Press Releases
Principal Investigator: Dr Likius Daniel
Institution Name: University of Namibia
Active Member Count: 5
Allocation Start: 2017-08-02
Allocation End: 2018-05-10
Used Hours: 747802
Project Name: UNAM Energy Initiative
Project Shortname: MATS1045
Discipline Name: Material Science
Material Science Research Centre of the University of Namibia. Under the supervision of Dr. Daniel Likius, this center is to provide students with specialized knowledge and skills in the field of Material Science for Energy and Environment. Materials Science is concerned with the science of developing materials which meet and exceed performance expectations for specific functions. At the center, we are involved in synthesis, characterization, computational and design ceramics that have the potential materials for energy and environment. High-performance computing and advanced data technologies are powerful tools in enhancing the our research here at UNAM. Through CHPC, our project is mainly depend on the system named Lengau owing to its speed of 1000 teraflops is very helpful to our research and we manage to collect data in very short time as it is very faster. With the help of CHPC, are now able to presenting our finding with concreted evidence at the national and international level (in Mauritius in July 2018). This is because we are now able to collect data at faster rate compare to the software that we use to used before the CHPC. therefore we appreciated with what CHPC is doing for us..
Principal Investigator: Prof Richard Betz
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 9
Allocation Start: 2016-05-16
Allocation End: 2018-06-28
Used Hours: 61602
Project Name: Artificial Photosynthesis
Project Shortname: CHEM0872
Discipline Name: Chemistry
The research group of Dr R Betz is working on the field of artificial photosynthesis. The latter process is the last of the big processes of life that has not been modeled successfully on a laboratory scale but whose knowledge could become crucial due to the concerning effects climate change could have on the supply of food and breathable oxygen based on natural foliage. The project embarks on a hitherto-unknown take on the problem and is progressing nicely. Stay tuned!
Principal Investigator: Prof Paulette Bloomer
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2017-06-22
Allocation End: 2018-04-17
Used Hours: 167141
Project Name: Molecular Ecology and Evolution Programme
Project Shortname: CBBI1030
Discipline Name: Bioinformatics
The Molecular Ecology and Evolution Programme (MEEP) is a research group in the Division of Genetics, Department of Biochemistry, Genetics and Microbiology at the University of Pretoria. We investigate the evolutionary history and current genetic diversity of many vertebrate species (marine and terrestrial), using genetics and genomics tools, and try to link the patterns we see with ecological and human-mediated events. We currently have two projects (Cape buffalo and bowhead whales) that make use of the CHPC resources, with additional projects in the pipeline.
Genomics of Cape Buffalo is a hot topic, and is of interest to the general public and wildlife ranchers in particular. Cape buffalo are bred on private game ranchers for a one or a few economically important traits, such as horn length and body size. The effects of this artificial selection, as well as breeding South African buffalo with East African buffalo, is unknown. We can use genomics to evaluate the risks and benefits of these practices for the short and long term (evolutionary) conservation prospects of the species
The genetic work on the bowhead whale uses empirical and simulation data to investigate the effects that different Nearctic human cultures exploiting the whale had on the abundance of the population. This means that genetic data may have more resolution than previously thought and is sufficient to detect subtle changes in population size in relation to exploitation and climate change. This is of great importance as there are many applications. We believe that the work will have sufficient impact to be of interest to the general public in South Africa and internationally.
Principal Investigator: Prof Bryan Sewell
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2016-05-11
Allocation End: 2018-08-30
Used Hours: 9229
Project Name: Enzyme Structures and Mechanisms
Project Shortname: CHEM0871
Discipline Name: Other
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https://theconversation.com/want-to-develop-vaccines-in-africa-then-invest-in-expertise-and-infrastructure-167660
Principal Investigator: Dr Bahareh Honarparvar
Institution Name: University of KwaZulu-Natal
Active Member Count: 0
Allocation Start: 2016-01-23
Allocation End: 2018-04-20
Used Hours: 10601889
Project Name: Computer-aided HIV/TB drug design
Project Shortname: CHEM0808
Discipline Name: Health Sciences
My research interest is mainly focused on applying a range of computational chemistry approaches for structure-based design. CHPC is beneficial to my research members to increase their research output and publications and graduation. My research members use commercial software packages such as Materials Studio,Gaussian and Amber. All these commercial software packages are installed in CHPC.
Principal Investigator: Dr Deshenthree Chetty
Institution Name: Mintek
Active Member Count: 1
Allocation Start: 2016-09-29
Allocation End: 2018-06-06
Used Hours: 90984
Project Name: 3D image analysis
Project Shortname: ERTH0939
Discipline Name: Earth Sciences
Mintek undertakes research into the acquisition and analysis of 3D images generated by X-ray computed tomography scanning. The analysis of such images leads to quantification of parameters related to mineral processing. These include mineral abundance, mineral grain size distribution, and liberation parameters. The ability to provide these as 3D information allows closer correlation with processing attributes, compared with standard 2D measurements used in the field of process mineralogy. Owing to the large size of 3D images generated, the CHPC allows timely processing of these images. The project has examined several algorithms for processing, in ongoing work.
Principal Investigator: Dr Melaku Tesfaye Yigiletu
Institution Name: South African Weather Service
Active Member Count: 2
Allocation Start: 2016-07-07
Allocation End: 2018-06-15
Used Hours: 209590
Project Name: South African Weather Service Air Quality Modelling and Forecasting (SAWS–AQMF)
Project Shortname: ERTH0912
Discipline Name: Earth Sciences
The blanket of air which surrounds the planet earth is known as the Earth's atmosphere; it helps protect the Earth and allows life to exist. Though trace gases and atmospheric aerosols comprise a small proportion of the Earth's atmosphere mixture; they are primarily accountable for some of the most significant physico-chemical characteristics of the Earth's atmosphere; and in turn, play a substantial role in our climate system. The presence of aerosols and trace gases in the Earth's atmosphere with undesirable amount is regarded as atmospheric pollution. As the air pollutant concentration increases, the quality (cleanness) of the air we breathe will be degraded. This air quality deterioration has several direct and indirect impacts. The South African Weather Service (SAWS) Air Quality Modelling and Forecasting (AQMF) group has developed a research program which principally aim to dealing with the air quality degradation impacts on: human health, Earth-atmosphere system, ecological processes as well as human socio-economic activities. The SAWS-AQMF research activities fundamentally deal with climate-chemistry coupled modelling systems. Such models are computationally highly demanding; hence the CHPC platform is crucial for the achievement of the group research programme. The SAWS-AQMF currently is involved in a number of national/international research projects that deals with: (a) the quantification of air pollution related national burden of diseases (this project is at its final stage); (b) assessing the climate impacts of different air pollutants, both in a continental and subcontinental scales (this project is progressing well); (c) WMO initiated international programme known as Air Quality Prediction and Forecasting Improvement for Africa (AQPREFIA) (this project is progressing well). Beside these, the SAWS–AQMF group is currently testing the implementation of different modelling system for the national air quality forecast as well as for provision of services to the general public and specific sectors.
Principal Investigator: Prof Edet Archibong
Institution Name: University of Namibia
Active Member Count: 4
Allocation Start: 2016-12-15
Allocation End: 2018-06-06
Used Hours: 148589
Project Name: (1) Computational Study of Semiconductor Clusters. (2) Computational Study of Bio-active Molecules Extracted from Plants
Project Shortname: CHEM0969
Discipline Name: Chemistry
At the Computational Chemistry Group of the University of Namibia (UNAM), Namibia, we have investigated the reactions of ozone and thiozone with phenols in the gas phase and also taken solvent effects into consideration. Namibia is an arid country in southern Africa with facilities for reclaiming water directly from domestic sewage. Ozonation is one of the processes used to disinfect the waste water and also to eliminate dissolved organic compounds. Despite its importance in drinking water processing, the mode of ozone reaction in water is not completely known and the subject still remains a grey area for research studies.
Based on the above, the Computational Chemistry group at UNAM/Namibia has embarked on the investigation of the reactions of ozone with compounds that could be found in recycled water and also in the atmosphere (of course, the importance of atmospheric ozone, cannot be overemphasized). Specifically, we are studying the reactions of ozone and thiozone with phenols (phenol, thiophenol, catechol, resorcinol) and their derivatives.
Computational studies prove to be important in these studies because several of the intermediates in the ozone/phenols reactions are short lived and difficult to isolate experimentally. Thus, these intermediates are modeled on computers and their thermodynamic and kinetic stability investigated.
The computing facilities provided by CHPC in South Africa (SA) allow our group to study these large chemical systems using decent level of theory. Using the Lengau clusters, one of our M.Sc students has nearly completed his research work which exciting results which should be published soon. The assistance and provision of computer time by CHPC in SA enable our group to engage in contemporary research which have universal benefit.
At present, the research work is progressing well and we expect to send our results for publication very soon. Also, one of our M.Sc students will complete his studies this year (2018), thanks to CHPC in SA.
Principal Investigator: Dr Natasha Wood
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2016-01-23
Allocation End: 2018-05-03
Used Hours: 503177
Project Name: Molecular Modelling of HIV glycoproteins
Project Shortname: CBBI0805
Discipline Name: Bioinformatics
The HIV Molecular Dynamics research group forms part of the Computational Biology division within the Department of Integrative Biomedical Sciences (IBMS) at the University of Cape Town. This small, but dynamic, group focussed on generating computer simulations of the HIV surface protein, which forms the first contact between the virus and the human CD4+ immune cells. This surface protein, Envelope, is covered with carbohydrates that are added by the human cell machinery during its formation. Since these carbohydrates are added by the host, they are not marked as foreign by the human immune system as would be the case for other infectious agents. Therefore, these carbohydrates that cover Envelope, are often called the HIV shield, as they protect the virus from being recognised by the immune system. However, in recent years, antibodies have been identified which bind to specific carbohydrates on the Envelope surface and by so doing, block the virus from entering, and infecting, a human CD4+ cell.
Our research focusses on running computer simulations of the Envelope protein to try and understand why certain antibodies bind to specific carbohydrates and others do not. This knowledge will then guide further research on designing agents (including potential vaccines) that could elicit specific antibody responses and thereby block HIV infection and thus the spread of the virus.
The research depends on running carbohydrate processing pipelines and molecular dynamics simulations, which require substantial computational resources. Over 500,000 CPU hours of processing has been carried out using the CHPC resources thus far, and the project would not have been possible without it.
Future work will include developing further processing pipelines so that this, relatively niche, research field will become more accessible to all HIV researchers around Africa and the world.
Principal Investigator: Prof Joanna Dames
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2016-12-12
Allocation End: 2018-06-15
Used Hours: 21759
Project Name: Mycorrhizal Interactions
Project Shortname: CBBI0966
Discipline Name: Bioinformatics
The Mycorrhizal Research group is based at Rhodes University, Grahamstown.
Mycorrhizal fungi form a symbiotic relationship with the roots of the majority of plant species. The interaction between these soil fungi, other soil microbes and plants results in many beneficial growth effects making an important contribution to sustainable agriculture, horticulture, and environmental rehabilitation. There are several types of mycorrhizal relationships depending on the fungi and host plants involved. Little is known about the biodiversity of these fungi in South African soils. The use of next-generation sequencing provides an opportunity to unravel this biodiversity in order to better understand factors which impact on the relationship. The CHPC platform has assisted in analysis of biodiversity of fungi in general and mycorrhizal fungi in particular as well as some interactions with soil bacteria.
Principal Investigator: Dr William Horowitz
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2017-01-16
Allocation End: 2018-03-28
Used Hours: 525605
Project Name: Probing the Frontiers of Nuclear Physics
Project Shortname: PHYS0974
Discipline Name: Physics
The CHPC provides critical computing power for the research programme of Dr. W. A. Horowitz. The goal of Dr. Horowitz's research is to unlock the secrets of nuclear matter under extreme conditions, for example in the centre of neutron stars or at a trillion degrees. Why a trillion degrees? That's the temperature of the universe a microsecond after the Big Bang, when the fundamental matter making up space was very different from what we experience every day. Instead of the usual protons and neutrons that make up normal nuclear matter, something very different is at work. The goal is to understand what exactly makes up this nuclear matter in extreme conditions and also to determine the impact of the dynamics of this matter on the early evolution of the universe. The incredible computing power of the CHPC allows for the world's most precise predictions for the behavior of certain particles known as quarks when the universe is at a trillion degrees. These predictions have been compared with measurements made at the world's premier atom smashers, such as the Large Hadron Collider in Europe, and it was shown that the data do in fact agree with calculations made at the CHPC. As a result, we're learning that the hottest stuff in the universe is still very strongly-coupled, like the most perfect trillion degree soup ever created.
Principal Investigator: Dr Bubacarr Bah
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 8
Allocation Start: 2017-01-20
Allocation End: 2018-07-27
Used Hours: 140538
Project Name: Large Scale Computations in Data Science
Project Shortname: CSCI0972
Discipline Name: Applied and Computational Mathematics
The research program in Large Scale Computations in Data Science provides for the main computational tasks of the Data Science Research Group at AIMS South Africa. The computational tasks include training of Deep Learning (DL) algorithms and storage of huge datasets. The training of DL algorithms is to learn underlying models from data for prediction purposes. These computational tasks come from applications that members of the Data Science Group are working on, which include neuroscience, renewable energy, finance, ecology, etc.
In particular, in the neuroscience application we wish to predict the chance of recovery of coma patients from their EEG data; while in the renewable energy project we wish to predict power output from potential wind and solar farms using wind and solar data of South Africa. The neuroscience project will help automate the process of classification of coma patients of those that have a potential to recover from those that don't. We hope also that this will make the classification process more accurate than what exist currently. The power prediction project will help in the integration of renewable energy resources to existing electricity grids. The project outcome will be the development of tools that will accurately predict power output from renewable sources. This will help in the planning of energy companies.
My research involves using Deep Learning techniques, which require a lot training on very huge datasets. Most of the training we do cannot run on a standard desktop or laptop hence we need a HPC facility like CHPC. A couple of my students have finished their research and a couple more are progressing significantly well in their research thanks to CHPC resources.
Principal Investigator: Prof KHALED ABOU-EL-HOSSEIN
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 1
Allocation Start: 2017-01-16
Allocation End: 2020-01-15
Used Hours: 8203
Project Name: Ultra-High Precision Machining of Optical Materials
Project Shortname: MATS0971
Discipline Name: Material Science
We at the Nelson Mandela University are absolutely thankful to the Centre of High Performance Computing for facilitating the use of their computing facilities. This have allowed us to conduct high performance simulations at the molecular level of some optical materials used in the aerospace and optical industries. The simulation results have been useful to understand the behaviour of optical materials when they are shaped into optical components without the the need to run extremely expensive laboratory experiments.
A number of PhD students who have been helped by CHPC have already graduated from the Machatronics of Nelson Mandela University
Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 31
Allocation Start: 2016-01-30
Allocation End: 2018-04-17
Used Hours: 6468989
Project Name: Computational and statistical methodologies for human and environmental health prediction
Project Shortname: CBBI0818
Discipline Name: Bioinformatics
Computational and statistical methodologies for human and environmental health prediction research programme (CBBI0818) is running from the University of Cape Town, South Africa. This research programme is fundamentally aiming
1) to determinate the environment and genetics variation that cause human species to look different, having difference in allergy, drug responses and treatment.
2) to identify and quantify the pattern of inheritance of the observed trait, drug response and treatment variation among human.
These are addressed through the design of machine learnings and artificial intelligent methodologies and statistical approaches to analysis DNA data of thousands affected/unaffected subjects within a geographical region. In doing so, this programme will contribute to human health by increasing understanding of the genetic and environmental underpinnings of complex traits (or diseases), drug/treatment responses and drug/dosage responses and forecasting individual's health and traits such as the weather is forecasting today. The accumulation of experimental DNA data in Biology and new high throughput experiments are growing rapidly and give a huge number of data difficult to manage, to store and to analyse this existing and future dispersed information. Therefore, high-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring the field of bioinformatics to use high-performance computing resources and carry out data management and analysis tasks on large scale data. Today, the use of HPC has critically increased our researcher portfolio to meet the international standard with respect to large scale genomic era. This programme has already developed a number of genomic-based software tools that address African genetic variation challenges and provided advanced trainings around parallel programming with respect to large-scale genomic data to African postgraduate students/researchers .
Principal Investigator: Prof Johan W. Joubert
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2016-01-23
Allocation End: 2018-06-13
Used Hours: 267074
Project Name: Mobility modelling using vehicle telematics
Project Shortname: MECH0803
Discipline Name: Other
Government (all spheres) is tasked with the challenge of deciding where to invest in infrastructure (for housing/transport/economic development etc). The real hard part is to balance two questions. Firstly, "who gets the benefit of infrastructure?" and, secondly, "who PAYS for those benefits?".
In our research programme we develop agent-based transport models that are able to depict and imitate the complex, multi-modal and large-scale transport scenarios in a South African context. Each individual - from the Metrorail commuter, to the private car owner, to the minibus taxi driver, to the commercial vehicle delivering your goodies at the Woolies Foods - are represented in such a transport model. The goal of our ongoing research is to assist government and industry make better informed, evidence-based decisions about the intended, and unintended consequences of specific transport interventions.
Since every individual is modelled the computational burden is substantial and the CHPC allows us to overcome the data preparation and simulation challenges of executing the large-scale, MATSim models.
Principal Investigator: Prof Gerard Tromp
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2017-03-13
Allocation End: 2018-09-05
Used Hours: 2368
Project Name: South African Tuberculosis Bioinformatics Initiative
Project Shortname: CBBI0999
Discipline Name: Bioinformatics
The South African Tuberculosis Bioinformatics Initiative (SATBBI), funded by the Strategic Health Innovation Partnership program of the South African Medical Research Council, performs bioinformatic analyses in support of tuberculosis research in South Africa. The analyses range from biostatistical support in experiment design and data analysis to complex analyses of sequence data from RNA and DNA.
Tuberculosis (TB) is a significant contributor to disease burden and death in South Africa, which has among the highest prevalence of the disease in the world. Our research helps a variety of other TB researchers be more effective in their research, and is also aimed at improving our understanding of the biological responses when individuals become infected with the TB bacterium as well as when they are treated. These analyses include trying to predict who will respond well or poorly to treatment, or who is likely to get ill or not after exposure.
The CHPC is an invaluable resource for our research program. It permits us to perform computationally intensive parts of or research that are otherwise impossible using our own resources, or in a timely manner. It is similar to a homeowner being able to rent some equipment for a do-it-yourself renovation job; at best without the tool the job will take a lot longer, at worst the job is impossible.
We are currently preparing our results for publication.
Principal Investigator: Prof Erick Strauss
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2016-04-06
Allocation End: 2018-06-15
Used Hours: 40837
Project Name: CoA biosynthesis and oxidative stress resistance as drug targets in pathogens
Project Shortname: CHEM0841
Discipline Name: Chemistry
Research in the Strauss group is focused on increasing understanding of the production of the essential metabolic cofactor coenzyme A (CoA) - which is produced from one of the B-vitamins - in a number of pathogens relevant to human health, like those causing TB and malaria.
By learning how CoA is produced in these organisms we can also potentially learn how to disrupt this production. If this can be done, it could provide us with new drugs to target these important pathogens.
Part of this entails understanding the CoA biosynthesis enzymes at a structural and chemical level, which can be facilitated by molecular modelling on resources such as the CHPC.
Principal Investigator: Dr Jean-Baptiste Ramond
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2016-11-09
Allocation End: 2018-06-13
Used Hours: 225973
Project Name: Metagenomics & metaproteomics of Desert soils
Project Shortname: CBBI0951
Discipline Name: Bioinformatics
Desert environments represent one third of the Earth's surface and South Africa is 80% arid. With Climate Change, arid land surface is expected to expand globally.
In these polyextreme environments, microorganisms dominate and are key actors in nutrient cycling.
Our project therefore aims at better understanding the roles of microbial communities in desert environments as well as their potential role in the mysterious Fairy Circle phenomenon formation.
To achieve this, we have generated a vast amount of data with high-throughput sequencing technologies and mass spectrometry.
We actually rely on CHPC's state-of-the-art computing facility and power to analyze these huge datasets.
Since its inception, this project has allowed the graduation of 2 students and the publication of 1 research article and 3 postdoctoral researchers and one student are still working on it.
Principal Investigator: Prof Wimpie Odendaal
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2016-09-30
Allocation End: 2018-04-17
Used Hours: 356799
Project Name: Electromagnetic radiation and scattering
Project Shortname: MECH0938
Discipline Name: Electrical Engineering
The Electromagnetism Group at the University of Pretoria has a long standing specialization in a wide variety of microwave components and antennas. The Group also has research experience in computational methods and antenna measurement techniques. Current research activities include: Electromagnetic measurements and numerical modelling of wideband antennas. The main purpose of this study is to contribute towards the development of high performance ultra-wide band antennas and systems; Measured RCS data of electrically large conducting airframes are used to investigate and validate the performance of several full-wave and asymptotic computational numerical methods. A very accurate laser scanned CAD model of the airframe is used for the simulations to reduce the number of uncertainties. This activity validated a number of numerical methods to model the RCS of realistic radar targets for practical applications and also formulated guidelines for researchers and engineers to assist with selecting the most appropriate method for different, scattering scenarios and applications. The numerical studies of the electrical large airframes are computationally extremely expensive, making the CHPC a critical resource to enable this research.
Principal Investigator: Prof Evans Adei
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 3
Allocation Start: 2017-08-03
Allocation End: 2018-06-06
Used Hours: 309585
Project Name: Materials For Energy and Fine Chemicals
Project Shortname: CHEM1046
Discipline Name: Chemistry
Three KNUST Kumasi students are involved in a Royal Society-DFID sponsored collaborative research and training that aims to train a cadre of African scientists in the use of state-of the-art computer modelling and advanced experimental techniques to design, develop new materials for solar cells and energy storage devices and the production of low-carbon sustainable fuels or chemical feedstock.
The initiative seeks to foster a sustainable research networks between research groups/Laboratories in the sub-Saharan Africa (University of Botswana, University of Namibia and KNUST Kumasi Ghana) and the UK (University of Cardiff) in order to strengthen research and training capacity in sub-Saharan African institution higher education through skills transfer between partner organizations of the research consortia.
In the past year apart from the over 300,000 CPU hrs allocated by CHPC which has appreciably increased our students' productivity, the 4-weeks CHPC on-site training which two of our students received in April 2018 on top of the 3-days off-site CHPC training at the University of Namibia in August 2017 have enhanced their computational skills set particularly with the use of the Guassian QM software package, a licence of which we are in the process of acquiring for our research group.
However with our limited HPC resource here at KNUST Kumasi Ghana we hope that CHPC will continue to support us with HPC resources in the short and medium terms to enable us use more realistic models in our calculations. So far one of the students has completed his MPhil and has been upgraded to Ph.D. while two others are about submit their paperwork for an upgrade. The CHPC will be duly acknowledged in our publications emanating from our research work and relevant reports.
Principal Investigator: Dr Kiprono Kiptiemoi Korir
Institution Name: Moi University, Eldoret, Kenya
Active Member Count: 4
Allocation Start: 2016-05-09
Allocation End: 2018-05-05
Used Hours: 382790
Project Name: Thermal characterization of MoS2 nanostructures: an ab initio study
Project Shortname: MATS0868
Discipline Name: Material Science
This group draws it's members from Moi Universiy, Computational Material Science Group (CMSG), in addition we have a collaborator Slimane Haffad from University of Beijaia - Algeria. Our research activities focus on nanomaterials for energy related applications, gas sensing, electronics, CO2 capture and storage. We also work on prediction and characterization of ultra-hard materials.
Since the discovery of nanomaterials in the early 1990's, various noble applications of these wonder materials have been demonstrated in various fields. However, the process of development of devices addressing major problems ailing the society, such as, energy and pollution has been rather slow due to lack of comprehensive understanding of such systems. Therefore, an in depth study of this group of materials is needed to establish better understanding that may lead to development of new principles, characterization techniques, and methods, which may lead to breakthroughs in addressing some of the bottle-necks currently associated with nanomaterials.
In this work, materials for various applications are simulated via approaches grounded on principles of quantum and classical mechanics, which have been shown to accurately predict materials properties. These predictive approaches require High Performance Computing facility like CHPC to solve mathematical formulaes, such as Schrodinger and Newtonian equations, which yield various properties of interest such as electronic, optical and others properties.
The first phase of the study was focused on structural optimization of molybdenum disulphate (MoS2) with gold nano-particles, and it was shown that interaction between the two systems was chemical, with gold nanoparticles enhancing the electronic properties of the two dimensional MoS2 layer, making it ideal for nano-electronic application. Currently, our efforts are focused on understanding the effects of these gold nano-particles on the thermal properties of the MoS2 layer.
Principal Investigator: Prof Penny Govender
Institution Name: University of Johannesburg
Active Member Count: 11
Allocation Start: 2016-01-23
Allocation End: 2018-04-17
Used Hours: 5021542
Project Name: Design of MOFs-based sorbent materials for capturing carbon dioxide
Project Shortname: CHEM0797
Discipline Name: Material Science
Environmental and energy problems are important topics globally due to the fast development of urbanization, huge population increases and industrialization. Recently, water pollution is a major issue in developing countries, particularly in regions where people rely on groundwater for domestic and drinking purposes. Almost 40 % of the world's population is facing water shortage. Most countries depend on the low-efficient power generation from the burning fossil fuels as their source of energy. The burning of fossil fuels normally generates a huge amount of CO2, which induces environmental concerns, such as greenhouse effect. As non-renewable natural resources, fossil fuels cannot be sustainable and depleted shortly in the next century owing to their environmental issues and high consumption rate. This has led to the investigation of photocatalysis as a possible solution to the problem. Despite significant concern and substantial efforts, the design of semiconductor photocatalyst materials that is both efficient and robust enough for water/wastewater treatment and energy production is still lacking. Due to the complexity of the experimental process, it is difficult to know the mechanism and origin of the enhanced photocatalytic performance. The first-principles approach is highly desirable in the area of materials science, particularly for understanding both the photocatalysis of nanomaterials, as well as the subsequent physical and chemical properties. Density functional theory (DFT) calculations was used as the method of clarification as it has already proven its superiority in studying the structural stabilities, electronic properties, work functions, charge transfer, and carrier effective mass of several semiconductor photocatalyst materials due to its reduced computational cost in calculating the electron density rather than the wave function.
Principal Investigator: Dr Krishna Govender
Institution Name: University of Johannesburg
Active Member Count: 6
Allocation Start: 2016-04-07
Allocation End: 2019-03-31
Used Hours: 287765
Project Name: Computational approaches to design novel anticancer agents
Project Shortname: CHEM0792
Discipline Name: Chemistry
The work involves benchmarking compuatational chemistry and material science codes installed on LENGAU.
This work provides users with a means to choose the appropriate number of cores for a particular jobs run on the cluster.
It also shows users places were the codes fail to scale correctly, suggesting that people should not go past the scaling threshold.
The benchmark results also show users the optimal number of cores that need to be used in order to make full use of the cluster nodes.
Principal Investigator: Prof Jeanet Conradie
Institution Name: University of the Free State
Active Member Count: 2
Allocation Start: 2016-10-25
Allocation End: 2018-03-20
Used Hours: 2404159
Project Name: Computational chemistry of transition metal complexes
Project Shortname: CHEM0947
Discipline Name: Chemistry
Certain metal-containing molecules show electrical conductivity in the solid state. Density functional theory calculations shed light on why the electrical conductivity of certain rhodium complexes was much smaller than in the similar iridium complexes. The electron flow was found to occur along the metal-metal bonds. The findings were published in international scientific journals and contribute to the knowledge base of the understanding on a molecular level of the metal-metal interactions in certain compounds. Results can be used in the design of electrical conductors. Calculations on big molecular models is high performance computing intensive and would not be possible on a desktop computer. This study is ongoing and depends on the availability of HPC facilities such as the CHPC of South Africa.
Principal Investigator: Prof Marile Landman
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2016-06-28
Allocation End: 2018-06-06
Used Hours: 110503
Project Name: Organometallic complexes and surfactants
Project Shortname: CHEM0906
Discipline Name: Chemistry
The research of Marina van der Merwe, a PhD student under the supervision of Prof Marilé Landman, at the University of Pretoria, focuses on the properties of PIBSA-based surfactants. Experimental studies have shown a specific trend in stability of these surfactants in a water/oil emulsion. The aim of the computational part of the project was to correlate specific parameters of the computational study to explain this experimental stability trend. The CHPC facilities were used to compute a number of the PIBSA derivatives and based on the results, explanations for the stability trend were proposed. In principal, most of the calculations could be done with Materials Studio of Accelrys. Marina is finalizing her PhD thesis and plans to submit within the next two months.
Principal Investigator: Dr Jenny-Lee Panayides
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 5
Allocation Start: 2016-09-16
Allocation End: 2018-03-20
Used Hours: 629264
Project Name: Lead Discovery & Process Development Programme
Project Shortname: CHEM0934
Discipline Name: Chemistry
Alzheimer's disease is the most common form of dementia. To date there is no cure for the disease and only symptomatic treatments are available. Using in silico computational and in vitro biological screening techniques, a team from CSIR Biosciences and the University of Pretoria are currently testing thousands of compounds to identify new pharmacophores for development into drugs for the treatment of Alzheimer's disease.
Using the computational resources provided by the CHPC, very large numbers of compounds can be tested with greater accuracy than what is possible with standard computational hardware. Hit compounds identified through this screening effort will be optimized using computer aided drug design, to improve their effectiveness against a particular target within the human body prior to the expensive and time consuming synthesis of the compounds for advanced biological screening. During this optimisation process many aspects will be considered, including the ability of the human body to absorb the compound and possible toxic side-effects. Thus, utilization of the CHPC resources can potentially accelerate drug development in a significantly more cost effective manner.
Principal Investigator: Dr Steven Hussey
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2017-04-10
Allocation End: 2018-06-06
Used Hours: 47917
Project Name: Forestry Molecular Genetics - transcriptional and epigenetic regulation of wood formation
Project Shortname: CBBI1010
Discipline Name: Bioinformatics
The Forest Molecular Genetics Programme is a joint venture of the University of Pretoria and South African forestry industry partners aimed at developing biotechnology applications for tree improvement. It focuses on the genetic basis of tree growth, wood formation and defence against pests and pathogens. The SA forestry industry produces over 20 million tons of wood per year for a wide array of renewable products such as timber, pulp, paper, packaging, cellulose, textiles, pharmaceuticals and food additives. Increasingly, there is interest in using trees as biorefineries, i.e. energy-efficient production platforms for high-value biopolymers and biochemicals. Timber from genetically improved plantations can also be processed into advanced building materials for sustainable housing and construction. In part, the Programme aims to understand the biology of wood formation and how it is regulated at various levels. For example, the metabolism and incorporation of carbon-rich compounds formed from photosynthesis into cellular structures such as wood, the role of networks of genes coordinating the activation of genes at the correct stages of growth and wood formation, and how the epigenome or degree of "packaging" of DNA influences the expression of genes. An important part in understanding these process is the use of DNA sequencing technologies that produce data requiring high-performance computation to analyze it. These tools were central to decoding the genome or DNA sequence of Eucalyptus grandis, an important fast-growing tree. Our Programme has relied on the Centre for High Performance Computing to help identify regions of the Eucalyptus genome that contain functional regions in the "dark matter" of the Eucalyptus genome that are important for gene expression. We are also aiming to understand how cellular organelles participate in wood formation, and in this regard we have analyzed gene expression patterns associated with the poorly understood plastid organelles found in wood.
Principal Investigator: Prof Charalampos (Haris) Skokos
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2017-04-13
Allocation End: 2018-06-06
Used Hours: 1190471
Project Name: Chaotic behavior of Hamiltonian systems
Project Shortname: CSCI1007
Discipline Name: Applied and Computational Mathematics
Using modern numerical techniques of Nonlinear Dynamics and Chaos Theory we investigate in a unified mathematical way the behavior of models describing the energy transport in disordered and granular media, as well as the properties of new elastic materials like graphene and molecules like the DNA. This research is performed by members of the 'Nonlinear Dynamics and Chaos Group' in the Department of Mathematics and Applied Mathematics at the University of Cape Town. The performed investigations constitute an innovative combination of Applied Mathematics, Chaos Theory, Hamiltonian Dynamics and Nonlinear Lattice Dynamics. Their outcomes will provide answers to some fundamental questions about the effect of chaos on the energy transport in disordered and granular media, and on the behavior of graphene and DNA. Some of the questions we try to address are: Does the presence of impurities and nonlinearities enhance or suppress the propagation of energy (e.g. heat) in solids, of light in crystals, and of vibrations in granular material? How does the ratio of the different base pairs in DNA chains affect their structural stability and the temperature at which the double-stranded DNA breaks to single-stranded DNA?
Principal Investigator: Prof Mario Santos
Institution Name: University of Western Cape
Active Member Count: 14
Allocation Start: 2016-10-17
Allocation End: 2018-04-24
Used Hours: 472911
Project Name: Cosmology with Radio Telescopes
Project Shortname: ASTR0945
Discipline Name: Astrophysics
The Centre for Radio Cosmology (CRC) at UWC aims to fully explore the use of the next generation of radio telescopes for measurements in cosmology, in particular with MeerKAT and SKA. CRC staff is closely involved in the South African and international SKA projects. About 10 postdoctoral researchers and 10 PhD/MSc students are doing their research within the CRC. Our work at the CHPC is mostly focused on running simulations of signals we expect to observe with MeerKAT/SKA and test how well radio telescopes can constrain certain cosmological models. This is a crucial component in the process to use these telescopes for cosmology since we need to understand the signals we are observing. The project include simulations of the hydrogen emission from the early universe, simulations of the contaminants, simulations of the telescope itself and analysis of the constraining power of such telescopes on cosmological models.
Principal Investigator: Dr Babatunde J. Abiodun
Institution Name: University of Cape Town
Active Member Count: 15
Allocation Start: 2016-06-20
Allocation End: 2018-06-28
Used Hours: 1908114
Project Name: CSAG-Atmospheric Modelling
Project Shortname: ERTH0904
Discipline Name: Earth Sciences
The Climate System Analysis Group (CSAG) Atmospheric Modelling project consists of CSAG researchers and students working on model development and applications. Our group is a unique research group within Africa (CSAG http://www.csag.uct.ac.za/). We are a mix of specialties who put the needs of developing nation users at the forefront of everything we do. As a result, we seek to apply our core research to meet the knowledge needs of responding to climate variability and change.
In the project, we develop, evaluate, and apply of dynamic and statistical climate models over Africa. Climate models are powerful tools for understanding the complexity of our earth climate system. We use various form of climate model, ranging from uniform-grid Global Climate Models (GCMs), Regional Climate Models (RCMs) and adaptive-grid GCMs (VGCM) that has capability to increase its grid resolution locally over a region of interest. Given the complexity and computational demand of these models we rely on high performance Computers like those at the Meraka CHPC to our models.
Our research goal is to understand the dynamics of climate extremes (i.e. droughts, extreme rainfall, heatwaves, and pollution episodes) and the impacts of vegetation changes on regional climate. The highlights of our past research, carried-out using the Meraka CHPC resources, include: development and application of a VGCM for studying rainfall producing systems in West Africa (Abiodun et al, 2010) and tropical cyclone over the South-West Indian Ocean (Maoyi et al., 2017); application of RCMs in studying the transport of atmospheric NOx and HNO3 over Cape Town (Abiodun et al., 2014), extreme rainfall events over Western Cape (Abiodun et al., 2014), and potential impacts of climate change on extreme precipitation over four African coastal cities (Abiodun., 2017). The project, which has graduated more than 20 postgraduate students in last five years, it is currently support 10 postgraduate students who are working towards graduating this year or next year.
Principal Investigator: Prof George Amolo
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 12
Allocation Start: 2016-05-05
Allocation End: 2018-03-28
Used Hours: 2211107
Project Name: Properties of Materials for Green Energy Harnessing
Project Shortname: MATS862
Discipline Name: Material Science
Africa faces several challenges that need to be addressed to better the lives of citizens of our continent. One of them is the provision of clean and affordable energy that has less negative impacts to the environment. In order to make this a reality there should be training of adequate local skills and expertise. The CHPC has provided my Kenyan research team with computational resources to perform investigations into the properties of materials that have potential to act as energy conversion materials. Such materials are useful for the conversion of solar radiation into energy used by solar cells and those that can be used to store hydrogen.
In this period alone my group has directly produced 3 Msc and 2 PhD. Several other graduate students are making good progression towards completion of their degrees. These graduate students have found employment in Kenyan universities and contributed towards numbers within the Materials Research Society of Kenya (MRSK). It is expected that with sufficient numbers of materials scientists, the National Research Foundation (NRF) in Kenya will provide funds for flagship projects in the development of energy conversion devices
ab initio techniques have been used to study the structural, electronic and optical properties of materials traditionally used for solar energy conversion. These have been TiO2, NiO, SnO2, all being transitional metal based, requiring special approaches. Studying these materials is expected to provide skills and knowhow to handle novel and emerging materials.
Some efforts have been invested to potential materials for hydrogen storage. This has involved both lithium and magnesium hydrides with better reproduction of the properties of magnesium hydrides than lithium hydride.
Recently the catalytic properties of copper nanowires and clusters on TiO2 surface as well as the lanthanide doping of graphene for spintronic applications have been carried out and reported.
Principal Investigator: Prof Felix Spanier
Institution Name: North-West University
Active Member Count: 5
Allocation Start: 2016-08-07
Allocation End: 2018-03-28
Used Hours: 3637352
Project Name: Acceleration and transport of high-energy particles in the universe
Project Shortname: ASTR0804
Discipline Name: Astrophysics
South Africa has moved a bit closer to the stars in the recent years by founding its own space agency SANSA. But there is more to space exploration than just building rockets. One important point is the understanding and possible forecast of space weather - the influence of high energy particles emanating from the Sun.
Researchers from the NWU have been doing extensive simulations to understand one aspect of space weather: The transport of cosmic rays in high-frequency turbulence. The Centre for Space Research has a decade long tradition in this kind of study and the youngest generation of researchers could benefit from CHPC's newest acquisition the Lengau cluster.
This type of research requires sophisticated and large-scale plasma models, which can only be handled with state-of-the-art supercomputers. CHPC has played a pivotal role in enabling NWU's researchers to get to the next level. Especially the new PhDs Alex Ivascenko and Cedric Schreiner have found new interesting details about the electron transport in the solar wind. They could show that the solar wind behaves vastly different at smallest scales and that this affects the transport of electrons significantly.
While this seems like a purely academic scenario, it still has an impact on building satellites and spacecrafts in the long run: Any space equipment has to be shielded against electron impacts and understanding the whereabouts of electrons from the Sun is an important piece of the puzzle. Especially for South Africa as aspiring space nation.
Future simulations will try to figure out how particle transport changes with a quiet Sun (weak turbulence) and solar eruptions (strong turbulence). The ultimate goal in any of these simulations is to predict when the Sun will emit large particle fluxes that may harm space equipment.
The tools and methods used in this project also have another important role: Understanding plasma simulations and high-performance computing is ever more important for industry.
Principal Investigator: Prof Peter Teske
Institution Name: University of Johannesburg
Active Member Count: 3
Allocation Start: 2017-02-06
Allocation End: 2018-06-28
Used Hours: 1349605
Project Name: Coevolution of mangroves and mangrove-associated crabs
Project Shortname: CBBI0979
Discipline Name: Bioinformatics
Who?
Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg
What?
Analysis of DNA and RNA data from a large portion of animal genomes.
Why?
To improve the management of commercially exploited species, optimise conservation efforts aimed at saving endangered species from extinction, and understand evolutionary relationships in nature.
How?
Genomic data sets generated using massive parallel sequencing technology results can only be assembled by means of supercomputers. Using CHPC, we are able to assemble a huge number of short reads into a meaningful sequence that reflects their order in the animal genome.
Progress?
CHPC and the valuable expertise it has gathered in one place has allowed our small lab to punch well above its weight, and we are now on our way of becoming an international player in the field of genomics who are being noticed by much larger (and much better funded) international research groups. We are looking forward to publishing several high-impact studies during the next few months that we would not have been able to complete without CHPC.
Principal Investigator: Prof Wim Delva
Institution Name: SACEMA / Stellenbosch University
Active Member Count: 3
Allocation Start: 2016-11-09
Allocation End: 2018-05-03
Used Hours: 209780
Project Name: Simpact-in-parallel
Project Shortname: CBBI0949
Discipline Name: Health Sciences
The Simpact project is a collaboration of researchers from the South African Centre for Epidemiological Modelling and Analysis (SACEMA) at Stellenbosch University, the Center for Statistics (CenStat) at Hasselt University, the International Centre for Reproductive Health (ICRH) at Ghent University, and the Vaccine & Infectious Disease Institute at the University of Antwerp who conduct research on HIV and HIV-HSV2 co-infection.
Understanding the structure and the dynamics of sexual transmission networks is a key step towards the design and implementation of effective HIV and HIV-HSV2 co-infection prevention measures. The project aims to inform prevention and treatment policy decisions through Individual Based Model (IBM) simulations. These IBMs are "conceptualized" to be an effective platform that enable policy implementations which are informed by assessment of output from simulation of prevention/treatment interventions under different strategies and/or scenarios which are impossible to test in the real world.
Meanwhile, the field of phylodynamics is emerging with much potential to enhance our understanding of HIV transmission dynamics by using sequence data. Phylodynamics methods allow estimation of epidemiological features such as time trends of HIV prevalence and HIV incidence, reproductive number, among others.
Our team has been working on a unified simulation framework that bridges these two schools of thought in order to "marry" multiple data sources. It is envisaged that this unified framework will enable improvement in epidemiological estimates by model calibration to multiple data sources (bio-behavioural and sequence data).
The utilisation of the HPC is invaluable in the success of this project. Notable, by adding a phylodynamic component to the IBM simulation will have an added simulation layer where molecular evolution of HIV will be simulated across the transmission networks. This framework is by nature highly stochastic hence repeated runs are needed to account for stochasticity hence time and memory consuming.
Principal Investigator: Dr Michelle Gordon
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2016-09-01
Allocation End: 2018-06-28
Used Hours: 45512
Project Name: Structural Implications of Mutations in HIV-1
Project Shortname: CBBI0928
Discipline Name: Bioinformatics
Our research group is based at the Nelson R Mandela Medical School at the University of KwaZulu-Natal and focusses on the effects of mutations that cause antiretroviral drug resistance on the structure of HIV-1 proteins. The drugs that patients take as part of their treatment against HIV-1 can stop working because the virus is always changing (mutating). We are looking at how these mutations also change the structure of the virus. To do this, we make a structural model of the affected viral protein using specialised software that uses a lot of computational power. By using the CHPC, I am able to access their high powered server, as well as the software for performing the molecular modelling.
With the information gained from this analysis, we can design new drugs that can work against these mutated viruses.
Principal Investigator: Dr Dominic Stratford
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2017-03-07
Allocation End: 2018-07-27
Used Hours: 29116
Project Name: Application of deformation-based models in paleoanthropology
Project Shortname: CSCI0984
Discipline Name: Imaging
As members of the Sterkfontein Research team, we are investigating 3-million-year-old fossil specimens from the caves and quarries at Sterkfontein, 50 km northwest of Johannesburg. Because it is one of the richest fossil complex site in Africa, this fossil assemblage is critical to challenge long-standing questions in human evolution. Who were our ancestors? Where and when did they live? Did they look like us? Did they walk on two legs, as humans do today? In addition to basic descriptions and traditional metrical analyses, recent incorporation and validation of computer-based techniques for reconstructing and comparing morphological pattern have substantially improved the quality of data delivered by fossil remains. In our project, we use high-resolution imaging techniques (e.g., microtomographic-based scanner) to non-invasively explore the fossil specimens and apply 3D modelling techniques to comparatively describe the anatomy of our ancestors. In that perspective, the access to a supercomputer through the CHPC resources is essential for running our analyses and provide new evidence of human evolution in South Africa.
Principal Investigator: Dr Kevin Lobb
Institution Name: Rhodes University
Active Member Count: 10
Allocation Start: 2016-01-23
Allocation End: 2018-03-13
Used Hours: 2120364
Project Name: Computational Mechanistic Chemistry and Drug Discovery
Project Shortname: CHEM0802
Discipline Name: Chemistry
There are two main areas of research conducted by this group in the Chemistry Department at Rhodes University. The first is in the area of drug discovery (with main focus on HIV and Malaria), and the second relates to the study of mechanism, and finding out how certain chemical processes occur in nature.
The interaction of ligands and substrate is the first step in the process of drug discovery, and identifying molecules which have the most promising interaction is the focus since these molecules will have the greatest potential therapeutic effect. These lead structures may be altered systematically to improve both the interaction and other properties they must have to be useful as drugs. To this end the group constructs virtual libraries of compounds and screens these against biological targets, and evaluates promising results using a variety of techniques that require the computational time provided by the CHPC.
Understanding how reactions occur is crucial in being able to harness the potential of chemical change. The uses of this understanding range from having more accurate analytical techniques to being able to synthesize new compounds in a way that is both more energy efficient and where less unwanted waste occurs. This research focuses on transformations where the mechanism of the reaction is not known. Using the CHPC complex reactions are explored at the molecular level, and after the identification of many possible reaction steps and calculation of the energy changes, the steps are pieced together to show the processes occurring for a specific chemical change.
These two areas of research are not unrelated. Enzymes (including parasitic enzymes) mediate chemical processes. The understanding of the mechanisms of these processes informs the design of new potential therapeutic agents.
Principal Investigator: Prof Willem PEROLD
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2016-10-31
Allocation End: 2018-04-17
Used Hours: 814109
Project Name: Simulation of advanced semiconductor materials for the optimisation of photovoltaic devices
Project Shortname: MATS0948
Discipline Name: Electrical Engineering
Energy is one of the most important elements humans need for living and development. Fossil fuel reserves are expected to deplete and researches have shown that sunlight is a potent and dependable source of energy for the future. The most effective way to harvest energy of sunlight and make it useful is by using photovoltaic devices. There are now three generations of photovoltaic solar cells, however, despite remarkable progress observed from the first to the third generation, photovoltaic energy production cost is still higher than that of fossil fuel or hydroelectric technologies. If the solar cell efficiency can be augmented by adding very cheaper materials then the energy production costs will fall. It is well known that to enhance solar cell efficiency, one need to increase its ability to absorb incident light photons. Our staff here at the Electrical and Electronic Engineering Departement, Faculty of engineering, Stellenbosh University is working to see how light absorbed by silicon based solar cells can be significantly increased by adding silver metallic nanoparticles with particular shapes and sizes into silicon layer of the solar cell. For a good and complete description of our systems, we use both Finite Difference Time Domain (FDTD) based on electromagnetism and quantum mechanics simulations. To simulate our systems using these methods an important quantity of numerical resources must be used and fortunately we have found that on the CHPC system. Our works clearly demonstrate that solar cells properties are well ameliorated by adding cubic, spheroidal and spherical silver metallic nanoparticles into standard solar cells.
Principal Investigator: Prof Ozlem Tastan Bishop
Institution Name: Rhodes University
Active Member Count: 18
Allocation Start: 2016-09-05
Allocation End: 2018-08-15
Used Hours: 22719456
Project Name: Structural Bioinformatics for Drug Discovery
Project Shortname: CBBI0867
Discipline Name: Bioinformatics
Research Unit in Bioinformatics (RUBi) at Rhodes University is specialized in structural bioinformatics research. Structural bioinformatics focuses on the identification and analysis of structure, dynamics and interaction of biological macromolecules in 3D space. While doing so, it aims to make connections between sequence – structure and function of macromolecules. Information on structure is particularly important as you can derive enormous amounts of information.
RUBi's main interest is drug discovery. Computer aided drug design technology has greatly revolutionised the drug research and development process. Traditional computational drug discovery approach includes large scale structure based and/or ligand based in silico docking combined with molecular dynamics and binding free energy calculations. All these computationally expensive calculations require to use HPC facilities.
In the last few years, RUBi has been developing some novel protocols by merging computational chemistry, structural bioinformatics and biophysics approaches and combining with traditional methods. These combined approaches also require HPC facilities. We expect that our protocols will advance our and others research. We have already been testing the combined approaches in different cases and a number of hit compounds identified; including identification of South African natural compounds as hits to cancer, malaria, trypanosoma and HIV.
Principal Investigator: Dr Charles Hefer
Institution Name: Agricultural Research Council
Active Member Count: 3
Allocation Start: 2016-01-23
Allocation End: 2018-04-24
Used Hours: 1127816
Project Name: Agricultural Genomics
Project Shortname: CBBI0794
Discipline Name: Bioinformatics
At the Agricultural Research Council, we make use of the CHPC it assist in identifying genetic markers in agricultural commodities. These markers are then used in breeding programs where breeders of specific crops perform selection of animals and or plant carrying these makers. The marker are generally associated with specific traits, for example growth or disease resistance, which are then bred into specific populations. These populations are then used to improve the general value of the crops and or animals.
Principal Investigator: Dr Abu Abrahams
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 2
Allocation Start: 2016-04-08
Allocation End: 2018-06-06
Used Hours: 2445272
Project Name: Synthesis and characterisation of lanthanide complexes with Di-(2-picolyl)amine and its derivatives
Project Shortname: CHEM0844
Discipline Name: Chemistry
Who: Rare earth coordination chemistry research group of Nelson Mandela University
What and why: The study of chemical and structural properties of the inorganic complexes with rare earth elements in order to identify trends in reactivity and identify potential applications in the fields of catalysis, medicine (diagnostic, anti-bacterial) and luminescence. Specifically complexes of rare earth elements with the ligand bis(2-pyridylmethyl)amine are being investigated due to this class of complexes displaying applications in the fields of catalysis, nuclear waste processing and medicine (solution structure elucidation). Increased utilisation of rare earth elements could also support the local economy, since rare earth elements may also be mined in South Africa.
How: The CHPC provides access to advanced computational resources which allows for the extraction of information from modelled systems of novel compounds, which may allow for the prediction of experimentally-determined properties. The latter process of physical experimentation are often time-consuming and expensive, whereas computational modelling may be performed on multiple systems simultaneously and may provide information of sufficient accuracy to inform the user of the most beneficial course of action to take when performing any physical experiments. In addition, modelling may also provide answers to fundamental questions which we may not yet be able to observe physically. In addition, advanced computational chemistry software packages (such as Gaussian 9/16 and ORCA) allow users with limited knowledge theoretical physics and computer programming to find answers to their chemical problems.
The experimental structures and composition of several monomeric- and dimeric- complexes containing the rare earth elements: Y, La, Nd, Dy, Ho and Lu, and preliminary geometry optimisations are well on their way to completion. An incremental refinement strategy implementing larger basis sets has proven feasible and will be carried out next.
Principal Investigator: Dr Josefine Wilms
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 6
Allocation Start: 2017-01-16
Allocation End: 2018-06-28
Used Hours: 11396
Project Name: Ocean and Climate modelling
Project Shortname: CSIR0936
Discipline Name: Applied and Computational Mathematics
The Modelling and Digital Science unit at the CSIR is using the CHPC to run a global climate model. This model provides runoff values on a global scale which we use to develop a river-routing algorithm. This algorithm was then implemented back into CCAM.
The routing algorithm informs us on where rivers will form and where they will output freshwater into the ocean. Fresh water deposits influences water density and may influence the currents. The currents influence the climate. We therefore are able to simulate what will happen if freshwater deposits into the ocean changes significantly with time.
Principal Investigator: Prof Hasani Chauke
Institution Name: University of Limpopo
Active Member Count: 6
Allocation Start: 2017-08-03
Allocation End: 2018-06-06
Used Hours: 868014
Project Name: Computational Modelling of Minerals, Metals and Alloys
Project Shortname: MATS1047
Discipline Name: Material Science
The research programme is conducted at the Materials Modelling Centre (MMC), University of Limpopo. The centre is a research unit focusing on computational modelling studies of various materials properties, for over two decade. Professor Hasani Chauke, the primary investigator under the minerals and alloy development programme, currently holds a Royal Society-Newton Advanced Fellowship position. The area of specialization is on mineral processing and metal alloys development using first-principles and molecular dynamics based methods, which employs various academic and commercial software with different types of interfaces.
Alloy development based projects focuses on the discovery of new materials and improving strength of materials such as ductility and elasticity which lead to fabrication of components for applications in automotive, aerospace and medical industries. In the mining area, the focus is to design ligands that can be used to enhance the floatation process for maximum recovery of mineral ore. The computer interfaces are linked to local servers and also benefit from the centre for high performance computing (CHPC). One of the major motivations of the research programme at MMC recently, is to run large scale simulations, and this requires high level computational power. Currently, the computer servers at MMC are linked to CHPC to allow such large scale calculations to be completed in a much shorter time. Most of the work carried are project at Honours (mini projects), Masters (MSc) and Doctoral (PhD) studies.
Principal Investigator: Prof Nicola Mulder
Institution Name: University of Cape Town
Active Member Count: 11
Allocation Start: 2016-01-29
Allocation End: 2018-03-20
Used Hours: 8715434
Project Name: H3ABioNet
Project Shortname: CBBI0825
Discipline Name: Bioinformatics
One of the key projects run at the CHPC is the design of a new genotyping array for African populations. This required the processing and analysis of >5,000 whole genomes from individuals across Africa. The most intensive component of this more recently has been the evaluation of the completed chip using imputation, which requires chunking of chromosomes to run in parallel in order to reduce the overall processing time. The chip has now been manufactured and researchers across Africa are enabled to generate what we hope is more useful data for their indigenous populations. This, in turn, will facilitate novel discoveries of diseases in African populations, which differ from their European counterparts due to the large genetic diversity on the continent.
The metaproteomics data analysis is also being done on samples of biomedical interest. These studies are aiming to determine the role of the microbiome in diseases as well as in the susceptibility to sexually transmitted diseases, including HIV. Again, this has the potential to facilitate novel discoveries for diseases in Africa and to identify biomarkers of disease which could be used to develop better diagnostics.
Principal Investigator: Dr Coleen Moloney
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2016-07-29
Allocation End: 2018-06-06
Used Hours: 40895
Project Name: Marine Ecosystem Modelling
Project Shortname: ERTH0920
Discipline Name: Environmental Sciences
A PhD student, Nandipha Mhlongo, at the University of Cape Town is working in collaboration with researchers from the French Institute for Research Development to apply a computer model to understand changes in the distribution and abundance of one of South Africa's main commercial fish species, the Cape anchovy. Ms Mhlongo is a scientist from the Fisheries Branch of the Dept of Agriculture, Forestry and Fisheries, responsible for providing advice to assist in fisheries management. Because many factors influence fish populations and the ocean is continuously varying, it is not possible to rely solely on observations at sea to understand marine populations. Computer models combine theory with data and provide a "virtual laboratory" to explore interactions and impacts. The computer models require vast amounts of storage and computer processing time - this is provided by the CHPC. The project is ongoing.
Principal Investigator: Prof Philip Machanick
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2016-08-15
Allocation End: 2018-08-15
Used Hours: 80270
Project Name: Motif quality assessment
Project Shortname: CBBI0922
Discipline Name: Bioinformatics
Caleb Kibet, recent PhD Bioinformatics graduate, now back home in Kenya, and Philip Machanick, Department of Computer Science, Rhodes University, are jointly working on tools and techniques in bioinformatics, the application of computer science to biology.
We are working on better characterizing how transcription is regulated. Transcription is a core part of how DNA encodes for protein, and understanding how this is regulated is important for both genetic components of diseases and designing medication. Our work is at the level of proving toolkits that can be applied by other researchers, though we do also work on problems in collaboration with other researchers.
CHPC provides a computational resource that makes it possible to do work of this kind without having source everything ourselves or waste time doing routine system administration. It is also very useful that my PhD student can wrap up his work and produce another publication from a remote location.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2016-05-13
Allocation End: 2018-04-17
Used Hours: 1468982
Project Name: CFD Modelling of Concentrated Solar Power Applications
Project Shortname: MECH0873
Discipline Name: Computational Mechanics
Central tower concentrated solar power plants are the most promising concentrated solar option in terms of increasing its performance and bringing costs down. For the former, new receivers and heat transfer fluids are being developed and for the latter the mirrors or heliostats (of which there can be hundreds of thousands) are being redesigned to be cheaper. In order to do this redesign, knowledge must be gained in predicting the peak loads that these reflectors will experience during all orientations and wind conditions. Computational Fluid Dynamics (CFD) is used in this project to determine the variation of the wind by considering a simulation technique called Large Eddy Simulation (LES). In LES, individual turbulent vortices are tracked as they pass over the heliostat structure to see how they change the surface pressure, and hence the force and moment experienced by the structure. This gives a time-varying response that can be used to size the actuators required to rotate these reflectors towards the sun under windy conditions. Researchers at the University of Pretoria's Clean Energy Research group under the leadership of Prof Ken Craig are using the resources at the CHPC to speed up these calculations. The CFD results are then used as input to finite element structural calculations of these structures to determine both their dynamical behaviour and whether they can withstand the resulting stresses without deflecting too much. The latter is important in their ability to keep the sunlight focused on the tower. This project has been ongoing since 2013 with the involvement of CHPC resources since 2016. The project has already delivered one masters student (Dawie Marais) with another masters student (Joshua Wolmarans) nearing completion. PhD student Pierre Poulain is also nearing the end of this investigation into LES modelling of the atmospheric boundary layer.
Principal Investigator: Dr Adam Skelton
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2016-01-23
Allocation End: 2018-04-17
Used Hours: 4900034
Project Name: Molecular modelling of biomolecules and materials
Project Shortname: CHEM0798
Discipline Name: Chemistry
I am Dr. Adam Skelton and I work at the College of Health Science university of KwaZulu-Natal. I work on understanding the behaviour of biological and material systems on the molecular level.
A particlar interest is in using molecular simulation to direct the rationale design of functionalized nanoparticles for a range of applications such as drug delivery, water treatment and catalysis. In particular, drug delivery is the use of nanoparticles to carry antiviral or antibacterial drugs into parts of the body that are difficult for conventional drugs to reach. Drug-delivery is, therefore, of huge importance in South Africa, especially in the battle against HIV and Tubercolosis.
The research requires running a series of computar simulations, which may take hours at a time. CHPC has had a great impact since it provides me with the facilities to perform such simulations.
Since the project started, my group has published more than 15 papers in international journals and has provided deep insight into biological and material systems on the molecular level.
Principal Investigator: Dr Hamilton Ganesan
Institution Name: Inqaba Biotec
Active Member Count: 1
Allocation Start: 2016-04-13
Allocation End: 2019-03-31
Used Hours: 38355
Project Name: General Analysis
Project Shortname: CBBI0843
Discipline Name: Bioinformatics
Having access to the resources at the CHPC (man and computer) was like a bridge between raw data and meaningful results. I appreciate the time taken to properly understand my companies needs and then allocate resources to us appropriately. Thank you CHPC for making life better for us!
Principal Investigator: Prof Tien-Chien Jen
Institution Name: University of Johannesburg
Active Member Count: 13
Allocation Start: 2017-03-07
Allocation End: 2018-04-28
Used Hours: 144125
Project Name: Developing an Innovative Metal Matrix Composite Membrane for Hydrogen Purification
Project Shortname: MATS0991
Discipline Name: Material Science
The University of Johannesburg has developed an ever-growing research group (also known as Jenano) consisting of undergraduates, masters, doctorate candidates and post-doctorate researchers from the Department of Mechanical Engineering Science. These young researchers under the supervision of Professor Tien-Chien Jen are investigating multiple research fields, some of these fields are the Hydrogen generation and advance manufacturing technology methods such as cold gas dynamic spray (surface spray coating), atomic layer deposition, photo-catalysis and dry manufacturing techniques. The group attempts to understand the process of these technologies, material structure and properties, and industrial application studies. These research fields are used to advance, optimise, and identify parameters and properties of each specific category from macro to nano scales. Furthermore, these studies contribute to both research scale and industrial scale studies. The research as contributed to multiple international collaboration projects, such from BRICS, NRF and Case Western Reserve, focusing on development and investigation of cutting-edge technologies. These specific research fields are reliant on the chpc resources for the multi-scale numerical modelling of these cutting-edge technology products and manufacturing processes. The research field has produced findings in multiple cutting-edge technologies, such as water purification biomimetic membrane, superconductor, ultra-thin film fabrication, hydrogen generation, hydrogen vehicle, construction coatings, and thermosiphon manufacturing equipment. These chpc resources have been critical in producing multiple international conference publication, peer-reviewed journals, and international collaborations. In future work these chpc resources will play a major and crucial part in the development of various cutting-edge technology investigations.
Principal Investigator: Dr Samson Khene
Institution Name: Rhodes University
Active Member Count: 6
Allocation Start: 2017-01-16
Allocation End: 2018-04-17
Used Hours: 191847
Project Name: Synthesis, Spectroscopy and Nonlinear Optical Properties of Phthalocyanines
Project Shortname: CHEM0975
Discipline Name: Chemistry
Many of today's optical sensors are based on optical materials in which non-linear optics may play a role. Defects in the cable can have an effect of reducing the light (which carries information) in an optical fiber or cable. This phenomenon is also present in a variety of non-linear active materials or molecules. This nonlinear reduction of light phenomenon can be used as a sensing method for detection and correction of signals that are sent in cables. The aim of our research (at Rhodes University in the Chemistry department) is to make and study molecules which will help improve signal transmission using a nonlinear process. This work will not be possible if it was not supported by CHPC facilities.
Principal Investigator: Dr Gebremedhn Gebreyesus Hagoss
Institution Name: University of Ghana
Active Member Count: 4
Allocation Start: 2017-06-12
Allocation End: 2018-05-10
Used Hours: 780392
Project Name: Atomistic simulations and condensed matter
Project Shortname: MATS1031
Discipline Name: Physics
The condensed matter research group at the Physics Department in the University of Ghana is focused on the study of the structural, electronic, magnetic, and optical properties of two- and three-dimensional materials. Computational simulations of the properties of these materials is carried out using Quantum Espresso (http://www.quantum-espresso.org) which is a state-of-the-art open-source computational software package. Our experimental research also covers the synthesis and characterization of these materials. Hence, we verify and validate our computational results against our experimental results.
Our computational work would not be possible without the enhanced computing resources available at the CHPC in South Africa. This is due to the fact that the materials we are studying require calculations on systems that contain comparatively large numbers of atoms. Typically, we do preliminary calculations on our computer and laptops with small number of atoms. Once the basic results are validated, the actual job is then transferred to the CHPC. The job is monitored at least once a day and the results downloaded when completed.
Our main areas of research are:
1. Electronic structure and optical properties of transition-metal oxides.
Experiments are carried on the the synthesis and characterization of pure and doped zinc peroxide and zinc oxide for oxygen and carbon-dioxide gas sensors, light-emitting applications, energy generation and storage and other applications. We are also investigating the structural, electronic, optical, and magnetic properties of these materials using the first-principle calculations.
2. Two-dimensional Materials Research
In this project, we focus on the effect of introducing lanthanide atoms into monolayer HfS2, especially on the modifications of the electronic, optical, and magnetic properties of the material.
Two dimensional materials also promise a wide range of applications, including light-emitting applications, energy generation and storage, wear- and corrosion resistant surfaces, and gas and radiation sensors.
Principal Investigator: Dr Steve Peterson
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2016-04-05
Allocation End: 2018-04-17
Used Hours: 2845756
Project Name: Development of a Prompt Gamma Imaging Device
Project Shortname: PHYS0830
Discipline Name: Physics
The UCT Prompt Gamma Imaging (PGI) Group is a part of the Measure Research Unit based in the Department of Physics at the University of Cape Town. PGI is a new form of imaging that will be used in conjunction with proton radiation therapy cancer treatments. The protons that are used to attack the cancer cells produce gamma-rays that we are detecting and using to produce images of the dose deposited in the patient. PGI is still a technology in development and relies heavily on computing resources for both detector design and image reconstruction.
Principal Investigator: Mr Theo Fischer
Institution Name: eScience
Active Member Count: 3
Allocation Start: 2016-04-18
Allocation End: 2018-03-20
Used Hours: 1710768
Project Name: Acid Deposition
Project Shortname: ERTH0851
Discipline Name: Earth Sciences
The modelling of acid deposition arising from sources of acidic precursors like SO2, NOx and NH3 emitted over Southern Africa has been verified at hand of wet and dry deposition data (Josipovic 2005-2007) to enable estimation of the impact of atmospheric deposition on the agricultural soils of the interior as well potential salinity impacts to the runoff from various catchment areas.
Acid deposition has been studied over the Highveld region of South Africa due to its high density of acid emissions arising mostly from power generation and petrochemical plants (Abanda, 2000; CE, et al., 2001; Josipovic, et al., 2011; Josipovic, et al., 2011; Kornelius & Scorgie, 2009; Zunckel, et al., 2000). It has been measured extensively to determine impacts to agricultural soil especially. Although deposition of acid species arising from power generation has been modelled using dispersion models, modelling of atmospheric chemistry and acid deposition has not been undertaken to any meaningful extent in South Africa before.
This study uses the WRFChem (coupled atmospheric chemical model) to model emissions of acidic precursors, their chemical conversion, as well as their wet and dry depositions. WRFChem allows for feedback mechanisms between emissions and meteorological processes like cloud formation and therefore provides a more dynamic and realistic scenario for modelling acid deposition.
The importance of this investigation is two-fold. Firstly, it arises from the economic and environmental impact of the deposition of anthropogenic salt emissions on water users in the strategic heartland of South Africa. And on the contrary/secondly, the expensive decisions arising from the location and technology of new power stations and industrial plant (such as the possible need to retrofit flu gas desulphurisation). Both the costs and the benefits are very high and hold very significant implications for our national economy.
Principal Investigator: Dr Ikechukwu Achilonu
Institution Name: University of the Witwatersrand
Active Member Count: 6
Allocation Start: 2016-04-13
Allocation End: 2018-06-15
Used Hours: 30204
Project Name: Computational approach to modelling druggable proteins of neglected tropical diseases parasites and ESKAPE pathogens
Project Shortname: CHEM0849
Discipline Name: Bioinformatics
Ligandin function of Plasmodium falciparum glutathione transferase towards known anti-malaria drugs
Tshireletso Mentor and Ikechukwu Achilonu*
Protein Structure-Function Research Unit, Faculty of Science
University of the Witwatersrand, Johannesburg
Malaria, caused by Plasmodium, remains one of the main causes of infectious parasite related death worldwide. Malaria is prevalent in most tropical regions, especially endemic to Sub-Saharan Africa of the 214 million cases and 438 000 malaria related deaths observed in 2015. Chloroquine was the main drug used for malaria treatment, prior to the prevalence of its resistance. To retard the development of resistance, drugs such as amodiaquine, lumefantrine, or sulfadoxine/pyrimethamine are combined with artemisinin. P. falciparum encodes a single glutathione transferase (GST) gene. PfGST is a cytosolic GST that functions in detoxification. The crystal structure of PfGST is indicative of a similar canonical fold apparent within other cytosolic GSTs. According to the expression profile of P. falciparum, PfGST is expressed adequately throughout the erythrocytic cycle of the parasite life cycle as well as within a period of the sporogonic cyle. This study aims to assess the molecular basis of ligandin function of PfGST towards known anti-malaria drugs using molecular modelling approach. This project will heavily relys of the CHPC cluster and access to the Schrodinger molecular modelling suite, including the induced fit ligand docking and the Glide docking for MMGBS calculation. The stability of the complex will be assessed using Desmond molecular dynamics (MD) simulation (~ 50-100 ns time frame). The project is at molecular dynamics stage. We have shown that there is significant interaction between PfGST and known anti-malaria drugs. The complexes will be subjected to MD simulation using the Schrödinger Desmond implemented in the CHPC. This will enable us understand the stability of the complexes and be able to infer potential disruption of the redox system of the parasite.
Principal Investigator: Prof Zenixole Tshentu
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 5
Allocation Start: 2016-05-05
Allocation End: 2018-05-10
Used Hours: 673011
Project Name: Metal-ligand, anion-cation interactions and protein-ligand studies
Project Shortname: CHEM0864
Discipline Name: Chemistry
The facilities at CHPC have allowed us to carry out smart design of the following:
1. Cations for anionic complexes towards the design of separating agents for platinum group metals. This contributes to the need to improve separation methods for the mining sector as current mineral ores provide less yield of the precious metals requiring better processing methods.
2. Ligands for metal ions in the design of selective extractants of base metals and platinum group metals. This aspect also contributes to developing the much needed chemistry for the mining sector.
3. Design of ligand scaffolds and their respective gold(I) complexes for targeting the protease enzyme by a dual action approach of active site ligand binding and allosteric binding of gold(I). This moves coordination chemistry towards the doorstep of targeting HIV.
My research group at the Department of Chemistry at Nelson Mandela University contributes to both the development of fundamental coordination chemistry of metal ions (or complex anions) as well as application of the metal ions. We are very grateful to the CHPC otherwise the projects would not be successful without the important computational facilities.
Principal Investigator: Prof Gert Kruger
Institution Name: University of KwaZulu-Natal
Active Member Count: 8
Allocation Start: 2016-04-04
Allocation End: 2018-05-08
Used Hours: 2367265
Project Name: CPRU molecular modeling
Project Shortname: HEAL0839
Discipline Name: Health Sciences
(Who) The Catalysis and Peptide Research Unit at UKZN (http://cpru.ukzn.ac.za/Homepage.aspx) is currently working on the mechanism of action on the HIV PR with respect to the natural substrates.
(What) We use an quantum chemical/molecular mechanics hybrid (Oniom) approach that gives us high level results on the thermodnamics and kinetics of the reaction. Our model enables us to study application of both electronics and sterics to change the bond strenght and binding energies of new potential inhibitors.
The same approach is followed for transpeptidases, essential enzymes for the inhibition of TB.
(Why) HIV is a major health threat in SA and new drugs is required due to the constant development of drug resistance. Similarly, TB and TB co-infection with HIV is a mojor health issue.
(How) Our theoretical studies will allow us to test a computational model that correctly describes the interactions between the respective enzymes and existing drugs. We are improving our computational model to the extent where are now in a position to start proposing new potential drug leads for synthesis. This can only be done with large computational resources provided by the CHPC.
Principal Investigator: Prof Mmantsae Diale
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2016-10-14
Allocation End: 2018-04-18
Used Hours: 1695192
Project Name: Electronic Structure of hematite and surface doped hematite
Project Shortname: MATS0944
Discipline Name: Physics
The solar energy collection and conversion group of the Department of Physics, University of
Pretoria, led by Prof Mmantsae Diale, are investigating the possible use of rust as a semiconductor electrode to make a photoelectrochemical (PEC) device used to split water into hydrogen and oxygen. Water is made out of oxygen and hydrogen molecules. Water-splitting is a process of producing hydrogen fuel from water, where the driving energy is solar. In this work, a PhD student, Joseph Simfukwe, a lecturer at the Copperbelt University in Zambia is the lead researcher. This work is in collaborative with Empa in Switzerland, led by Dr Artur Braun. The scientific name for rust is hematite. Hematite (α-Fe2O3) has been identified as a better replacement of titanium dioxide (TiO2) in the PEC water splitting and solar energy harvesting, reducing dependence on the use of fossil fuels. Its many advantages as an electrode includes abundance, cost, non-toxicity and stability to chemical corrosion in large pH range. The study, using the quantum-espresso simulation package, requires large and high performance computers, since the structure of hematite is very complicated, and results in large size files which cannot be processed on a single computer. The calculations also takes a long time. Therefore this study is only possible with the help of the CHPC.
The project has thus far produced a publication in MRS Advances after a successful presentation of the work in 2017 Materials Research Society (MRS) fall conference, where Joseph Simfukwe was awarded the best poster prize. We remain grateful for the support from CHPC without which our research may not be possible.
Principal Investigator: Dr Morne Du Plessis
Institution Name: National Zoological Gardens of South Africa
Active Member Count: 7
Allocation Start: 2016-04-01
Allocation End: 2018-06-20
Used Hours: 168879
Project Name: Wildlife Comparative Genomics and Bioinformatics
Project Shortname: CBBI0831
Discipline Name: Bioinformatics
The Wildlife Comparative Genomics and Bioinformatics group currently utilises the CHPC as a resource to develop methodologies and workflows that will enhance the groups capacity to conduct research in the area of wildlife conservation as well as biodiversity research. The primary use of this resource is to assemble and organise large volumes of biological data, mostly in the form of DNA sequences, in a manner whereby the similarities within and across species can be explored and understood. The CHPC is therefore instrumental in allowing for the evaluation of large, complex datasets that would otherwise be difficult to explore. Ultimately these variations are explored within the context of a number of research questions, with the common aim of ensuring the survival of, often critically endangered species.
Principal Investigator: Dr Fabio Cinti
Institution Name: NITHEP
Active Member Count: 1
Allocation Start: 2016-06-01
Allocation End: 2018-06-28
Used Hours: 32092
Project Name: Quantum Monte Carlo for ultra-cold atoms
Project Shortname: PHYS0892
Discipline Name: Physics
Can we manipulate atomic clouds controlling the interactions strength among themselves? If so, what kind of new effects may be observed?
Despite they might be thought as trivial, such questions are keeping busy the most advanced research laboratories as well as brilliant theoretical physicists all over the world. Recently, new experiments have been coming across fascinating behaviors in atoms as Erbium and Dysprosium which will be helping us out to give the ultimate answer. Considering the magnetic properties of these lanthanide elements, scientists observed as they are capable of interact at large distances (50 to 100 nanometers). Surprisingly, the interactions at play assemble atoms in filaments that remain stable for extremely long times.
Starting from these observations, and making a large use of the HPC facility it has been studying the mechanisms that rule the physics of such fascinating structures. As an interesting example, filaments are quantum objects and display peculiar effects, such as the absence of viscosity, called superfluidity, at very low temperatures. Making use of advanced numerical methods, we obtained a phase diagram that proposes other interesting states, like a homogeneous fluid and atomic grapes or clusters, modifying the interaction strength or the system density. This studes, which will serve a guide for future experiments on other elements, has been recently published in the prestigious scientific journal Physics Review Letters.
The present outcomes are a first and important step for a definite answer to the initial questions. Such answers will give the opportunity to control with exquisite precision the bricks of matter we are made of, opening new routes and hopefully revolutions in quantum technology.
Principal Investigator: Prof Rosemary Dorrington
Institution Name: Rhodes University
Active Member Count: 6
Allocation Start: 2016-12-13
Allocation End: 2018-05-10
Used Hours: 59396
Project Name: Marine Natural Products Research
Project Shortname: CBBI0963
Discipline Name: Bioinformatics
Marine Natural Products Research Group, Department of Biochemistry and Microbiology, Rhodes University
The Marine Natural Products Research Platform covers the broad field of marine biodiscovery, focusing on the potential of bioactive secondary metabolites produced by marine organisms endemic to the Agulhas Bioregion as lead compounds for drug discovery.
Overview and aims
More than half of new pharmaceutical drugs on the market or in clinical trials are natural products and their derivatives and the majority of these are now coming from marine macrofauna and their associated microbiomes. The Maine Natural Produces research programme is active across the broad field of marine biodiscovery, focusing on exploring the potential of marine invertebrates and their associated microorganisms as sources of novel bioactive small molecules. Research projects include: (1) Biodiversity mapping of benthic habitats in the Agulhas bioregion, focusing on invertebrates, ascidians, soft corals and their associated microbiota; (2) Isolation and characterization of bioactive secondary metabolites of marine organisms; (3) screening marine natural product libraries for anti-viral, anti-cancer and antibacterial activity and (4) elucidating the metabolic pathways that result in the production of lead compounds to pave the way for engineering recombinant systems for their production for the pharmaceutical industry. Associated projects focus on the application of high throughput metagenomic and analytical chemistry technologies to map patterns and processes in marine ecosystems to provide tools for sustainable development of our ocean economy. All of these research activities require access to high performance computing facilities to curate, process and analyse large Next Generation Sequencing (NGS) datasets. Primarily, we have used the CHPC facilities to analyse NGS amplicon library data to characterise the microbial communities of both marine and terrestrial systems.
Principal Investigator: Prof Alexander Quandt
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2016-05-31
Allocation End: 2018-06-06
Used Hours: 41153
Project Name: First principles simulations of renewable energy devices
Project Shortname: MATS0882
Discipline Name: Material Science
Several researchers from the simulations focus area of the Materials for Energy Research Group (MERG) at the University of the Witwatersrand are using HPC facilities to study the interaction of light with materials, and the formation of charged double layers in supercapacitors. The PI is Prof. Alexander Quandt, and the submitting members of this project are PhD students Nkosinathi Malaza and Patrick Mwonga.
The studies carried out by this team of researchers are based on first principles methods like Density Functional Theory (DFT), which means that the only input to these simulations are the starting positions of the ionic cores and the total number of electrons forming a model solid. All of the elastic, electronic, magnetic and optical properties of these model systems may be determined using first principles methods, and can be directly compared to experimental data.
The goal is to use the unmatched accuracy of first principles methods to improve our current understanding of collective electronic excitations in solids called plasmons, to improve the efficiency of standard inorganic solar cells, and to improve the energy storage capacity of supercapacitors. All of these studies are supplemented by experimental work carried out by various other researchers from MERG.
So far the group has only sporadically used CHCP facilities, but with the resources needed to carry out their simulations, they start to struggle with their own domestic computing facilities and will have to use CHPC facilities more frequently, and also more extensively.
In the last 2 years the group has published 3 papers, 3 book chapters, 3 conference papers and presented 10 invited talks on international conferences, which were related to the present project. Only one of these papers actually used CHPC facilities so far.
Principal Investigator: Dr Gerhard Venter
Institution Name: University of Cape Town
Active Member Count: 8
Allocation Start: 2016-01-23
Allocation End: 2018-04-17
Used Hours: 2239970
Project Name: Simulation of Ionic Liquids
Project Shortname: CHEM0791
Discipline Name: Chemistry
Dr Venter's research group is part of the Scientific Computing Research Unit at the University of Cape Town and uses computer simulation to study the chemical and physical properties of biopolymers in a special class of solvents, called "ionic liquids". These simulations provide insight into the intermolecular interactions and chemical behaviour that control the dissolution and subsequent reactivity of these naturally occuring polymers. A better understanding of these processes can lead to the rational design of new, environmentally friendly solvents systems that can dissolve biomass and enhance its reactivity. The dissolution of biomass is the first step in converting naturally occuring polymers to biofuels and other platform chemicals.
High performance computing is required for all research conducted in this group and without the resources and infrastructure provided by the Centre for High Performance Computing (CHPC), the research will not be possible.
Principal Investigator: Dr Roelf Du Toit Strauss
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2016-07-28
Allocation End: 2018-04-17
Used Hours: 4287118
Project Name: Computational Space Weather
Project Shortname: PHYS0918
Discipline Name: Physics
One of the biggest hurdles faced by manned exploration of space is the high levels of natural radiation present in the solar system. This is not only an important consideration faced by future astronauts on board spacecraft, but also by future colonizers of Mars, and inhabitants of future moon bases and space stations. This important risk is acknowledged by both SpaceX and NASA, and planned bases and spacecraft try to accommodate so-called "space storm shelters", where space dwellers can hide from dangerous radiation levels. At the Centre for Space Research of the North-West University, South Africa, we are doing our part to mitigate these possible harmful effects by developing state-of-the-art numerical models that can simulate and predict the levels of harmful natural radiation. To simulate the intensity of these so-called "cosmic ray" particles, complicated and large-scale numerical models are run on large scale computer clusters, such as the Lengau cluster of the Centre for High Performance Computing (CHPC) in Cape Town, South Africa.
Principal Investigator: Dr Marde Helbig
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2016-05-25
Allocation End: 2018-08-24
Used Hours: 297655
Project Name: Solving Multi-objective optimization problems using CI algorithms
Project Shortname: CSCI0874
Discipline Name: Computer Science
The Computational Intelligence Research Group (CIRG) at the University of Pretoria focusses on using computational intelligence algorithms to solve a variety of problems.
This project focusses on solving optimisation problems that have more than two objectives and where at least two objectives are in conflict with one another. Furthermore, the objectives and/or constraints change over time. These types of problems can be applied in a wide range of applications areas such as production plants (scheduling the jobs at the plant), delivery services (vehicle routing optimization), costing (electricity costing optimization), water treatment (optimizing the treatment of water based on what the water will be used for), and stock market (portfolio optimization or prediction of stock movement).
When developing algorithms to solve these kinds of problems they must be evaluated on benchmark functions against other algorithms. Furthermore, performance measures have to be calculated for the various algorithms and the data has to be statistically analysed. CHPC resources are used to run these simulations to obtain the data, which is required to write publications.
Principal Investigator: Prof Thirumala Govender
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2016-01-23
Allocation End: 2018-07-19
Used Hours: 110122
Project Name: IN SILICO EVALUATION OF NANO DRUG DELIVERY SYSTEMS
Project Shortname: MATS0816
Discipline Name: Material Science
The Novel Drug Delivery Unit (NDDU) at University of KwaZulu-Natal is led by Professor Thirumala Govender, a Professor of Pharmaceutics, Head of the UKZN NanoHealth Pillar and Evaluator on the Medicine Control Council of South Africa. The NDDU currently focuses on developing advanced medicine formulations to overcome antibiotic resistance. Antibiotic resistance, considered a global crisis currently, affects the development of human society and has high cost implications to government in terms of finances and resources.
Our group has designed various types of novel pharmaceutical materials as well as advanced and new generation "smart" nano drug delivery systems such as nanomicelles, nanoplexes, polymersomes etc. with superior architectural designs which have been prepared by our team and have shown superior activity against sensitive and resistant bacteria. The group philosophy is to use a multidisciplinary integrated approach that will minimize the cost of research and maximize therapeutic outcomes.
Hence the facilities provided by CHPC allows our group to integrate molecular modeling with our research that involves extensive in vitro and invivo animal evaluation of our novel medicines, and is being recognized locally and internationally for excellence.
Principal Investigator: Prof Gerhard Venter
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2016-05-31
Allocation End: 2018-04-28
Used Hours: 3027500
Project Name: Finite Element Analysis and Numerical Design Optimization
Project Shortname: MECH0883
Discipline Name: Computational Mechanics
The Materials, Optimization and Design (MOD) research group is a part of the Department of Mechanical and Mechatronic Engineering Faculty at Stellenbosch University. The research group's members work on a diverse group of projects related to structural analysis and optimization. The fields covered by the group are Finite element analysis, Computational fluid dynamics, numerical design optimization, material characterization for numerical modelling purposes and meta-modelling, etc.
Projects have dealt or are dealing with:
• inflatable structures (inflatable wings, dunnage bags, etc.)
• morphing wings/hydrofoils
• soft robotics
• large radio astronomy antennas
• heart valves
• composites
• vertical axis wind turbines
• particle swarm optimization
• railway bogies
• mining truck tires
• material testing methods
• high-pressure water supply lines
• heat exchanger header boxes for industrial heat exchangers, etc.
The primary goal of the group is to produce or facilitate advanced engineering design.
Principal Investigator: Dr Eric Maluta
Institution Name: University of Venda
Active Member Count: 13
Allocation Start: 2016-01-30
Allocation End: 2018-03-20
Used Hours: 1178922
Project Name: Energy Material Modeling in the Application of different Photovoltaic Technologies
Project Shortname: MATS0827
Discipline Name: Physics
our current research projects are based on the computational studies of semiconductors, energy materials and dye sensitized solar cells. We are currently working on dye uptake on the TiO2 semiconductor, Band gab engineering and the study of charge transfer at TiO2/dye-molecule interfaces in these types of solar cells. Apart from the computational studies of energy materials and dye solar cells, I am working on the analysis of solar radiation and renewable energy hybrid systems for rural development. Our main research aim is the improvement of the efficiency of PV materials and cost reduction in order to improve the use of this renewable technology for electricity generations. All our calculation are performed using the CHPC facilities. The research work has already produce few publications, Honours projects and two Masters research projects. The research involves Honours, Masters and PhD students.
Principal Investigator: Prof Francis Dejene
Institution Name: University of the Free State
Active Member Count: 4
Allocation Start: 2016-01-23
Allocation End: 2018-05-05
Used Hours: 2223910
Project Name: Experimental and computational studies on material properties of semiconductors and phosphor
Project Shortname: MATS0817
Discipline Name: Physics
Our research group at UFS (Qwa-Qwa) campus is composed of a staff member, 3 postdoc, 11 PhD and 2 MSc students. The research group is currently involved with several experimental and computational parallel research, which are on preparation by simple reproducible processes and characterization of new and smart materials for phosphorescence, photovoltaic, sensors, nanoparticles for energy, energy storage and Field emission Display applications e.g TV's. Our objective is to train postgraduate students in the field of luminescence materials and renewable energy. This programme inspires and motivates a number of students to follow careers in science and material science to enable them work with ESKOM and other energy companies in future. The resources CHPC provides has added significant impetus in the research conducted in my group. The work on this project mainly focuses in developing models that can be used to either complement experimental investigations or provide fundamental explanations to experimentally observed properties.
The HPC at CHPC is very helpful by guiding in input parameters for experimental synthesis in eliminating experimental material waste; saving time required for experimental work and allows calculations that are more detailed. Hence our envisaged tasks within this project work focused more on calculations related to energy, luminescence/optical properties of materials. This is mainly because these are the properties currently investigated experimentally within my group. Through collaboration with an expert on CHPC applications, we are now able to provide fundamental explanations to some of the phenomena that we could only speculate from experimental observations. The project has been a success since various papers were published and some students graduated. We have also developed collaboration with University of the Western Cape, Nelson Mandela Metropolitan University, University of Nairobi, University of Eldoret, JKUAT Physics, University of Addis Ababa, Tokyo Institute of Science and Technology, ICTP and Tsukuba University
Principal Investigator: Dr Hezekiel Kumalo
Institution Name: University of KwaZulu-Natal
Active Member Count: 7
Allocation Start: 2017-04-10
Allocation End: 2018-05-10
Used Hours: 120902
Project Name: Molecular modeling and computer aided drug design
Project Shortname: HEAL1009
Discipline Name: Health Sciences
(Molecular modeling and computer aided drug design from university of kwazulu Natal)
The group covers a wide range of computational and molecular modeling research areas with main focus on biological systems and drug design approaches.
Main interest is related to design and study of biologically and therapeutically oriented targets. This is achieved by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We are involved in projects such Understanding drug resistance mechanisms via different computational tools QM/MM MD simulations Quantitative Structure Activity Relationship (QSAR) Conformational Analysis of biomolecules Bioinformatics tools applications Development Projects Approaches to enhance binding free energy calculations results Developing parameters for biomolecules: on-going projects Software implementations: on-going projects. All the projects that we do in the group contribute to the training of pharmaceutical scientists with specific skills for both the pharmaceutical industry and academia. This has the potential of stimulating the local pharmaceutical industries in South Africa to manufacture pharmaceuticals of quality, excellence and affordability for optimum and cost effective patient health, instead of being dependent on multinational pharmaceutical companies. We are still young group therefore funding is problem, therefore for the resources at CHPC allows us to generate hypotheses for subsequent experimental testing in a much quicker manner and higher throughput than using experiment alone to generate hypotheses that you'd like to test. It has h given us an opportunity to be able explain experimental data we could not explain easily such the binding landscapes of different enzymes and the mechanism of action for different inhibitors
Principal Investigator: Dr Phillip Nyawere
Institution Name: Kabarak University, Nakuru, Kenya
Active Member Count: 2
Allocation Start: 2017-03-07
Allocation End: 2018-06-28
Used Hours: 40488
Project Name: Barium Floride and Perovskites
Project Shortname: MATS0996
Discipline Name: Physics
Barium Flouride and Perovskites Group is based in Kenya and it is working in collaboration with five universities that is Rongo University, Kenyatta University, Kabarak University, Masinde Muliro and Kisii University. This group brings together both supervisors (lecturers) and students at Masters and PhD levels. Though so far only one student appears in CHPC cluster, there are several students that are on board and are soon requiring computational hours allocated to them.
This group is interested in studying perovskite materials and their applications in solar cells. We are also interesting in superconducting materials. We are looking at such materials in terms of energy generation, for example wind energy generation.
Our research could be done experimentally but due to poorly equipped laboratories, we prefer use of computational methods. This method is convenient to us and very accurate compared to experimental data.
With the availability of CHPC cluster, we have made many advances in our research group and this machine has enabled quick calculations for our levels of research.
Our first PhD student, Elicah is writing her thesis after publishing her first paper and has submitted her second paper. It is expected that she will graduate towards the end of 2019.
Principal Investigator: Prof Kevern Cochrane
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2016-07-01
Allocation End: 2018-06-06
Used Hours: 101856
Project Name: Fisheries management in the southern Benguela system under climate change scenarios
Project Shortname: ENVI0908
Discipline Name: Environmental Sciences
Our research group is based at the Department of Ichthyology and Fisheries Science, Rhodes University. Our collaborators include researchers from different South African Universities and from international universities and research institutes. The group has been active in the project Global Understanding and Learning for Local Solutions (GULLS), which aims to contribute to reduction of vulnerability of marine coastal communities to climate change. The project study areas are five hotspots in the southern hemisphere, of which the ocean area off South Africa is one. Among several objectives, our work explores optimal management approaches to reduce vulnerability of fisheries in the Southern Benguela to future changes, using the Atlantis modelling framework. This modelling framework is computationally intensive and a model run takes at least 5 hours to complete, moreover, only 2 simultaneous runs can be conducted on a normal computer while still being able to use the computer on other tasks. Therefore, having access to the CHPC has been essential for our research, which would have been affected by serious constraints and delays without access to the cluster.
The Atlantis in the Benguela and Agulhas Current systems (ABACuS v2) model has been used to evaluate future trends in abundance of important fisheries resources under climate change, as well as the robustness of indicators under environmental variability and climate change. Progress to date has been good and further work focusing on the likely effects of climate change on future trends in upwelling and primary production is underway. The programme will also contribute to the Model Intercomparison Project – Fisheries sector, which aims to use different ecosystem models from different regions of the world to understand and predict the future effects of climate change on marine ecosystems.
Principal Investigator: Dr Aniekan Ukpong
Institution Name: University of KwaZulu-Natal
Active Member Count: 8
Allocation Start: 2016-10-10
Allocation End: 2018-04-17
Used Hours: 1038821
Project Name: Theoretical and Computational Condensed Matter and Materials Physics
Project Shortname: MATS0941
Discipline Name: Physics
The theoretical and computational condensed matter and materials physics group at the School of Chemistry and Physics, University of KwaZulu-Natal develops and implements state-of-the-art models for studying complex materials. We take special interest in the rich phenomena involved in the interaction of the electron cloud of atoms, molecules and solids with static and dynamic electric and magnetic fields. Our main tool is quantum mechanics as formulated within density functional theory, and we implement it computationally. Our analyses allow us to gain unique insights to complex materials, and their associated phenomena, which can be a predictive guide to experiments.
Our research focuses on the electronic structure of heterostructure multilayer nanoparticles, atomic dynamics in ceramic glass composites, alloys development, and applied spectroscopy. We study charge and spin transport for the development of topological insulators, metallic and semiconducting properties. We also study the response of electronic systems to applied electric and magnetic fields. Our emphasis is on finding answers to questions that arise from materials research in disparate areas of modern society. Finding suitable answers involve doing calculations that help to reveal how electrons behave in materials that contain a very large number of atoms. Such calculations are impossible to perform on laptops or desktop computers. Our use of high performance computing has allowed us to develop technical capabilities in technology areas such as electronics, energy, water purification and nanomedicine, as well as coal beneficiation.
Particularly, in our spintronics research, we have recently predicted the existence of a new robust phase for transporting electrons, which is suitable for storing information efficiently. This finding may pave the way for a whole new family of energy-efficient magnetic recording devices based on artificially-assembled materials.
Principal Investigator: Dr Parvesh Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2016-01-23
Allocation End: 2018-08-30
Used Hours: 23925
Project Name: Molecular dynamics and docking studies of organic compounds
Project Shortname: CHEM0795
Discipline Name: Chemistry
I initiated my independent research group in the School of Chemistry and Physcids at UKZN in 2014. Currently, I am supervising 13 postgraduate students (seven PhD's and five Masters) in addition to 2 Honors and two Post-doctoral fellows. My research interest includes the designing and synthesis of heterocyclic scaffolds. Specifically, we are targeting the chemical agents that have potential to act as anti-bacterial, anti-tuberculosis, anti-cancer, anti-malarial and anti-diabetic agents. We are employing different computer-based technologies such as molecular docking, QSAR, QSPR and pharmacophore modelling to predict novel chemical assemblies from the online databases. The identified lead molecules are synthesized in our organic laboratory and tested in vitro. All the computer simulations are performed on the CHPC cluster, This computing facility has been very useful to find very useful information that was not possible to solve had we not this facility available. Running these jobs on normal computers either would have taken months to finish or would die in middle. With this supercomputing facility in our hand, we not only managed to run complex calculations but obtained constructive scientific explanations for our experimental results. Consequently, we managed to this compiled data in reputed chemistry journals. Moreover, my post graduate students has learnt different computational tools that are being used in drug design and drug discovery field. I am highly grateful to chpc for providing us this wonderful facility.
Principal Investigator: Prof Raymond Hewer
Institution Name: University of KwaZulu-Natal
Active Member Count: 7
Allocation Start: 2016-05-19
Allocation End: 2018-06-28
Used Hours: 46787
Project Name: The design and discovery of small-molecule inhibitors of HIV-1 integrase activity
Project Shortname: CHEM0877
Discipline Name: Chemistry
Our research group, led by Dr Raymond Hewer, within the Discipline of Biochemistry at the University of KwaZulu Natal seeks to design and discover novel compounds with therapeutic potential against HIV-1 and Alzheimer's Disease; two diseases that represent a high burden of disease in South Africa. Our primary approach to identify new compounds involves the use of state-of-art molecular modelling programs which we access through agreement with the CHPC. A number of compounds identified in this manner have proven to be effective in vitro with findings published in various Journal articles.
Principal Investigator: Dr Quinn Reynolds
Institution Name: Mintek
Active Member Count: 2
Allocation Start: 2016-01-23
Allocation End: 2018-04-24
Used Hours: 112982
Project Name: Computational Modelling of Furnace Phenomena
Project Shortname: MINTEK776
Discipline Name: Applied and Computational Mathematics
TAMING THE FIRE
Researchers at Mintek are using the CHPC's powerful supercomputers to solve some of the most radical engineering problems in existence.
Pyrometallurgy is the field of extractive metallurgy which specialises in using high temperatures to transform ores or wastes into useful industrial commodities such as pure metals and alloys, and forms a key link in the minerals beneficiation chain in South Africa's resource-rich economy. It also pushes the boundaries of human ingenuity. Electric furnaces used in pyrometallurgy routinely heat rocky raw materials to temperatures above their melting points – 1500 degrees Celsius or higher – forming liquids similar to volcanic lava which must not only be safely contained and handled, but also chemically reacted with other materials in order to release the products of value. Furnaces are complex pieces of equipment operating under extreme conditions hazardous to both people and instruments, and it is often difficult or impossible to measure information from them experimentally – that's where high performance computing steps in.
By building advanced mathematical and numerical models of the many interconnected phenomena happening inside furnaces, researchers on this project use virtual experimentation and prototyping to make pyrometallurgy more energy efficient, less harmful to the environment, and more capable of processing everything from raw ores to complex wastes. Computational modelling facilitated by the CHPC is an invaluable tool that gives us the ability to stand at the center of the fire and learn its secrets.
Principal Investigator: Prof Phuti Ngoepe
Institution Name: University of Limpopo
Active Member Count: 28
Allocation Start: 2016-04-22
Allocation End: 2018-04-04
Used Hours: 22828431
Project Name: Computational Modelling of Materials: Energy Storage
Project Shortname: MATS0856
Discipline Name: Material Science
Materials Modelling Centre (MMC), at the University of Limpopo (UL), employs High Performance Computing (HPC) methods to design and predict properties of valuable materials. Firstly, the demand of lithium ion batteries is increasing significantly owing to rapidly expanding automotive and energy storage markets. MMC simulates fabrication of lithium ion battery cathode particles made of nickel, manganese and cobalt, which are similar to those grown in production plant reactors. This is intended to reduce deterioration and breakage of such cathodes during charging and discharging in order to extend distances to be covered by electric vehicles in one charge. The work is conducted to support the production of cathode precursors at a pilot plant hosted by UL and supported by the Department of Science and Technology. Batteries beyond lithium ion, with higher capacity are also being investigated. Secondly, high recoveries of precious group metals from mines with the less understood platreef, particularly in Limpopo province, are not easily achieved. MMC, in collaboration with various research groups, use HPC to simulate the design of near green reagents for better recovery. A proof of concept on how simulations reproduce experimental approaches in such designs has been conducted on known sulphide minerals. The concept is being extended to explore ores with precious metal minerals containing less sulphur, with intention of enhancing their recoveries. Lastly, titanium powder metallurgy facilitates convenient manufacturing of alloys. MMC employs simulations to predict properties of high temperature titanium platinum based shape memory alloys. Furthermore, growth of titanium nanoclusters is modeled and provides valuable insights on titanium growth in a pilot plant at the Council for the Scientific and Industrial Research. Simulations across these three themes, are highly computer intensive and are achievable by use of HPC where UL postgraduate students are main beneficiaries.
Principal Investigator: Dr Lucy Kiruri
Institution Name: Kenyatta University, Nairobi, Kenya
Active Member Count: 0
Allocation Start: 2017-06-18
Allocation End: 2018-06-15
Used Hours: 477640
Project Name: KU Computational Chemistry Research Group
Project Shortname: CHEM1032
Discipline Name: Chemistry
CHEM1032: KU Computational Chemistry Research Group
The members of the group are in 3 different areas of Molecular modeling, namely ab initio, Molecular Mechanics and Molecular Dynamics.
Katana Chengo is a 3rd year Ph.D. student. His work entails DFT study of Cationic iron half-sandwich complexes of mixed donor ligands. This involves geometry optimization and frequency calculations with the aim of determining the best coordination site of the mixed donor ligands.
Isaac is a first year Masters student working on re-engineering existing drugs of Mycobacterium tuberculosis by introducing organometallic fragment into their molecular structure and determining drug-likeness computationally. The computations are based on Density Functional Theory (DFT) methods such as B3LYP, CAM-B3LYP, and PBEPBE with the standard Pople's polarized split valence basis set 6-31++G**.
George work entails running a molecular dynamics (MD) simulation to see how my protein molecule responds to various bound ligands. He has finished his work, and he will start his Ph.D. program in September 2018.
Lucy has done calculations on Barakol and anhydrobarakol using gaussian16. The work involves geometry optimization and frequency calculations. The project aims to determine the stability of the two molecules. She is preparing a manuscript.
The CHPC is invaluable in fast-tracking our work since we were using core i5 desktop before where calculations would take much longer. Since the start of using the CHPC, we have made much progress on the work.
Principal Investigator: Prof Warren du Plessis
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2017-03-07
Allocation End: 2018-04-17
Used Hours: 777712
Project Name: Electronic Warfare (EW) Technologies
Project Shortname: MECH0989
Discipline Name: Electrical Engineering
RCS simulation data for simple targets have been generated. These data will be used to support research into innovative methods to reduce the number of simulation points required to obtain accurate RCS results, and into the data available from RCS measurements.
Principal Investigator: Prof Martin Nieuwoudt
Institution Name: SACEMA / Stellenbosch University
Active Member Count: 1
Allocation Start: 2016-01-23
Allocation End: 2018-04-17
Used Hours: 572413
Project Name: Computational Biosystems
Project Shortname: CBBI0807
Discipline Name: Bioinformatics
This is a composite project with a number of sub-components. The Principal Investigator (PI) is Prof Martin Nieuwoudt from the Institute for Biomedical Engineering, Stellenbosch University. The PI's research focus is in the simulation and modelling of non-linear biological processes using large disparate datasets. As the above activities are (very) computationally intensive they cannot be undertaken without access to large scale resources.
To date two student projects have been completed:
1. A Masters Degree in Electronic Engineering with Distinction, by Floris van Zyl in 2017. This was named, 'Characterisation of the dielectric properties of Rhinceros tissue using computer simulation and physical tissue phantom models'. This project focussed on the development of de novo animal tracking technology. This student intends doing a PhD, presumably as a continuation of the subject matter.
2. A PhD in Mathematics, by Eva Ujeneza, currently in the final stages of completion. This is named, Modeling long term Immunological response to antiretroviral therapy for HIV infection. Two publications are currently in near final stages and will be submitted to international journals in the very near future.
Several as yet incomplete projects are underway that will require access to CHPC resources in the future. For example, a graduate Mechatronic Engineering students is busy with the design and computational flow dynamics (CFD) modelling of a novel mammalian-tissue and TB co-culturing device. The CFD modelling will require access to significant computational resources.
In fairness, CHPC access is not required at the present moment, i.e. not within the next month. However, we do sincerely request that the project account for Computational Biosystems be left active so that resources may be applied for as soon as they are required.
Principal Investigator: Prof Ignacy Cukrowski
Institution Name: University of Pretoria
Active Member Count: 9
Allocation Start: 2016-06-10
Allocation End: 2018-05-05
Used Hours: 5369764
Project Name: Understanding chemistry from QM study of molecular systems
Project Shortname: CHEM0897
Discipline Name: Chemistry
Activities in chemistry (in science in general) can be seen as made of two distinctive approaches: 1) development of new theories and methodologies that should lead to better understanding of concepts and chemical process (reactions) and 2) practical implementation of known chemical processes and performing, in principle, routine operations. Our research group in the Department of Chemistry, University of Pretoria, that consists of Prof I Cukrowski (the leader), several PhD, MSc and Honours students as well as a postdoctoral Fellow) is involved in fundamental studies focused on (a) understanding chemical bonds from the electron density distribution throughout a molecule (there are many kinds of bonds but still there is no clue for an ultimate theory of bond; there are various approximate quantum chemical bonding models that can be used only to answer certain questions about particular type of a bond); to this effect several novel methodologies were developed by our group and they are being tested on numerous molecular systems, and (b) modelling reaction mechanisms (to understand on atomic and molecular fragment level how it works or why it does not work) that might be of significance in the development of new drugs in, e.g. tuberculosis (a highly contagious disease that remains a significant public health problem globally) or Alzheimer disease with reported cases growing rapidly throughout the world. Although we started modelling of reaction mechanisms only recently, a significant progress has been made and about 8 research papers are already under preparation. Any pioneering theoretical work, such is ours, requires a large number of real-life molecular systems (made of tenth of atoms) that have to be computationally 'processed' under specific conditions. This, in turn, requires expensive computational resources, such as CHPC, with a dedicated staff to assure it is available to research groups 24/7.
Principal Investigator: Dr John Mack
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2016-01-23
Allocation End: 2018-06-06
Used Hours: 19727
Project Name: Rational design of phthalocyanine, porphyrin and BODIPY dyes
Project Shortname: CHEM0796
Discipline Name: Chemistry
The Centre for Nanotechnology Innovation (CNI) at Rhodes University under director Prof. Tebello Nyokong carries out research related to the use of molecular dyes in biomedical applications, such as cancer treatment through photodynamic therapy, the use of antimicrobial photodynamic chemotherapy for treating hospital superbugs and as sensors for ions that are harmful to human health.
Other applications of interest include wastewater treatment and the development of optical limiters to protect human vision,such as in aviation safety in protecting pilots from the irresponsible use of laser pointers during runway approaches. It is important to understand trends in the electronic and optical properties that make the molecular dyes suitable for these particular applications. The resources of the Centre for High Performance computing help to facilitate this by making it possible to carry out molecular modelling calculations that can be used to predict how changes to the structures of the molecular dyes will modify their properties. The flexibility that CHPC provides where memory allocations are concerned is often vital.
The CNI currently has three staff members, twelve PhD, fourteen MSc and four Honours students, and four postdoctoral fellows, and usually publishes over forty peer-reviewed publications per year. This rose to a high of sixty-five in 2017 with ten involving the use of CHPC resources.
Principal Investigator: Dr Febe de Wet
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2017-01-30
Allocation End: 2018-09-05
Used Hours: 24094
Project Name: Automatic transcription of broadcast data
Project Shortname: CSIR0978
Discipline Name: Other
The Human Language Technology (HLT) Research Group at the CSIR Meraka Institute develop speech and language-related technologies for the South African context to enhance access to information and communication. Given the multilingual nature of South Africa, HLTs can make information and services accessible to a larger proportion of the South African population in a sustainable way, by reaching people in remote locations, people who are not necessarily trained in using technology, or people who are not fluent in English. HLTs can also provide access to information to people with disabilities. HLT can support language diversity and providing of information in multiple languages in an affordable and equitable fashion. The development of all 11 official languages is a national priority, which requires significant attention to HLT in all of these languages. HLT can be of significant economic importance – both by empowering citizens of the country to work more productively, and by forming the core of an exportable set of technologies (since such technologies are currently not available to most of the developing world).
The HLT Research Group operates in a vibrant environment consisting of researchers, developers, project managers and students from backgrounds as diverse as engineering, linguistics and sociology. We conduct basic and applied research into projects related to the following areas of research: automatic speech recognition, text-to-speech synthesis, natural language processing, machine translation, human language analytics, text and speech resource development, speech and language technology system design and implementation, and usability and user experience evaluation of speech and language technology.
Principal Investigator: Prof Mahmoud soliman
Institution Name: University of KwaZulu-Natal
Active Member Count: 26
Allocation Start: 2016-01-23
Allocation End: 2018-04-18
Used Hours: 13126492
Project Name: Drug Design, development and modelling
Project Shortname: HEAL0790
Discipline Name: Health Sciences
The research scope of the Molecular Bio-Computation and Drug Design Research Lab covers a wide range of computational and molecular modeling research areas with main focus on biological systems and drug design approaches. Main interest is related to design and study of biologically and therapeutically oriented targets by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We show keen interest in diseases of global burden and of high prevalence within the south African populace such as HIV/AIDS, Tuberculosis and Cancer. The computational resources provided by CHPC is employed in performing molecular dynamic calculations and the accompanying post molecular dynamic simulation analysis.
Principal Investigator: Dr Thabang Ntho
Institution Name: Mintek
Active Member Count: 8
Allocation Start: 2016-01-23
Allocation End: 2018-04-28
Used Hours: 980478
Project Name: Hydrogen Storage Materials and Catalysis
Project Shortname: MATS0799
Discipline Name: Material Science
In the Advanced Materials Division, at Mintek, we use density functional theory (DFT) and other simulation methods mostly to accelerate our research in finding or engineering new catalytic and alloy materials that can address South African needs in a variety of areas including health (shape memory alloys), water purification, energy (fuel cells), etc. The CHPC offers us the tools and platform to focus on our work to rapidly achieve results via the use of the Lengau super-computer. So far virtual experiments (simulations) have allowed us to validate some of our experimental findings while helping us cut down on the number of laboratory experiments needed to reach project scientific aims and objectives.
Principal Investigator: Dr Tiri Chinyoka
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2016-10-10
Allocation End: 2018-05-05
Used Hours: 2660878
Project Name: Analysis and Solution of Computational Fluid Dynamics Problems via the Finite Volume Method and the OpenFOAM Software
Project Shortname: MECH0943
Discipline Name: Applied and Computational Mathematics
The research group's focus is centered on the complex flow of equally complex fluids and their commercial and industrial applications. Examples of completed projects include flows around aircraft landing gears in the modelling of noise reduction as well as complex flows of polymeric fluids generally as obtaining in the polymer, pharmaceutical and food industries. The scientific modelling of the complex flows of such complex fluids reduces to equally complicated systems of mathematical equations. These mathematical model equations cannot be solved by hand even for the most basic small scale applications. It is therefore necessary to develop scientific computing methods to simulate and solve these problems. This is where the group finds important linkages with the CHPC. The CHPC provides high speed computing facilities to assist in solving our mathematical equations. The computing speed is of fundamental importance as the relevant computations can take weeks or months on an average desktop computer. The collaboration with the CHPC has therefore enabled the group to resolve very complex problems with relative ease.
Principal Investigator: Prof Ray Everson
Institution Name: North-West University
Active Member Count: 2
Allocation Start: 2016-05-09
Allocation End: 2018-06-13
Used Hours: 177219
Project Name: CO2 Capture in Circulating Fluidized Beds
Project Shortname: MECH0866
Discipline Name: Chemical Engineering
High Performance Computing key in SO2 and CO2 Abatement Technologies
Coal-Fired Power Plants are the largest sources of SO2 and CO2 into the atmosphere. Regulatory requirements are forcing big industrial pollutant emitters to implement abatement technologies for cleaning outlet gas from these toxic and climate warming gases. The School of Chemical and Minerals Engineering at the North-West University are working with Industrial Companies in South Africa to improve devices for cleaning pollutants from outlet gases.
An effective method of removing SO2 and CO2 from flue gas originating from the burning of coal is the use of Lime. Fine Lime particles mixed with flue gas is capable of reacting and absorbing these toxic gases. The process of mixing Lime particles with flue gas and allowing the reactions to take place is facilitated in a device called a Circulating Fluidized Bed (CFB). The CFD consist of a riser section in which the particles are introduced to the flue gas and a downcomer where the particles are separated from the clean gas and reintroduced to the flue gas in the riser.
The flow in which the Lime particles interact with the flue gas is called a solid-gas two-phase flow. These two-phase flows are very complex to control especially with the aim of ensuring a uniform particle distribution through the flue gas, which will ensure the most efficient reaction. Computational Fluid Dynamics (CFD) is used to model this kind of complex two-phase flows to better understand and to predict efficiencies of the process. Due to the big size of industrial CFBs very power computers are needed to solve two-phase flows using CFD. World wide the research in gas-solid two-phase flows of plant sized equipment relies heavily on the availability of super computers. This is where the Super Computer facility of CHPC plays a critical role to enable these kinds of flow simulations. The software available on CHPC for two-phase flow applications include OpenFOAM, STARCCM+, MFIX and NEPTUNE_CFD. Current activities include the simulation of the first plant scale Flue Gas Desulfurization unit operating with dry Lime particles in a CFB to be commissioned in South Africa end of 2018.
Principal Investigator: Prof Fourie Joubert
Institution Name: University of Pretoria
Active Member Count: 25
Allocation Start: 2016-06-27
Allocation End: 2018-04-24
Used Hours: 1011659
Project Name: NGS Bioinformatics
Project Shortname: CBBI0905
Discipline Name: Bioinformatics
Users from the University of Pretoria use bioinformatics approaches at the CHPC to study organisms such as viruses, bacteria, fungi, insects, plants, animals and humans.
The work done has a wide range of applications to human health, agriculture and biotechnology and has led to various oral and poster presentations at national and international conferences.
The availability of high-performance computer resources enables biological researchers to perform work that would not otherwise be possible, contributing significantly to the national bioeconomy.
Principal Investigator: Prof Nelishia Pillay
Institution Name: University of Pretoria
Active Member Count: 7
Allocation Start: 2016-01-23
Allocation End: 2018-05-17
Used Hours: 4031508
Project Name: Nature Inspired Computing Optimization
Project Shortname: CSCI0806
Discipline Name: Computer Science
The NICOG (Nature Inspired Computing Research Group) at the University of KwaZulu-Natal and University of Pretoria is using facilities provided by the CHPC to implement distributed multicore architectures to implement evolutionary algorithms and evolutionary algorithm hyper-heuristics to solve real-world industry problems such as packing, scheduling, forecasting, data mining, computer security and routing problems. This research has provided a platform to initiate collaborations with both industry and international institutions working in the area of operations research.
One of the areas in which this research has made an impact is educational timetabling. The algorithms developed have been used to find solutions to university course, examination and practical scheduling problems. One of these approaches developed has automated the creation of heuristics, which are usually derived by humans involving a time consuming process, to solve educational timetabling problems. The approaches developed have also proven to be effective in the field of computer security to detect network intrusions, i.e. whether an intrusion has occurred as well as the type of intrusion.
Principal Investigator: Prof Serestina Viriri
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2016-04-05
Allocation End: 2018-02-21
Used Hours: 21145
Project Name: Computer Vision and Image Processing
Project Shortname: CSCI0836
Discipline Name: Computer Science
Computer Vision and Image Processing Research Group based at UKZN, intend to use this platform with Deep learning related research work.
Principal Investigator: Dr Evans Benecha
Institution Name: University of South Africa
Active Member Count: 5
Allocation Start: 2017-05-25
Allocation End: 2018-05-23
Used Hours: 516533
Project Name: Defect engineering in novel 2-D materials
Project Shortname: MATS1025
Discipline Name: Physics
The research programme titled "Defect engineering in novel 2-D materials" focuses on investigation of the properties of defects in single layered materials - usually one atom thick. The group spearheading this research is headed Dr Evans Benecha and it consists of senior researchers, postdocs and graduate students from the University of South Africa. Single atom layered materials possess interesting properties as opposed to many atom thick materials. For example, graphene – which a single layer of carbon atoms –enables electrons to flow much faster than silicon, is the world's strongest material, harder than diamond, yet lightweight and flexible. This unique combination of superior properties makes it a credible material for new technologies in a wide range of fields. Some of the envisaged applications of graphene as well as other single atom layered materials include making of medical implants, solar cells, stronger sports equipment, and batteries; just to name a few. However, the properties of these materials are not well understood for these applications to be realized. Dr Benecha and his group's approach towards understanding these materials involves use of large computational resources, and access to the CHPC computing facility has significantly reduced the time needed to generate and analyze data. The results from this project will not only assist in the current understanding of the role of defects in these materials, but will also help to reveal potential new functionalities.
Principal Investigator: Dr Thishana Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2016-01-23
Allocation End: 2018-06-06
Used Hours: 52323
Project Name: Combined kinetics,quantum-chemical investigation of reaction mechanisms involving catalysts
Project Shortname: CHEM0821
Discipline Name: Chemistry
The TS Computational Chemistry Research Group (University of Kwazulu-Natal, School of Chemistry and Physics) carries out quantum chemical modelling of homogenously catalysed organic reactions in the inter-domain field of Physical-Organic Chemistry. Computational Chemistry can be classified as 'Green Chemistry' as it is sustainable and does not generate chemical waste. The focus of this research group is primarily on catalytic asymmetric synthesis that have many applications in the pharmaceutical and fine chemical industry. The optimisation of a catalyst offers a good understanding of the factors that are responsible for the rate and selectivity of a reaction. Theoretical calculations, together with experimental kinetic measurements, often can pin down the mechanism. Using this methodology, it is possible to understand, and more importantly, design effective catalysts for a number of asymmetric, catalytic processes. The CHPC provides the facilities: hardware, in the form of the Lengau cluster and software programs such as Gaussian16, amongst many others. Thus far the current project has yielded two publications since 2016.
Principal Investigator: Dr John Bosco Habarulema
Institution Name: South African National Space Agency
Active Member Count: 3
Allocation Start: 2016-06-08
Allocation End: 2018-08-15
Used Hours: 120054
Project Name: Regional Total Electron Content modelling and mapping
Project Shortname: PHYS0896
Discipline Name: Physics
The project aimed at understanding and modelling electron density changes in the ionosphere is being carried out at the South African National Space Agency.
In general, instrumentation for electron density measurements is scarce which necessitates the utilisation of other methods such as modelling that would involve some interpolation and extrapolation over regions that are not sufficiently covered. One of the importance of such work is to be able to do high frequency planning and predictions which are useful for aviation applications. Because of the size of the data involved and high computation power requirements, usage of CHPC comes in handy. A background model has so far been crafted and the next phases will deal with some assimilation to make the model the realistic day to day representation of the ionospheric changes.
Principal Investigator: Dr Daniel Wilke
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2017-04-10
Allocation End: 2018-12-12
Used Hours: 118361
Project Name: Particle Technology and Engineering
Project Shortname: MECH1008
Discipline Name: Computational Mechanics
Discrete element modeling (DEM) remains underutilized due to the computational demands. We recently demonstrated the utility of DEM to assist in understanding the commerical mixing process called Resonant Acoustic Mixing (RAM), which has made significant impact in obtaining homogenous mixing. However, this trademarked process remains poorly understood. The aim of this study was to conducted an experimental and numerical investigation into resonant acoustic mixing and shed light into the dominant parameters that affect mixing as this technology is directly relevant to The National Metrology Institute of South Africa. As they recently acquired a Resonant Acoustic Mixer. A small experimental facility was setup at the University of Pretoria to calibrate a DEM model, which was then extensively used in a sensitivity study.
Principal Investigator: Dr Mary-Jane Bopape
Institution Name: South African Weather Service
Active Member Count: 7
Allocation Start: 2017-05-11
Allocation End: 2018-06-06
Used Hours: 374845
Project Name: Very Short Range Forecasting
Project Shortname: ERTH1022
Discipline Name: Earth Sciences
Extreme weather events can have a disastrous impact on the society and the economy, by causing deaths, injury, damage to property and undermine food, water and energy security. Adverse weather early warning systems can help society prepare for adverse weather and climate events, and to better adapt to a changing climate. The South African Weather Service (SAWS) is the national weather forecast and climate prediction agency and only atmospheric alerting authority in South Africa. SAWS uses a combination of observations and models to advance the society's ability to anticipate potential impact of weather, climate, water and related fields. In this research programme the focus is on the use a number of models to understand how they perform when simulating weather over South Africa. Simulations conducted so far focused on extreme weather events and one student is analysing heavy rainfall events over the East Rand. Other models will also be implemented by SAWS at the CHPC to allow SAWS make strategic decisions on which models to consider as the main operational model. The use of the CHPC cluster is necessary for SAWS to be able to advance the weather and climate services it provides. It may be noted that SAWS has its own HPC system, however this system is used up by operational simulations and gives no allowance for any simulations to be conducted for research purposes.
Principal Investigator: Prof Daniel Joubert
Institution Name: University of the Witwatersrand
Active Member Count: 17
Allocation Start: 2016-01-23
Allocation End: 2018-03-20
Used Hours: 28648158
Project Name: Energy Materials: Numerical explorations
Project Shortname: MATS0800
Discipline Name: Physics
Imagine designing a material atom by atom. Imagine analysing the properties of tomorrow's novel materials before they exist. Computational materials science plays an important role at every of level of the design and engineering of new materials. The rapid advances in computer processing power and memory has given virtual, fundamental, materials design a boost. The first problem faced in designing a virtual material, a material that has not yet been made, is to find the stable configurations in which the atoms in the mix will settle into. The designer must find the configuration of electrons and nuclei, the building blocks of atoms, which result from the interactions among a number of particles that, even for a small piece of material, exceeds the number of particles of sand on all the beaches in the world. This daunting task has a simple solution. Instead of finding the configuration of the real material, the problem is solved for a fictitious material where the constituent particles do not interact. All that is necessary is to find the particle density distribution of the fictitious material, which by design, is the same as that of the real material. A Noble prize was awarded for this idea to the chemists Walter Kohn and John Pople in 1998.
A group of postgraduate students at the University of the Witwatersrand use the computer power at the national Centre for High Performance Computing to conduct virtual experiments on existing and novel materials to examine their potential as energy harvesters. They examine the potential of a selection of materials that can be used as cheap components in solar cells, materials that can generate electricity from waste heat and materials that can be used to split water molecules to extract hydrogen for energy production.
Principal Investigator: Prof Giuseppe Pellicane
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2016-05-30
Allocation End: 2018-04-24
Used Hours: 1013561
Project Name: Computational Study of Structure-Property Relationships in polymer blends relevant to OPV devices
Project Shortname: MATS0887
Discipline Name: Physics
Designing novel organic materials for Organic Photovoltaic devices (OPV) relevant to solar cells by a combined experimental and computational effort is as major outcome in the field of renewable, sustainable and non-polluting sources of energies. In fact, solar energy is an inexhaustible and green energy source and organic molecules allow for a cheap device preparation cost and exhibit relative ease of processability: these two factors meet the requirements for industrial production and large scale diffusion of solar energy as a viable and economic energy source. Nevertheless, the study of organic conducting materials is important for achieving a fundamental understanding of charge transport phenomena at the molecular level, which represents a remarkable scientific progress in the physics and chemistry of semiconductor devices.
As a team of researchers, our group is based at UKZN, and we are working on Theoretical and Computational studies of Complex fluids. We are involved in addressing the research questions of this research proposal. A number of publications in scientific journals are obviously expected as a result of this research endeavour, and we already produced a number of them, even if they are still limited to the computer simulation study of simplified models of polymer blends, where we try to understand the effect of the geometry of the polymer on the blend morphology. We are also presenting the research outcomes of the project in international conferences/workshops, that will allow for broadcast of vital research data on solar cells with the international scientific community and will be beneficial to the global progress towards a green and sustainable earth planet. We acknowledge the skilled and resourceful personnel at CHPC, and the generous allocation of computational resources granted to us by them, which are instrumental to fulfill the goals of this project.
Principal Investigator: Mr Randall Paton
Institution Name: University of the Witwatersrand
Active Member Count: 5
Allocation Start: 2016-04-21
Allocation End: 2018-02-28
Used Hours: 1337341
Project Name: Compressible Gas Dynamics
Project Shortname: MECH0847
Discipline Name: Other
Our group examines high-speed or highly transient phenomena in air with applications in supersonic aircraft, human safety, and industry. The use of high-performance computing allows assessment of flow domains difficult, expensive, or impossible to repeatably test using physical experiments and is an invaluable tool in developing the science of compressible gas dynamics further. Recent work by Masters and Doctoral students has included:
- The development of a design for laboratory blast wave shock tube using high-resolution simulation. This design more accurately models blast characteristics than any previous method while allowing the study of reflection and diffraction behaviour
- The modelling of expansion wave diffraction using the Large Eddy Simulation technique. This challenging but powerful technique has historically seen low usage due to high computational demand entailed and thus this study was only really practically possible using HPC. The behaviour of moving expansion waves has also remained largely unstudied to date and so this work is also very novel
- The modelling of the diffraction of shock waves from shock tubes with non-orthogonal exit surfaces. While an extensive experimental campaign complemented this study, the vortex arch formed in these diffractions (a feature never before identified) could only be confirmed using the visualisation afforded by high-resolution simulation
- The high spation and temporal resolution modelling of the aerodynamic effects of high acceleration on various bodies both due to propulsion and drag
Principal Investigator: Dr Henry Otunga
Institution Name: Maseno University, Kisumu, Kenya
Active Member Count: 1
Allocation Start: 2016-06-07
Allocation End: 2018-05-31
Used Hours: 408664
Project Name: Computational Study of Hematite Clusters
Project Shortname: MATS0888
Discipline Name: Material Science
Sunlight is the most abundant renewable energy resource and considered to be the ultimate solution to address the global energy problem: The Tetrawatt Challenge. However, the vision of solar
energy providing a substantial fraction of global energy infrastructure is still far from being realized. The major challenge is to develop an efficient and cost-effective approach for storing
solar energy that can be used on demand on a global scale. Splitting water photoelectrochemically is a promising way in which solar energy can be harvested and stored through
photocurrent-driven chemical bond rearrangement leading to the formation of molecular hydrogen (2H2O→2H2+O2, E0=1.23 eV, Standard Hydrogen Electrode, SHE), which can be used directly as fuel or as
an intermediate in the production of other fuels.
Hematite (alpha-Fe2O3) has emerged as a candidate photoanode material due to several favorable features: a band gap of about 2.0 eV (which allows for a large fraction of solar spectrum to be
absorbed), excellent stability under aqueous environments, and abundance in nature. Converting energy from the Sun to electricity efficiently via photoelectrochemical splitting of water is based on photo-induced charge separation at an interface (semiconductor/water interface) and the mobility of photogenerated carriers (electron-hole pairs). However, in bulk hematite, the separated charges recombine very fast (very short lifetimes of electron-hole pairs) and have very low mobility, hindering the conversion efficieny. These limitations can be dealt with by nanostructuring hematite, by growing ultrathin films of hematite, and by introducing impurity atoms i hematite. In this work, the structure and energetics of various size clusters of Fe2O3 have been investigated using the plane-wave pseudopotential approach to Density Functional Theory (DFT) and ab initio Molecular Dynamics (MD).
These calculations require a significant amount of compute resources in terms of memory and cpu scaling. In this respect, I am grateful to the CHPC for granting me access to their supercomputing facilities and I hope for more collaboration in future.
Principal Investigator: Ms Robyn Jacob
Institution Name: SA Sugercane Research Institute
Active Member Count: 2
Allocation Start: 2016-11-09
Allocation End: 2018-06-06
Used Hours: 81003
Project Name: Saccharum Genomics
Project Shortname: CBBI0956
Discipline Name: Bioinformatics
The South African Sugarcane Research Institute (SASRI) is an agricultural research institute located in KwaZulu-Natal. The sugarcane industry is a substantial agricultural activity in South Africa and contributes significantly to the country's gross domestic product. In a genomic context, sugarcane has been classed as an "orphan crop" as, despite its economic importance, no reference genome assembly currently exists. The sugarcane genome is large and very complex due mostly to the polyploid nature of the crop. SASRI actively engages in sugarcane genomics research facilitated in part by the computing resources provided at The Centre for High Performance Computing (CHPC). One of our aims is to harness the wealth of both in-house and publicly available genomic and transcriptomic data in order to construct a reference transcriptome for use in sugarcane RNA-seq studies.
We have progressed well towards our aim of constructing a reference sugarcane transcriptome utilising homology to related plant species' and the wealth of sugarcane short-read sequencing data available. We are currently conducting a differential expression analysis to uncover the molecular mechanisms involved in resistance of some sugarcane varieties against the lepidopteran stem-borer pest, Eldana saccharina.
Our experience with the CHPC has been very good and the platform is well suited to deal with large genomic and transcriptomic datasets and the software tools required for downstream analyses.
Principal Investigator: Prof Shazrene Mohamed
Institution Name: South African Astronomical Observatory
Active Member Count: 1
Allocation Start: 2016-05-25
Allocation End: 2018-06-28
Used Hours: 31484
Project Name: 3D rad-hydro simulations of the outflows of evolved stars
Project Shortname: ASTR0880
Discipline Name: Astrophysics
The computational stellar astrophysics group (PI. S. Mohamed) is currently based at the South African Astronomical Observatory and the University of Cape Town. The research uses supercomputers, powerful computational machines at the CHPC, to simulate the complex physics involved in the interactions of stars in the final phases of evolution. The interactions include exchanges with a nearby companion star or planet that can lead to the formation of spirals, disks, jets and even violent stellar explosions. By comparing the models with observations from powerful telescopes, these simulations help us understand how solar systems evolve and ultimately, the fate of our own star, the sun.
Principal Investigator: Prof MESFIN ABAYNEH KEBEDE
Institution Name: University of South Africa
Active Member Count: 3
Allocation Start: 2016-04-21
Allocation End: 2018-08-31
Used Hours: 74364
Project Name: Electrode materials for energy storage systems
Project Shortname: MATS0855
Discipline Name: Material Science
Electrode materials for energy storage systems research program is led by Dr Mesfin Kebede a principal researcher at CSIR.
Electrode materials for energy storage systems is focusing on studying the structural and electrochemical properties of electrode materials for lithium ion battery.
The computational work on electrode materials is very useful to complement the experimental work. The intention is to get strong understanding on the electrode materials using computational calculations.
Before going to laboratory and carryout experiments, it is very useful to do computational research. The computational research work reduces the expenses for chemicals and also save the time to be spend in the experiment. Sometimes, we can get very important information from the computational work than the experimental work. Therefore, the computational research work is very useful.
So far, the progress on the research program is satisfactory and more computational work is still necessary to design materials with enhanced properties and performance.
Who? (identity of the research group and institution)
The computational studies are undertaken within the Smart Places cluster at Energy Centre of the CSIR.
What? (a brief description of the nature of the work)
The works involves the search and identification of suitable materials composition of potential cathode material to be used Li-ion rechargeable batteries that will yield enhanced properties and high performance.
Why? (explain why the work is being done, and sufficiently important to justify use of public resources)
The computational studies serve as a key guideline towards setting up well informed experimental work aimed at synthesizing electrode material that possess improved electrochemical properties such as stability, capacity and cycleability. As a result, first-principles calculations provide the experimental group with a competitive advantage over other researchers elsewhere and position CSIR and South Africa in the forefront of cutting-edge materials research.
How? (give a very brief and superficial description of the process, and how it relies on the CHPC)
Despite systems interruptions sometimes, the current and other envisaged work relies heavily on the Materials Studio software license only accessible through CHPC. The access to computational tools and technical support have proved to be quiet useful in our research endeavours.
How is the project progressing?
So far, despite previous hiccups due to other researchers leaving CSIR employment, we have regrouped and refocused our research efforts as demonstrated by current collaborations with some of the experts in the computational modelling field. We are convinced with the preliminary work that more exciting predictions will lead us to niche research areas that have potential to be registered as intellectual property.
Principal Investigator: Dr Katherine de Villiers
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2016-01-23
Allocation End: 2018-08-15
Used Hours: 29730
Project Name: Investigations of drugable targets relevant to antimalarial action
Project Shortname: CHEM0801
Discipline Name: Chemistry
The Bioinorganic research group (Haem Team) at Stellenbosch University (Dept. Chemistry and Polymer Science) is led by Dr Katherine de Villiers. Our primary research focus is towards understanding mechanism(s) of action of clinical antimalarials so that we are better informed when designing altogether new treatments. The latter is important because of resistance by the malaria parasite. The disease burden caused by malaria is a particular challenge in Africa, and this motivates our research efforts further. We have made use of the CHPC facilities to enable us to investigate drug-target interactions that would otherwise not be possible via experiment. In particular, we have used a program called Materials Studio to investigate the interaction of antimalarials to the surface of crystals of synthetic malaria pigment.
Principal Investigator: Dr Melvin Ferreira
Institution Name: North-West University
Active Member Count: 2
Allocation Start: 2016-10-17
Allocation End: 2018-06-15
Used Hours: 102732
Project Name: Telecommunication and Network Resource Engineering (TaNRE)
Project Shortname: MECH0942
Discipline Name: Electrical Engineering
The TeleNet research group is hosted in the School of Electrical, Electronic and Computer Engineering, North-West University, Potchefstroom campus. Our main research theme revolves around the effective utilisation of telecommunication and network resources. Our main areas of work can be categorised as follows:
1. Access Network planning, both in the fixed networks (e.g. Passive Optical Networks) and wireless networks (e.g. 5G, TV white space networks)
2. Radio Frequency spectrum management and monitoring
3. Wireless mesh and sensor networks
4. Information theory, especially Forward Error Correction and Network Coding
Currently the group consists of 4 researchers, of which three are Computer and Electronic Engineers and one is Industrial Engineer with a background in Business Mathematics and Informatics. The group currently has 12 Masters degree students and 2 Doctoral students.
The work conducted on the CHPC involves the implementation and parallelisation of radio frequency propagation models. Radio frequency propagation models are used to model the path loss experienced between a radio transmitter and receiver. The path loss is reduction in power experienced at the receiver due to distance, frequency, terrain profile and atmospheric conditions to name a few.
As telecommunication networks become more complex, the parameters that need to be modeled increase in number and resolution. This results in computational explosion of the problem. Propagation modelling is a required initial step is most wireless network planning and radio frequency spectrum management tasks.
Apart from human capital development of our students, the time to model large scale propagation predictions have reduced to hours, from previously spending weeks on high-end desktop machines.
To date we have implemented parallel implementations of the Hata-Davidson and Longley-Rice Irregular Terrrain Model (both in Area and Point-to-point mode). Currently we are identifying additional propagation models for parallelisation and improving computational efficiency of the current implementations.
Principal Investigator: Prof Regina Maphanga
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 4
Allocation Start: 2016-07-28
Allocation End: 2018-05-05
Used Hours: 96232
Project Name: Energy Storage Materials
Project Shortname: MATS0919
Discipline Name: Material Science
The group is called Advanced Mathematical Modelling based at Modelling and Digital Science unit of CSIR and uses multiscale methods to develop novel energy storage materials with desired properties and enhanced properties for existing materials. The envisaged outcome of this project is to develop energy storage materials models with improved performance and consistency, which will be cheaper and environmentally benign. The ever-increasing global energy needs and depleting fossil-fuel resources demand the pursuit of sustainable energy alternatives, including renewable sources to replace carbon intensive energy sources. Sustainable and renewable energy is considered to be the most effective way to minimize CO2 emissions. Hence, finding sustainable energy storage technologies is vital for optimally harnessing the renewable energy.
Computational methodologies are very effective in predicting material-structure-property correlations. In this project simulation methods and models based on parallel computing are developed to probe battery materials properties. Centre for High Performance Computing (CHPC) resources are used to develop these parallel methods and algorithms for large and complex material models. Thus, CHPC resources provide a platform to simulate the evolution of material properties at a wide range of external conditions that are not accessible experimentally and fast track acquisition of results. The major of aim of this project is to create a predictive, reliable and robust set of models of materials for energy storage across the materials modelling length scale, leading to integrated multi-scale capability.
Principal Investigator: Dr Chris Lennard
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2016-07-01
Allocation End: 2018-08-30
Used Hours: 13869
Project Name: Wind Atlas for South Africa
Project Shortname: ERTH0909
Discipline Name: Earth Sciences
The Wind Atlas for South Africa project (WASA) is a collaboration between the Danish Technological University and the University of Cape Town, CSIR and SAWS that is developing a wind energy resource map across the entire country. The current WASA resource map covers only parts of the Northern, Eastern and Western Cape and is being expanded in two phases to include (1) KZN and the southern Free state then (2) the remainder of the country. UCT is responsible for the creation of the course scale wind resource map using a regional climate model during phase 2 and 3 of the project. As the simulations are computationally very expensive these are being run on the CHPC infrastructure. The phase 2 map will be produced during 2018 and the final, country-wide map during 2020.
Principal Investigator: Dr GENITO MAURE
Institution Name: Eduardo Mondlane University
Active Member Count: 3
Allocation Start: 2016-07-29
Allocation End: 2018-04-17
Used Hours: 77760
Project Name: Air Pollution and Impacts
Project Shortname: ERTH0917
Discipline Name: Earth Sciences
The "Air Pollution and Impacts" is a project undertaken by the Environment and Climate Research Group from the Eduardo Mondlane University in Maputo – Mozambique. It aims to understand better the feedbacks of the Southern African climate and atmospheric pollution, specifically the tiny solid and liquid particles released by different sources in this region, which remains uncertain for the region despite its already notorious high pollution levels. The research applies state–of–the–art physical climate models that incorporate complex interactions between pollution and climate, which result in different responses of the solar radiation amount reaching the Earth as well as of precipitation patterns. Because of the complexity of interactions in the models, the computational demand is extremely high and only the CHPC has such capacity to host such a project in the region. Thus far, the project has successfully completed its first phase that comprised test simulations of the impacts of wildfires over the Niassa Reserve. Other simulations on pollution source-pathway-receptor analysis is also ongoing.
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 2
Allocation Start: 2017-03-07
Allocation End: 2018-03-20
Used Hours: 4537524
Project Name: Structural, electronic, magnetic properties and anisotropy energy in some metallic and non-metallic heterostructures
Project Shortname: MATS0988
Discipline Name: Material Science
Research in Single-Molecule Magnets (SMM) is motivated by the discovery that a single molecule could behave like a tiny magnet. Such nanoscale magnetism can be exploited in the design of smallest possible magnetic device. Since this scientific breakthrough, there have been efforts at making SMM that have widespread potential technological implications such as in quantum computing, magnetic refrigeration and biomedical applications such as MRI as well as in high-density information storage. Our work is an effort in this direction, and is aimed at investigating and optimizing conditions necessary for the stability of SMM of TbPc2 on a suitable substrate, using the ab-initio density functional theory approach. TbPc2 is one of the most experimentally studied SMM which, owing to a large unquenched orbital moment and a strong spin-orbit coupling, displays single-ion anisotropies and magnetic stability at considerably larger temperatures. A recent experimental study have shown that TbPc2 molecule deposited on antiferromagnetic FeMn films exhibits magnetic hysteresis and exchange bias as consequence of coupling to the uncompensated interfacial Fe spins. To our knowledge, no ab-initio studies have been done on TbPc2 molecule attached on FeMn films up till now. Therefore, atomic level study of TbPc2/FeMn systems is desirable, as this will elucidate the fundamental atomic mechanisms responsible for the observed molecular magnetization. Furthermore, our understanding of such mechanism will assist in the design and search for other room-temperature single-molecular magnets with wide ranging potential technological applications. The CSIR-CHPC/Lengau facility is very crucial to the research as it provides the computational platform on which the calculations are being performed. Furthermore, the personnel at the HPC have been extremely helpful in ensuring that the research proceeds without any significant disruptions.
Principal Investigator: Prof Andries Engelbrecht
Institution Name: Stellenbosch University
Active Member Count: 6
Allocation Start: 2016-07-08
Allocation End: 2019-04-19
Used Hours: 832731
Project Name: Computational Intelligence for Optimization
Project Shortname: CSCI0886
Discipline Name: Computer Science
The computational intelligence research group at the University of Pretoria develops swarm-inspired optimisation algorithms to solve complex problems, where the search landscapes change over time, and where more than one constrained objective have to be simultaneously satisfied. Before these algorithms can be used, they have to be extensively benchmarked and analysed. Such analyses led to further improvements of the algorithms, that are now ready for real-world application.
Principal Investigator: Prof Thuto Mosuang
Institution Name: University of Limpopo
Active Member Count: 6
Allocation Start: 2016-05-20
Allocation End: 2018-06-06
Used Hours: 29259
Project Name: Computational studies of various ultra-hard materials
Project Shortname: MATS0875
Discipline Name: Material Science
Advanced materials for energy and sensing research group at the Department of Physics of the University of Limpopo.
Project description: The project intends to explore different materials which could be used in solar energy generation. Structural, optical, electronic, mechanical, and dynamical properties play a crucial role in identifying suitable candidate materials. Computational first principle and conventional molecular dynamics methods will be used to predict materials with notable qualities. Scanning Probe Microscopy will further be utilized and modelled to probe the desired solar cell properties. Electrical measurements will then be applied to the convincing candidate materials for final confirmation.
This project intends to foster research at Honours, Masters and PhD level using fundamental Physics and Chemistry applied to different materials. The materials developed are bound to expand national and global knowledge on advanced materials and efficient solar energy usage. It is through this project that notable challenges experienced by ESKOM in supplying the communities with efficient energy are being addressed. In addition to this knowledge base and theory on energy conservation and storage will be created. Postgraduate training and human capacity development will also be notable impacts of this project.
CHPC resources as a national facility comes handy to our research group as supercomputers are a challenge for less established researchers to access. With CHPC resources my group is able to perform good calculations and further present our results mostly in the Annual South African Institute of Physics Conferences.
Currently the project is having one Masters student (male) working on stability and defects in graphene. A PhD female student is working on structural, optical, and electronic excited properties of CuS and CuSe. Their findings will be mapped with some experimental results to have a clear understanding of the nature of solar cell materials.
Principal Investigator: Prof Krishna Bisetty
Institution Name: Durban University of Technology
Active Member Count: 8
Allocation Start: 2016-01-03
Allocation End: 2018-04-04
Used Hours: 3952893
Project Name: Computational Modelling & Bioanalytical Chemistry
Project Shortname: CHEM0820
Discipline Name: Chemistry
Our research focuses on smart biodevice platforms in biosensor technology using experimental and computational methods. This is achieved by incorporating nanostructured electrode materials into electroactive polymers for the design of biosensors for applications in the environmental, food and health sectors. The broader goals are to design, model and fabricate doped smart materials to improve drug delivery and biosensing systems. In this regard, we make use of aptamers to selectively detect the presence of specific biomolecules or compounds in a given environment, by producing an electrical signal that is equivalent to changes reflected in the biologically sensitive element or receiver. Due to the diagnostic methods not being able to produce reliable results, high level computational tools such as molecular dynamics simulations, molecular docking and density functional codes available on the CHPC cluster are used as a guide to design novel aptamers from biomacro-molecules. This has led to our current invention involving the development of an aptasensor specifically to target capsaicin, a chemical compound responsible for the pungency in various chilli-based food samples.
Principal Investigator: Prof Alan Christoffels
Institution Name: University of Western Cape
Active Member Count: 3
Allocation Start: 2016-01-30
Allocation End: 2018-08-09
Used Hours: 434694
Project Name: Bioinformatics and Public Health
Project Shortname: CBBI0819
Discipline Name: Bioinformatics
The Christoffels' lab is based at the the South African National Bioinformatics Institute on the University of the Western Cape Campus. We use computational tools to understand host-pathogen interactions. We are developing methods to analyse genomics data with a view to understand bacterial drug resistance. We also use existing tools to gain insight into functional aspects of bacterial biology. Identification of drug targets in bacterial genomes include gleaning information from the genetic data in bacterial genomes but also looking more closely at protein structure. In this context the resources at CHPC has helped us to take a closer look at the molecular level to understand how proteins and drugs communicate with each other. Of particular interest has been the effect of modifications to an enzyme that metabolize tuberculosis (TB) drugs. DNA sequencing has identified mutations in this enzyme specifically in people of mixed ancestry. The implication is that such mutations could result in the enzyme breaking down the drug too fast or too slow- this impacts the effect of the TB treatment. We have modelled the enzyme and the drug together and assessed the impact of mutations on the function and integrity of this enzyme-drug complex. The computation required to simulate the molecular interaction between the drug and the enzyme (and within the enzyme) is heavily dependent on the compute power based at the CHPC. This work has been key to motivate for additional experiments to validate this work. We continue to explore the use of analytics to inform drug development. Our methods are now moving to the use of machine learning approaches to extract features from structural information to predict the likelihood of a molecule being druggable. This work has application in the plethora of herbal compounds being published from crude extracts.
Principal Investigator: Prof Veikko Uahengo
Institution Name: University of Namibia
Active Member Count: 11
Allocation Start: 2017-08-02
Allocation End: 2018-06-06
Used Hours: 343476
Project Name: Solar Materials
Project Shortname: MATS1043
Discipline Name: Material Science
The group is working on Solar materials, based at the University of Namibia (UNAM). The group is targeting local available materials with photocatalytic properties used in the development solar materials. The raw materials such as zinc oxides and copper oxides are used nowadays to harvest energy from the sun, after smart engineering of their band gaps. These materials are abundant in Namibia, and currently they are exported in their raw for without even a single percentage of value addition. Importantly, energy has become critical in our ever fast growing societies which are becoming highly dependent on energy for technological advancement. Thus, local available resources must be exploited for value addition and also to solve our own problems, for the benefits of our societies. The CHPC has become a powerful intermediator making life very easier for researchers, because it is used into predicting which system is suitable for a certain functionality, then the simulations can be used to determine experimental work, eliminating those which are neither possible (experimentally) or not good enough for that particular functionality. This saves a lot of money in chemicals and solvents along the way. Thus far, the progress of the projects have ran smoothly and achieved milestaones, that could not be possible without this Facility.
Principal Investigator: Prof Carlos Bezuidenhout
Institution Name: North-West University
Active Member Count: 8
Allocation Start: 2016-06-14
Allocation End: 2018-04-26
Used Hours: 229597
Project Name: Metagenomics studies of Microbes
Project Shortname: CBBI0890
Discipline Name: Other
Researchers in the Microbiology research group at the North-West University in Potchefstroom are using the CHPC facility to analyse large data sets. The programme involves amongst others: Whole genome mapping of bacteria for horizontal gene transfer; Whole genome mapping of a novel Xanthomonas plant pathogen; Mapping of plasmids; Microbiome analysis of agricultural soils; Microbiome analysis of water and sediment Environmental metagenomics of drinking water production facilities; Transcriptome analysis of Bt Resistant Busseola fusca. The research focus on water and food security and safety. These are important issues and obtaining local data is critical. Whereas large data sets could be generated quite routinely it is the data mining and analysis that requires sufficient computing capacity, such as that provided by the CHPC. Several papers had been published or are in the final draft stage. Having this capacity also provide this research group (CBB10890 – Metagenomics studies of Microbes) with competitive advantage is applications for funding.
Principal Investigator: Prof SALAM TITINCHI
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2017-02-08
Allocation End: 2018-09-05
Used Hours: 152380
Project Name: Molecular structure and Excited state Investigation
Project Shortname: CHEM0977
Discipline Name: Chemistry
Photochromism is a phenomenon in which a molecule change color when subjected to e.g. light, this new color means different molecule due to change in structure due to absorption of light . Also, this structure changes when light is being absorbed means the molecule goes from stable to less stable structure. These new molecules generated by light could serve as energy storage molecules and they give such energy when light source is switched off.
This photochromism phenomenon has many applications in material science such as in electronic devices they may act as photo-switches, optical memories, storage and display devices such as keypad buttons. These species are also used as printing inks in security fields in which the ink is invisible under normal light but it becomes visible under UV irradiation.
This project aims to prepare molecules called Chalcones these molecules when subjected to light change structure and give colored molecule called Chromene. The Chromene reverse back to Chalcone when light source is switched off . The project has several phases, one of these phases is 3D structure modeling to enhance the understanding of the physical properties of photchromic molecules this will be done by computer modeling using computer code such as Gaussian 9 and 16 available in CHPC.
Another phase of the research is to study the structure of the excited states which is generated from the light absorbed by the first molecule i.e. Chalcone . This study will help in understanding the photo -reaction of Chalcone to Chromene and open the future to design new molecules as photo-switches.
The CHPC as a huge computer is helping us to overcome problems encountered in desk top type computers . So far we managed to resolve a problem with the aid of CHPC that the desk top failed to give a reasonable result and the modeling process is continuing to finalize the required computations for the project.
Principal Investigator: Prof Denis Pollney
Institution Name: Rhodes University
Active Member Count: 4
Allocation Start: 2016-08-11
Allocation End: 2018-04-17
Used Hours: 1406584
Project Name: Gravitational waves from binary black hole mergers
Project Shortname: ASTR0921
Discipline Name: Astrophysics
Black hole mergers are the most prominent sources of gravitational waves (GW), and have been the subject of much excitement in recent years. In 2015, the first observation of a pair of colliding black holes was observed by the LIGO gravitational wave detector and was the subject of the 2017 Nobel Prize in Physics. Since then, a half dozen other merger events have been recorded delivering a wealth of information about these object to astrophysicists.
The Rhodes Mathematics Department is part of an international collaboration developing, running, and interpreting computer models of black holes in order to better understand their properties and their gravitational wave emissions. There is a great deal of work to be done to understand subtle features of GW signals which may to a new understanding of our classical theory of gravity, including the possibility or modifications to the century old theory of general relativity.
Our group has focussed on studying GWs from systems that may mimic the signatures of binary black holes. Objects called ``boson stars'' represent a particularly simple form of matter that can yield very similar signals. By characterizing subtle differences between signals generated by these objects we hope to remove an important source of ambiguity and confirming our classical understanding of gravity.
High accuracy demands large computational resources. Expanded fully, the Einstein equations of general relativity involve 20000 computations at each point within a spacetime. As a result, these simulations are carried out at some of the world's largest supercomputers, including the one at the CHPC. Our simulation code, developed with collaborators around the world, is contributing to an international effort to understand these systems. And locally developed techniques, including ``characteristic matching'' -- a method of evolving spacetimes without boundaries -- are leading to new levels of precision in our ability to model black hole systems.
Principal Investigator: Dr Theodor Loots
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2016-04-04
Allocation End: 2019-02-28
Used Hours: 1316635
Project Name: The arc length of statistical functions
Project Shortname: CSCI0829
Discipline Name: Applied and Computational Mathematics
In the StatDistT research group of the Department of Statistics, at the University of Pretoria, a specialised unit exists having computational and methodological statistics as focus. The StatDistT group are led by Prof. Andriette Bekker, and with Dr. Theodor Loots working in the above mentioned focus area.
Part of the work investigated by this unit, includes the establishment of non-parametric methods which relies on empirical rather than exact distributions. The construction of these empirical distributions often rely on computer-intensive methods, which makes it ideal for Lengau at the CHPC. Techniques such as the bootstrap and kernel density estimates are often used, which will be investigated in higher dimensions in the future.
One of the main research questions is how Statistics may benefit from high performance computing, so that under the assumption of unlimited computing power, it is to be understood if we can "do better". It is not difficult to imagine that in a couple of decades from now, desktop computers will have similar computing capacity than high-performance computers, but what will Statistics have braught to the table by then? Will it still be stuck in a world where "it takes to long" or "it is to difficult to compute", or would it have moved on to "we already have ... in place"?
Principal Investigator: Dr Madison Lasich
Institution Name: Mangosuthu University of Technology
Active Member Count: 7
Allocation Start: 2017-06-08
Allocation End: 2018-06-06
Used Hours: 142461
Project Name: Chem Thermo
Project Shortname: CHEM1028
Discipline Name: Chemical Engineering
The Thermodynamics, Materials and Separations Research Group based at Mangosuthu University of Technology focuses on studying the thermophysical properties of matter, with a view to developing novel materials and improving industrial separation processes. In particular, research thus far has examined polymer membranes, clay adsorbents, and aqueous crystals. The use of molecular simulations (by way of the CHPC's resources) enables us to obtain insights not achievable in the laboratory. A key goal of this research is to develop new materials and products which can benefit the local economy. Our research is ongoing, and so far we have had several papers accepted to international conferences.
Principal Investigator: Prof Kevin Naidoo
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2016-04-05
Allocation End: 2018-03-28
Used Hours: 2215100
Project Name: Reaction Dynamics of Complex Systems
Project Shortname: CHEM0840
Discipline Name: Chemistry
The research groups within the Scientific Computing Research Unit (SCRU) are mostly interested in the development and applications of methods useful to Life Scientists and Material Scientists. We develop computational and informatics software using methods in applied mathematics and physics to construct algorithmic solutions useful to chemists and biologists. Our Cancer Translational Science Laboratory applies the computation and informatics technologies to provide models for experimental scientists aiming to achieve Translational Research goals in medical and chemical science.
SCRU is able to leverage the large-scale parallel compute capacity of the CHPC to solve frontier challenges in computational chemistry and scientific computing. In particular, by running across many compute cores we are able to efficiently approximate the Schrodinger equation for large systems. By using parallelised multiscale ab initio/MM molecular reaction dynamics (FEARCF) we calculate the reaction mechanisms of enzymes and develop an electronic understanding furthering insight towards inhibitor development.
Principal Investigator: Prof Francois Engelbrecht
Institution Name: University of the Witwatersrand
Active Member Count: 14
Allocation Start: 2017-01-30
Allocation End: 2018-06-15
Used Hours: 22416317
Project Name: Development of the first African-based earth system model VRESM and its projections of future climate change over Africa
Project Shortname: ERTH0859
Discipline Name: Earth Sciences
New African-based Earth System Model
The first African-based Earth System Model is under development at the Council for Scientific and Industrial Research (CSIR) in South Africa, through a collaboration with the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Australia and South Africa's Centre for High Performance Computing (CHPC). Earth System Models are used to simulate global climate change, including the feedbacks between the atmosphere, ocean, land-surface and carbo n cycle that may occur whilst he planet is warming. What is making the CSIR Earth System Model unique is that it is the only model being developed in Africa, through an African and Southern Hemisphere lens. The reliable simulation of critical African climate issues, such as the occurrence of drought in southern Africa in response to El Niño events, the flooding that sporadically occur over Mozambique in response to landfalling tropical cyclones, is key in the development of the new model. The model development process is also focussed on the Southern Ocean's role in regulating southern African climate, as well as the global climate through the absorption of carbon dioxide in the ocean. The development and application of an Earth System Model is a computationally extensive endeavour, and was impossible to undertake in South Africa before the Lengau cluster of the CHPC became available in 2018. The CSIR-CHPC partnership towards development of the new model has in 2017 led in the generation of the largest set of projections of future climate change over Africa ever generated in Africa. These simulations have provided new insight into the plausible impacts of climate change in South Africa, including how the frequencies of droughts, heat-waves and landfalling tropical cyclones may change over the next few decades. These projections were key in informing South Africa's Third National Communication on Climate Change, which was finalised early in 2018 under the science leadership of the CSIR. The CSIR and CHPC are now set to make Africa's first contributions to the international Coupled Model Intercomparioson Project Phase Six (CMIP6) of the World Climate Research Programme in 2019.
Principal Investigator: Prof Zander Myburg
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2017-04-24
Allocation End: 2018-06-06
Used Hours: 8962
Project Name: Forest Molecular Genetics (FMG) Programme
Project Shortname: CBBI1015
Discipline Name: Bioinformatics
We are not ready to make a press release since both projects are ongoing.
Principal Investigator: Prof Catharine Esterhuysen
Institution Name: Stellenbosch University
Active Member Count: 8
Allocation Start: 2016-01-23
Allocation End: 2018-03-20
Used Hours: 3053373
Project Name: Computational chemistry analysis of intermolecular interactions
Project Shortname: CHEM0789
Discipline Name: Chemistry
Intermolecular interactions play a fundamentally important role in the properties of solid materials. For instance, molecules are taken up into porous materials as a result of the interactions between these species, while the manner in which they interact has an influence on the sorption ability of the porous material. Calculations performed using the CHPC's computational facility have allowed us to explain the role that intermolecular interactions play in the unusual sorption properties of various porous compounds. We have also been able to establish methodologies for determining the behaviour of radicals and polymorphism in a variety of compounds, including cage compounds. We are slowly moving toward the goal of explaining catalytic and biological processes through understanding the role of intermolecular interactions in the mechanism in order to predict improved catalysts and biologically active compounds.
Principal Investigator: Prof Gerrit Basson
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2017-03-07
Allocation End: 2018-04-28
Used Hours: 727222
Project Name: CFD modelling of Hydraulic Structures in Rivers
Project Shortname: MECH0985
Discipline Name: Computational Mechanics
The research group consists of 3 PhD students at the Department of Civil Engineering, Stellenbosch University, who are actively investigating the highly dynamic behaviour of hydraulic structures in rivers. Key aspects which are being investigated include, fluid-structure interaction, sediment dynamics and aeration. The work is of an academic nature and aims to expand the knowledge of these unique structures in addition to supporting engineers by providing them with new data and testing novel concepts.
One of the fields of the research is the modelling of bridge pier scour in alluvial rivers to ensure that bridges are protected against collapse caused by the undercutting action of scouring in rivers. The CHPC has allowed a new numerical model to be developed for the prediction of sediment transport in rivers with vortices induced by obstructions.
The CHPC assists in the research by allowing the research team to more extensively (and speedily) explore this behaviour than would otherwise be the case.
Principal Investigator: Prof Rajshekhar Karpoormath
Institution Name: University of KwaZulu-Natal
Active Member Count: 9
Allocation Start: 2016-04-01
Allocation End: 2018-06-15
Used Hours: 82746
Project Name: Design of small novel organic compounds as potential drug candidates
Project Shortname: HEAL0835
Discipline Name: Health Sciences
To say in short for non technical audience, The use of CHPC saves your 90% computational time if you are trying a normal desktop at your place. You can enjoy the saved time.
Principal Investigator: Prof Yoshan Moodley
Institution Name: University of Venda
Active Member Count: 6
Allocation Start: 2016-07-15
Allocation End: 2018-06-06
Used Hours: 26621
Project Name: Mammalian Evolutionary Genomics
Project Shortname: CBBI0911
Discipline Name: Bioinformatics
The University of Venda leads the way in Conservation Genomics
Genetic information stored in the DNA of organisms can be used to help in their conservation. Using information contained in the whole genome of animals, researchers and students at UniVen's Department of Zoology are unlocking the genetic secrets required to more effectively conserve the world's endangered wildlife species. This is because genetic information can be used to check on how healthy a population is, and how related a population is to other populations. This is essential information for conservation managers on the ground who need to make decisions on how to manage populations and to identify the individuals most suitable for relocation to other populations.
Our group is unique in the Republic since no other university is yet able to carry out such work on non-model animals at the whole genome level. The Department has thus become a centre of excellence, generating postgraduate students with the rare skills of understanding, manipulating and interpreting genome level data.
The amount of data contained in just one genome is massive - approximately 3 billion DNA base molecules. This becomes even more complex when populations of individual genomes are analysed together. The service of the CHPC in this regard could be invaluable to the success of the group, especially if our larger memory requirements can be met.
Ongoing projects include population genomic appraisals of the highly endangered black rhinoceros in southern Africa; an assessment of relatedness between African forest and savanna elephants; divergence between Asian leopards and genetic exchanges between brown and polar bears. Thus far, one Masters student has completed his thesis.
Principal Investigator: Prof Tahir Pillay
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2016-05-25
Allocation End: 2018-05-10
Used Hours: 1119143
Project Name: Molecular Modelling of ligands and receptors
Project Shortname: HEAL0876
Discipline Name: Health Sciences
Prof Tahir Pillay's research group in the Department of Chemical Pathology, University of Pretoria is actively working in the field of pharmacoinformatics applications in disease. The groups has used the facility of CHPC since 2014. The research group uses several pharmacoinformatics tools to design computational models followed by screening of small molecular databases and simulations.
Inherited and acquired disease such as HIV, Mycobacterium tuberculosis and Alzheimer's diseases pose serious challenges. According to WHO, in 2012, there were an estimated 8.6 million new cases of tuberculosis (TB) and 1.3 million people died from TB. Acquired immunodeficiency syndrome (AIDS) is an epidemic disease with an estimated two million deaths each year and remains one of the world's most significant public health challenges, particularly in low- and middle-income countries. To date, there is no selective therapy which can securely treat or control such disease. In this context and in this field of research it is imperative to search for more lead molecules to treat such disease.
They are using several techniques including pharmacophore-based virtual screening, molecular docking, molecular dynamics and quantum chemical approach to identify novel promising molecules from the free and commercial small molecule databases. Several computational approaches are used to validate the screened molecules.
The project has already achieved several outcomes in form of research articles and conference presentations.
In the CHPC, the group's research makes extensive use of Schrodinger, Amber, Gromacs etc. and they have published a number of research articles in international journals. Their research work is entirely dependent on pharmacoinformatics tools available in the CHPC server. The Department of Chemical Pathology does not have the high performance computing infrastructure to carry out this research as it requires the computational tools and capability of the CHPC. Hence, this research group is completely dependent on access to the CHPC server to fulfil the objectives of the envisaged projects. They are very pleased with the services available in the CHPC server and are grateful to the entire CHPC team for their efforts and support.
Principal Investigator: Mr Adebayo Azeez Adeniyi
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2016-11-10
Allocation End: 2018-03-28
Used Hours: 1518626
Project Name: Drug Discovery Research Using Quantum and Molecular Dynamic Simulation
Project Shortname: CHEM0958
Discipline Name: Chemistry
Dr Adebayo Adeniyi is the PI of the research group on: Drug Discovery Research Using Quantum and Molecular Dynamic Simulation. The focus of their research is centred around the application of computational tools in the area of drug design and discovery, electrochemistry, spectroscopy and electronic properties of molecules. The computational tools are used to search the library of many existing molecules in the database to know which of them will be an effective replacement for existing drugs that are found to be less active or that the pathogens have developed resistance to. It has lead to a more speedy drug discovery, less expensive and is know to be a faster and efficient way of screening million of molecules against pathogenic targets. Many of our application of computational tools has giving better insight into the behaviour of drug candidates in the target enzyme of the pathogens. We have also used the computational tools to look at the effects of introducing new groups of atoms into a molecule and how it has increased the effectiveness of the drug candidates. Another interesting part of the works we have done is to make use of the computational tools to study the change in the properties of the target enzymes as a result of changing in their shape (i.e. conformation) and what are the shapes of these targets that result into their cross resistance to existing drugs (i.e. making existing drug ineffective) and what need to be done to get better drug candidates against such conformations. In all these aspects of research, the HPC facilities are our major resources, we have made used of installed softwares like AMBER, GAUSSIAN and many other installed programs on HPC to make all these areas of research possible. Many of our great discovery through the application of HPC facilities have been shared with the scientific audience all over the world through research articles publication that is up to six in 2017 and also through conferences presentations.
Principal Investigator: Dr Ndumiso Mhlongo
Institution Name: University of KwaZulu-Natal
Active Member Count: 1
Allocation Start: 2017-03-15
Allocation End: 2018-06-06
Used Hours: 28444
Project Name: Biomolecular Modelling Research Unit
Project Shortname: HEAL1002
Discipline Name: Health Sciences
Biomolecular Modelling Research Unit is located at the University of KwaZulu-Natal, Howard College Campus and headed by Dr Ndumiso N. Mhlongo. This research group employs CHPC resources to conduct molecular dynamics simulations to analyse the dynamical properties of macro-molecules such as folding and allosteric regulations; ligand-receptor interactions; atom-to-atom interactions; protein-protein interaction;virtual screening and molecular docking of active molecules; QSAR etc, for the design and development of inhibitors against diseases and disorders. Through the use of CHPC resources, we have designed potential inhibitors against M. tuberculosis and cancer treatment. These have made contributions to discovery new inhibitors & new knowledge which could directly translate into real health benefits of the society.
Principal Investigator: Dr Gwynneth Matcher
Institution Name: Rhodes University
Active Member Count: 5
Allocation Start: 2016-11-09
Allocation End: 2018-06-06
Used Hours: 87787
Project Name: Microbial Ecology in Antarctic and aquatic ecosystems
Project Shortname: CBBI0952
Discipline Name: Environmental Sciences
Our research group, at Rhodes University, focuses on Antarctic microbial ecology. Antarctica experiences extreme physical conditions (e.g. low temperatures, high UV radiation, etc.) all of which impose enormous survival pressures on the fauna and flora. What is not commonly known is that the vast majority of the biomass in Antarctica is represented by microbes which, for most regions, have not been investigated. In order to provide accurate and holistic distribution patterns of the biota in Antarctica, these knowledge gaps need to be filled in. The relative simplicity of the trophic systems found in Antarctica make these ecosystems particularly vulnerable to the effects of global climate change. In order to assess the effect of global climate change on biodiversity, the current biodiversity of microbial species and their contribution to ecosystem functioning (e.g. decomposition, nutrient cycling, etc.) needs to be established. In addition to global climate change, increasing human presence in Antarctica further threaten the ecosystems. Mitigation of these impacts has generally focussed on processes involving higher organisms such as plants and invertebrates with little attention given to the consequence of microbial contamination. The introduction of non-indigenous microorganisms into these delicate ecosystems has several serious and long-standing ramifications. The most obvious is the extinction of endemic microbial species due to invasive species which will not only result in irrevocable losses of endemic species, but the alteration of microbial population structures will also dramatically affect the functioning of ecosystems. Assessing anthropogenic impacts is thus of critical importance and research to this end will inform future environmental protection policies in Antarctica. Our research assesses microbial populations using sequence analysis of target genes. The data generated is analysed on the CHPC servers and allows us to identify which microbial species are present and their role in the functioning of these ecosystems.
Principal Investigator: Prof Ed Sturrock
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2016-09-07
Allocation End: 2018-06-28
Used Hours: 51442
Project Name: Structural elucidation of Angiotensin Converting Enzyme using cryo-electron microscopy
Project Shortname: HEAL0931
Discipline Name: Health Sciences
Proteases are enzymes that play an important role in a variety of biological processes. The angiotensin converting enzyme (ACE), for example, is comprised of two parts, the N- and C-domain, which respectively function in scar tissue formation and blood pressure regulation. Conditions such as cardiovascular disease, diabetes, obesity and tuberculosis can lead to excessive scar tissue formation, known as fibrosis, which ultimately prevents organ function. Currently, there is no specific treatment for fibrosis and affected individuals have a mean survival period of 2-4 years. In 2010, 31.1% of the global adult population were suffering from hypertension. It is a major risk factor for stroke and cardiovascular disease with an especially high burden in middle- to low income countries. The Zinc metalloprotease group at the UCT IDM (Department of Integrative Biomedical Sciences), headed by Prof Edward D Sturrock, has a long-standing interest in ACE. Although ACE inhibitors reduce fibrosis and are widely used to treat hypertension, some patients experience side-effects of rash and severe swelling below the skin surface. Sturrock and co-workers therefore designed drugs to specifically block the C-domain for hypertension or the N-domain for fibrosis treatment but their advancement to clinical trials is hampered by a poor understanding of their mechanism of action. Assisted by the CHPC's computational resources, they simulated the interaction between these molecules and ACE using molecular dynamics simulations. This relies on the principles of physics and requires high computational power to simulate how thousands of protein atoms move at a given temperature and pressure. They found that a promising anti-fibrotic compound's binding was guided by opening of the N-domain's three-dimensional structure through a so-called 'breathing' motion. In future, they will utilize these findings to further the clinical development of anti-hypertensive and anti-fibrotic treatments with reduced side-effect profiles.
Principal Investigator: Mr Muaaz Bhamjee
Institution Name: University of Johannesburg
Active Member Count: 3
Allocation Start: 2016-04-05
Allocation End: 2018-04-17
Used Hours: 266065
Project Name: Modelling of Multiphase Flow in Process Equipment
Project Shortname: MECH0837
Discipline Name: Computational Mechanics
The research group is from the Department of Mechanical Engineering Science at the University of Johannesburg. The primary area of interest in the research is the use of coupled computational fluid dynamics and computational granular dynamics models to investigate the complex multiphase interaction in process equipment. The models are based on multiple continuum and meso-scopic based approaches which are couple with models such as the Discrete Element Method, Immersed Boundary Method and Eulerian Dense Discrete Phase Models. Both commercial and open-source software has been used in the research. Primarily the research has been focussed on hydrocyclones. However, the research is moving onto fluidised beds, spiral concentrators, highly concentrated slurry flows and gas cyclones. The models are benchmarked (for accuracy) against experimental measurements as well as for computational efficiency. Accurate and computationally efficient modelling of such phenomena is vital to the design of hydrocyclones which is crucial to the mining industry. The research group has produced numerous publications and has supported the research of four post-graduate students. Research into the computational efficiency of the models is continuing with the aid of the Centre for High Performance Computing (CHPC) facilities. Due to the complex physics and fidelity required in the problems tackled by the research group large computational resources are required. The CHPC provides a computational resource platform that is vital to the ongoing work and success of the research group.
Principal Investigator: Dr George Manyali
Institution Name: Masinde Muliro University of Science and Technology, Kakamega, Kenya
Active Member Count: 11
Allocation Start: 2016-01-23
Allocation End: 2018-05-31
Used Hours: 258295
Project Name: Ab Initio study of Thermoelectric Materials
Project Shortname: MATS0712
Discipline Name: Material Science
The Computational and Theoretical Physics (CTheP) Group at the Department of Physics, Masinde Muliro University of Science and Technology, comprised of a team of researchers and students dedicated to the development and application of computational modeling to outstanding problems in materials science. In general, the group seeks a deeper understanding of quantum-mechanical descriptions of interacting electrons and nuclei in order to predict and design properties of materials and devices using density functional theory as a tool for the first-principles simulation. This kind of simulations generates volumes of data which cannot be handled by the common desktop computers. High-performance computing provides the computational environment that includes parallel processing, large memory, and storage of the big data. Therefore, Center for High-Performance Computing facility in Cape Town, South Africa, plays a vital role in providing the resources that aid the discovery of new materials and accelerates its application in the industry, an achievement that would have been in vain with desktop computers. Some specific projects for our group include characterization of already known thermoelectric materials. The information gained from this project is used as identifiers in search for new thermoelectric materials with the tailored figure-of-merit. Such materials are used to enhance the efficiency of thermoelectric generator power system for renewable energy. Such outcomes of our projects have an impact on the livelihood of the rural communities in Kenya, and generally, supports the Agenda Four of the Kenyan economic blueprint that was recently availed by the president of the Republic Kenya.
Principal Investigator: Prof Moritz Braun
Institution Name: University of South Africa
Active Member Count: 3
Allocation Start: 2016-09-06
Allocation End: 2018-03-20
Used Hours: 2558630
Project Name: Density Functional studies using a variety of different methods and considering materials of current interest
Project Shortname: MATS0924
Discipline Name: Physics
Using calculations based on quantum mechanics, we have investigated various two dimensional materials. These calculations were performed on the CHPC super computing facilities.
The simulations described the chemical doping and modification of ReS2, ReSe2, MoS2 and boronitride materials. The properties of these materials were modified with resultant improvement in their electronic, optical and/or magnetic properties.
Being able to modify the properties of the above mentioned materials promises to allow the creation of new materials with fine tuned properties. These materials would be of interest in advanced semiconductors, opto-electronic devices or magneto-optical devices.
Principal Investigator: Prof Abu Yaya
Institution Name: University of Ghana
Active Member Count: 4
Allocation Start: 2017-03-07
Allocation End: 2018-04-03
Used Hours: 808035
Project Name: DFT modeling of weak interactions; a case study for Carbon nanosystems
Project Shortname: MATS0990
Discipline Name: Material Science
This research team is made up of members from the University of Ghana and the University of Agriculture, Abeokuta, Nigeria.
The work involves the use of computer models for the understanding of how the human DNA are arrange (known as pi-pi stacking) and also how materials bond together to form stronger materials which are used for building and electronics applications.
Without a computer with large memories which are known as clusters, it will not be possible to understand this behaviour. Eventhough this can be done by experiment, this will take years to really understand but with computer models, it will be faster, just days or weeks. Therefore computer modelling is used as a microscope in order to understand the real picture of a situation or problem.
Our project tries to understand interactions which play a crucial role in arrangements of DNA, proteins, and the stacking of polymers (plastics)
This is important in understanding genetic disorders and other life threatening diseases that are linked to DNA and proteins. Secondly, we are also able to understand how materials mix together to form stronger materials which are used for applications such as aeroplanes, cars, flats screen televisions, mobile phones and buildings or civil structures (High-rise buildings)
Thankfully, with the resources available at CHPC, we are able to understand and shed light on these complex interactions that mimic nature.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2017-07-21
Allocation End: 2018-06-06
Used Hours: 38591
Project Name: CFD modelling of atmospheric stability for wind farms
Project Shortname: MECH1040
Discipline Name: Computational Mechanics
The CFD modelling of atmospheric stability for wind farms conducted at the CHPC is headed by Principal Investigator Prof Ken Craig who collaborated with researcher Hendri Breedt, both from the University of Pretoria. The program focuses on using Computational Fluid Dynamics for wind farm site selection, especially when taking atmospheric stability into account.
Wind energy has become one of the dominant forms of renewable energy because of the rapid reduction in costs associated with wind turbines and wind farm development.
In the wind resource and wind turbine suitability industry Computational Fluid Dynamics has gained widespread use to model the airflow at proposed wind farm locations. These models typically focus on the neutrally stratified surface layer and ignore physical process such as buoyancy and the Coriolis force. These physical processes are integral to the accurate description of the atmospheric boundary layer and reductions in uncertainties of turbine suitability and power production calculations can be achieved if these processes are included.
These reductions lead to greater energy generation and more optimised wind farms which are critical for the successful rollout of this energy form. The large physical size of the wind farm terrains leads to large computational domains used in the simulations. The CHPC provides the computational capacity provided to run the simulations
The program resulted in the successful submission of the student's Master thesis (cum laude) as well as a submitted journal article to the Journal of Wind Engineering & Industrial Aerodynamics. The models developed will form part of ongoing research of atmospheric stability models used in the commercial wind resource industry.
Principal Investigator: Dr Stefan du Plessis
Institution Name: Stellenbosch University
Active Member Count: 6
Allocation Start: 2016-01-23
Allocation End: 2018-04-24
Used Hours: 52488
Project Name: Shared Roots
Project Shortname: HEAL0793
Discipline Name: Health Sciences
Shared Roots is a collaborative research project undertaken by researchers from the disciplines of of psychiatry, psychology, neurology, genetics and bioinformatics at Stellenbosch University and researchers from the South African National Bioinformatics Institute (SANBI). It is a MRC Flagship funded study and the principal investigator on the study is the executive head of the department of psychiatry Professor Soraya Seedat. Dr Stéfan du Plessis is responsible for the neuroimaging component. Our study included participants with posttraumatic stress disorder (PTSD), schizophrenia and Parkinson's disease. It is known that individuals with mental and neurological disorders have higher rates of heart disease and stroke than the general population. It is not clear why this is the case. Our study therefore aims to collect information about all the potential factors that can play a role, to better understand risk and resilience, and enable the development of treatment strategies. To achieve this goal we will combine state-of-the-art research techniques such as genetic evaluations and the latest neuroimaging techniques. This will be combined in analysis with information evaluating these brain disorders, general health and lifestyle factors.
For our neuroimaging component, we scanned over 600 participants using Magnetic Resonance Imaging (MRI). Here we investigate potential brain changes associated with increased metabolic risk. We proceeded to calculate precise measurements of around 70 known brain regions using the MRI scans, which will be compared between cases and healthy controls. Processing takes around 24 hours for each scan. To finish in a timely manner, we used the Centre for High Performance Computing Rosebank, Cape Town, Sun Intel Lengau cluster.
Recruitment closed end 2017. The processing of the MRI scans was completed early in 2018. Our first manuscript is planned for submission at the end of 2018.
Principal Investigator: Dr Yabebal Fantaye
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 3
Allocation Start: 2017-03-28
Allocation End: 2018-04-17
Used Hours: 155261
Project Name: Machine Learning
Project Shortname: ASTR1005
Discipline Name: Data Science
My group is based at AIMS South Africa, in Muizenberg. We focus on two main research areas: applying deep learning to foreground mitigation in the MeerKAT/SKA experiment and semantic segmentation of objects from earth observation satellite images, particularly focusing on the African continent. Radio Frequency Interference (RFI) is one of the main source of foreground contamination to the MeerKAT/SKA astronomical signal. Building a reliable and fast RFI flagging software is indispensable to extracting high quality science from these experiments. My group work in this regard is producing large radio data simulations with RFI contamination, and comparing the speed and accuracy of existing RFI masking algorithms to what we develop. The second component of our research is developing deep learning machine vision to segmenting buildings, farm lands, water bodies and other useful structures from satellite observations of African cities. This is useful to identify and monitor informal settlements in big African cities as well as extracting timely data about urban and rural dynamics in Africa. One of my student is completing his MSc thesis on this area using over 150k CHPC CPU and GPU hours. We have already acquired high resolution satellite images of four main cities in Africa from SANSA to test the deep learning architectures we developed.
Principal Investigator: Prof Jaco Dirker
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2017-06-08
Allocation End: 2018-04-17
Used Hours: 192333
Project Name: Heat Transfer Enhancement in Thermal Systems
Project Shortname: MECH1029
Discipline Name: Computational Mechanics
Renewable energy exploration and the responsible usage of existing energy resources are vital for sustainable economic and industrial development. Future energy needs will require continual improvement in energy processing technologies and storage systems. The Clean Energy Research Group at the University of Pretoria aims to contribute to such efforts by conducting both applied and fundamental research using experimental and numerical techniques. One of the group's focus areas is that of large scale thermal energy storage and conversion systems which have lower associated costs than electric energy storage systems. This, however, requires improved heat transfer mechanisms to match demand side energy consumption rates and has led to the need for geometric optimization and innovation in heat exchanger equipment and thermal energy storage modules. This is the driving force behind the exciting investigations supported by the CHPC whereby the effects of heat transfer enhancement due to turbulator inclusion and the augmentation of latent phase change material energy cycling are considered. For this purpose, high performance computing is required to solve complicated and detailed energy transfer, mass transfer, and fluid dynamics equations in the transient domain using computational codes such as those included in commercial simulation packages such as Ansys Fluent. Detailed simulation results of flow eddies and phase transition fronts, as well as design space exploration results will assist in deriving smaller, more efficient energy transfer components which have lower capital and operating costs in both solar renewable energy systems and fossil fuel based systems. Among the early successes include the improvement of local and average heat transfer coefficients by more than 50% which, if implemented, would result in a significant size reduction of heat exchanger equipment.
Principal Investigator: Prof Richard Tia
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 10
Allocation Start: 2017-08-02
Allocation End: 2018-03-20
Used Hours: 211067
Project Name: Computational Chemistry and Materials Science
Project Shortname: CHEM1044
Discipline Name: Chemistry
We have not yet obtained results that can form the basis of a press release but with the progress made in the our work, especially the work pertaining to the conversion and utilization of carbon dioxide, it should be possible to make a press release in the near future. With increasing interest of the scientific community and government agencies on the mitigation of rising carbon dioxide levels and the attractiveness of using carbon dioxide as a feed-stock for industrial processes, this work might be very suitable for a press release as and when we get interesting results.
Our research activities fall under two broad areas, namely;
1. Molecular modeling - Exploring the mechanisms of organic, inorganic and organometallic reactions.
These studies afford important molecular-level mechanistic details of industrially-relevant chemical reactions that are difficult, if not impossible, to obtain experimentally. Molecular level understanding enable chemical reactions to be guided quickly and efficiently along desirable pathways, with the effect of producing the right product with minimal energy consumption and minimal environmental impact. A key aspect of this work is the development of homogeneous transition metal catalysts for the depolymerization of lignin, an abundant natural resource, for fuel.
2. Materials modeling
The atomic- and molecular-level mechanistic insight gained from these studies are useful for the design of novel catalysts for the conversion of CO2 and other green-house gases as well as stranded gases from the petroleum refining into useful fuels. This addresses the problem of global warming as well as providing an environmentally friendly alternative sources of fuel.
The research objectives described here are very computationally-demanding and using the CHPC resources is highly beneficial. Without that, we would not be able to carry out some of these calculations.
Principal Investigator: Dr Donald Mkhonto
Institution Name: Tshwane University of Technology
Active Member Count: 2
Allocation Start: 2016-07-25
Allocation End: 2018-02-21
Used Hours: 12317
Project Name: Electronic Structure and Atomistic Simulations of Minerals and Mineral Surfaces
Project Shortname: MATS0916
Discipline Name: Physics
Materials Modelling is done at Tshwane University of Technology in the department of Physics with Dr. Donald Mkhonto as the Principal investigator. Employing computational materials science techniques to study both bulk structure and surfaces of materials and minerals in general; Computational Materials Science at the department is aimed at using simulation methods to predict properties of different materials at different conditions that may be difficult and expensive experimentally. The methods allow us to calculate and predict materials properties at different length scales (from Angstrom to Micrometer length, that is from few atoms to thousands of atoms) While computational codes and hardware used for the kind of study may be expensive to academics, the use of CHPC (Centre For High Performance Computing) as provided by the government of South Africa is of vital importance and assist invaluably in terms of both physical computer infrastructure and software. We are able to introduce students (both undergraduate and post graduate) to computational materials science as an alternative and partner to experimental work and materials design.
Principal Investigator: Prof Steve Koch
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2016-08-16
Allocation End: 2018-08-30
Used Hours: 70705
Project Name: NP Equivalence Scales
Project Shortname: ECON0910
Discipline Name: Economics and Finance
Research into the Health and Household Behaviours (ReHHaB) in the Department of Economics at the University of Pretoria focuses its research into households, and their welfare. The majority of our research considers health, but it also examines household budgets and energy consumption; we also make extensive use of non-standard statistical methods, including nonparametric analysis and continuous regression splines. As part of our research, the group has been examining the appropriateness of per capita measures of welfare. Our research so far suggests that such measures present an unfortunately skewed view of poverty in South Africa; although an unequal country, it not as unequal as currently suggested. We are currently examining the robustness of our findings, but we should have that research publicly available soon.
Principal Investigator: Dr Sunita Kruger
Institution Name: University of Johannesburg
Active Member Count: 1
Allocation Start: 2017-03-07
Allocation End: 2018-04-26
Used Hours: 66692
Project Name: Environmental Heat Transfer
Project Shortname: MECH0995
Discipline Name: Computational Mechanics
This research group in the Mechanical Engineering Science Department of the University of Johannesburg is currently focusing on environmental heat transfer. Specifically heat transfer in naturally ventilated greenhouses. Greenhouses are used to protect plants from adverse weather conditions and insects. Ventilation of greenhouses are of vital importance to ensure quality crop production. If temperatures in a greenhouse is too high, poor plant growth may result, and an increased need for frequent watering. A mechanical ventilation system might be required to cool the inside of the greenhouse. Natural ventilation is an alternative option used to ventilate greenhouses. Natural ventilation uses temperature and wind to control the indoor climate of greenhouses. Unfortunately greenhouses are extremely energy intensive. Energy costs are the third highest cost related to greenhouse crop cultivation. Reducing the operating costs of energy associated with greenhouse cultivation may result in a price reduction of greenhouse cultivated crops. Conducting experimental work on ventilation of greenhouses can be costly and cumbersome. Using computational methods such as CFD (Computational Fluid Dynamics) to obtain qualitative and quantitative assessment of greenhouses can reduce costs and time involved. The computer cluster at the Centre for High Performance Computing has been used to conduct the numerical investigation using CFD. Currently research is being conducted on a large commercial greenhouse. Smaller greenhouses containing a single span are also being investigated.
Principal Investigator: Dr Francois van Heerden
Institution Name: Nuclear Energy Cooperation of SA
Active Member Count: 2
Allocation Start: 2016-01-23
Allocation End: 2018-04-17
Used Hours: 117307
Project Name: Research Reactor Fuel Burnup and Material Activation
Project Shortname: INDY0788
Discipline Name: Physics
The Radiation and Reactor Theory (RRT) group at the South African Nuclear Energy Corporation (Necsa) provides calculational support for the SAFARI-1 research reactor, and perform research in the general area of nuclear analysis. We also develop and maintain our own suite of reactor simulation software, called OSCAR. This suite is the primary operational support tool for the SAFARI-1 reactor, and is used at a number of international facilities, which range from small university based research reactors, to larger national facilities.
During the past year, CHPC computing resources were utilized for a project facilitated by the International Atomic Energy Agency (IAEA) through a Collaborative Research Project (CRP) aimed at the collection of experimental data suitable for code benchmarking and validation. We are participating by providing experimental data from our own facility, the SAFARI-1 research reactor, and by calculating a number of experimental benchmarks from other member states. This particular CRP focuses on fuel depletion and material activation, which is important for the economic and safe operation of research reactors. Most of the primary analysis work has been completed, and we are well on target to deliver final reports in the last research meeting scheduled for October 2018. These reports will eventually be incorporated in a formal technical publication by the IAEA, available to all member states.
The latest version of our tool set, OSCAR-5, provides a platform that combines different analysis codes, from fast diffusion solvers suitable for fuel depletion tasks, to high fidelity particle transport solvers, which can be used to do detailed local activation analysis, in a consistent manner. High Performance Computing plays an important role in the data preparation step for the diffusion solver, and in the use of transport solvers to estimate neutron flux distributions in the core.
Principal Investigator: Prof Eric van Steen
Institution Name: University of Cape Town
Active Member Count: 6
Allocation Start: 2016-01-23
Allocation End: 2018-03-20
Used Hours: 4099144
Project Name: Lateral interactions on surfaces
Project Shortname: CHEM0780
Discipline Name: Chemistry
Heterogeneous catalysis has in the past been regarded as a black-art since the uncertainty around the roles of the various components in the catalyst. In this research project, the role of the various components interacting with the catalytically active materials are being studied using theoretical methods (DFT) to give a better understanding of the interaction within the catalyst system, and guide the experiments to prove certain concepts. As such, my group performs calculations of importance to the development of fuel cell technology, viz. 1) interactions between adsorbed species on platinum surfaces and 2) interaction between surfaces in these catalysts. Furthermore, my group investigates the role of promoters in cobalt-based Fischer-Tropsch synthesis by investigating their location in the surface (e.g. platinum) or on the surface (as a ligand mimicking the effect of a catalyst support).
Although the group is only looking at model systems, the insight generated by our research are applicable to realistic catalyst systems (in our case in particular to fuel cell research and catalysts for the Fischer-Tropsch synthesis). These model calculations can only be performed at a CHPC, due to the complexity and scale of the calculations.
Principal Investigator: Prof Walter Meyer
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2016-05-04
Allocation End: 2018-06-06
Used Hours: 48245
Project Name: Dynamics of primary radiation induced defects in semiconductors
Project Shortname: MATS0860
Discipline Name: Physics
Semiconductors used in electronic devices play a crucial role in almost all current technology, ranging from power generation (in solar cells) to power switching and conversion to smart phones, computers and satellite communications. In order to function, the semiconductors require a highly perfect crystal lattice with impurity atoms placed at exact locations in the device. Any unwanted impurities and crystal defects may degrade performance and cause devices to malfunction. These defects may be caused during manufacturing processes but also by harsh environments, e.g. space. On the other hand, some defects also have properties that may be exploited in promising future technology including spintronics and quantum computing. In summary, defects in semiconductors play an important role in both current and future technology.
The aim of the Electronic Materials Group in the Physics Department of the University of Pretoria is to understand the properties of defects on a fundamental level. In order to achieve this deep understanding, both experimental and theoretical techniques are used. Thanks to the power of modern computers, a technique called "Density Functional Theory", or DFT for short, may be used to calculate the expected properties of a specific defect. These properties may be compared to experimental results to test the validity of the theoretical assumptions. The results can lead us to build better models of how defects in semiconductors influence device performance, how devices can be engineered to reduce their susceptibility to defects and to find properties of defects which may make them useful in technologies such as spintronics and quantum computing.
The main disadvantage of DFT is that it requires a very large number of calculations, which have only recently become feasible for computers to perform within a reasonable time. The research currently uses the high performance computer at the CHPC and a free scientific programme Quantum-ESPRESSO to calculate the properties of these defects.
The first step is to perform these calculations on simple defects in well-known materials such as silicon, in order to test the applicability of the theory. Currently the calculations are progressing well and the results are promising. Once we have shown the reliability of these results, we will continue to investigate more complicated defects as well as novel materials.
Principal Investigator: Dr Melanie Rademeyer
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2016-01-30
Allocation End: 2019-02-06
Used Hours: 94122
Project Name: Properties of organic-inorganic hybrids
Project Shortname: MATS0823
Discipline Name: Material Science
The Material Science Research Group at the University of Pretoria, lead by Prof Melanie Rademeyer, focuses, among others, on the computation of the magnetic properties of organic-inorganic hybrid materials. Magnetic materials are important materials due to their potential technological applications, and organic-inorganic hybrid materials offer a unique opportunity in terms of the material design approach followed.
The successful calculation of the magnetic properties of these materials will allow for the identification of hybrid materials with promising magnetic properties. The materials identified via the computational method will then be synthesised in the laboratory and their magnetic properties measured experimentally via SQUID magnetometry.
The computational method involves the use of the single crystal structure of the material, as well as quantum mechanical and statistical thermodynamic calculations.
Significant progress has been made, with the magnetic properties of a number of organic-inorganic hybrid compounds having been calculated successfully employing the resources offered by the CHPC.
Principal Investigator: Prof Don Cowan
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2016-09-08
Allocation End: 2018-08-15
Used Hours: 240711
Project Name: Meta-omics of extreme environments
Project Shortname: CBBI0932
Discipline Name: Bioinformatics
The Centre for microbial Ecology and Genomics is based at the University of Pretoria. We are interested in to carry out research concerning the microbial ecology and their diversity in the extreme environments, in particular the Antarctic and Namib Deserts. The resident "extremophile" microorganisms, given their unique functional (metabolic) potential are important indicators of extreme environmental conditions and potential impact of global climate change. We have, thus far, successfully characterized sediment and also marine microbial diversity, including their respective metabolic capacities, with the use of metagenomic analyses. The study of large metagenomic datasets require substantial computational power. Fortunately, these services are provided by the CHPC, without which we will not be able to optimally-perform our research.
Principal Investigator: Prof Claude Carignan
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2016-11-24
Allocation End: 2018-05-12
Used Hours: 56398
Project Name: Numerical Simulations of Barred Galaxies
Project Shortname: ASTR0961
Discipline Name: Astrophysics
Claude Carignan and his group (Nathan Deg, Toky Randriamampandry) at UCT have used carefully crafted simulations run at CHPC to generate one of the first mass models of NGC 1300. This is a particularly exciting achievement as the orientation of this barred galaxy prevents other methods from successfully modeling this galaxy. Their technique can be applied to a range of barred galaxies that could not be modeled otherwise.
Nathan Deg and Claude Carignan, working with Lawrence Widrow (Queen's University) have developed a new method for generating initial conditions for galaxy simulations. This program, call GalactICS (Galaxy Initial ConditionS) can make equilibrium galaxies with a spherical dark matter halo and bulge, two stellar disks, and a gas disk. Other methods for making such initial conditions generally require some time to relax to equilibrium, while GalactICS begins in equilibrium. This program is useful for studying dynamical processes, like bar formation, modeling real galaxies, controlled merging experiments, etc.
In addition, Claude Carignan and Nathan Deg have been working with Sarah Blyth, Nadine Hank, and Simon Krüger to analyze simulations of merging galaxies. They are attempting to characterize how asymmetric these mergers are, how this asymmetry parameter varies with observational systematics, like the angle the merger is observed at, and what the asymmetry parameter can tell us about the galaxies involved in the merger.
Principal Investigator: Prof Rebecca Garland
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2016-04-20
Allocation End: 2018-04-17
Used Hours: 450337
Project Name: Simulating atmospheric composition
Project Shortname: ERTH0846
Discipline Name: Earth Sciences
Air pollution can have large negative impacts on human health, agriculture, ecosystems, visibility and climate. In South Africa, although ambient air quality is regulated, many areas are out of compliance with the National Ambient Air Quality Standards. In order to protect human health and mitigate impacts, it is critical to improve air quality. The Constitution provides that everyone has a right to have an environment that is not harmful to their health. The Atmospheric Composition Focus Area (ACFA) in the CSIR Climate Studies, Modelling and Environmental Health Research Group aims to provide the evidence base to quantify the impacts of air quality and to improve air quality.
The group uses the CHPC to run an air quality model to simulate urban and regional air quality at high resolution. This chemical transport model simulates the physics and chemistry of the atmosphere. The processes represented within the model are complex, and thus computationally intensive, which makes use of the CHPC facility a necessity. The CSIR ACFA is the only group in South Africa routinely running a chemical transport model to simulate air quality.
Using the CHPC resources, the team has been able to simulate the impact of policy interventions on air quality in cities. Additionally, the team has simulated the health risk from air pollution regionally in South Africa. In the past, this has been done using monitoring station data only, which then limits the analysis to only those living directly around the station. The team has also simulated the impact of climate change on air pollution. These simulations use the climate projections for the CSIR's VrESM, which is also run at CHPC, to provide meteorology input into the air quality model.
These outputs directly provide the evidence base needed for decision makers to draft and implement policies and interventions to effectively improve air quality as well as understand its impacts, now and into the future.
Principal Investigator: Prof Cornie van Sittert
Institution Name: North-West University
Active Member Count: 16
Allocation Start: 2016-01-23
Allocation End: 2018-03-20
Used Hours: 5561291
Project Name: Computational Chemistry within LAMM at NWU (Potchefstroom)
Project Shortname: CHEM0778
Discipline Name: Chemistry
Since the 1880 the main source of energy for South Africa was coal and at present coal provides 77% of South Africa's primary energy needs. However, the electricity comes at a very high cost, namely air pollution and the influence of the air pollution to human health. In 2004 the South African government reformed the legislation with regard to air pollution. In an effort to contribute to the management of air quality new energy sources must be investigated. These new energy sources must be affordable, clean and renewable. Some of these alternative energy sources are fuel cells and batteries. Electricity from fuel cells and batteries are obtainable through the use of electrochemistry, where free energy of spontaneous reactions is transformed into electricity. A potential replacement form of energy is the hybrid sulphur (HyS) cycle. The HyS cycle is a two-step water-splitting process, which could be used for the production of hydrogen. In the HyS cycle, the anode material used is platinum. However, because platinum is a rare and expensive metal, it is not an economical viable option for long term and large scale production of hydrogen. Hence, various attempts to reduce or eliminate the platinum content, while not compromising the process performance has been made. In the order to understand the electrochemistry on the anode and make informed decisions on the type and amount of metal to be used in various platinum alloys, investigations on a fundamental level is needed. These type of investigations could be classified as computational chemistry. The resources needed for these type of investigations, namely various types of hardware and software is of cardinal importance. Although resources are available at NWU, it is not nearly enough to fully support the research covered in the Laboratory of Applied Molecular Modelling (LAMM). So if we as researchers within the LAMM did not have access to the CHPC resources the progress of our research will be much slower.
Principal Investigator: Prof Thulani Makhalanyane
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2017-05-24
Allocation End: 2018-08-20
Used Hours: 77611
Project Name: Metagenomics of extreme environments
Project Shortname: CBBI1023
Discipline Name: Bioinformatics
The Centre for Microbial Ecology and Genomics has recently launched a continuation of projects aimed at understanding the contribution of microorganisms in environmentally extreme environments. These projects, which range from studies aimed at understanding the role of microbial communities in Antarctic biogeochemical cycling to studies on the gut microbiota of South African individuals, all rely on the analysis of next generation sequencing data. Using metagenomics, which provides access to over 99% of isolates which cannot be cultured using standard laboratory conditions, these studies aim to assess genes implicated in carbon and nitrogen cycling in a range of soils. Several outputs from these studies have generated high impact publications in leading journals.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2017-03-10
Allocation End: 2018-05-23
Used Hours: 2206381
Project Name: CFD modelling of falling-film bioreactors
Project Shortname: MECH1001
Discipline Name: Computational Mechanics
This project stemmed from a passenger transport initiative of Transnet Engineering, known "in-house" as the MC25. While the project's initial phase would consist of a low to medium speed commuter connecting the business hubs of Gauteng to Polokwane, hereby opening the job-market in order to address the high unemployment rate in the country, Transnet's vision would ultimately be a high-speed rail network connecting South Africa's major cities. The optimisation of this train's nose is to serve as a technology demonstrator for this ultimate future goal. The optimisation goals are drag reduction, a financial consideration, and cross-wind stability, a safety consideration. Given the complex nature of the problem, Transnet joined hands with the University of Pretoria and the CHPC to make this vision a reality. While it is usually aeroplanes that seem to fascinate the public, it is the aerodynamics of high-speed trains that are truly challenging, mainly due to the very "dirty" external flow field surrounding the train due to the presence of the ground, the very thick boundary layer flowing over the train surface and the very long trailing wake. This implies that not only would the computational domain for a train have to be very large, but the flow phenomena that would need to be captured are very complex also. Transnet required the development of in-house expertise in the field of fluids and approached Professor Ken Craig of the University of Pretoria to guide Andrea Beneke's research. Because of the very large and complex nature of the required, cluster computing from the CHPC was a necessity. While the geometry of the train nose has already been optimized for windless conditions, it is Transnet's hope that a train nose that is stable under cross-wind conditions will soon be completed also – taking South-Africa one step closer to the future.
Principal Investigator: Prof Christine Lochner
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2016-06-29
Allocation End: 2019-03-13
Used Hours: 15137
Project Name: Compulsivity-Impulsivity
Project Shortname: HEAL0907
Discipline Name: Imaging
A key criticism of the Diagnostic and Statistical Manual of Mental Disorders (DSM) is that although it is useful for research and in the practice, its criteria are based upon the description of superficial behavioural signs and symptoms but lacks a biological footing. Recent years have witnessed increasing attempts to address inclusion of biological data that may be similar across disorders. So instead of focusing on behavioural symptomatology only, the current trend is to consider 'neurocognitive endophenotypes', such as compulsivity and impulsivity, that may be derived from neuroimaging data instead of using behavioural data only, and using them 'transdiagnostically', to identify commonalities across disorders. With this project we aim to explore these proposed endophenotypes further by focusing on three psychiatric disorders with apparent compulsive / impulsive features (i.e. obsessive-compulsive disorder, gambling disorder and substance use disorder). Findings may contribute to our understanding of the underpinnings of disorders with such characteristics, and may also render data that are useful in treatment.
The project renders an opportunity for different units - i.e. from Stellenbosch University (e.g. MRC Unit on Risk and Resilience in Mental Disorders, the Department of Psychiatry), the University of Cape Town (the Department of Psychiatry and Mental Health) and the Cape Universities Brain Imaging Centre (CUBIC) to collaborate. The research team thus includes basic scientists, neuroimaging experts, researchers with M-degrees in Research Psychology, a clinical psychologist, a general practitioner and a psychiatrist.
The work is crucially important in establishing expertise in South African neuroimaging, and specifically with regards to structural imaging, diffusion tensor imaging (DTI), magnetic resonance spectroscopy (MRS) and functional MRI in psychiatric disorders.
CHPC creates a user-friendly platform for creating the scripts required to run the Tortoise and other methods used for analysis of MRI data. The project is funded by the National Research Foundation of SA.
Principal Investigator: Dr Leigh Johnson
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2017-08-10
Allocation End: 2018-04-26
Used Hours: 474422
Project Name: MicroCOSM: Microsimulation for the Control of South African Morbidity and Mortality
Project Shortname: HEAL1049
Discipline Name: Health Sciences
Research led by Cari van Schalkwyk (Stellenbosch University) shows that although HIV and human papillomavirus (HPV) frequently occur in the same individuals, this is mainly because both viruses are sexually transmitted, and not because HIV alters the risk of HPV acquisition or vice versa. These findings have important implications for HIV prevention, as they suggest that HPV vaccination is unlikely to be successful as an HIV prevention strategy. These findings depend on detailed mathematical models that simulate samples of the South African population and their sexual networks in order to estimate the rates at which people become infected with HIV and other sexually transmitted infections. Such models require substantial computing power, and the CHPC is critical to the conduct of these simulations.
Principal Investigator: Prof Tulio de Oliveira
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2017-08-18
Allocation End: 2018-06-06
Used Hours: 31093
Project Name: Pathogen Bioinformatics
Project Shortname: CBBI1053
Discipline Name: Bioinformatics
The KwaZulu-Natal Research Innovation and Sequencing Platform is a new organization at the University of KwaZulu-Natal, whose purpose is to spearhead top quality research in South Africa and the rest of the continent. This is partly an effort to reverse the South African brain drain that has been observed. KRISP assists biological researchers in achieving their scientific goals through a process of specialization and collaboration. KRISP has an array of both wet-lab and computational specialists as well as international collaborators to support this effort.
Some of our current research focuses on the geospatial organisation and modelling the spread and clustering of diseases such as TB and HIV through a combination of genetic and social data. The impact of this is a more rational approach to curbing and treating for the aforementioned, especially in countries where the economy is a major limiting factor.
With interesting questions and added parameters, comes the need for more computing power. With the enormous influx of biological data and the exceptional cost of hardware, it becomes prudent to rely on external resources such as the CHPC. A platform on which cutting-edge scientific questions can be addressed by a robust cycle of observation, analysis and criticism.
Principal Investigator: Dr Andre Stander
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2017-08-22
Allocation End: 2018-06-06
Used Hours: 41918
Project Name: In silico estimation of ligand binding energies against cancer- and malaria-associated proteins
Project Shortname: CHEM1055
Discipline Name: Health Sciences
The research group of Dr Stander at the Department of Physiology specializes in in silico drug design and in vitro testing of new anti-cancer compounds.
The use of the CHPC Lengau cluster has enabled this research group to speed up docking times to help identify more compounds and also perfect free energy calculations. The latter part is especially important in predicting binding affinity of new compounds and can thus better discriminate between inactive and active compounds and therefore reduce costs associated with the synthesis of inactive compounds.
Using specialized molecular modelling software and collaboration with industry, new potent and selective bomodomain 4 and sirtuin 1 inhibitors were identified and synthesized for in vitro testing. The new compounds are active against a variety of cancer cell lines including breast and prostate cancer, leukemia and neuroblastoma at sub micromolar levels. Additionally, new inhibitors that target Qi site of cytochrome bc1 of the malaria parasite were designed and show potent nanomolar activity against blood stage parasites with no in vitro effects against human cells at 10 micromolar.
Principal Investigator: Prof Nithaya Chetty
Institution Name: University of Pretoria
Active Member Count: 0
Allocation Start: 2017-08-22
Allocation End: 2018-06-15
Used Hours: 1397990
Project Name: Advanced Computational Resources for members of ASESMA
Project Shortname: MATS1050
Discipline Name: Material Science
ASESMA is a series of workshops held every two years in different sub-Saharan countries, designed to foster a collaborative network for research and higher education in Africa. Participants are drawn from across the continent through a competitive process, and the lecturers and mentors are outstanding scientists from across the world including Africa. ASESMA has shown that it is possible to build a network in a particular scientific area across sub-Saharan Africa with world-class research with a relatively low budget. It already is expanding to involve more chemistry and materials science, and the next school will be an introduction into biological systems. These are steps toward fulfilling the vision of building African Networks for Computational Materials and Biological Sciences. The greatest asset is the commitment of the lecturers and mentors, the team work of the local organisers and the idealism of the participants who rank amongst the brightest of young minds from Africa, many of whom come from impoverished backgrounds but still dare to reach for the stars. This is an inspiring story for all who get involved.
The core guiding principle is that computation makes it possible for world-class research to be done with modest investment, and it is an essential part of education for the future. There is tremendous goodwill of scientists world-wide and there is great potential in the young people of Africa who only need the opportunities to take part in the global community of science! The use of the CHPC facility, which is the largest HPC facility in Africa, permits a large number of such computations to be performed significantly faster and with significantly more available memory than would be possible with desktop computers.
ASESMA is sponsored for the years by the International Union of Pure and Applied Physics (IUPAP) as a joint mission of the Commissions on Physics Development (C13), Computational Physics (C20), Physics Education (C14) and the Structure and Dynamics of Condensed Matter C(12). ASESMA is grateful to Jim Gubernatis, Kennedy Reed and the late Peter Borcherds for their significant role in helping set ASESMA as a biennial school moving through various African countries and with IUPAP as the principal sponsor. The ICTP has been instrumental in administering and managing ASESMA. The Quantum Espresso development group is credited for their excellent and versatile open source plane wave density functional codes that form the cornerstone of the work of ASESMA.
Principal Investigator: Prof Sanushka Naidoo
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2017-08-30
Allocation End: 2018-06-15
Used Hours: 71868
Project Name: Eucalyptus and Pine Pathogen Interactions
Project Shortname: CBBI1057
Discipline Name: Environmental Sciences
The Eucalyptus and Pine Pathogen Interactions research group, from the University of Pretoria, focusses on investigating the molecular interactions of economically important forest tree species with pests and pathogens of interest to the South African forestry industry. One of the most pressing threats to global pine cultivation is the pitch canker fungus, Fusarium circinatum, which can have a devastating effect in both the field and nursery. Many strategies are currently employed to manage F. circinatum in the field and nursery, with limited success. Investigation of the host-pathogen interaction between Pinus spp. and F. circinatum is crucial for development of effective disease management strategies. To this end, RNA-sequencing data was generated for six pine species, with varying levels of resistance, during F. circinatum challenge. As with many non-model organisms, however, investigation of host-pathogen interactions in Pinus spp. is hampered by limited genomic resources. Fortunately, advances in bioinformatics has made it possible to leverage the inherent redundancy in next generation sequencing data to assemble the reference transcriptome. A transcriptome assembly and annotation work-flow was established on the CHPC using data for Pinus pinaster. More than 20 preliminary transcriptomes were assembled, using Trinity and Trans-ABYSS at different k-mers. Preliminary assemblies were concatenated, and redundancy reduced using the EvidentialGene pipeline. The resulting assembly was annotated, and non-pine transcripts removed, using the EnTAP pipeline to produce a high-quality P. pinaster reference transcriptome. Read data was mapped back to the assembled transcriptome to investigate host expression during F. circinatum challenge. The established work-flow will be used to investigate host responses for the remaining species to allow comparison of host responses between species.
Principal Investigator: Dr Eduard Grebe
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2017-09-15
Allocation End: 2018-09-05
Used Hours: 3496
Project Name: HIV Incidence estimation
Project Shortname: CBBI1062
Discipline Name: Health Sciences
The HIV incidence estimation group at the DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis at Stellenbosch University has conducted a number of important studies using the resources of the CHPC.
A novel method for estimating age-specific HIV incidence, which utilises an optimal weighting of incidence estimates using biomarkers of 'recent' infection and estimates using a demographic approach (the age/time structure of prevalence) was recently demonstrated using survey data from KwaZulu-Natal and published in the PLOS ONE journal in September 2018.
The group also utilised CHPC computational infrastructure in characterising tests for recent infection, including the use of a novel approach to estimating the key performance characteristics from repeat blood donor data, which was reported at the prestigious CROI conference held in Boston, MA, USA in March 2018.
The CHPC proved an invaluable resource, since these methods rely on "big data" approaches that are not feasible on personal computers.
Principal Investigator: Dr Chris Barnett
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2017-09-28
Allocation End: 2018-05-23
Used Hours: 11832
Project Name: Analysis of disease related polymers
Project Shortname: CBBI1063
Discipline Name: Bioinformatics
I investigate the shapes, structures, and properties of molecules by using computational modelling techniques. I'm particularly interested in complex sugars (glycans), which are interesting to study because they are involved in intricate molecular recognition processes in cells, for example, playing a role in cell signalling, adhesion, and immunity.
Further understanding of these molecules and the complex systems they are involved in may lead to the generation of additional diagnostic markers and inhibitors that can be used to combat disease.
The CHPC provides a platform for being able to run large-scale and highly parallel simulations which is a great help in making rapid progress towards solving research questions. The CHPC is also a test bed when carrying out computation on and developing algorithms for large datasets.
Principal Investigator: Dr Willem Gerber
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2017-09-28
Allocation End: 2018-08-30
Used Hours: 109506
Project Name: Computational investigation of transition state metal catalysis
Project Shortname: CHEM1061
Discipline Name: Chemistry
The research group of Dr WJ Gerber was founded in 2010 at the Department of Chemistry and Polymer Science at Stellenbosch University. The main aim of this research group is to use computational chemistry at various levels of theory to elucidate inorganic reaction kinetics (ligand exchange/oxidative addition and reductive elimination/general redox reactions), mechanism and thermodynamics. With an understanding of these interrelated topics pertaining to transition metal complex reactions more efficient catalyst can be designed and better optimize separation/purification of platinum group metals pertinent to the mining industry. To achieve these goals requires relatively large computational resources as supplied by the CHPC in the past year which greatly assist with the progress of several projects.
Principal Investigator: Dr Adeniyi ogunlaja
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 3
Allocation Start: 2017-11-07
Allocation End: 2018-09-20
Used Hours: 18053
Project Name: Chemistry and Material Science
Project Shortname: MATS1070
Discipline Name: Chemistry
Refractory polyaromatic hydrocarbons found in fuels such as dibenzothiophene, quinoline and its alkylated derivatives emits nitrous oxides and sulfur oxides to the environment when combusted, thereby reducing air quality. Desulfurization by means of oxidative desulfurization and adsorptive denitrogenation has been proposed to complement the hydrodesulfurization (HDS) and hydrodenitrogenation (HDN) processes, currently employed to remove sulfur and nitrogen compounds in fuels. At Nelson Mandela University analytical chemistry research group, we design materials that can selectively remove these sulfur and nitrogen compounds. Molecular modelling based upon the density functional theory (DFT) was employed to understand the mode of adsorption (interaction) between synthesised materials and the various compounds to be removed from fuels. Computational study assists with the understanding of the electronic and thermodynamic properties of synthesised materials prior to application. It also gives an insight as to the specific properties to be targeted when designing adsorbents for environmental clean-up. So far, progress has been made around the design and adsorption of some toxic molecules in fuels. HPC assist our group to build models that could be employed in explaining complex phenomena. It has also enabled us to ask big questions around activity of our materials and to test for possible answers computationally. CHPC has created the platform for where researchers like me could assess the HPC and has also assisted me and my students with solving problems some computation problems.
Principal Investigator: Prof Mohsen Sharifpur
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2017-11-15
Allocation End: 2018-04-17
Used Hours: 198367
Project Name: Computational Heat transfer
Project Shortname: MECH1073
Discipline Name: Computational Mechanics
The research group was established as the Clean Energy Research Group in the Department of Mechanical and Aeronautical Engineering at UP, as an internationally leading laboratory. According to the Essential Science Indicators of ISI Web of Knowledge for "highly cited researcher" (3 February 2014 – present): The group is ranked amongst the top 1% of the world in engineering in three fields: (a) citations, (b) number of papers and (c) citations per paper.
Choosing correct boundary conditions, flow field characteristics and employing right thermal fluid properties can affect the simulation of convection heat transfer using nanofluids. Nanofluids have shown higher heat transfer performance in comparison with conventional heat transfer fluids. The suspension of the nanoparticles in nanofluids creates a larger interaction surface to the volume ratio. These advantages introduce nanofluids as a desirable heat transfer fluid in the cooling and heating industries. The other part of the research is concerned with the use of nanoparticles in boiling and condensation flows. Due to the complexity of such types of flows, new development is needed in this section. The important aspect will be the phase change of liquid phase. The liquid can be distilled water, coolants such as Ethylene glycol and refrigerant such as R141 and other types of liquid. The variety of base fluid can lead to understanding of many critical applications of nanofluid in industry. Such simulations need to be run for long in order to model the mass transfer in interfacial surface and reach statistical convergence. CHPC resources are a lot valuable since we couldn't do these runs on our research group machine. These are still in progress: Model development for nano-scale heat transfer, Study and development of a new method for particles in pool boiling with different base fluid and various inclination angles.
Principal Investigator: Dr David Pearton
Institution Name: Oceanographic Research Institute (ORI)
Active Member Count: 2
Allocation Start: 2017-11-16
Allocation End: 2018-09-12
Used Hours: 19156
Project Name: Responses of South African Coral Reefs to Climate Change
Project Shortname: CBBI1072
Discipline Name: Environmental Sciences
The Oceanographic Research Institute (ORI), part of the South African Association for Marine Biological Research (SAAMBR) has been involved in researching and protecting South Africa's marine biodiversity since 1959. One of ORI's flagship programmes is the Coral Reef programme which has conducted pioneering research on the coral reefs of South Africa and the Western Indian Ocean.
Coral reefs all over the world are under significant pressure from a wide variety of sources including global changes such as warming oceans and ocean acidification as well as local threats such as overfishing and pollution. This has resulted in mass global bleaching events and a worldwide decrease of 50% in coral reef cover in the past 50 years. South Africa's coral reefs are considered high latitude marginal reefs and, as such, are good models for how corals can adapt or acclimate to environmental extremes.
ORI is conducting research on how South African corals from different evolutionary backgrounds respond to climate change. To do this we are conducting experimental studies exposing corals to different predicted warming and ocean acidification scenarios and seeing how they respond physiologically and genetically. In order to look at the genetic response we have to determine which genes are turned on and off under normal vs warm or acidic conditions. To do this we use a technique called RNA-Seq that combines cutting edge next generations sequencing with advanced algorithms and high performance computing to determine the level of expression of every gene. This allows us to understand on a fundamental level how the corals are responding to climate change and what their potential for adaptation might be. This will allow us to predict what might happen to our corals in a changing world and how best to protect and preserve these unique ecosystems.
Principal Investigator: Prof Chris Meyer
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2017-12-07
Allocation End: 2018-09-12
Used Hours: 685457
Project Name: Development of CFD models
Project Shortname: MECH1077
Discipline Name: Computational Mechanics
The research activity is led by Prof CJ Meyer from Stellenbosch University and is focused on developing computational models of industrial thermo- and fluid dynamic processes. There is a specific emphasis on the use of free software under the GNU General Public License. The industrial processes under consideration are those relevant to specific segments of industry in South Africa most notably power generation. Current projects include the simulation of biomass combustion processes where models are developed to ease the computational costs of the various stages of combustion by using neural networks. A significant reduction in the size of the computational model is achieved with an associated reduction of computational time. The project has come to an end as the PhD student, Philip du Toit has completed his research and graduated in early 2018.
Principal Investigator: Mr Anban Pillay
Institution Name: University of KwaZulu-Natal
Active Member Count: 12
Allocation Start: 2018-01-09
Allocation End: 2019-09-18
Used Hours: 102599
Project Name: Deep Learning Approaches
Project Shortname: CSCI1078
Discipline Name: Computer Science
The Deep Learning research group belongs to the Centre for Artificial Intelligence Research Node at the University of KwaZulu-Natal. The Centre for Artificial Intelligence Research (CAIR) (CAIR.za.net) is a South African distributed Research Network that conducts foundational, directed and applied research into various aspects of Artificial Intelligence.
The research group conducts foundational research in machine learning in general and deep learning in particular. Deep learning projects require substantial computing resources and the CHPC is vital to its success.
The projects involve various area of deep learning that include deep reinforcement learning, convolutional and recurrent neural networks. Application areas include image processing, natural language processing and speech recognition.
Several students are busy with projects at present.
Principal Investigator: Mr Randall Paton
Institution Name: University of the Witwatersrand
Active Member Count: 5
Allocation Start: 2016-04-07
Allocation End: 2018-03-20
Used Hours: 1418047
Project Name: Compressible Gas Dynamics
Project Shortname: MECH0847
Discipline Name: Other
Our group examines high-speed or highly transient phenomena in air with applications in supersonic aircraft, human safety, and industry. The use of high-performance computing allows assessment of flow domains difficult, expensive, or impossible to repeatably test using physical experiments and is an invaluable tool in developing the science of compressible gas dynamics further. Recent work by Masters and Doctoral students has included:
- The development of a design for laboratory blast wave shock tube using high-resolution simulation. This design more accurately models blast characteristics than any previous method while allowing the study of reflection and diffraction behaviour
- The modelling of expansion wave diffraction using the Large Eddy Simulation technique. This challenging but powerful technique has historically seen low usage due to high computational demand entailed and thus this study was only really practically possible using HPC. The behaviour of moving expansion waves has also remained largely unstudied to date and so this work is also very novel
- The modelling of the diffraction of shock waves from shock tubes with non-orthogonal exit surfaces. While an extensive experimental campaign complemented this study, the vortex arch formed in these diffractions (a feature never before identified) could only be confirmed using the visualisation afforded by high-resolution simulation
- The high spation and temporal resolution modelling of the aerodynamic effects of high acceleration on various bodies both due to propulsion and drag
Principal Investigator: Dr Nana Ama Browne Klutse
Institution Name: Ghana Space Science and Technology Institute
Active Member Count: 2
Allocation Start: 2018-02-14
Allocation End: 2018-10-10
Used Hours: 98628
Project Name: Regional Climate modeling over Africa
Project Shortname: ERTH1087
Discipline Name: Earth Sciences
The CHPC system has provided access to a supervisor from the Department of Physics, University of Ghana and my students from the West African Science Service Center on Climate Change and Adapted Land Use (WASCAL). We are climate scientists but do not have the system in our countries to run our experiments. We model the climate and the impact on water and land. The CHPC has made our research possible.
We thank the South African government and all partners involved in CHPC for making this possible. We also thank the hard working scientists, engineers and the general staff of the CHPC for keeping up the good services.
Principal Investigator: Prof Beatriz Garcia de la Torre
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2018-02-26
Allocation End: 2018-10-10
Used Hours: 14831
Project Name: Peptide Chemistry
Project Shortname: CHEM1090
Discipline Name: Chemistry
Our research group is based at the University of KwaZulu-Natal, Durban. Our group major focus on the synthesis of new
peptides and further understand their stability, interactions with ions and lipids using different in-silico methods.
Bacterial infection is one of the major cause of death in South Africa and other African countries. Designing the new
antibacterial peptides and understand their interaction with lipids and protein target is very important. We first design
peptides in-silico and test their stability by performing in-silico studies using CHPC resources.
Currently, we using CHPC for three projects, one project calculations have been finished we are in the phase of
manuscript writing for the other two projects we are still performing the calculations
Principal Investigator: Dr Kevin Lobb
Institution Name: Rhodes University
Active Member Count: 12
Allocation Start: 2018-03-08
Allocation End: 2018-10-10
Used Hours: 526352
Project Name: Computational Mechanistic Chemistry and Drug Discovery
Project Shortname: CHEM0802
Discipline Name: Chemistry
We are a diverse research group at Rhodes University mostly of individuals from South Africa but also from France, Nigeria, Zimbabwe and India. We study three main aspects:
1. How reactions occur (mechanism) including a focus on how terpenes (which are found in essential oils) are formed in plants;
2. Chemical libraries and can these libraries help us to identify new treatments for diseases such as Alzheimer's Disease, HIV and TB
3. Conformation and how this affects biological activity of drugs such as the immunosuppressant cyclosporine.
Principal Investigator: Dr Jenny-Lee Panayides
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 5
Allocation Start: 2018-03-13
Allocation End: 2018-10-17
Used Hours: 455098
Project Name: Lead Discovery & Process Development Programme
Project Shortname: CHEM0934
Discipline Name: Chemistry
Alzheimer's disease is the most common form of dementia. To date there is no cure for the disease and only symptomatic treatments are available. Using in silico computational and in vitro biological screening techniques, a team from CSIR Biosciences and the University of Pretoria are currently testing thousands of compounds to identify new pharmacophores for development into drugs for the treatment of Alzheimer's disease.
Using the computational resources provided by the CHPC, very large numbers of compounds can be tested with greater accuracy than what is possible with standard computational hardware. Hit compounds identified through this screening effort will be optimized using computer aided drug design, to improve their effectiveness against a particular target within the human body prior to the expensive and time consuming synthesis of the compounds for advanced biological screening. During this optimisation process many aspects will be considered, including the ability of the human body to absorb the compound and possible toxic side-effects. Thus, utilization of the CHPC resources can potentially accelerate drug development in a significantly more cost effective manner.
Principal Investigator: Prof Nicola Mulder
Institution Name: University of Cape Town
Active Member Count: 14
Allocation Start: 2018-03-13
Allocation End: 2018-11-22
Used Hours: 1650668
Project Name: H3ABioNet
Project Shortname: CBBI0825
Discipline Name: Bioinformatics
H3ABioNet undertook the design of a new genotyping array for African populations. This required the processing and analysis of 3,500 whole genome sequences from African populations across the continent. The CHPC was used for processing of the next generation sequence data, including alignment, variant calling, refinement and phasing. This was all necessary to produce a clean, high quality dataset from which to select representative mutations for the array. The array has now been manufactured and more than 20,000 samples have been processed. This is enabling researchers working on African data to make new discoveries on the genetic basis of diseases.
Principal Investigator: Prof Cornie van Sittert
Institution Name: North-West University
Active Member Count: 18
Allocation Start: 2018-03-13
Allocation End: 2018-10-17
Used Hours: 5065394
Project Name: Computational Chemistry within LAMM at NWU (Potchefstroom)
Project Shortname: CHEM0778
Discipline Name: Chemistry
Since the 1880 the main source of energy for South Africa was coal and at present coal provides 77% of South Africa's primary energy needs. However, the electricity comes at a very high cost, namely air pollution and the influence of the air pollution to human health. In 2004 the South African government reformed the legislation with regard to air pollution. In an effort to contribute to the management of air quality new energy sources must be investigated. These new energy sources must be affordable, clean and renewable. Some of these alternative energy sources are fuel cells and batteries. Electricity from fuel cells and batteries are obtainable through the use of electrochemistry, where free energy of spontaneous reactions is transformed into electricity. A potential replacement form of energy is the hybrid sulphur (HyS) cycle. The HyS cycle is a two-step water-splitting process, which could be used for the production of hydrogen. In the HyS cycle, the anode material used is platinum. However, because platinum is a rare and expensive metal, it is not an economical viable option for long term and large scale production of hydrogen. Hence, various attempts to reduce or eliminate the platinum content, while not compromising the process performance has been made. In the order to understand the electrochemistry on the anode and make informed decisions on the type and amount of metal to be used in various platinum alloys, investigations on a fundamental level is needed. These type of investigations could be classified as computational chemistry. The resources needed for these type of investigations, namely various types of hardware and software is of cardinal importance. Although resources are available at NWU, it is not nearly enough to fully support the research covered in the Laboratory of Applied Molecular Modelling (LAMM). So if we as researchers within the LAMM did not have access to the CHPC resources the progress of our research will be much slower.
Principal Investigator: Prof Penny Govender
Institution Name: University of Johannesburg
Active Member Count: 13
Allocation Start: 2018-03-14
Allocation End: 2018-10-17
Used Hours: 644210
Project Name: Design of MOFs-based sorbent materials for capturing carbon dioxide
Project Shortname: CHEM0797
Discipline Name: Material Science
Our group focuses on the modelling of material that may be used for water remediation. One of the current global challenges is the accessibility of safe drinking water for humankind and animals. Although water is available in some areas it is still not conducive for human consumption therefore the need for water purification. Current methods are either too expensive and even more chemically intensive. By using modelling methods we can easily probe and simulate materials that may be used to the best of their abilities for maximum remediation.
The availability of the CHPC resources has been priceless for the sucess of my research group as this is the only mode of resource we have for access to software as well as a platform to submit our calculations. Without these resources we would not be able to start or finish our research therefore access to the CHPC is pivotal for our productivity and assisting in finding ways to meet the global challenge of ensuring clean water is made available to even the poorest of the poor.
Dr KK Govender who is assigned to the Science domain has also been exceptional in the services that he has rendered for our constant access to the facility with minor hiccups. The turn around time for assistance is short and the knowledge shared to the students is also found to be limitless and most beneficial.
We are extremely grateful for this facility which has helped us to expedite the field of computational chemistry in South Africa and we hope that the access will continue for a long while yet.
Principal Investigator: Prof Eric van Steen
Institution Name: University of Cape Town
Active Member Count: 6
Allocation Start: 2018-03-13
Allocation End: 2018-10-17
Used Hours: 233000
Project Name: Lateral interactions on surfaces
Project Shortname: CHEM0780
Discipline Name: Chemistry
Most compounds used in our day-to-day life has been manufactured using a catalyst, i.e. a compound which ensures that the compound is produced faster and more efficiently (both from an energetic and environmental viewpoint). The evaluation of the suitability of a materials as a catalyst is a ginormous task and has been much of a black art up to now. Theoretical calculations using the CHPC gives us a better understanding of the functioning of catalysts and aids us in searching for better catalysts.
One of the aspects dealt with in this project is improving the catalyst for fuel cells. The slow part in the process has been identified as the conversion of oxygen into water. We are probing ways to improve this reaction thereby improving the efficiency of fuel cells.
Principal Investigator: Prof Catharine Esterhuysen
Institution Name: Stellenbosch University
Active Member Count: 8
Allocation Start: 2018-03-13
Allocation End: 2018-10-17
Used Hours: 535774
Project Name: Computational chemistry analysis of intermolecular interactions
Project Shortname: CHEM0789
Discipline Name: Chemistry
The nature and strength of intermolecular interactions are related to the properties of materials in the solid state. In the Supramolecular Chemistry group at Stellenbosch University we use computational chemistry methods to analyse the interactions to predict a variety of interesting properties. The focus of much of our work is on the interactions between porous materials and compounds such as carbon dioxide (CO2). Since CO2 is known to be the primary contributor to global warming the separation and sequestration of carbon dioxide is one of the Grand Challenges in science and engineering. However, a severe obstacle in the practical capture of CO2 is the large energetic penalty involved in its selective separation. We therefore aim to obtain a fundamental understanding of the chemical processes involved in CO2 sorption (a generic term describing both adsorption, involving molecules trapped on surfaces, and absorption, where the molecules are drawn into a bulk phase) by porous materials, which is vital to develop improved materials for carbon dioxide sequestration. In order to study the interactions between the porous materials and the gaseous 'guests' we utilise the BIOVIA Materials Studio software suite available at the CHPC. Experimental structural data are used as a basis to calculate the sites that the guests will occupy inside the framework and to analyse the strengths of the interactions, which are then used to understand and hence predict sorption properties. We have been able to show that electrostatic interactions are particularly important in stabilising CO2 inside a framework, with the interior structure of the porous material being more important for sequestration than the size of the pores. We are currently investigating the effect of using mixtures of gases in the selective sorption of CO2.
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2018-03-13
Allocation End: 2018-10-17
Used Hours: 2000201
Project Name: Structural, electronic, magnetic properties and anisotropy energy in some metallic and non-metallic heterostructures
Project Shortname: MATS0988
Discipline Name: Material Science
Research in Single-Molecule Magnets (SMM) is motivated by the discovery that a single molecule could behave like a tiny magnet. Such nanoscale magnetism can be exploited in the design of smallest possible magnetic device. Molecules of TbPc2 and CuPc (Pc=C32H16N8) have received considerable experimental and theoretical research attention due to the relative stability of their magnetic structures at temperature suitable for practical applications. Such stability is crucial for the applications of SMM in quantum computing, magnetic resonance imaging (MRI) as well as in high-density information storage, among others. Of importance however, is the choice of suitable substrate which preserves their nanomagnetism. This is necessary to fully exploit the potential benefits of these SMM. Our work therefore, focuses at investigating and optimizing conditions necessary for the stability of SMM of TbPc2 and CuPc (Pc=C32H16N8) molecule on varieties of substrates, using computational approach. To our knowledge, no ab-initio studies have been done on TbPc2 molecule attached on FeMn films up till now. Therefore, atomic level study of TbPc2/substrate (i.e. substrate = FeMn , graphene, silicene, and other two-dimensional materials) is desirable, as this will elucidate the fundamental atomic mechanisms responsible for the observed molecular level magnetization. Furthermore, the understanding of such mechanism will assist in the design and search for other room-temperature single-molecular magnets with wide ranging potential technological applications. So far, the project has established atomic level mechanism underlying the stability of SMM/FeMn and SMM/graphene systems. Other substrates are currently under investigations. The CSIR-HPC/Lengau facility is very crucial to the research as it provides the computational platform on which the calculations are being performed. The research study is a collaboration between Dr. Brice Rodrigue Malonda Boungou of Universite Marien NGouabi, Congo-Brazzaville and Dr. Abdulrafiu Raji of the University of South Africa (UNISA), South Africa.
Principal Investigator: Prof Daniel Joubert
Institution Name: University of the Witwatersrand
Active Member Count: 19
Allocation Start: 2018-03-13
Allocation End: 2018-10-17
Used Hours: 9106960
Project Name: Energy Materials: Numerical explorations
Project Shortname: MATS0800
Discipline Name: Physics
Imagine designing a material atom by atom. Imagine analysing the properties of tomorrow's novel materials before they exist. Computational materials science plays an important role at every of level of the design and engineering of new materials. The rapid advances in computer processing power and memory has given virtual, fundamental, materials design a boost. The first problem faced in designing a virtual material, a material that has not yet been made, is to find the stable configurations in which the atoms in the mix will settle into. The designer must find the configuration of electrons and nuclei, the building blocks of atoms, which result from the interactions among a number of particles that, even for a small piece of material, exceeds the number of particles of sand on all the beaches in the world. This daunting task has a simple solution. Instead of finding the configuration of the real material, the problem is solved for a fictitious material where the constituent particles do not interact. All that is necessary is to find the particle density distribution of the fictitious material, which by design, is the same as that of the real material. A Noble prize was awarded for this idea to the chemists Walter Kohn and John Pople in 1998. A group of postgraduate students at the University of the Witwatersrand use the computer power at the national Centre for High Performance Computing to conduct virtual experiments on existing and novel materials to examine their potential as energy harvesters. They examine the potential of a selection of materials that can be used as cheap components in solar cells, materials that can generate electricity from waste heat and materials that can be used to split water molecules to extract hydrogen for energy production.
Principal Investigator: Prof Moritz Braun
Institution Name: University of South Africa
Active Member Count: 3
Allocation Start: 2018-03-14
Allocation End: 2018-11-22
Used Hours: 1265710
Project Name: Density Functional studies using a variety of different methods and considering materials of current interest
Project Shortname: MATS0924
Discipline Name: Physics
My group is the high performance and computing research group based in University of South Africa. The research focus of our group are on theoretical Physics, computational Physics, inverse Scattering, few-Body Physics and materials science.
The group has actively leveraged on the research facility provided by the CHPC to carry out materials science research and provide validation to some theoretical physics questions. The kind of research carried out within the group would lead to materials design and discovery as well as answer pedagogical scientific queries.
Solving the many-body electron problem is an non-trivial problem for interacting systems which provides appropriate description of most materials. This can be done with the help of computing in a self-consistent manner. Thus, materials science problem such as this, leverages on the CHPC resources to provide meaningful contribution.
Progress has been achieved in the 2D materials, bulk materials and pedagogical problems we are engaged in. Recently, we investigated ZnTiO3 based material which is of importance in the development of solar based device. We were able to describe this material and provide valuable insights towards to the experimental realization of the system.
Principal Investigator: Mr Randall Paton
Institution Name: University of the Witwatersrand
Active Member Count: 4
Allocation Start: 2018-03-13
Allocation End: 2018-10-17
Used Hours: 412594
Project Name: Compressible Gas Dynamics
Project Shortname: MECH0847
Discipline Name: Other
Compressible gas use occurs in the everyday world, such as the pneumatic lifts used for car bonnets, but the dynamics of these gases at high speeds remains an area of active research. With the drive for greater efficiency and minimal environmental impact, innovation in all aspects of life is needed. One possible avenue is changes to transport through the development of high-speed trains and aircraft. In these contexts, high-speed travel would be subsonic (slower than the speed of sound) for trains and possibly supersonic (faster than the speed of sound) for aircraft. The speed of sound is around 1 000 kph.
Experimental testing is generally too expensive to be practical when studying the loads on supersonic bodies. Computational Fluid Dynamics (CFD) provides an excellent alternative allowing users to conduct experiments using a computer instead. In the Flow Research Unit at Wits University, the use of high performance computing has enabled detailed modelling of the effects of extreme acceleration resulting from the high aerodynamic forces in these regimes to be quantified. These studies would not have been practically possible using conventional computers as each simulation would have required upwards of 3 months, 24 hours a day while execution on the CHPC reduced this to around 1 week per case. This work is reaching conclusion now and further publications from the work are expected.
Principal Investigator: Prof Jeanet Conradie
Institution Name: University of the Free State
Active Member Count: 3
Allocation Start: 2018-03-14
Allocation End: 2018-10-17
Used Hours: 1539294
Project Name: Computational chemistry of transition metal complexes
Project Shortname: CHEM0947
Discipline Name: Chemistry
DFT work focused inter alia on 2-pyridyl-(1,2,3)-triazole-containing metal(II) compounds. A detailed knowledge of the structure and properties of these compounds are essential for future evaluation to be used for medical applications (antimicrobial), chemical industrial use and dyes in dye-sensitized solar cells.
Principal Investigator: Mr Theo Fischer
Institution Name: eScience
Active Member Count: 3
Allocation Start: 2018-03-13
Allocation End: 2018-09-06
Used Hours: 170242
Project Name: Acid Deposition
Project Shortname: ERTH0851
Discipline Name: Earth Sciences
The Mpumalanga Highveld region is subject to intensive power generation and emissions from the oil from coal industry heavy industrial activity. As at 2010 the sulphur dioxide emissions by power generation alone amounted to 2.2 million tonnes, which is expected to increase further with additional coal power plants under consideration and existing ones running at capacity. Full oxidation and conversion to salt (SO2 -> SO4-> TDS) typically more than doubles the mass of SO2. Accordingly the annual mass of TDS that will eventually report to catchments and oceans amounted to over 4.5 million tons, whereas the natural annual average total salt load in the runoff from the entire 38 5050 km2 Vaal Dam catchment is only about 0.18 million tons.The importance of this investigation arises from the economic and environmental impact of the deposition of anthropogenically emitted salts on water users in the strategic heartland of South Africa on the one hand, and the expensive decisions arising from the location and technology of new power stations and industrial plant (such as the possible need to retrofit flu gas desulphurisation) on the other. Both the costs and the benefits are high and hold very significant implications for our national economy. Rational decision making therefore requires evaluation of the costs associated with both deposition impacts and the cost of reducing them. The latter is well known, but since the potential problem was first highlighted in 1983, the impact on water resources has not been quantified. . A major purpose of this study is to do so, followed by estimation of the economic impact on Rand Water consumers.
Principal Investigator: Prof Josua Meyer
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2018-03-14
Allocation End: 2018-10-17
Used Hours: 931811
Project Name: Fundamentals of forced and mixed convection in heat exchangers
Project Shortname: MECH1094
Discipline Name: Computational Mechanics
In-tube condensation is widely seen in many industries such as desalination, power plants and air conditioning. Thoroughly understanding of the condensation phenomenon would lead to better design of the systems which consequently causes the improvement of system efficiency. Although in majority of applications the circular tubes are used, there are some particular cases, like in air-cooled steam condensers, in which non-circular tubes such as rectangular tubes and flattened tubes are utilized. It has been proved that the thermal efficiency of such tubes are better as compared to the conventional circular tubes under specific operating conditions.
This work is being done by the Clean Energy Research Group (CERG) at the University of Pretoria. This group is involved in experimental and numerical heat transfer research focused on clean energy applications. CERG, falling under the Department of Mechanical and Aeronautical Engineering at the University of Pretoria, has a number of world class experimental facilities focused on heat transfer, balanced by a Computational Fluid Dynamics (CFD) division. The Group members have developed, designed and built five unique, state of-the-art experimental set-ups, which are being used for leading-edge heat transfer research.
Due to lack of water resources in South Africa, the research works on the optimizing and performance enhancement of systems working with water as the working fluid should be greatly developed. Such activities will definitely lead to lower energy and water consumption within the country in the future.
It is the purpose of this research work to numerically investigate the effect of inclination on condensation of steam inside a long flattened channel. Thoroughly understanding of this problem via numerical simulations would assist in proper design of ACCs with low cost and time compared to experimentation.
At the moment, most of the work has been done, and a research paper is going to be prepared.
Principal Investigator: Prof Richard Tia
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 12
Allocation Start: 2018-03-15
Allocation End: 2018-10-24
Used Hours: 706567
Project Name: Computational Chemistry and Materials Science
Project Shortname: CHEM1044
Discipline Name: Chemistry
We have not yet obtained results that can form the basis of a press release but with the progress made in the our work, especially the work pertaining to the conversion and utilization of carbon dioxide, it should be possible to make a press release in the near future. With increasing interest of the scientific community and government agencies on the mitigation of rising carbon dioxide levels and the attractiveness of using carbon dioxide as a feed-stock for industrial processes, this work might be very suitable for a press release as and when we get interesting results.
Our research activities fall under two broad areas, namely;
1. Molecular modeling - Exploring the mechanisms of organic, inorganic and organometallic reactions.
These studies afford important molecular-level mechanistic details of industrially-relevant chemical reactions that are difficult, if not impossible, to obtain experimentally. Molecular level understanding enable chemical reactions to be guided quickly and efficiently along desirable pathways, with the effect of producing the right product with minimal energy consumption and minimal environmental impact. A key aspect of this work is the development of homogeneous transition metal catalysts for the depolymerization of lignin, an abundant natural resource, for fuel.
2. Materials modeling
The atomic- and molecular-level mechanistic insight gained from these studies are useful for the design of novel catalysts for the conversion of CO2 and other green-house gases as well as stranded gases from the petroleum refining into useful fuels. This addresses the problem of global warming as well as providing an environmentally friendly alternative sources of fuel.
The research objectives described here are very computationally-demanding and using the CHPC resources is highly beneficial. Without that, we would not be able to carry out some of these calculations.
Principal Investigator: Dr Eric Maluta
Institution Name: University of Venda
Active Member Count: 15
Allocation Start: 2018-03-16
Allocation End: 2018-10-24
Used Hours: 440003
Project Name: Energy Material Modeling in the Application of different Photovoltaic Technologies
Project Shortname: MATS0827
Discipline Name: Physics
Our computational research group at the University of Venda, focuses on the computational studies of semiconductors, energy materials, water splitting and dye sensitized solar cells. We are currently currently working on the TiO2 semiconductor, Band gap engineering and the study of charge transfer at TiO2/dye-molecule interfaces in these types of solar cells.
Developing a cheaper solar cell will help the rural villages to be able to buy and use these types of solar cells. We hope that by understanding the factors affecting the solar cells, we can find solutions to improve their efficiency.
Our main goal is to manufacture a simple solar cell, which will be locally South African. The calculations based on the CHPC will helped us to perform the experiments simple. The calculations makes us to understand the system we are working on and it becomes easy to implement it during experiment. We hope that soon we will be able to develop new solar cells and materials.
Principal Investigator: Mr Adebayo Azeez Adeniyi
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2018-03-20
Allocation End: 2018-10-24
Used Hours: 714863
Project Name: Drug Discovery Research Using Quantum and Molecular Dynamic Simulation
Project Shortname: CHEM0958
Discipline Name: Chemistry
The CHPC research group CHEM0958 (Drug Discovery Research Using Quantum and Molecular Dynamic Simulation) is made up of the three additional users besides the principal investigation. As the principal investigator, I am currently at University of the Free State, while two of my users are at University of KwaZulu-Natal, Westville Campus.
Our CHPC research group (CHEM0958) is focussing on the application of quantum and statistical methods to study the electronic, molecular and spectroscopic properties of molecules and their potential therapeutic applications against selected enzymes rated to Cancer and Alzheimer diseases. The application of our molecules also cover the possibility of been used in dye sensitizer solar cell and also as catalyst. We are regular users of CHPC quantum packages like Gaussian and molecular dynamics packages like Amber.
We have also published three research articles in the year 2018 through the application of CHPC facilities. We also have some other research outputs that are under review.
Two of my group users will be obtaining their PhD degree this year. CHPC has contributed significantly to their research thesis.
Principal Investigator: Prof George Amolo
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 11
Allocation Start: 2018-03-20
Allocation End: 2018-10-24
Used Hours: 950287
Project Name: Properties of Materials for Green Energy Harnessing
Project Shortname: MATS862
Discipline Name: Material Science
The MATS862 group continues research activities with a focus on materials for energy conversion. This group consists of materials scientists of Kenyan origin as well as graduate students pursuing their studies at universities in Kenya. The provision of high performance computing resources and support to carry out research work through computational modeling in materials science cannot be taken for granted and we are truly grateful to the South African Government. The latest initiatives from Kenya have been to obtain codes that require proprietary licenses to legally enable their hosting at the CHPC and enhance further research.
In the recent past the work has looked at materials for thermoelectric conversion as well as potential catalysts for the photo-oxidation of water. It is expected that studying such materials is likely to inform experimental work as to the direction of possible investigations thus minimising past trial and error.
The search for alternative and cleaner forms of energy has gathered moment in many parts of the world due to concerns of environmental degradation and the development of technologies from innovation trends. In order to perform these kinds of development there is need to create infrastructural and human capacity to meet challenges that may arise.
Projects selected for investigations are based on research gaps or questions to be answered in order to enhance research output rather than mere. reproduction. Once a suitable material system is identified the appropriate scripts are created in the CHPC and simulations run to extract scientific information. Some simulations can take months to run to completion. The CHPC is therefore required to provide the computational resources consistently without interruption.
Good progressing has been made and dissemination made in various conferences and in the form of publications
Principal Investigator: Prof Kevin Naidoo
Institution Name: University of Cape Town
Active Member Count: 7
Allocation Start: 2018-03-20
Allocation End: 2018-10-24
Used Hours: 2106205
Project Name: Reaction Dynamics of Complex Systems
Project Shortname: CHEM0840
Discipline Name: Chemistry
My group develops software and algorithms for biomedical and life science applications. Our unsupervised methods are able to identify cancer subtypes that will assist oncologist in the treatment of breast cancer patients. Our methods to design cancer therapeutics are been put to the test in our enzymology laboratories in preparation for cancer cell line tests.
Principal Investigator: Dr Chris Barnett
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2018-03-22
Allocation End: 2018-10-24
Used Hours: 14581
Project Name: Analysis of disease related polymers
Project Shortname: CBBI1063
Discipline Name: Bioinformatics
I investigate the shapes, structures, and properties of molecules by using computational modelling techniques. I'm particularly interested in complex sugars (glycans), which are interesting to study because they are involved in intricate molecular recognition processes in cells, for example, playing a role in cell signalling, adhesion, and immunity.
Further understanding of these molecules and the complex systems they are involved in may lead to the generation of additional diagnostic markers and inhibitors that can be used to combat disease.
The CHPC provides a platform for being able to run large-scale and highly parallel simulations which is a great help in making rapid progress towards solving research questions. The CHPC is also a test bed when carrying out computation on and developing algorithms for large datasets.
Principal Investigator: Prof Felix Spanier
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2018-03-22
Allocation End: 2018-10-24
Used Hours: 1596282
Project Name: Acceleration and transport of high-energy particles in the universe
Project Shortname: ASTR0804
Discipline Name: Astrophysics
South Africa has moved a bit closer to the stars in the recent years by founding its own space agency SANSA. But there is more to space exploration than just building rockets. One important point is the understanding and possible forecast of space weather - the influence of high energy particles emanating from the Sun.
Researchers from the NWU have been doing extensive simulations to understand one aspect of space weather: The transport of cosmic rays in high-frequency turbulence. The Centre for Space Research has a decade long tradition in this kind of study and the youngest generation of researchers could benefit from CHPC's newest acquisition the Lengau cluster.
This type of research requires sophisticated and large-scale plasma models, which can only be handled with state-of-the-art supercomputers. CHPC has played a pivotal role in enabling NWU's researchers to get to the next level. Especially the new PhDs Alex Ivascenko and Cedric Schreiner have found new interesting details about the electron transport in the solar wind. They could show that the solar wind behaves vastly different at smallest scales and that this affects the transport of electrons significantly.
While this seems like a purely academic scenario, it still has an impact on building satellites and spacecrafts in the long run: Any space equipment has to be shielded against electron impacts and understanding the whereabouts of electrons from the Sun is an important piece of the puzzle. Especially for South Africa as aspiring space nation.
Future simulations will try to figure out how particle transport changes with a quiet Sun (weak turbulence) and solar eruptions (strong turbulence). The ultimate goal in any of these simulations is to predict when the Sun will emit large particle fluxes that may harm space equipment.
The tools and methods used in this project also have another important role: Understanding plasma simulations and high-performance computing is ever more important for industrial purposes. And teaching these skills to young students will make a difference.
Principal Investigator: Dr Rose Modiba
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 4
Allocation Start: 2018-03-28
Allocation End: 2018-10-24
Used Hours: 78855
Project Name: Computational modelling of light metals
Project Shortname: MATS1097
Discipline Name: Material Science
Light metal group at the CSIR use computational simulation packages through CHCP to do studies on the structural stabilities of materials in order to predict the stable phases. The generated results can be used as a guide in the labs without performing a lot of experiments. The Materials Studio code at CHCP is used to determine the structural, elastic and optical properties of the materials and compare with the available experimental results to validate our findings, then new alloying elements are added and new information is generated which can be used in the labs. Interestingly, the jobs submitted at CHCP complete faster which makes it possible for us to do more research and comparison quicker. The determined results up to so far yielded a good correlation with the experiments.
Principal Investigator: Prof Abu Yaya
Institution Name: University of Ghana
Active Member Count: 4
Allocation Start: 2018-03-28
Allocation End: 2018-10-24
Used Hours: 361561
Project Name: DFT modeling of weak interactions; a case study for Carbon nanosystems
Project Shortname: MATS0990
Discipline Name: Material Science
The research group is made up of researchers from the University of Ghana and the Bells University of Technology, Ota, Nigeria.
Members are focused on using a series of computers (over 500) which has be name Lengau to investigate tiny particles (nanomaterials) which are otherwise not visible to the eyes but can be modeled with these computers for use in electronic devices such as mobile phones, CD recorders, flat screen television etc.
Currently the research is progressing steadily and are done with the first stage by making models which could be tested experimentally.
Principal Investigator: Prof Krishna Bisetty
Institution Name: Durban University of Technology
Active Member Count: 7
Allocation Start: 2018-04-02
Allocation End: 2018-11-15
Used Hours: 40947
Project Name: Computational Modelling & Bioanalytical Chemistry
Project Shortname: CHEM0820
Discipline Name: Chemistry
My current ongoing projects are as follows:
Mechanism of metal uptake and release for transferrin—metal family protein using QM/MM
Understanding the pH effect on the conformational diversity that may affect interaction between phenylalanine ammonia-lyase sensing and Capsaicin and sensing.
Designing electrochemical biosensors for the detection of different analytes with application in food industry.
Principal Investigator: Prof Jaco Dirker
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2018-03-27
Allocation End: 2018-10-24
Used Hours: 291493
Project Name: Heat Transfer Enhancement in Thermal Systems
Project Shortname: MECH1029
Discipline Name: Computational Mechanics
I apologize for missing the required feedback for this period. Kindly refer to the progress report that was submitted for the following period which reflects the state of the project at that time.
Principal Investigator: Prof Graham Jackson
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2018-04-04
Allocation End: 2018-10-31
Used Hours: 11307
Project Name: Insect neuropeptides
Project Shortname: CHEM1101
Discipline Name: Chemistry
Insect flight is under hormonal control. When needed, hormones are released and bind to trans-membrane receptors, which initiates energy mobilization. By understanding the structure and nature of the hormone/receptor binding it is possible to design species specific insecticides.
Principal Investigator: Prof Phuti Ngoepe
Institution Name: University of Limpopo
Active Member Count: 27
Allocation Start: 2018-04-05
Allocation End: 2019-01-10
Used Hours: 9363102
Project Name: Computational Modelling of Materials: Energy Storage
Project Shortname: MATS0856
Discipline Name: Material Science
The University of Limpopo Materials Modelling Centre (MMC) employs computational modelling for predicting and optimising properties of materials. The South African Research Chair, occupied by Professor Phuti Ngoepe, has enabled extension of high performance computing approach to value addition of materials. Different modelling time and length scales are employed on computing infrastructure at MMC and the Centre for High Performance Computing, in Cape Town. High energy density batteries are central to development of electric vehicles, solar energy storage and support of the electricity grid. Their enhanced performance is achieved with nano-architectured electrodes, and the MMC has developed some world leading approaches of modelling such nanostructures for Li-ion batteries and beyond. The models imitate and predict processes occurring in reactors of pilot and production plants for electrode materials. They further enable performance prediction, such as fast charge and long life of batteries. Efficient mineral processing methods, which address challenges of water, energy and environment in the mining sector are becoming imperative. The MMC studies mineral surface properties by simulations and predict and design reagents that optimise recoveries of sulphides from ores, especially the precious group metals. Lastly, the MMC investigates phase stabilities of precious and light metal alloys from a combination of energetics, elastic and vibrational properties. The approach has provided valuable information for aerospace applications, shape memory devices and powder metallurgy processing. The research themes, mentioned above, have been conducted in collaboration with Universities, national laboratories and industries, locally and internationally, particularly the UK, USA, Japan and China. Research contributions have generated many publications and presentations at local and international conferences, with several keynote addresses. More than 50 MSc and PhD students have graduated and have won conference awards at local and international conferences. Researchers have received numerous national accolades, and have contributed to science policy development in the country.
Principal Investigator: Prof Fernando Albericio
Institution Name: University of KwaZulu-Natal
Active Member Count: 1
Allocation Start: 2018-04-09
Allocation End: 2018-11-15
Used Hours: 6731
Project Name: Peptide chemistry and Organic chemistry
Project Shortname: CHEM1102
Discipline Name: Chemistry
We are Peptide Science Group at UKZN Westville campus. The project was brought up with an intend to learn computational chemistry. The project involves synthesis of several organic molecules towards application in oligonucleotide chemistry. With the help of computational tools we aim to predict the reaction mechanism. Since CHPC provides the server which speeds up the calculations and helps in achieving the preliminary results. The project so far had been very promising in its preliminary stage. We expect to be going ahead with these results for further analysis towards prediction of reaction mechanism.
Principal Investigator: Prof Juliet Hermes
Institution Name: SAEON
Active Member Count: 2
Allocation Start: 2018-04-10
Allocation End: 2018-10-31
Used Hours: 16796
Project Name: SAEON Coastal and Regional Ocean Modelling Programme
Project Shortname: ERTH1103
Discipline Name: Earth Sciences
The Coastal and Regional Ocean Modelling Programme is a modelling initiative of the South African Environmental Observation Network (SAEON) Egagasini Node based in Cape Town. The aim of this programme is to use ocean models to understand regional and coastal shelf dynamics. The ORCA025 configuration, extending from the Angola gyre, Mozambique channel and including the Southern Ocean is used in this programme. A high resolution grid is used which zooms the coastal region including the St Helena Bay region which is an important nursery ground for fish and also the main generation zone of low oxygen water. The low oxygen generated in the St Helena Bay region result in the formation of greenhouse gases including nitrous oxide which has a global warming potential about 265¬-310 times higher than that of carbon dioxide. With climate change there is also a need to understand implications for primary production and expansion of low oxygen regions in the ocean. The coupled ocean model in this programme is used to understand these processes and the results obtained can be used to fill knowledge gaps and advance coastal modelling. Currently the model is being validated and the next step is to increase resolution to capture fine scale processes.
Principal Investigator: Prof Rebecca Garland
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2018-04-10
Allocation End: 2018-10-31
Used Hours: 147753
Project Name: Simulating atmospheric composition
Project Shortname: ERTH0846
Discipline Name: Earth Sciences
Air pollution can have large negative impacts on human health, agriculture, ecosystems, visibility and climate. In South Africa, although ambient air quality is regulated, many areas are out of compliance with the National Ambient Air Quality Standards. In order to protect human health and mitigate impacts, it is critical to improve air quality. The Constitution provides that everyone has a right to have an environment that is not harmful to their health. The Atmospheric Composition Focus Area (ACFA) in the CSIR Climate Studies, Modelling and Environmental Health Research Group aims to provide the evidence base to quantify the impacts of air quality and to improve air quality. The group uses the CHPC to run an air quality model to simulate urban and regional air quality at high resolution. This chemical transport model simulates the physics and chemistry of the atmosphere. The processes represented within the model are complex, and thus computationally intensive, which makes use of the CHPC facility a necessity. The CSIR ACFA is the only group in South Africa routinely running a chemical transport model to simulate air quality. Using the CHPC resources, the team has been able to simulate the impact of policy interventions on air quality in cities. Additionally, the team has simulated the health risk from air pollution regionally in South Africa. In the past, this has been done using monitoring station data only, which then limits the analysis to only those living directly around the station. The team has also simulated the impact of climate change on air pollution. These simulations use the climate projections for the CSIR's VrESM, which is also run at CHPC, to provide meteorology input into the air quality model. These outputs directly provide the evidence base needed for decision makers to draft and implement policies and interventions to effectively improve air quality as well as understand its impacts, now and into the future.
Principal Investigator: Dr Adam Skelton
Institution Name: University of KwaZulu-Natal
Active Member Count: 11
Allocation Start: 2018-04-10
Allocation End: 2018-10-31
Used Hours: 742499
Project Name: Molecular modelling of biomolecules and materials
Project Shortname: CHEM0798
Discipline Name: Chemistry
I am Dr. Adam Skelton and I work at the College of Health Science university of KwaZulu-Natal. I work on understanding the behaviour of biological and material systems on the molecular level. A particular interest is in using molecular simulation to direct the rationale design of functionalized nanoparticles for a range of applications such as drug delivery, water treatment and catalysis. In particular, drug delivery is the use of nanoparticles to carry antiviral or antibacterial drugs into parts of the body that are difficult for conventional drugs to reach. Drug-delivery is, therefore, of huge importance in South Africa, especially in the battle against HIV and Tubercolosis. The research requires running a series of computar simulations, which may take hours at a time. CHPC has had a great impact since it provides me with the facilities to perform such simulations. Since the project started, my group has published more than 15 papers in international journals and has provided deep insight into biological and material systems on the molecular level.
Principal Investigator: Prof Mahmoud soliman
Institution Name: University of KwaZulu-Natal
Active Member Count: 34
Allocation Start: 2018-04-11
Allocation End: 2018-07-10
Used Hours: 2687850
Project Name: Drug Design, development and modelling
Project Shortname: HEAL0790
Discipline Name: Health Sciences
The research scope of the Molecular Bio-Computation and Drug Design Research Lab covers a wide range of computational and molecular modeling research areas with main focus on biological systems and drug design approaches. Main interest is related to design and study of biologically and therapeutically oriented targets by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We show keen interest in diseases of global burden and evident prevalence within the south African populace such as HIV/AIDS, Tuberculosis and Cancer. The computational resources provided by CHPC is employed in performing the molecular dynamic calculations and the corresponding post molecular dynamic simulation analysis
Principal Investigator: Prof Warren du Plessis
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2018-04-11
Allocation End: 2018-10-31
Used Hours: 510836
Project Name: Electronic Warfare (EW) Technologies
Project Shortname: MECH0989
Discipline Name: Electrical Engineering
Simulations of the radar cross section (RCS) of an object are extremely time consuming and memory intensive. The use of techniques to reduce the number of simulations which need to be performed is thus of tremendous interest. However, the problem is that baseline data need to be generated to allow the performance of such interpolation techniques to be determined, leading to a requirement for a large number of RCS simulations which require an enormous amount of computing time and resources. The availability of the CHPC has allowed Proff Warren du Plessis and Pieter Jacobs in the Department of Electrical, Electronic and Computer Engineering at the University of Pretoria to undertake such research in a way that other researchers without access to similar resources are unable to. For example, the first paper these researchers published on this topic did not make use of the CHPC and clearly demonstrated the way that this research would be constrained in terms of the number and complexity of objects which could be considered without access to additional computing resources. The initial results are excellent, suggesting that the time required for RCS simulations can be significant reduced without sacrificing accuracy. As stated above, one paper has already been published on this topic, with another paper in preparation and further papers planned.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2018-04-11
Allocation End: 2018-10-31
Used Hours: 2953389
Project Name: CFD modelling of falling-film bioreactors
Project Shortname: MECH1001
Discipline Name: Computational Mechanics
This project stemmed from a passenger transport initiative of Transnet Engineering, known "in-house" as the MC25. While the project's initial phase would consist of a low to medium speed commuter connecting the business hubs of Gauteng to Polokwane, hereby opening the job-market in order to address the high unemployment rate in the country, Transnet's vision would ultimately be a high-speed rail network connecting South Africa's major cities. The optimisation of this train's nose is to serve as a technology demonstrator for this ultimate future goal. The optimisation goals are drag reduction, a financial consideration, and cross-wind stability, a safety consideration. Given the complex nature of the problem, Transnet joined hands with the University of Pretoria and the CHPC to make this vision a reality. While it is usually aeroplanes that seem to fascinate the public, it is the aerodynamics of high-speed trains that are truly challenging, mainly due to the very "dirty" external flow field surrounding the train due to the presence of the ground, the very thick boundary layer flowing over the train surface and the very long trailing wake. This implies that not only would the computational domain for a train have to be very large, but the flow phenomena that would need to be captured are very complex also. Transnet required the development of in-house expertise in the field of fluids and approached Professor Ken Craig of the University of Pretoria to guide Andrea Beneke's research. Because of the very large and complex nature of the required, cluster computing from the CHPC was a necessity. While the geometry of the train nose has already been optimized for windless conditions, it is Transnet's hope that a train nose that is stable under cross-wind conditions will soon be completed also – taking South-Africa one step closer to the future.
Principal Investigator: Dr Roelf Du Toit Strauss
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2018-04-12
Allocation End: 2018-10-31
Used Hours: 2361991
Project Name: Computational Space Weather
Project Shortname: PHYS0918
Discipline Name: Physics
One of the biggest hurdles faced by manned exploration of space is the high levels of natural radiation present in the solar system. This is not only an important consideration faced by future astronauts on board spacecraft, but also by future colonizers of Mars, and inhabitants of future moon bases and space stations. This important risk is acknowledged by both SpaceX and NASA, and planned bases and spacecraft try to accommodate so-called "space storm shelters", where space dwellers can hide from dangerous radiation levels. At the Centre for Space Research of the North-West University, South Africa, we are doing our part to mitigate these possible harmful effects by developing state-of-the-art numerical models that can simulate and predict the levels of harmful natural radiation. To simulate the intensity of these so-called "cosmic ray" particles, complicated and large-scale numerical models are run on large scale computer clusters, such as the Lengau cluster of the Centre for High Performance Computing (CHPC) in Cape Town, South Africa.
Principal Investigator: Dr Bahareh Honarparvar
Institution Name: University of KwaZulu-Natal
Active Member Count: 9
Allocation Start: 2018-04-12
Allocation End: 2018-11-15
Used Hours: 1543254
Project Name: Computer-aided HIV/TB drug design
Project Shortname: CHEM0808
Discipline Name: Health Sciences
My research lies in the clear and coherent road map towards the application of computational methods to address problems in the biomedical field and drug discovery. I am motivated by the challenges in designing potential therapeutic compounds for the treatment of different diseases that can be brought to the market. I use software packages that are installed on CHPC for biomolecular simulation and drug design.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2018-04-12
Allocation End: 2018-10-31
Used Hours: 468966
Project Name: CFD Modelling of Concentrated Solar Power Applications
Project Shortname: MECH0873
Discipline Name: Computational Mechanics
Central tower solar power plants are the most promising concentrated solar with research into new receivers and heat transfer fluids and collectors (heliostats) being ongoing world-wide. Researchers at the University of Pretoria's Clean Energy Research group under the leadership of Prof Ken Craig are using the resources at the CHPC to speed up calculations of both heliostat analysis (involving wind loads and fluid-structure interaction) as well as those required for a new point-focus central receiver design being developed. For heliostats, knowledge has been gained in predicting the peak loads that these reflectors will experience during all orientations and wind conditions. Ongoing work is focused on further reducing the cost of these Computational Fluid Dynamics (CFD) hybrid Large Eddy Simulation (LES):Reynolds-Averaged Navier-Stokes models to make them feasible on smaller-scale computers. This project has been ongoing since 2013 with the involvement of CHPC resources since 2016. The project has already delivered one masters student (Dawie Marais) with another masters student (Joshua Wolmarans) nearing completion. PhD student Pierre Poulain is also nearing the end of this investigation into LES modelling of the atmospheric boundary layer. For central receivers, work is ongoing to enhance heat transfer. Of specific interest here is the use of jet impingement, especially in the transient mode through either passive or active excitation. This phenomenon of heat transfer enhancement, although conceptually simple, it very hard to model accurately, and here the resources of the CHPC are invaluable.
Principal Investigator: Dr Samson Khene
Institution Name: Rhodes University
Active Member Count: 7
Allocation Start: 2018-04-13
Allocation End: 2018-11-15
Used Hours: 351213
Project Name: Synthesis, Spectroscopy and Nonlinear Optical Properties of Phthalocyanines
Project Shortname: CHEM0975
Discipline Name: Chemistry
Many of today's optical sensors are based on optical materials in which non-linear optics may play a role. Defects in the cable can have an effect of reducing the light (which carries information) in an optical fiber or cable. This phenomenon is also present in a variety of non-linear active materials or molecules. This nonlinear reduction of light phenomenon can be used as a sensing method for detection and correction of signals that are sent in cables. The aim of our research (at Rhodes University in the Chemistry department) is to make and study molecules which will help improve signal transmission using a nonlinear process. This work will not be possible if it was not supported by CHPC facilities.
Principal Investigator: Dr GENITO MAURE
Institution Name: Eduardo Mondlane University
Active Member Count: 3
Allocation Start: 2018-04-16
Allocation End: 2018-11-22
Used Hours: 62988
Project Name: Air Pollution and Impacts
Project Shortname: ERTH0917
Discipline Name: Earth Sciences
The "Air Pollution and Impacts" is a project undertaken by the Environment and Climate Research Group from the Eduardo Mondlane University in Maputo – Mozambique. It aims to understand better the feedbacks of the Southern African climate and atmospheric pollution, specifically the tiny solid and liquid particles released by different sources in this region, which remains uncertain for the region despite its already notorious high pollution levels. The research applies state–of–the–art physical climate models that incorporate complex interactions between pollution and climate, which result in different responses of the solar radiation amount reaching the Earth as well as of precipitation patterns. Because of the complexity of interactions in the models, the computational demand is extremely high and only the CHPC has such capacity to host such a project in the region. Thus far, the project has successfully completed its first phase that comprised test simulations of the impacts of wildfires over the Niassa Reserve and is now ready to start cyclone trajectory simulations as well as SKA related work. Other simulations on pollution source-pathway-receptor analysis are also ongoing.
Principal Investigator: Dr Quinn Reynolds
Institution Name: Mintek
Active Member Count: 2
Allocation Start: 2018-04-16
Allocation End: 2018-10-31
Used Hours: 232002
Project Name: Computational Modelling of Furnace Phenomena
Project Shortname: MINTEK776
Discipline Name: Applied and Computational Mathematics
The Pyrometallurgy Division at Mintek engages in research, development, and technology transfer in the field of high-temperature metallurgical processing. This supports the beneficiation and value-enhancement of South Africa's extensive mineral resources.
In pyrometallurgy, furnaces are used to heat and melt rocky raw materials to temperatures in excess of 1500 degrees centigrade. Once in the molten state, the chemical reactions necessary to extract the valuable metal and mineral products they contain can be performed. The design and operation of such furnaces is an engineering grand challenge, and is greatly improved by the building of fundamental and applied knowledge of their behaviour using large computational models. Mintek's collaboration with the Centre for High Performance Computing has been invaluable in helping us push the envelope in pyrometallurgical process modelling.
A number of project milestones were met this year, including the development of enhanced models of plasma arc behaviour for electric furnace design, combined chemical reaction and fluid flow models for understanding secondary metallurgy processes, and computational fluid dynamics models for improving the methods used to remove molten material from furnace vessels.
Principal Investigator: Dr Aniekan Ukpong
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2018-04-16
Allocation End: 2018-10-31
Used Hours: 177660
Project Name: Theoretical and Computational Condensed Matter and Materials Physics
Project Shortname: MATS0941
Discipline Name: Physics
The theoretical and computational condensed matter and materials physics group at the School of Chemistry and Physics, University of KwaZulu-Natal develops and implements state-of-the-art models for studying complex materials. We take special interest in the rich physical phenomena involved in the interaction of the cloud of electron in atoms, molecules and solids with a static or dynamic electric and (or) magnetic field(s). Our main tool is quantum mechanics as formulated within density functional theory, and we implement it computationally using the HPC platform. Our data analyses allow us to gain unique insights to the physical properties of complex materials, and their associated electronic phenomena, which can be used as a predictive guide to experiments. Our research focuses on the electronic structure of heterostructure multilayer nanoparticles, atomic dynamics in ceramic glass composites, alloys development, and applied spectroscopy. We study charge and spin transport for the development of topological insulators, metallic and semiconducting properties. We also study the response of electronic systems to applied electric and magnetic fields. Our emphasis is on finding answers to questions that arise from materials research in disparate areas of modern society. Finding suitable answers involve doing calculations that help to reveal how electrons behave in materials that contain a very large number of atoms. Such calculations are impossible to perform on laptops or desktop computers. Our use of high performance computing has allowed us to develop technical capabilities in technology areas such as electronics, energy, water purification and nanomedicine, as well as coal beneficiation. Particularly, in our spintronics research, we have recently predicted the existence of a new robust phase for transporting electrons, which is suitable for storing information efficiently. This finding may pave the way for a whole new family of energy-efficient magnetic recording devices based on artificially-assembled materials.
Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 24
Allocation Start: 2018-04-16
Allocation End: 2019-03-08
Used Hours: 2305448
Project Name: Computational and statistical methodologies for human and environmental health prediction
Project Shortname: CBBI0818
Discipline Name: Bioinformatics
Computational and statistical methodologies for human and environmental health prediction research programme (CBBI0818) is running from the University of Cape Town, South Africa. This research programme is fundamentally aiming 1) to determinate the environment and genetic variation that cause human species to look different, having difference in allergy, drug responses and treatment. 2) to identify and quantify the pattern of inheritance of the observed trait, drug response and treatment variation among human. These are addressed through the design of machine learnings and artificial intelligent methodologies and statistical approaches to analysis DNA data of thousands affected/unaffected subjects within a geographical region. In doing so, this programme will contribute to human health by increasing understanding of the genetic and environmental underpinnings of complex traits (or diseases), drug/treatment responses and drug/dosage responses and forecasting individual's health and traits such as the weather is forecasting today. The accumulation of experimental DNA data in Biology and new high throughput experiments are growing rapidly and give a huge number of data difficult to manage, to store and to analyse this existing and future dispersed information. Therefore, high-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring the field of bioinformatics to use high-performance computing resources and carry out data management and analysis tasks on large scale data. Today, the use of HPC has critically increased our researcher portfolio to meet the international standard with respect to large scale genomic era. This programme has already developed a number of genomic-based software tools that address African genetic variation challenges and provided advanced trainings around parallel programming with respect to large-scale genomic data to African postgraduate students/researchers.
Principal Investigator: Prof Paulette Bloomer
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2018-04-16
Allocation End: 2019-03-08
Used Hours: 11900
Project Name: Molecular Ecology and Evolution Programme
Project Shortname: CBBI1030
Discipline Name: Bioinformatics
The Molecular Ecology and Evolution Programme (MEEP) is a research group in the Division of Genetics, Department of Biochemistry, Genetics and Microbiology at the University of Pretoria. We investigate the evolutionary history and current genetic diversity of many vertebrate species (marine and terrestrial), using genetics and genomics tools, and try to link the patterns we see with ecological and human-mediated events. We currently have two projects (Cape buffalo and bowhead whales) that make use of the CHPC resources, with additional projects in the pipeline. Genomics of Cape Buffalo is a hot topic, and is of interest to the general public and wildlife ranchers in particular. Cape buffalo are bred on private game ranchers for a one or a few economically important traits, such as horn length and body size. The effects of this artificial selection, as well as breeding South African buffalo with East African buffalo, is unknown. We can use genomics to evaluate the risks and benefits of these practices for the short and long term (evolutionary) conservation prospects of the species The genetic work on the bowhead whale uses empirical and simulation data to investigate the effects that different Nearctic human cultures exploiting the whale had on the abundance of the population. This means that genetic data may have more resolution than previously thought and is sufficient to detect subtle changes in population size in relation to exploitation and climate change. This is of great importance as there are many applications. We believe that the work will have sufficient impact to be of interest to the general public in South Africa and internationally.
Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 9
Allocation Start: 2018-04-16
Allocation End: 2019-03-08
Used Hours: 194180
Project Name: African Multi-Omics Data Science
Project Shortname: CBBI1039
Discipline Name: Bioinformatics
CBBI1039: UCT Applied Genomics (AGe) is a training programme, running from the University of Cape Town, South Africa. This research programme is fundamentally aiming 1) to provide postgraduate students with the knowledge skills and bioinformatics tools they need to understand the models of medical population genetics and of computational molecular biology; 2) to enable graduate students at the University of Cape Town, across the country and African continent to be able to relate the models and data of statistical genetics to the constraints of inheritance and the molecular mechanisms of genetic data, including DNA sequence data, next generation sequences and to develop the skills to work with these massive data sets. 3) to solicit the assistance of CHPC, South Africa, Cape Town in training the trainers along this proposed programme to efficiently use the resources and master the portable bash servers(PBS) and the implementation of large scale genomic project under CHPC's resources. The accumulation of experimental DNA data in Biology and new high throughput experiments are growing rapidly and give a huge number of data difficult to manage, to store and to analyse this existing and future dispersed information. Therefore, high-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring the field of bioinformatics to use high-performance computing resources and carry out data management and analysis tasks on large scale. Today, the use of HPC has increased our training portfolio to meet the international standard with respect to large scale genomic era in training and increasing data analysis skills of our students and other trainees across the continent. This programme has developed several genomic-based, Bioinformatics, programming courses that address the African training needs around large-scale genomic data in order to meet the international standard required in this field
Principal Investigator: Dr Stefan du Plessis
Institution Name: Stellenbosch University
Active Member Count: 7
Allocation Start: 2018-04-16
Allocation End: 2018-11-22
Used Hours: 22905
Project Name: Shared Roots
Project Shortname: HEAL0793
Discipline Name: Health Sciences
Understanding the SHARED ROOTS of Neuropsychiatric Disorders and Modifiable Risk Factors for Cardiovascular Disease.
Shared Roots is a collaborative research project undertaken by researchers from the departments of psychiatry, neurology and genetics at Stellenbosch University and researchers from the South African National Bioinformatics Institute (SANBI). It is a MRC Flagship funded study and the principal investigator on the study is the executive head of the department of psychiatry Professor Soraya Seedat. Dr Stéfan du Plessis is responsible for the neuroimaging component. Our study included participants with posttraumatic stress disorder (PTSD), schizophrenia or Parkinson's disease. It is known that individuals with mental illness as well as other common brain disorders have higher rates of heart disease and stroke than the general population. It is not clear why this is the case. Our study therefore aims to collect information about all the potential factors that can play a role, to better understand the increased risk and enable the development of treatment strategies. To achieve this goal we will combine state-of-the-art research techniques such as genetic evaluations and the latest neuroimaging techniques. This will be combined in analysis with information evaluating the brain disorders, general health and lifestyle factors.
For our neuroimaging component, we scanned over 600 participants using Magnetic Resonance Imaging (MRI). Here we investigate potential brain changes associated with increased metabolic risk. We proceeded to calculate precise measurements of around 70 known brain regions using the MRI scans, which will be compared between cases and healthy controls. Processing takes around 24 hours for each scan. To finish in a timely manner, we used the Centre for High Performance Computing Rosebank, Cape Town, Sun Intel Lengau cluster.
Currently we have closed recruitment end 2017. The processing of the MRI scans was completed early in 2018. We are now the data analysis phase. The results will be prepared for publication in international peer reviewed journals, of which the first manuscript is planned for submission end of 2018.
Principal Investigator: Prof Mmantsae Diale
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2018-04-16
Allocation End: 2019-02-21
Used Hours: 551296
Project Name: Electronic Structure of hematite and surface doped hematite
Project Shortname: MATS0944
Discipline Name: Physics
The ab initio studies of hematite and surface doped hematite
Hematite (α-Fe2O3) has been identified as a better replacement of TiO2 for use in the Photoelectrochemical (PEC), water splitting and solar energy harvesting. Previously, TiO2 was used as an anode, but its absorption in the UV limits solar energy harvesting. Hematite is thus a replacement due to its band gap of 2 eV; which absorbs in the visible section of the electromagnetic radiation. In addition, it is also cheap, non-toxic, abundant in the earth's crust and inert to chemical corrosion in wie pH range. However, α-Fe2O3, has a number of drawbacks, such as rapid carrier recombination and low electrical conductivity, among others. Doping plays a major role in the improvement of electrical conductivity of α-Fe2O3. In this study we seek to carry out a computational study of hematite and doped hematite with suitable elements using quantum espresso software package
The new developments in 2018 is the allocation of a South Africa Research Chair (SARChI) in clean and green energy to Prof M Diale. The research focus of the SARChI chair is on the collection and conversion of solar energy using material science and device engineering for national benefit; thus addressing country electricity-energy issues. The global energy crisis has reached the plateau which expects all the plus 7.5 billion people of the world to work together to address issues related to climate change. Efficient collection of "Solar Energy" incorporates many different technologies: from photovoltaics (PV), and artificial photosynthesis (AP); nanotechnology and material science to device engineering. The current rate of developments in this area has moved from unbeatable c-Si solar cells to Dye sensitized solar cells and Biohybrid systems. While PV technology system have matured, the problem continues to be storage. Currently, there is great growth on materials development for hydrogen production and harnessing the qualities of c-Si for solar cell by creation of hybrid systems. Equally important is the synergy between natural and artificial photosynthesis. The PV-AP-PEC system will form a basis for innovative research in solar energy collection and conversion, including storage. It is envisaged that the SARChI chair in clean and green energy will provide a major contribution within the University of Pretoria to boost research.
Using CHPC to study the electronic structure of hematite and surface doped hematite makes a valuable contribution to the quest for clean and green energy sources. As hematite is understood, we hope to know what must be done to increase the conductivity of the semiconductor that will be efficient in water splitting, where hydrogen production can be increased.
Principal Investigator: Mr Muaaz Bhamjee
Institution Name: University of Johannesburg
Active Member Count: 3
Allocation Start: 2018-04-16
Allocation End: 2018-10-31
Used Hours: 106822
Project Name: Modelling of Multiphase Flow in Process Equipment
Project Shortname: MECH0837
Discipline Name: Computational Mechanics
The research group is from the Department of Mechanical Engineering Science at the University of Johannesburg. The primary area of interest in the research is the use of coupled computational fluid dynamics and computational granular dynamics models to investigate the complex multiphase interaction in process equipment. The models are
based on multiple continuum and meso-scopic based approaches which are couple with models such as the Discrete Element Method, Immersed Boundary Method and Eulerian Dense Discrete Phase Models. Both commercial and open-source software has been used in the research. Primarily the research has been focused on
hydrocyclones. However, the research is moving onto fluidised beds, spiral concentrators, highly concentrated slurry flows and gas cyclones. The models are benchmarked accuracy) against experimental measurements as well as for computational efficiency. Accurate and computationally efficient modelling of such phenomena is vital to the design of hydrocyclones which is crucial to the mining industry. The research group has produced numerous publications and has supported the research of four post-graduate students. Research into the computational efficiency of the models is continuing with the aid of the Centre for High Performance Computing (CHPC) facilities. Due to the complex physics and fidelity required in the problems tackled by the research group large computational resources are required. The CHPC provides a computational platform that is vital to the ongoing work and success of the research group.
Principal Investigator: Prof Mario Santos
Institution Name: University of Western Cape
Active Member Count: 17
Allocation Start: 2018-04-16
Allocation End: 2018-10-31
Used Hours: 518635
Project Name: Cosmology with Radio Telescopes
Project Shortname: ASTR0945
Discipline Name: Astrophysics
The Centre for Radio Cosmology (CRC) at UWC aims to fully explore the use of the next generation of radio telescopes for measurements in cosmology, in particular with MeerKAT and SKA. CRC staff is closely involved in the South African and international SKA projects. About 10 postdoctoral researchers and 10 PhD/MSc students are doing their research within the CRC. Our work at the CHPC is mostly focused on running simulations of signals we expect to observe with MeerKAT/SKA and test how well radio telescopes can constrain certain cosmological models. This is a crucial component in the process to use these telescopes for cosmology since we need to understand the signals we are observing. The project include simulations of the hydrogen emission from the early universe, simulations of the contaminants, simulations of the telescope itself and analysis of the constraining power of such telescopes on cosmological models.
Principal Investigator: Prof Giuseppe Pellicane
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2018-04-17
Allocation End: 2018-11-07
Used Hours: 161252
Project Name: Computational Study of Structure-Property Relationships in polymer blends relevant to OPV devices
Project Shortname: MATS0887
Discipline Name: Physics
Designing novel organic materials for Organic Photovoltaic devices (OPV) relevant to solar cells by a combined experimental and computational effort is as major outcome in the field of renewable, sustainable and non-polluting sources of energies. In fact, solar energy is an inexhaustible and green energy source and organic molecules allow for a cheap device preparation cost and exhibit relative ease of processability: these two factors meet the requirements for industrial production and large scale diffusion of solar energy as a viable and economic energy source. Nevertheless, the study of organic conducting materials is important for achieving a fundamental understanding of charge transport phenomena at the molecular level, which represents a remarkable scientific progress in the physics and chemistry of semiconductor devices. As a team of researchers, our group is based at UKZN, and we are working on Theoretical and Computational studies of Complex fluids. We are involved in addressing the research questions of this research proposal. A number of publications in scientific journals are obviously expected as a result of this research endeavour, and we already produced a number of them, even if they are still limited to the computer simulation study of simplified models of polymer mixtures, where we blend different polymer species to try to understand the effect of the geometry of the polymer on the blend structural properties (for example, how the concentration of the two polymer species changes as a function of the distance from the interface of the material with air). We are also presenting the research outcomes of the project in international conferences/workshops, that will allow for broadcast of vital research data on solar cells with the international scientific community and will be beneficial to the global progress towards a green and sustainable earth planet. We acknowledge the skilled and resourceful personnel at CHPC, and the generous allocation of computational resources granted to us by them, which are instrumental to fulfill the goals of this project.
Principal Investigator: Dr Gerhard Venter
Institution Name: University of Cape Town
Active Member Count: 10
Allocation Start: 2018-04-17
Allocation End: 2018-11-07
Used Hours: 1537122
Project Name: Simulation of Ionic Liquids
Project Shortname: CHEM0791
Discipline Name: Chemistry
Dr Venter's research group is part of the Scientific Computing Research Unit at the University of Cape Town and uses computer simulation to study the chemical and physical properties of biopolymers in a special class of solvents, called "ionic liquids". These simulations provide insight into the intermolecular interactions and chemical behaviour that control the dissolution and subsequent reactivity of these naturally occuring polymers. A better understanding of these processes can lead to the rational design of new, environmentally friendly solvents systems that can dissolve biomass and enhance its reactivity. The dissolution of biomass is the first step in converting naturally occuring polymers to biofuels and other platform chemicals.
High performance computing is required for all research conducted in this group and without the resources and infrastructure provided by the Centre for High Performance Computing (CHPC), the research will not be possible.
Principal Investigator: Prof Fourie Joubert
Institution Name: University of Pretoria
Active Member Count: 32
Allocation Start: 2018-04-17
Allocation End: 2019-03-01
Used Hours: 237898
Project Name: NGS Bioinformatics
Project Shortname: CBBI0905
Discipline Name: Bioinformatics
The Centre for Bioinformatics and Computational Biology acts as host and support liaison for a wide series of projects, ranging from viruses and bacteria to plants and mammals. The work reported here includes a series of theses, papers and conference posters and talks. It includes human health, forest health, crop health and environmental health. The availability of high performance resources at the CHPC enables us to perform research that would not otherwise be possible.
Principal Investigator: Dr Francois van Heerden
Institution Name: Nuclear Energy Cooperation of SA
Active Member Count: 2
Allocation Start: 2018-04-18
Allocation End: 2019-10-01
Used Hours: 65158
Project Name: Research Reactor Fuel Burnup and Material Activation
Project Shortname: INDY0788
Discipline Name: Physics
The Radiation and Reactor Theory (RRT) group at the South African Nuclear Energy Corporation (Necsa) provides calculational support for the SAFARI-1 research reactor, and perform research in the general area of nuclear analysis. We also develop and maintain our own suite of reactor simulation software, called OSCAR. This suite is the primary operational support tool for the SAFARI-1 reactor, and is used at a number of international facilities, which range from small university based research reactors, to larger national facilities.
During the past year, CHPC computing resources were utilized for a project facilitated by the International Atomic Energy Agency (IAEA) through a Collaborative Research Project (CRP) aimed at the collection of experimental data suitable for code benchmarking and validation. We are participating by providing experimental data from our own facility, the SAFARI-1 research reactor, and by calculating a number of experimental benchmarks from other member states. This particular CRP focuses on fuel depletion and material activation, which is important for the economic and safe operation of research reactors. All analysis reports were delivered during the final Research Coordination Meeting held in October 2018 at the agency in Vienna. These reports will eventually be incorporated in a formal technical publication by the IAEA, available to all member states.
The latest version of our tool set, OSCAR-5, provides a platform that combines different analysis codes, from fast diffusion solvers suitable for fuel depletion tasks, to high fidelity particle transport solvers, which can be used to do detailed local activation analysis, in a consistent manner. High Performance Computing plays an important role in the data preparation step for the diffusion solver, and in the use of transport solvers to estimate neutron flux distributions in the core.
Principal Investigator: Dr Yabebal Fantaye
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 3
Allocation Start: 2018-04-19
Allocation End: 2018-11-22
Used Hours: 38239
Project Name: Machine Learning
Project Shortname: ASTR1005
Discipline Name: Data Science
Aerial image labelling has found relevance in diverse areas including urban
management, agriculture, climate, mining, and cartography. As a result,
research efforts have been intensified to find fast and accurate algorithms. The
current state-of-the-art results in this context have been achieved by deep
convolutional neural networks (CNNs). One of the main challenges in using deep CNNs
is the need for a large set of ground truth labels during the training phase.
Moreover, one has to choose optimal values for the many hyperparameters
involved in the model construction to get a good result.
Extending on the seminal work by Mnih & Hinton (2012), our work at CHPC is
focused on building robust CNN models to segment buildings from aerial images.
Principal Investigator: Dr Leigh Johnson
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2018-04-19
Allocation End: 2018-11-07
Used Hours: 219112
Project Name: MicroCOSM: Microsimulation for the Control of South African Morbidity and Mortality
Project Shortname: HEAL1049
Discipline Name: Health Sciences
The MicroCOSM project, based at the Centre for Infectious Disease Epidemiology and Research at the University of Cape Town, is a project to simulate the spread of infectious diseases, as well as the incidence of non-infectious diseases, in the South African population. By simulating the social and biological factors that contribute to disease transmission, we can better understand which sub-populations need to be targeted for special interventions. We can also evaluate the impact that various prevention and treatment programmes have had in South Africa to date, and evaluate the potential impact of new programmes. This simulation involves generating nationally representative samples of 20,000-40,000 South Africans and tracking them over their life course. Because this involves many individual-level calculations, the model requires substantial computing power, and the CHPC is therefore critical to the conduct of these simulations. We have recently published a report that describes the model and the simulation of HIV outcomes (https://www.biorxiv.org/content/early/2018/04/30/310763). This work lays the foundation for a more quantitative approach to understanding which sub-populations are currently at the greatest HIV risk, and to assessing what interventions are needed to reduce socioeconomic and racial inequality in health outcomes.
Principal Investigator: Dr Sunita Kruger
Institution Name: University of Johannesburg
Active Member Count: 1
Allocation Start: 2018-04-19
Allocation End: 2018-11-07
Used Hours: 11730
Project Name: Environmental Heat Transfer
Project Shortname: MECH0995
Discipline Name: Computational Mechanics
This research group in the Mechanical Engineering Science Department of the University of Johannesburg is currently focusing on environmental heat transfer. Specifically heat transfer in naturally ventilated greenhouses. Greenhouses are used to protect plants from adverse weather conditions and insects. Ventilation of greenhouses are of vital importance to ensure quality crop production. If temperatures in a greenhouse is too high, poor plant growth may result, and an increased need for frequent watering. A mechanical ventilation system might be required to cool the inside of the greenhouse. Natural ventilation is an alternative option used to ventilate greenhouses. Natural ventilation uses temperature and wind to control the indoor climate of greenhouses. Unfortunately greenhouses are extremely energy intensive. Energy costs are the third highest cost related to greenhouse crop cultivation. Reducing the operating costs of energy associated with greenhouse cultivation may result in a price reduction of greenhouse cultivated crops. Conducting experimental work on ventilation of greenhouses can be costly and cumbersome. Using computational methods such as CFD (Computational Fluid Dynamics) to obtain qualitative and quantitative assessment of greenhouses can reduce costs and time involved. The computer cluster at the Centre for High Performance Computing has been used to conduct the numerical investigation using CFD. Currently research is being conducted on a large commercial greenhouse. Smaller greenhouses containing a single span are also being investigated
Principal Investigator: Dr Nkululeko Emmanuel Damoyi
Institution Name: Mangosuthu University of Technology
Active Member Count: 2
Allocation Start: 2018-04-20
Allocation End: 2018-11-15
Used Hours: 54403
Project Name: Surface Reaction Mechanisms
Project Shortname: CHEM1105
Discipline Name: Chemistry
My name is Dr Nkululeko Damoyi and I teach Inorganic Chemistry in the department of Chemistry at Mangosuthu University of Technology (MUT). My present research is in Computational Chemistry (CC) and the modelling calculations are done through the Centre for High Performance Computing (CHPC) in Cape Town. Research is registered at CHPC under the name: Surface Reaction Mechanisms. Presently I am the only member of the group and some students will be included at the beginning of 2019. I supervise some MUT Btech students in small CC research projects although they use their laptops for calculations. Current research output is in a form of two publications in peer-reviewed journals.
A large production of alkanes, for example LPG gas, from imported crude oil and mined natural gas and coal exists in South Africa through a variety of industrial processes. The alkanes are used as starting materials for many other industrial organic compounds, such as plastics. However, the production of some of these industrial organic compounds is too costly and there is a high commercial demand for catalytic methods and new catalysts that would bring down the costs of production. Computer technological advances make it possible to do research in CC in order to model chemical reactions and predict chemical reaction properties which are difficult or impossible to determine from normal laboratory experiments. Most of our present research involves utilising CC to predict the likely chemical reaction mechanisms that produce valuable organic compounds from alkanes with use of catalysts and also without catalysts. Through CHPC we are able to use internet to connect to their cluster computers in order to run the calculations and from the results be able to model the energetics of chemical reactions and predict reaction mechanisms.
Principal Investigator: Dr William Horowitz
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2018-04-23
Allocation End: 2018-11-15
Used Hours: 28967
Project Name: Probing the Frontiers of Nuclear Physics
Project Shortname: PHYS0974
Discipline Name: Physics
The CHPC is generating novel predictions for the dynamics of the physics of a trillion degrees. A microsecond after the Big Bang, the entire universe existed at a temperature of 100,000 times hotter than the centre of the sun. At multi-billion Rand experiments in the United States and Europe, these extreme conditions are recreated. Tens of thousands of scientists around the world analyse this data, and the calculations from the CHPC allow these scientists to interpret their results. Surprisingly, it appears as though the hottest stuff in the universe is also the most perfect fluid while at the same time being extremely strongly coupled.
Principal Investigator: Prof Carlos Bezuidenhout
Institution Name: North-West University
Active Member Count: 12
Allocation Start: 2018-04-24
Allocation End: 2019-03-08
Used Hours: 93993
Project Name: Metagenomics studies of Microbes
Project Shortname: CBBI0890
Discipline Name: Other
Researchers in the Microbiology research group at the North-West University in Potchefstroom are using the CHPC facility to analyse large data sets. The programme involves amongst others: Whole genome mapping of bacteria for horizontal gene transfer; Whole genome mapping of a novel Xanthomonas plant pathogen; Mapping of plasmids; Microbiome analysis of agricultural soils; Microbiome analysis of water and sediment Environmental metagenomics of drinking water production facilities; Transcriptome analysis of Bt Resistant Busseola fusca. The research focus on water and food security and safety. These are important issues and obtaining local data is critical. Whereas large data sets could be generated quite routinely it is the data mining and analysis that requires sufficient computing capacity, such as that provided by the CHPC. Several papers had been published or are in the final draft stage. Having this capacity also provide this research group (CBB10890 – Metagenomics studies of Microbes) with competitive advantage is applications for funding.
Principal Investigator: Prof Juliet Pulliam
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2018-04-24
Allocation End: 2019-03-08
Used Hours: 39548
Project Name: South African Centre for Epidemiological Modelling and Analysis
Project Shortname: CBBI1106
Discipline Name: Other
The South African Centre for Epidemiological Modelling & Analysis (SACEMA) is a national research centre established under the Centre of Excellence programme of the Department of Science and Technology and the National Research Foundation, and based at Stellenbosch University. Our core mission is to improve health in South Africa and across the continent through model-based analysis. Trained in mathematics, biology, physics, economics, statistics, and epidemiology, our researchers bridge disciplines to understand disease dynamics and improve real-world outcomes. Over the past 10 years, SACEMA has developed a robust and impactful research program in quantitative infectious disease epidemiology. Our current research falls under two broad themes: at the scale of individual patients, we work on biomarkers, drug targets, and diagnostics, and at the population scale, we focus on transmission dynamics and interventions. SACEMA students and staff use the CHPC to run models of disease transmission, evaluate potential interventions, and validate novel analytical methods.
Principal Investigator: Dr Thabang Ntho
Institution Name: Mintek
Active Member Count: 10
Allocation Start: 2018-04-25
Allocation End: 2018-11-22
Used Hours: 395104
Project Name: Hydrogen Storage Materials and Catalysis
Project Shortname: MATS0799
Discipline Name: Material Science
In the Advanced Materials Division, at Mintek, we use density functional theory (DFT) and other simulation methods mostly to accelerate our research in finding or engineering new catalytic and alloy materials that can address South African needs in a variety of areas including health (shape memory alloys), water purification, energy (fuel cells), etc. The CHPC offers us the tools and platform to focus on our work to rapidly achieve results via the use of the Lengau super-computer. So far virtual experiments (simulations) have allowed us to validate some of our experimental findings while helping us cut down on the number of laboratory experiments needed to reach project scientific aims and objectives.
Principal Investigator: Dr Pieter Levecque
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2018-04-25
Allocation End: 2018-11-07
Used Hours: 11276
Project Name: Non carbon supports for electrocatalyts
Project Shortname: MATS1108
Discipline Name: Material Science
HySA/Catalysis is a research centre housed by the Catalysis Institute in the Department of Chemical Engineering at UCT. The purpose of the centre is to develop South African based intellectual property around fuel cells and water electrolysis. Fuel cells are regarded as an essential technology in future energy conversion. Hydrogen as a fuel can be produced from renewable sources and then turned into electricity using a fuel cell. This is particularly advantageous to store excess energy produced by solar panels, windmills etc. for use at low sun/wind conditions. The current performance of fuel cell systems has gotten to a level that they are ready for commercial deploy. However, one of the last hurdles is to extend the lifetime of some of the materials used. Carbon is the typical support material for the catalyst used but is prone to corrosion. One of the main research topics in our group is finding new support materials for fuel cells. Typical materials research follows a hit and miss approach that involves the practical preparation and testing of numerous materials until one is found with the required properties, this is very time and cost intensive. This project aims at rather following the 'catalyst by design' approach. In this we make use of modelling tools to screen the properties of certain material compositions before actually making them. The modelling involves placing different atoms in different crystal lattices and then calculating the bonding properties and structure. The amount and complexity of the calculations involved require the use of high performance computing facilities, like the ones offered by the Centre of High Performance Computing (CHPC) in Cape Town. This approach and the easy access to the CHPC facility and good support from them saves time and resources and makes the lab based development and testing of these materials a lot more targeted and efficient.
Principal Investigator: Dr Kiprono Kiptiemoi Korir
Institution Name: Moi University, Eldoret, Kenya
Active Member Count: 3
Allocation Start: 2018-04-26
Allocation End: 2018-11-07
Used Hours: 821455
Project Name: Thermal characterization of MoS2 nanostructures: an ab initio study
Project Shortname: MATS0868
Discipline Name: Material Science
his group draws it's members from Moi University, Computational Material Science Group (CMSG), in addition we have a collaborator Slimane Haffad from University of Beijaia- Algeria. Our research activities focuses mainly on nano-materials for energy related applications, gas sensing, electronics, CO2 capture and storage. We also work on prediction and characterization of ultra-hard materials.
The maintenance of life on earth, our food, oxygen, and fossil fuels depend upon the conversion of solar energy into chemical energy by biological photosynthesis carried out by green plants and photosynthetic bacteria. In this process sunlight and available abundant raw materials (water, carbon dioxide) are converted to oxygen and the reduced organic species that serve as food and fuel. A long-standing challenge has been the development of a practical artificial photosynthetic system that can roughly mimic the biological one, by being able to use sunlight to drive a thermodynamically uphill reaction of an abundant materials to produce a fuel. Since demonstration photo-catalytic water splitting using Titania by Akira Fijushima and Kenichi Honda in early 1970, efforts are still ongoing to enhance the process such that it is commercially viable.
In this work, graphene, and nano-materials of ZnO and MoS2 are simulated via approaches grounded on principles of quantum and classical mechanics, which have been shown to accurately predict materials properties. These predictive approaches requires huge computational effort as it entails solving mathematical formulas, such as Schrödinger and Newtonian equations. For this reason, availability of the state of the art High Performance Computing facility, such as CHPC is a critical component for implementation of this work. Solving Schrödinger and Newtonian equations can yield various properties of interest such as structural, mechanical, electronic, and optical properties that is essential for comprehensive characterization of these systems.
Currently, our efforts are focused on understanding the effects of dopants and nano-particles on the photo-catalytic performance of these systems, which may help in identifying the ideal candidate to be recommended to experimentalist for fabrication and testing.
Principal Investigator: Prof Tien-Chien Jen
Institution Name: University of Johannesburg
Active Member Count: 20
Allocation Start: 2018-04-25
Allocation End: 2018-12-14
Used Hours: 1311728
Project Name: Developing an Innovative Metal Matrix Composite Membrane for Hydrogen Purification
Project Shortname: MATS0991
Discipline Name: Material Science
Hydrogen is an excellent energy carrier because of its high enthalpy of combustion with less environmental impact. Hydrogen fuel can be directly used in cars, ships, aircraft, and other transportation equipment. Although there are many problems to be resolved for implementation of hydrogen technology, it is generally believed that hydrogen will become a key energy carrier in this century. Until sufficient quantities of hydrogen can be derived from renewable energy sources, it will have to come from hydrogen separation using existing fuels (e.g., diesel, natural gas) as the feedstock. Hydrogen separation units can generate highly purified hydrogen from the feedstock gas mixtures, however, a certain amount of CO and other chemicals will make it into the hydrogen stream and cause catalyst failure on the fuel cell electrode. This significantly deteriorates the activity of the catalyst layer, particularly for PEM fuel cells. This deterioration greatly reduces the efficiency of power generation and the life cycle of the fuel cell. Overcoming this obstacle is necessary for the wider use of highly efficient fuel cells.
The objective of this proposal is to develop a new composite metal membrane (CMM) that can achieve extremely high flux and selectivity of the hydrogen separation and achieve the lifetime goal set by the U.S. DOE. To accomplish these goals, a research team formed by the University of Johannesburg (UJ), Council for Scientific and Industrial Research (CSIR) and Hydrogen South Africa (HySA) will combine two major technologies: Electrostatic-Force-Assisted Cold Gas Dynamic Spraying (ECGDS) and Laser-Assisted Manufacturing (LAM) to develop this new type of membrane. The proposed new membrane will eliminate the hydrogen embrittlement, catalyst failure, and avoid the difficulty of forming a defect-free, ultrathin Pd film on the substrate surface.
The proposed CMM will exhibit superior reliability and can be produced with a relatively low-cost and scalable process. Along with the development process, numerous numerical methods are utilized to simulate the material properties and behaviour as well as the optimization fabrication procedure. To accomplish these task HPC services from CHPC plays a crucial role in understanding the numerous unknown phenomena's. This service enables the research to be simulated from feature scale to reactor scale .Note that this project is currently supported by the NRF for 2017-2019.
Principal Investigator: Prof Mohsen Sharifpur
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2018-04-28
Allocation End: 2018-11-15
Used Hours: 114037
Project Name: Computational Heat transfer
Project Shortname: MECH1073
Discipline Name: Computational Mechanics
The research group was established as the Clean Energy Research Group in the Department of Mechanical and Aeronautical Engineering at UP, as an internationally leading laboratory. According to the Essential Science Indicators of ISI Web of Knowledge for "highly cited researcher" (3 February 2014 – present): The group is ranked amongst the top 1% of the world in engineering in three fields: (a) citations, (b) number of papers and (c) citations per paper.
Choosing correct boundary conditions, flow field characteristics and employing the right thermal fluid properties can affect the simulation of convection heat transfer using nanofluids. Nanofluids have shown higher heat transfer performance in comparison with conventional heat transfer fluids. The suspension of the nanoparticles in nanofluids creates a larger interaction surface to the volume ratio. These advantages introduce nanofluids as a desirable heat transfer fluid in the cooling and heating industries. The other part of the research is concerned with the use of nanoparticles in boiling and condensation flows. Due to the complexity of such types of flows, new development is needed in this section. The important aspect will be the phase change of the liquid phase. The liquid can be distilled water, coolants such as Ethylene glycol and refrigerants such as R141 and other types of liquid. The variety of base fluid can lead to an understanding of many critical applications of nanofluid in industry. Such simulations need to be run for long to model the mass transfer in interfacial surface and reach statistical convergence. CHPC resources are a lot valuable since we couldn't do these runs on our research group machine. These are still in progress: Model development for nano-scale heat transfer, Study and development of a new method for particles in pool boiling with different base fluid and various inclination angles.
Principal Investigator: Prof Ignacy Cukrowski
Institution Name: University of Pretoria
Active Member Count: 7
Allocation Start: 2018-05-02
Allocation End: 2018-11-14
Used Hours: 1285294
Project Name: Understanding chemistry from QM study of molecular systems
Project Shortname: CHEM0897
Discipline Name: Chemistry
Activities in chemistry (in science in general) can be seen as made of two distinctive approaches: 1) development of new theories and methodologies that should lead to better understanding of concepts and chemical process (reactions) and 2) practical implementation of known chemical processes and performing, in principle, routine operations. Our research group in the Department of Chemistry, University of Pretoria, that consists of Prof I Cukrowski (the leader), several PhD, MSc and Honours students as well as a postdoctoral Fellow) is involved in fundamental studies focused on (a) understanding chemical bonds from the electron density distribution throughout a molecule (there are many kinds of bonds but still there is no clue for an ultimate theory of bond; there are various approximate quantum chemical bonding models that can be used only to answer certain questions about particular type of a bond); to this effect several novel methodologies were developed by our group and they are being tested on numerous molecular systems, and (b) modelling reaction mechanisms (to understand on atomic and molecular fragment level how it works or why it does not work) that might be of significance in the development of new drugs in, e.g. tuberculosis (a highly contagious disease that remains a significant public health problem globally) or Alzheimer disease with reported cases growing rapidly throughout the world. Although we started modelling of reaction mechanisms only recently, a significant progress has been made and about 8 research papers are already under preparation. Any pioneering theoretical work, such is ours, requires a large number of real-life molecular systems (made of tenth of atoms) that have to be computationally 'processed' under specific conditions. This, in turn, requires expensive computational resources, such as CHPC, with a dedicated staff to assure it is available to research groups 24/7.
Principal Investigator: Prof Regina Maphanga
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 3
Allocation Start: 2018-05-02
Allocation End: 2018-11-14
Used Hours: 58118
Project Name: Energy Storage Materials
Project Shortname: MATS0919
Discipline Name: Material Science
The group is called Advanced Mathematical Modelling based at Modelling and Digital Science unit of CSIR and uses multiscale methods to develop novel energy storage materials with desired properties and enhanced properties for existing materials. The envisaged outcome of this project is to develop energy storage materials models with improved performance and consistency, which will be cheaper and environmentally benign. The ever-increasing global energy needs and depleting fossil-fuel resources demand the pursuit of sustainable energy alternatives, including renewable sources to replace carbon intensive energy sources. Sustainable and renewable energy is considered to be the most effective way to minimize CO2 emissions. Hence, finding sustainable energy storage technologies is vital for optimally harnessing the renewable energy.
Computational methodologies are very effective in predicting material-structure-property correlations. In this project simulation methods and models based on parallel computing are developed to probe battery materials properties. Centre for High Performance Computing (CHPC) resources are used to develop these parallel methods and algorithms for large and complex material models. Thus, CHPC resources provide a platform to simulate the evolution of material properties at a wide range of external conditions that are not accessible experimentally and fast track acquisition of results. The major of aim of this project is to create a predictive, reliable and robust set of models of materials for energy storage across the materials modelling length scale, leading to integrated multi-scale capability.
Principal Investigator: Dr Tiri Chinyoka
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2018-05-02
Allocation End: 2018-11-22
Used Hours: 912759
Project Name: Analysis and Solution of Computational Fluid Dynamics Problems via the Finite Volume Method and the OpenFOAM Software
Project Shortname: MECH0943
Discipline Name: Applied and Computational Mathematics
The research group's focus is centered on the complex flow of equally complex fluids and their commercial and industrial applications. Examples of completed projects include flows around aircraft landing gears in the modelling of noise reduction as well as complex flows of polymeric fluids generally as obtaining in the polymer, pharmaceutical and food industries. The scientific modelling of the complex flows of such complex fluids reduces to equally complicated systems of mathematical equations. These mathematical model equations cannot be solved by hand even for the most basic small scale applications. It is therefore necessary to develop scientific computing methods to simulate and solve these problems. This is where the group finds important linkages with the CHPC. The CHPC provides high speed computing facilities to assist in solving our mathematical equations. The computing speed is of fundamental importance as the relevant computations can take weeks or months on an average desktop computer. The collaboration with the CHPC has therefore enabled the group to resolve very complex problems with relative ease.
Principal Investigator: Prof Gerhard Venter
Institution Name: Stellenbosch University
Active Member Count: 5
Allocation Start: 2018-05-03
Allocation End: 2018-11-14
Used Hours: 600732
Project Name: Finite Element Analysis and Numerical Design Optimization
Project Shortname: MECH0883
Discipline Name: Computational Mechanics
The Materials, Optimization and Design (MOD) research group is a part of the Department of Mechanical and Mechatronic Engineering Faculty at Stellenbosch University. The research group's members work on a diverse group of projects related to structural analysis and optimization. The fields covered by the group are Finite element analysis, Computational fluid dynamics, numerical design optimization, material characterization for numerical modelling purposes and meta-modelling, etc.
Projects have dealt or are dealing with:
* inflatable structures (inflatable wings, dunnage bags, etc.)
* morphing wings/hydrofoils
* soft robotics
* large radio astronomy antennas
* heart valves
* composites
* vertical axis wind turbines
* particle swarm optimization
* railway bogies
* mining truck tires
* material testing methods
* high-pressure water supply lines
* heat exchanger header boxes for industrial heat exchangers, etc.
The primary goal of the group is to produce or facilitate advanced engineering design.
Principal Investigator: Prof Claude Carignan
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2018-05-02
Allocation End: 2018-11-22
Used Hours: 41335
Project Name: Numerical Simulations of Barred Galaxies
Project Shortname: ASTR0961
Discipline Name: Astrophysics
Claude Carignan and his group (Nathan Deg, Toky Randriamampandry) at UCT have used carefully crafted simulations run at CHPC to generate one of the first mass models of NGC 1300. This is a particularly exciting achievement as the orientation of this barred galaxy prevents other methods from successfully modeling this galaxy. Their technique can be applied to a range of barred galaxies that could not be modeled otherwise.
Nathan Deg and Claude Carignan, working with Lawrence Widrow (Queen's University) have developed a new method for generating initial conditions for galaxy simulations. This program, called GalactICS (Galaxy Initial ConditionS) can make equilibrium galaxies with a spherical dark matter halo and bulge, two stellar disks, and a gas disk. Other methods for making such initial conditions generally require some time to relax to equilibrium, while GalactICS begins in equilibrium. This program is useful for studying dynamical processes, like bar formation, modeling real galaxies, controlled merging experiments, etc.
In addition, Claude Carignan and Nathan Deg have been working with Sarah Blyth, Nadine Hank, and Simon Krüger to analyze simulations of merging galaxies. They are attempting to characterize how asymmetric these mergers are, how this asymmetry parameter varies with observational systematics, like the angle the merger is observed at, and what the asymmetry parameter can tell us about the galaxies involved in the merger.
Principal Investigator: Dr Gebremedhn Gebreyesus Hagoss
Institution Name: University of Ghana
Active Member Count: 4
Allocation Start: 2018-05-04
Allocation End: 2018-11-29
Used Hours: 278797
Project Name: Atomistic simulations and condensed matter
Project Shortname: MATS1031
Discipline Name: Physics
The condensed matter research group at the Physics Department in the University of Ghana is focused on the study of the structural, electronic, magnetic, and optical properties of two- and three-dimensional materials. Computational simulations of the properties of these materials is carried out using Quantum Espresso (http://www.quantum-espresso.org) and ABINIT (https://www.abinit.org/) that are the state-of-the-art open-source computational software packages. Our experimental research also covers the synthesis and characterization of these materials. Hence, we verify and validate our computational results against our experimental results.
Our computational work would not be possible without the enhanced computing resources available at the CHPC in South Africa. This is due to the fact that the materials we are studying require calculations on systems that contain comparatively large numbers of atoms. Typically, we do preliminary calculations on our computer cluster here at the University of Ghana. Once the basic results are validated, the actual job is then transferred to the CHPC. The job is monitored at least once a day and the results downloaded when completed.
Our main areas of research are:
1. Electronic, magnetic, structural and optical properties of transition-metal oxides.
Experiments are carried on the the synthesis and characterisation of pure and doped zinc peroxide and zinc oxide for oxygen and carbon-dioxide gas sensors, light-emitting applications, energy generation and storage and other applications. We are also investigating the structural, electronic, optical, and magnetic properties of these materials using the first-principle calculations. Moreover, we are investigating the electronic, magnetic, optical and structural properties of ZrO2.
2. Modeling and Simulation of Perovskite Materials for Energy Applications
Perovskite solar cells (organometal CH3NH3PbX3 and mixed halide CH3NH3PbI2X, (X = Cl, Br, I)) have the best power conversion efficiency. However, there is environmental concern due to the existence of a toxic element, lead (Pb). Hence it is very important to search computationally for the replacement of Pb by environmentally friendly elements. We are investigating all the divalent metals (Co, Cu, Fe, Mg, Mn, Ni, Sn, Sr, and Zn) which could substitute Pb in an organometal and mixed halide perovskite and also investigating the electrical, structural and optical properties of the selected organometal and mixed halide perovskite.
3. Two-dimensional Materials Research
In this project, we focus on the effect of introducing lanthanide atoms annd spin orbit coupling effects into monolayer RSe2 and WS2.
Two dimensional materials also promise a wide range of applications, including light-emitting applications, energy generation and storage, wear- and corrosion resistant surfaces, and gas and radiation sensors.
Principal Investigator: Dr Hezekiel Kumalo
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2018-05-06
Allocation End: 2018-11-14
Used Hours: 734050
Project Name: Molecular modeling and computer aided drug design
Project Shortname: HEAL1009
Discipline Name: Health Sciences
The group covers a wide range of computational and molecular modeling research areas with main focus on biological systems and drug design approaches. Main interest is related to design and study of biologically and therapeutically oriented targets. This is achieved by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We are involved in projects such Understanding drug resistance mechanisms via different computational tools QM/MM MD simulations Quantitative Structure Activity Relationship (QSAR) Conformational Analysis of biomolecules Bioinformatics tools applications Development Projects Approaches to enhance binding free energy calculations results Developing parameters for biomolecules: on-going projects Software implementations: on-going projects. All the projects that we do in the group contribute to the training of pharmaceutical scientists with specific skills for both the pharmaceutical industry and academia. This has the potential of stimulating the local pharmaceutical industries in South Africa to manufacture pharmaceuticals of quality, excellence and affordability for optimum and cost effective patient health, instead of being dependent on multinational pharmaceutical companies. We are still small yet fast growing group however funding is problem, therefore for the resources at CHPC allows us to generate hypotheses for subsequent experimental testing in a much quicker manner and higher throughput than using experiment alone to generate hypotheses that you'd like to test. It has given us an opportunity to be able explain experimental data we could not explain easily such the binding landscapes of different enzymes and the mechanism of action for different inhibitors
Principal Investigator: Prof Tahir Pillay
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2018-05-13
Allocation End: 2018-11-14
Used Hours: 1219457
Project Name: Molecular Modelling of ligands and receptors
Project Shortname: HEAL0876
Discipline Name: Health Sciences
Tahir Pillay's research group in the Department of Chemical Technology, University of Pretoria is actively working on the field of pharmcoinformatics applications in the genetic and acquired diseases. We have been using the facility of CHPC since 2014. The research group uses several pharmacoinformatics tools to design computational models followed by screening of small molecular databases and simulations for therapeutic application in several diseases including HIV/AIDS, Tuberculosis, Alzheimer's, Malaria, etc. For this purpose we are extensively using Schrodinger, Amber, Gromacs etc. Therefore, the research work is entirely dependent on pharmacoinformatics tools available in the CHPC server. The department does not have sufficient infrastructure to carry out the research in the current project. Hence, our research group requires access to the CHPC server to fulfil the objectives of the current project. We are quite happy with the services available in the CHPC server and would like to thank entire team for their efforts and support.
Principal Investigator: Prof Nelishia Pillay
Institution Name: University of Pretoria
Active Member Count: 7
Allocation Start: 2018-05-11
Allocation End: 2018-12-20
Used Hours: 3299502
Project Name: Nature Inspired Computing Optimization
Project Shortname: CSCI0806
Discipline Name: Computer Science
Artificial intelligence is playing an imperative role in the fourth industrial revolution. One of the areas that is receiving attention is the automated design of machine learning techniques using artificial intelligence. The aim of this is twofold, firstly this will reduce the time researchers and practitioners will spend on design. Secondly this will facilitate the production of off-the-shelf tools for non-experts to use. This research has successfully applied evolutionary algorithms for the automated design of machine learning techniques to solve classification, network intrusion detection, financial forecasting, packing, airplane landing, vehicle routing and timetabling problems. Automated involves high runtimes and high performance computing is needed. As we move into the four industrial revolution the complexity of real-world problems is increase and this research has also investigated two new search techniques, namely, multi-space search and partial solution optimization, which overcome some of the challenges of traditional search techniques. Both these techniques require distributed computing to reduce runtimes.
Principal Investigator: Prof Zenixole Tshentu
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 6
Allocation Start: 2018-05-15
Allocation End: 2018-11-14
Used Hours: 128869
Project Name: Metal-ligand, anion-cation interactions and protein-ligand studies
Project Shortname: CHEM0864
Discipline Name: Chemistry
Our studies involve the design of reagents for a specific target. This requires computational methods to arrive at the relevant chemistry to employ for each target metal ion, anion, cation or protein.
Principal Investigator: Dr Likius Daniel
Institution Name: University of Namibia
Active Member Count: 5
Allocation Start: 2018-05-15
Allocation End: 2018-11-14
Used Hours: 313731
Project Name: UNAM Energy Initiative
Project Shortname: MATS1045
Discipline Name: Material Science
Material Science Research Centre of the University of Namibia. Under the supervision of Dr. Daniel Likius, this center is to provide students with specialized knowledge and skills in the field of Material Science for Energy and Environment. Materials Science is concerned with the science of developing materials which meet and exceed performance expectations for specific functions. At the center, we are involved in synthesis, characterization, computational and design ceramics that have the potential materials for energy and environment. High-performance computing and advanced data technologies are powerful tools in enhancing the research here at UNAM. Through CHPC, our project is mainly depend on the system named Lengau owing to its speed of 1000 teraflops is very helpful to our research and we manage to collect data in very short time as it is very faster. With the help of CHPC, are now able to presenting our finding with concreted evidence at the national and international level (in Mauritius in July 2018). This is because we are now able to collect data at faster rate compare to the software that we use to use before the CHPC. Therefore we appreciated with what CHPC is doing for us.
Principal Investigator: Prof Edet Archibong
Institution Name: University of Namibia
Active Member Count: 4
Allocation Start: 2018-05-16
Allocation End: 2018-11-21
Used Hours: 103168
Project Name: (1) Computational Study of Semiconductor Clusters. (2) Computational Study of Bio-active Molecules Extracted from Plants
Project Shortname: CHEM0969
Discipline Name: Chemistry
At the Computational Chemistry Group of the University of Namibia (UNAM), Namibia, we have investigated the reactions of ozone and thiozone with phenols in the gas phase and also taken solvent effects into consideration. Namibia is an arid country in southern Africa with facilities for reclaiming water directly from domestic sewage. Ozonation is one of the processes used to disinfect the waste water and also to eliminate dissolved organic compounds. Despite its importance in drinking water processing, the mode of ozone reaction in water is not completely known and the subject still remains a grey area for research studies.
Based on the above, the Computational Chemistry group at UNAM/Namibia has embarked on the investigation of the reactions of ozone with compounds that could be found in recycled water and also in the atmosphere (of course, the importance of atmospheric ozone, cannot be overemphasized). Specifically, we are studying the reactions of ozone and thiozone with phenols (phenol, thiophenol, catechol, resorcinol) and their derivatives.
Computational studies prove to be important in these studies because several of the intermediates in the ozone/phenols reactions are short lived and difficult to isolate experimentally. Thus, these intermediates are modeled on computers and their thermodynamic and kinetic stability investigated.
The computing facilities provided by CHPC in South Africa (SA) allow our group to study these large chemical systems using decent level of theory. Using the Lengau clusters, one of our M.Sc students has nearly completed his research work which exciting results which should be published soon. The assistance and provision of computer time by CHPC in SA enable our group to engage in contemporary research which have universal benefit.
At present, the research work is progressing well and we expect to send our results for publication very soon. Also, one of our M.Sc students will complete his studies this year (2018), thanks to CHPC in SA.
Principal Investigator: Prof Alexander Quandt
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2018-05-17
Allocation End: 2018-11-21
Used Hours: 780778
Project Name: First principles simulations of renewable energy devices
Project Shortname: MATS0882
Discipline Name: Material Science
We are a computational materials science group in the School of Physics at Wits University. We have a special research focus on renewable energy devices, as well as on the study of fundamental light-matter interactions. Under the umbrella of the Materials for Energy Research Group (MERG) our group collaborates with a number of experimental groups in Physics, Chemistry and Engineering, and the goal of these collaborations is to develop novel types of batteries, supercapacitors and solar cells.
We currently use CHPC facilities to study the formation and the physical/chemical properties of electrostatic double layers at the electrode surfaces in batteries and supercapacitors. To this end we use ab initio methods based on density functional theory rather than molecular dynamics simulations. This is a numerical approach, which has not been studied very much in the literature up to now. Due to the size of the model systems that we study, which comprise model electrodes, solvent molecules and ions, our ab initio simulations require a lot of computational resources, which cannot be provided by a small domestic compute cluster anymore.
Note that many of the fundamental electrochemical processes like double layer capacitance and pseudo-capacitance are not very well understood up to now. But simulations of such processes based on inexpensive numerical methods running on a typical domestic compute clusters have the serious disadvantage that they heavily rely on empirical parameters, and that they also use very crude models of the chemical bonding. Such a procedure is not accurate enough to provide us with a realistic description of fundamental electrode processes, in particular when these processes involve the transfer of electrons to/from the electrode. Thus there is an urgent need to study these fundamental electrochemical processes with the most accurate numerical methods available, and also for reasonably large model systems, which amounts to a numerical challenge that requires CHPC support.
From a more general and more practical point of view, a deeper understanding of fundamental electrode processes is also crucial for the improvement of commercially available batteries and supercapacitors, and for the development of novel types of electrochemical storage systems.
Principal Investigator: Prof Gert Kruger
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2018-05-17
Allocation End: 2018-11-21
Used Hours: 190999
Project Name: CPRU molecular modeling
Project Shortname: HEAL0839
Discipline Name: Health Sciences
(Who) The Catalysis and Peptide Research Unit at UKZN (http://cpru.ukzn.ac.za/Homepage.aspx) is currently working on the mechanism of action on the HIV PR with respect to the natural substrates. (What) We use an quantum chemical/molecular mechanics hybrid (Oniom) approach that gives us high level results on the thermodnamics and kinetics of the reaction. Our model enables us to study application of both electronics and sterics to change the bond strenght and binding energies of new potential inhibitors. The same approach is followed for transpeptidases, essential enzymes for the inhibition of TB. (Why) HIV is a major health threat in SA and new drugs is required due to the constant development of drug resistance. Similarly, TB and TB co-infection with HIV is a mojor health issue. (How) Our theoretical studies will allow us to test a computational model that correctly describes the interactions between the respective enzymes and existing drugs. We are improving our computational model to the extent where are now in a position to start proposing new potential drug leads for synthesis. This can only be done with large computational resources provided by the CHPC.
Principal Investigator: Prof Walter Meyer
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2018-05-17
Allocation End: 2018-11-21
Used Hours: 151780
Project Name: Dynamics of primary radiation induced defects in semiconductors
Project Shortname: MATS0860
Discipline Name: Physics
Press release:
Semiconductors used in electronic devices play a crucial role in almost all current technology, ranging from power generation (in solar cells) to power switching and conversion to smart phones, computers and satellite communications. In order to function, the semiconductors require a highly perfect crystal lattice with impurity atoms placed at exact locations in the device. Any unwanted impurities and crystal defects may degrade performance and cause devices to malfunction. These defects may be caused during manufacturing processes but also by harsh environments, e.g. space. On the other hand, some defects also have properties that may be exploited in promising future technology including spintronics and quantum computing. In summary, defects in semiconductors play an important role in both current and future technology.
The aim of the Electronic Materials Group in the Physics Department of the University of Pretoria is to understand the properties of defects on a fundamental level. In order to achieve this deep understanding, both experimental and theoretical techniques are used. Thanks to the power of modern computers, a technique called "Density Functional Theory", or DFT for short, may be used to calculate the expected properties of a specific defect. These properties may be compared to experimental results to test the validity of the theoretical assumptions. The results can lead us to build better models of how defects in semiconductors influence device performance, how devices can be engineered to reduce their susceptibility to defects and to find properties of defects which may make them useful in technologies such as spintronics and quantum computing.
The main disadvantage of DFT is that it requires a very large number of calculations, which have only recently become feasible for computers to perform within a reasonable time. The research currently uses the high performance computer at the CHPC and a free scientific programme Quantum-ESPRESSO to calculate the properties of these defects.
The first step is to perform these calculations on simple defects in well-known materials such as silicon, in order to test the applicability of the theory. Currently the calculations are progressing well and the results are promising. Once we have shown the reliability of these results, we will continue to investigate more complicated defects as well as novel materials.
Principal Investigator: Dr Sean February
Institution Name: SKA
Active Member Count: 3
Allocation Start: 2018-05-19
Allocation End: 2018-11-21
Used Hours: 3868
Project Name: MeerKAT Open Time Projects - Feasibility Study
Project Shortname: ASTR1114
Discipline Name: Astrophysics
The South African Radio Astronomy Observatory manages the currently operating 64-dish MeerKAT telescope located in Carnarvon in the Karoo. It is expected that approximately 30% of MeerKAT's observing time will be taken up by smaller research groups who do not necessarily have the computing capacity to carry out the required processing of the data. The point of this research programme is to provide an avenue for such projects to perform at least a portion of their processing. For ease of software deployment and for scientific reproducibility, we will make use of the container technology uDocker. Initial testing: a typical radio-astronomer's software environment (including the underlying operating system) has been exported locally, transferred to Lengau, and successfully executed on a compute node. Future plans include more rigorous benchmarking in the form of typical data reductions, from the initial container export stage all the way to the final data product.
Principal Investigator: Dr Evans Benecha
Institution Name: University of South Africa
Active Member Count: 6
Allocation Start: 2018-05-21
Allocation End: 2018-11-21
Used Hours: 340867
Project Name: Defect engineering in novel 2-D materials
Project Shortname: MATS1025
Discipline Name: Physics
The research programme titled "Defect engineering in novel 2-D materials" focuses on investigation of the properties of defects in ultra thin layered materials - usually one to few atoms thick. The group spearheading this research is headed Dr Evans Benecha and it consists of senior researchers, postdocs and graduate students from the University of South Africa. Single atom layered materials possess interesting properties as opposed to bulk materials. For example, graphene – which a single layer of carbon atoms –enables electrons to flow much faster than silicon, is the world's strongest material, harder than diamond, yet lightweight and flexible. This unique combination of superior properties makes it a credible material for new technologies in a wide range of fields. Some of the envisaged applications of graphene as well as other single atom layered materials include making of medical implants, solar cells, stronger sports equipment, and batteries; just to name a few. However, for these applications to be realialized, the properties of these materials need to be well understood. Dr Benecha and his group's approach towards understanding these materials involves use of large computational resources; access to the CHPC computing facility has significantly reduced the time needed to generate and analyze data. The results from this project will not only assist in the current understanding of the role of defects in these materials, but will also help to reveal potential new functionalities.
Principal Investigator: Dr Lelanie Smith
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2018-05-21
Allocation End: 2019-03-15
Used Hours: 117996
Project Name: Aeronautical Research
Project Shortname: MECH1118
Discipline Name: Other
Within the Aeronautical engineering group at the University of Pretoria, the research is focused on novel aircraft configurations. Dr L Smith specifically looks at these configurations and the physics that make them fuel efficient using CFD.
In application studies of this work, passenger aircraft are considered and the size and complexity associated with the domain and flow physics when solving these problems are quite time consuming. Even before expanding to design exploration and optimisation models.
The CHPC is an incredible resource to truly make this process achievable. Currently we have 2 Master students using it, but the hope is that in the next year we have one more M student and a PhD student in the group.
Principal Investigator: Ms Robyn Jacob
Institution Name: SA Sugercane Research Institute
Active Member Count: 3
Allocation Start: 2018-05-22
Allocation End: 2019-03-01
Used Hours: 7571
Project Name: Saccharum Genomics
Project Shortname: CBBI0956
Discipline Name: Bioinformatics
The South African Sugarcane Research Institute (SASRI) is an agricultural research institute located in KwaZulu-Natal. The sugarcane industry is a substantial agricultural activity in South Africa and contributes significantly to the country's gross domestic product. Among pest and disease pressures affecting the South African sugarcane industry, Eldana saccharina (a lepidopteran stem borer) is inflicting the worst damages. We are utilising the CHPC to investigate the sugarcane response mechanisms to boring of the stems by the Eldana larvae. Little is known about the initial steps of infestation and this applied research project will deliver new knowledge in that domain. The project will make use of de novo transcriptome assembly and the differential expression analysis of a resistant versus a susceptible sugarcane variety challenged with the borer. Ultimately, this novel knowledge will be used to devise improved breeding methods that will deliver more resistant sugarcane varieties to the industry.
Principal Investigator: Dr Madison Lasich
Institution Name: Mangosuthu University of Technology
Active Member Count: 8
Allocation Start: 2018-05-22
Allocation End: 2018-11-29
Used Hours: 337246
Project Name: Chem Thermo
Project Shortname: CHEM1028
Discipline Name: Chemical Engineering
The Thermodynamics, Materials and Separations Research Group at MUT has made progress in studying the behaviour of confined fluids using computer simulations. Our research suggests that bentonite may have potential for use as an adsorbent to purify noble gases, and recent work has shed light on the corrosion suffered by concrete infrastructure exposed to hydrogen sulphide. The use of molecular simulations enables us to gain insights at the molecular level, which would not be easily achieved in a laboratory. Future work will examine systems of interest to natural gas exploitation and polymer applications, as well as systems of a more theoretical interest, such as Korteweg fluids (a class of material which includes magmas and quantum condensates). Such work would not be possible without the computing facilities of the CHPC in Cape Town, as many-body molecular simulations require significant amounts of computing time to perform.
Principal Investigator: Prof Charalampos (Haris) Skokos
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2018-05-22
Allocation End: 2018-12-20
Used Hours: 1185485
Project Name: Chaotic behavior of Hamiltonian systems
Project Shortname: CSCI1007
Discipline Name: Applied and Computational Mathematics
Using modern numerical techniques of Nonlinear Dynamics and Chaos Theory we investigate in a unified mathematical way the behavior of models describing the energy transport in disordered and granular media, as well as the properties of new elastic materials like graphene and molecules like the DNA. This research is performed by members of the 'Nonlinear Dynamics and Chaos Group' in the Department of Mathematics and Applied Mathematics at the University of Cape Town. The performed investigations constitute an innovative combination of Applied Mathematics, Chaos Theory, Hamiltonian Dynamics and Nonlinear Lattice Dynamics. Their outcomes will provide answers to some fundamental questions about the effect of chaos on the energy transport in disordered and granular media, and on the behavior of graphene and DNA. Some of the questions we try to address are: Does the presence of impurities and nonlinearities enhance or suppress the propagation of energy (e.g. heat) in solids, of light in crystals, and of vibrations in granular material? How does the ratio of the different base pairs in DNA chains affect their structural stability and the temperature at which the double-stranded DNA breaks to single-stranded DNA?
Principal Investigator: Dr Andre Stander
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2018-05-22
Allocation End: 2018-11-22
Used Hours: 183785
Project Name: In silico estimation of ligand binding energies against cancer- and malaria-associated proteins
Project Shortname: CHEM1055
Discipline Name: Health Sciences
Development of a new protein forcefield that improves protein-ligand simulations and interactions. It will play a crucial role in identifying of medicinally relevant compounds.
Principal Investigator: Dr Ndumiso Mhlongo
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2018-05-22
Allocation End: 2018-11-22
Used Hours: 271826
Project Name: Biomolecular Modelling Research Unit
Project Shortname: HEAL1002
Discipline Name: Health Sciences
This research group employs CHPC resources to conduct molecular dynamics simulations to analyse the dynamical properties of macro-molecules such as folding and allosteric regulations; ligand-receptor interactions; atom-to-atom interactions; protein-protein interaction;virtual screening and molecular docking of active molecules; QSAR etc, for the design and development of inhibitors against diseases and disorders. Through the use of CHPC resources, we design potential inhibitors against tuberculosis and cancer. These have made contributions to discovery new inhibitors & new knowledge which could directly translate into real health benefits of the society.
Principal Investigator: Prof Willem PEROLD
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2018-05-24
Allocation End: 2018-12-14
Used Hours: 199123
Project Name: Simulation of advanced semiconductor materials for the optimisation of photovoltaic devices
Project Shortname: MATS0948
Discipline Name: Electrical Engineering
Most of the energy actually used around the world comes from non-renewable fossil fuel reserves. However, their extraction negatively impacts our environment and their depletion has been predicted. To reduce pollution due to energy production and our reliance on non-renewable energy sources, the development of technologies to harvest the large amount of energy that sunlight contains has emerged as the best solution. The most practical way to capture and store energy from sun is by using photovoltaic solar cell devices. Photovoltaic solar cell market is much diversified but to make it competitive with fossil fuels, the cost needs to be diminished. This can be achieved by building solar cells with lower amount of material and higher efficiency. Fortunately, plasmonic solar cells made by adding metallic nanoparticles into standard photovoltaic solar cells offer a good way to build such solar cell systems. Metallic nanoparticles support surface plasmons that offer several mechanisms to trap incident light into a solar cell. Our staff here at the Electrical and Electronic Engineering Department, Faculty of Engineering, Stellenbosch University is working to see how light absorbed by silicon based solar cells can be significantly increased by adding silver or aluminium nanoparticles with particular shapes and sizes into silicon layer of the solar cell. For a good and complete description of our systems, we use both Finite Difference Time Domain (FDTD) based on electromagnetism and quantum mechanics simulations. To simulate our systems using these methods an important quantity of numerical resources must be used and fortunately we have found that on the CHPC system. Our works clearly demonstrate that solar cells properties are well ameliorated by adding cubic, spheroidal and spherical metallic nanoparticles into standard solar cells.
Principal Investigator: Dr Henry Otunga
Institution Name: Maseno University, Kisumu, Kenya
Active Member Count: 1
Allocation Start: 2018-05-24
Allocation End: 2018-11-27
Used Hours: 3997
Project Name: Computational Study of Hematite Clusters
Project Shortname: MATS0888
Discipline Name: Material Science
Sunlight is the most abundant renewable energy resource and considered to be the ultimate solution to address the global energy problem: The Tetrawatt Challenge. However, the vision of solar
energy providing a substantial fraction of global energy infrastructure is still far from being realized. The major challenge is to develop an efficient and cost-effective approach for storing
solar energy that can be used on demand on a global scale. Splitting water photoelectrochemically is a promising way in which solar energy can be harvested and stored through
photocurrent-driven chemical bond rearrangement leading to the formation of molecular hydrogen (2H2O→2H2+O2, E0=1.23 eV, Standard Hydrogen Electrode, SHE), which can be used directly as fuel or as an intermediate in the production of other fuels.
Hematite (alpha-Fe2O3) has emerged as a candidate photoanode material due to several favorable features: a band gap of about 2.0 eV (which allows for a large fraction of solar spectrum to be
absorbed), excellent stability under aqueous environments, and abundance in nature. Converting energy from the Sun to electricity efficiently via photoelectrochemical splitting of water is based on photo-induced charge separation at an interface (semiconductor/water interface) and the mobility of photogenerated carriers (electron-hole pairs). However, in bulk hematite, the separated charges recombine very fast (very short lifetimes of electron-hole pairs) and have very low mobility, hindering the conversion efficieny. These limitations can be dealt with by nanostructuring hematite, by growing ultrathin films of hematite, and by introducing impurity atoms in hematite. In this work, the structure and energetics of various size clusters of Fe2O3 have been investigated using the plane-wave pseudopotential approach to Density Functional Theory (DFT) and ab initio Molecular Dynamics (MD). These calculations require a significant amount of compute resources in terms of memory and cpu scaling. In this respect, I am grateful to the CHPC for granting me access to their supercomputing facilities and I hope for more collaboration in future.
Principal Investigator: Dr Abu Abrahams
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 3
Allocation Start: 2018-05-25
Allocation End: 2018-11-27
Used Hours: 626132
Project Name: Synthesis and characterisation of lanthanide complexes with Di-(2-picolyl)amine and its derivatives
Project Shortname: CHEM0844
Discipline Name: Chemistry
No changes from previous submission:
Who: Rare earth coordination chemistry research group of Nelson Mandela University What and why: The study of chemical and structural properties of the inorganic complexes with rare earth elements in order to identify trends in reactivity and identify potential applications in the fields of catalysis, medicine (diagnostic, anti-bacterial) and luminescence. Specifically complexes of rare earth elements with the ligand bis(2-pyridylmethyl)amine are being investigated due to this class of complexes displaying applications in the fields of catalysis, nuclear waste processing and medicine (solution structure elucidation). Increased utilisation of rare earth elements could also support the local economy, since rare earth elements may also be mined in South Africa. How: The CHPC provides access to advanced computational resources which allows for the extraction of information from modelled systems of novel compounds, which may allow for the prediction of experimentally-determined properties. The latter process of physical experimentation are often time-consuming and expensive, whereas computational modelling may be performed on multiple systems simultaneously and may provide information of sufficient accuracy to inform the user of the most beneficial course of action to take when performing any physical experiments. In addition, modelling may also provide answers to fundamental questions which we may not yet be able to observe physically. In addition, advanced computational chemistry software packages (such as Gaussian 9/16 and ORCA) allow users with limited knowledge theoretical physics and computer programming to find answers to their chemical problems. The experimental structures and composition of several monomeric- and dimeric- complexes containing the rare earth elements: Y, La, Nd, Dy, Ho and Lu, and preliminary geometry optimisations are well on their way to completion. An incremental refinement strategy implementing larger basis sets has proven feasible and will be carried out next.
Principal Investigator: Dr George Manyali
Institution Name: Masinde Muliro University of Science and Technology, Kakamega, Kenya
Active Member Count: 10
Allocation Start: 2018-05-28
Allocation End: 2018-11-28
Used Hours: 449559
Project Name: Ab Initio study of Thermoelectric Materials
Project Shortname: MATS0712
Discipline Name: Material Science
The Computational and Theoretical Physics (CTheP) Group at the Department of Physics, Masinde Muliro University of Science and Technology, comprised of a team of researchers and students dedicated to the development and application of computational modeling to outstanding problems in materials science. In general, the group seeks a deeper understanding of quantum-mechanical descriptions of interacting electrons and nuclei in order to predict and design properties of materials and devices using density functional theory as a tool for the first-principles simulation. This kind of simulations generates volumes of data which cannot be handled by the common desktop computers. High-performance computing provides the computational environment that includes parallel processing, large memory, and storage of the big data. Therefore, Center for High-Performance Computing facility in Cape Town, South Africa, plays a vital role in providing the resources that aid the discovery of new materials and accelerates its application in the industry, an achievement that would have been in vain with desktop computers. Some specific projects for our group include characterization of already known thermoelectric materials. The information gained from this project is used as identifiers in search for new thermoelectric materials with the tailored figure-of-merit. Such materials are used to enhance the efficiency of thermoelectric generator power system for renewable energy. Such outcomes of our projects have an impact on the livelihood of the rural communities in Kenya, and generally, supports the Agenda Four of the Kenyan economic blueprint that was recently availed by the president of the Republic Kenya.
Principal Investigator: Dr Thishana Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 6
Allocation Start: 2018-05-28
Allocation End: 2018-12-14
Used Hours: 51141
Project Name: Combined kinetics,quantum-chemical investigation of reaction mechanisms involving catalysts
Project Shortname: CHEM0821
Discipline Name: Chemistry
The TS Computational Chemistry Research Group (University of Kwazulu-Natal, School of Chemistry and Physics) carries out quantum chemical modelling of homogenously catalysed organic reactions in the inter-domain field of Physical-Organic Chemistry. Computational Chemistry can be classified as 'Green Chemistry' as it is sustainable and does not generate chemical waste. The focus of this research group is primarily on catalytic asymmetric synthesis that have many applications in the pharmaceutical and fine chemical industry. The optimisation of a catalyst offers a good understanding of the factors that are responsible for the rate and selectivity of a reaction. Theoretical calculations, together with experimental kinetic measurements, often can pin down the mechanism. Using this methodology, it is possible to understand, and more importantly, design effective catalysts for a number of asymmetric, catalytic processes. The CHPC provides the facilities: hardware, in the form of the Lengau cluster and software programs such as Gaussian16, amongst many others. Thus far the current project has yielded three publications since 2016.
Principal Investigator: Prof Hasani Chauke
Institution Name: University of Limpopo
Active Member Count: 7
Allocation Start: 2018-05-29
Allocation End: 2019-03-08
Used Hours: 1005328
Project Name: Computational Modelling of Minerals, Metals and Alloys
Project Shortname: MATS1047
Discipline Name: Material Science
The research programme is conducted at the Materials Modelling Centre (MMC), University of Limpopo. The centre is a research unit focusing on computational modelling studies of various materials properties, for over two decade. Professor Hasani Chauke, the primary investigator under the minerals and alloy development programme (MATS1047), currently hold a Royal Society-Newton Advanced Fellowship position. The area of specialization is on mineral processing and metal alloys development using first-principles and molecular dynamics based methods, which employs various academic and commercial software's with different types of interfaces. The computer interfaces are linked to local servers and also benefit from the centre for high performance computing (CHPC). One of the major motivations of the research programme at MMC recently, is to run large scale simulations, and this requires high level computational power. Currently, the computer servers at MMC are linked to CHPC to allow such large scale calculations to run at a much less computational time. Most of the work carried are project at Honours (mini projects), Masters (MSc) and Doctoral (PhD) studies.
Principal Investigator: Dr John Mack
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2018-05-31
Allocation End: 2018-12-11
Used Hours: 1613
Project Name: Rational design of phthalocyanine, porphyrin and BODIPY dyes
Project Shortname: CHEM0796
Discipline Name: Chemistry
The Centre for Nanotechnology Innovation (CNI) at Rhodes University under director Prof. Tebello Nyokong carries out research related to the use of molecular dyes in biomedical applications, such as cancer treatment through photodynamic therapy, the use of antimicrobial photodynamic chemotherapy for treating hospital superbugs and as sensors for ions that are harmful to human health. Other applications of interest include wastewater treatment and the development of optical limiters to protect human vision,such as in aviation safety in protecting pilots from the irresponsible use of laser pointers during runway approaches. It is important to understand trends in the electronic and optical properties that make the molecular dyes suitable for these particular applications. The resources of the Centre for High Performance computing help to facilitate this by making it possible to carry out molecular modelling calculations that can be used to predict how changes to the structures of the molecular dyes will modify their properties. The flexibility that CHPC provides where memory allocations are concerned is often vital. The CNI currently has three staff members, twelve PhD, fourteen MSc and four Honours students, and four postdoctoral fellows, and usually publishes over forty peer-reviewed publications per year. This rose to a high of sixty-five in 2017 with ten involving the use of CHPC resources.
Principal Investigator: Prof Rosemary Dorrington
Institution Name: Rhodes University
Active Member Count: 7
Allocation Start: 2018-06-04
Allocation End: 2019-03-08
Used Hours: 1842
Project Name: Marine Natural Products Research
Project Shortname: CBBI0963
Discipline Name: Bioinformatics
Marine Natural Products Research Group, Department of Biochemistry and Microbiology, Rhodes University
The Marine Natural Products Research Platform covers the broad field of marine biodiscovery, focusing on the potential of bioactive secondary metabolites produced by marine organisms endemic to the Agulhas Bioregion as lead compounds for drug discovery. Overview and aims More than half of new pharmaceutical drugs on the market or in clinical trials are natural products and their derivatives and the majority of these are now coming from marine macrofauna and their associated microbiomes. The Maine Natural Produces research programme is active across the broad field of marine biodiscovery, focusing on exploring the potential of marine invertebrates and their associated microorganisms as sources of novel bioactive small molecules. Research projects include: (1) Biodiversity mapping of benthic habitats in the Agulhas bioregion, focusing on invertebrates, ascidians, soft corals and their associated microbiota; (2) Isolation and characterization of bioactive secondary metabolites of marine organisms; (3) screening marine natural product libraries for anti-viral, anti-cancer and antibacterial activity and (4) elucidating the metabolic pathways that result in the production of lead compounds to pave the way for engineering recombinant systems for their production for the pharmaceutical industry. Associated projects focus on the application of high throughput metagenomic and analytical chemistry technologies to map patterns and processes in marine ecosystems to provide tools for sustainable development of our ocean economy. All of these research activities require access to high performance computing facilities to curate, process and analyse large Next Generation Sequencing (NGS) datasets. Primarily, we have used the CHPC facilities to analyse NGS amplicon library data to characterise the microbial communities of both marine and terrestrial systems.
Principal Investigator: Dr Steven Hussey
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2018-06-04
Allocation End: 2019-03-08
Used Hours: 4061
Project Name: Forestry Molecular Genetics - transcriptional and epigenetic regulation of wood formation
Project Shortname: CBBI1010
Discipline Name: Bioinformatics
The Forest Molecular Genetics Programme is a joint venture of the University of Pretoria and South African forestry industry partners aimed at developing biotechnology applications for tree improvement. It focuses on the genetic basis of tree growth, wood formation and defence against pests and pathogens. The SA forestry industry produces over 20 million tons of wood per year for a wide array of renewable products such as timber, pulp, paper, packaging, cellulose, textiles, pharmaceuticals and food additives. Increasingly, there is interest in using trees as biorefineries, i.e. energy-efficient production platforms for high-value biopolymers and biochemicals. Timber from genetically improved plantations can also be processed into advanced building materials for sustainable housing and construction. In part, the Programme aims to understand the biology of wood formation and how it is regulated at various levels. For example, the metabolism and incorporation of carbon-rich compounds formed from photosynthesis into cellular structures such as wood, the role of networks of genes coordinating the activation of genes at the correct stages of growth and wood formation, and how the epigenome or degree of "packaging" of DNA influences the expression of genes. An important part in understanding these process is the use of DNA sequencing technologies that produce data requiring high-performance computation to analyze it. These tools were central to decoding the genome or DNA sequence of Eucalyptus grandis, an important fast-growing tree. Our Programme has relied on the Centre for High Performance Computing to help identify regions of the Eucalyptus genome that contain functional regions in the "dark matter" of the Eucalyptus genome that are important for gene expression. We have also started to understand for the first time how cellular organelles participate in wood formation, and in this regard we have analyzed gene expression patterns associated with the poorly understood plastid organelles found in wood.
Principal Investigator: Dr Gwynneth Matcher
Institution Name: Rhodes University
Active Member Count: 5
Allocation Start: 2018-06-04
Allocation End: 2019-03-08
Used Hours: 18444
Project Name: Microbial Ecology in Antarctic and aquatic ecosystems
Project Shortname: CBBI0952
Discipline Name: Environmental Sciences
Our research is on microbial ecology and population dynamics in Antarctic and sub-Antarctic ecosystems. Our research sites are within the Jutulsessen and Ahlmanriggen mountain ranges (Western Dronning Maud Land, Antarctica) as well as Marion Island (which is a sub-Antarctic Island). This research is being conducted at Rhodes University. The main focus of our research is the characterization and comparative analysis of microbial populations from soil and aquatic ecosystems which are currently completely unknown. In addition to discovering what microbes occur in these extreme environments, we also aim to elucidate their role in the functioning of these fragile ecosystems. Antarctica terrestrial environments are dominated by microbes and the relative trophic simplicity present in these habitats presents a unique opportunity for fundamental research into ecosystem functioning and the factors which influence biodiversity and habitat efficacy in extreme environments. The relative simplicity of the trophic systems found in Antarctica make these ecosystems particularly vulnerable to perturbations such as global climate change. The response of polar biota to changing environmental conditions is of significant importance as alterations in the biodiversity and functional richness of microbial soil populations will have significant implications on soil respiration rates and ecosystem functioning as a whole. In order to assess the effect of global climate change on biodiversity, the current biodiversity and abundances of microbial species present in a given environment and their contribution to ecosystem functioning needs to be established. The microbial populations in target sites are assessed by sequence analysis of their 16S rRNA genes which allows for identification of the microbes present. This data is analysed on the CHPC platform using software (Mothur) and is correlated with other data in order to assess the structure and potential functioning of these populations.
Principal Investigator: Prof Marile Landman
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2018-06-04
Allocation End: 2019-01-22
Used Hours: 4275
Project Name: Organometallic complexes and surfactants
Project Shortname: CHEM0906
Discipline Name: Chemistry
The research group of Prof Marilé Landman in the Department of Chemistry at the University of Pretoria has been active in investigating the interactions of a series of PIBSA-based surfactants with various components of high internal phase emulsions using molecular modelling methods. Dr Marina van der Merwe was the PhD student working on this project and has recently graduated with a PhD degree on this work. Quantum and classical mechanics codes were used for model building, geometry optimisation and molecular dynamics (MD) to study modes of surface adsorption; all these codes are contained within a single platform materials modelling suite - Material Studio™. The surface affinity of several low energy conformers of hypothetically possible ionised forms of the polymeric surfactants i.e. neutral, protonated (cationic), deprotonated (anionic) and zwitterionic, was probed on simulated surfaces of aqueous ammonium nitrate, pure water, and predicted growth faces of crystalline ammonium nitrate. Averaged values of the interaction energies were used for efficacy comparison. According to the hypothesis tested, i.e. comparative adsorption of additives to the surface of the supersaturated solution of salt and to water as well as crystal growth inhibition, it was found that all experimentally active surfactants had lower adsorption energies to water than to the model salt solution. It can be concluded that the overall surfactant efficiency in this series is determined by the polarised nature of the secondary amide domain, intrinsic dipole moment and surfactant stability. This mechanism of surface stabilization seems highly plausible and a further study is required to test its validity.
Principal Investigator: Prof Veikko Uahengo
Institution Name: University of Namibia
Active Member Count: 9
Allocation Start: 2018-06-04
Allocation End: 2019-02-06
Used Hours: 1223537
Project Name: Solar Materials
Project Shortname: MATS1043
Discipline Name: Material Science
The research group from the University of Namibia, is a Material Chemistry based group working on metal oxides of copper and zinc. The group is focusing in harnessing the properties of these materials for a variety of applications, ranging from catalysts, photocatalyst, solar materials (thin films) and biological activities. This is done through different synthetic or fabrication methods such as sol gel, molecular precursor methods, through introduction of different dopants. In the end, this will not only harness the applications of these abundant and easy-to-make materials, but it will also add values to these locally available materials, which are normally exported in their raw forms.
Our research employs quantum-mechanical simulations based on density functional theory (DFT) to help identify new solar harvesting materials. Currently, our focus lies on ZnO and ZnP2, two compounds that have promising electronic and optic properties. Modelling them from a theoretical point of view gives complementary insight into processes that govern photon absorption, electron-hole creation, and transportation of charges across the bulk. We have shown how basic DFT is inadequate to model our two zinc compounds and have identified Hubbard corrections (or hybrid functionals) as the next step forward. Once the modelling of the basic properties has been done, we shall move to performing doping, creating surfaces and possibly create band-aligned structures, to improve the photovoltaic properties of ZnO and ZnP2.
Furthermore, some students are looking into improving the light absorption efficiency of inorganic complex dyes by tuning the optical properties of these complexes to absorb in the visible region. In addition to ZnO and ZnP2, the group has also looked into the TiO2 doped with sliver-nanoparticles to improve its photo voltaic properties, with the results so far outstanding. This work is sandwiched between Cardiff University and UNAM, for which ideas are shared among the two teams, as well as other member within the scope of our collaborative consortium.
The CHPC (has) and is still a major contributing factor to our work, because before we start with experimental work, we have to simulate the designs of our materials and see which ones are most suitable, in terms of energetics and dynamics, then select thereafter, thus by using the HPC facilities we are managing to select the favorable cases, leaving us with straight forward choices. This is not only saving us time, but it is also saving us money, which we use to buy chemicals for experiments. Instead of trying out all possible cases experimentally, simulation/computation can do it easily and leave you with the most possible cases (experimentally).
Principal Investigator: Prof Evans Adei
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 7
Allocation Start: 2018-06-04
Allocation End: 2019-01-22
Used Hours: 265383
Project Name: Materials For Energy and Fine Chemicals
Project Shortname: CHEM1046
Discipline Name: Chemistry
At the present reporting period, there has not been any new development that merits a press release.
Principal Investigator: Mr Jean Pitot
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2018-06-05
Allocation End: 2019-01-22
Used Hours: 56910
Project Name: SAFFIRE Programme
Project Shortname: MECH1121
Discipline Name: Computational Mechanics
The University of KwaZulu-Natal's Aerospace Systems Research Group (ASReG) is at the forefront of rocket propulsion research in academia, both in South Africa and Africa as a whole. Located at the University's Discipline of Mechanical Engineering, ASReG primarily conducts research in the areas of liquid and hybrid rocket propulsion, as well sounding rocket development.
The SAFFIRE Programme aims to develop South Africa's first fully-integrated liquid rocket engine, which is being designed for use in a small satellite launch vehicle. The long-term intention of the Programme is for the engine to enable the indigenous development of a South African space launch capability.
To meet its developmental goals, the Programme requires the simulation of complex computational models to predict the fluid dynamic, thermochemical and structural performance of various engine components. These simulations are typically very computationally-expensive, and require extensive computational resources to run within a reasonable time frame. The CHPC offers the only realistic means of obtaining access to such resources.
The Programme is progressing well, and 2019 will see the graduation of two masters students.
Principal Investigator: Dr Vuyani Moses
Institution Name: Rhodes University
Active Member Count: 10
Allocation Start: 2018-06-05
Allocation End: 2019-03-08
Used Hours: 2308891
Project Name: Bioinformatics and Computational Chemistry Applications
Project Shortname: CBBI1122
Discipline Name: Bioinformatics
We are newly created research group which falls under the Rhodes university research Unit in Bioinformatics (Rubi). Our interests are using computational techniques to solve biological problems such as drug discovery and biofuel production.
Principal Investigator: Dr Lucy Kiruri
Institution Name: Kenyatta University, Nairobi, Kenya
Active Member Count: 6
Allocation Start: 2018-06-05
Allocation End: 2019-02-28
Used Hours: 1355256
Project Name: KU Computational Chemistry Research Group
Project Shortname: CHEM1032
Discipline Name: Chemistry
CHEM1032: KU Computational Chemistry Research Group –Jan 2019
The members of the group are in 3 different areas of Computational Chemistry, namely ab initio, Molecular Mechanics and Molecular Dynamics. Most of the work done is medicinal (anti tuberculosis drugs, Malaria project, and water purification).
Katana Chengo in his 4th year Ph.D program. student. His work entails DFT study of Cationic iron half sandwich complexes of mixed donor ligands.
Wycliffe Omwansu is also a PhD student and he started running jobs in the cluster 3 months ago under my group. He is on Molecular Dynamics applied to study conformational transitions (structural changes) in some biomolecules that are important in how malaria is transmitted. The system contains approximately 20,000 atoms and he gromacs 5.1.2 to do classical simulations. Up to this point, he has been able to simulate a 6µs trajectory, and he is likely to proceed to 8µs.
Nonetheless, he is working on his first paper "Hydration Water Networks and Conformational Transitions in an Odorant Binding Protein: A Molecular Dynamics Study". The paper looks at the role of water in structural changes of biomolecules: residence correlation times, velocity auto-correlation function, first second and their Legendre polynomial or orientation distribution functions, etc.
Isaac Odhiambo is a second year Masters student working on engineering existing drugs of Mycobacterium tuberculosis by introducing organometallic fragment into their molecular structure and determining drug-likeness computationally. The computations are based on Density Functional Theory (DFT) methods such as B3LYP, CAM-B3LYP and PBEPBE with the standard Pople's polarized split valence basis set 6-31++G**.
George Omolloh work entails running a molecular dynamics (MD) simulation to see how my protein molecule responds to various bound ligands. He has finished his work and he will start his Ph.D. program soon.
Abraham Samoei joined my group last month. His project is on water purification.
I have done calculations on Barakol and anhydrobarakol using g16. The work involves geometry optimization and frequency calculations. The aim of the project is to determine the stability of the two molecules. I am preparing a manuscript.
The CHPC is invaluable in fast tracking our work since we were using core i5 desktop before where calculations would take much longer. Since the start of using the CHPC we've made a lot of progress on the work.
Principal Investigator: Dr Deshenthree Chetty
Institution Name: Mintek
Active Member Count: 1
Allocation Start: 2018-06-04
Allocation End: 2019-01-22
Used Hours: 4121
Project Name: 3D image analysis
Project Shortname: ERTH0939
Discipline Name: Earth Sciences
MINTEK is developing software to rapidly process 3D images of ore samples to ultimately extract quantitative data from the images. While scans can be completed rapidly, the large volume of data contained in these images traditionally requires many hours to process into the desired measurements. The processed images along with the data extracted will be of benefit for processing of ores to extract commodities of value.
Principal Investigator: Prof Sanushka Naidoo
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2018-06-05
Allocation End: 2019-03-08
Used Hours: 136887
Project Name: Eucalyptus and Pine Pathogen Interactions
Project Shortname: CBBI1057
Discipline Name: Environmental Sciences
The Eucalyptus and Pine Pathogen Interactions research group, from the University of Pretoria, focusses on investigating the molecular interactions of economically important forest tree species with pests and pathogens of interest to the South African forestry industry. One of the most pressing threats to global pine cultivation is the pitch canker fungus, Fusarium circinatum, which can have a devastating effect in both the field and nursery. Many strategies are currently employed to manage F. circinatum in the field and nursery, with limited success. Investigation of the host-pathogen interaction between Pinus spp. and F. circinatum is crucial for development of effective disease management strategies. To this end, RNA-sequencing data was generated for six pine species, with varying levels of resistance, during F. circinatum challenge. As with many non-model organisms, however, investigation of host-pathogen interactions in Pinus spp. is hampered by limited genomic resources. Fortunately, advances in bioinformatics has made it possible to leverage the inherent redundancy in next generation sequencing data to assemble the reference transcriptome. A transcriptome assembly and annotation work-flow was established on the CHPC using data for Pinus pinaster. The established work-flow is being used to investigate host responses for the remaining species to allow comparison of host responses between species and has also been applied to Pinus nigra challenged with Diplodea pathogens. Additionally, a work-flow was established to identify and characterise the expressed genes in a fungal phyllosphere community in interaction with Eucalyptus from previously sequenced data.
Principal Investigator: Dr Mary-Jane Bopape
Institution Name: South African Weather Service
Active Member Count: 8
Allocation Start: 2018-06-08
Allocation End: 2019-01-22
Used Hours: 154735
Project Name: Very Short Range Forecasting
Project Shortname: ERTH1022
Discipline Name: Earth Sciences
The mandate of the South African Weather Service (SAWS) is to provide weather climate and air quality services and solutions. To do so, SAWS uses a numerical weather and climate models. The organisation has been working on comparing simulation of high impact weather events made using 3 different models to inform the strategic direction the organisation takes on modelling. Preliminary results indicate that all the three models are very comparable when simulating these high impact weather events. The study is progressing and will be concluded in March 2019. From April 2019, work will begin on studying atmospheric processes as simulated by the chosen model, and SAWS will also start working on modifying the chosen model.
Principal Investigator: Prof Nithaya Chetty
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2018-06-07
Allocation End: 2019-07-19
Used Hours: 828409
Project Name: Advanced Computational Resources for members of ASESMA
Project Shortname: MATS1050
Discipline Name: Material Science
Work on 2 dimensional materials is now firmly established as an area of excellence at the University of Pretoria. Focus on the past year has been mainly on MoS2. Recently (over the past two years) a 2 dimensional bi-layer of zeolite has been experimentally synthesised by scientists in the USA. This is an area of promising new research for computational studies, and we have now begun to focus on this new class of materials for the coming year. Catalysis, filtering of ions (especially in aqueous solution), storage of ions (for example Li), etc are important areas of investigation for the future. 2 PhD students have graduated, and 1 postdoctoral fellow has completed his studies at the University of Pretoria in these areas of endeavour.
Principal Investigator: Prof Rajshekhar Karpoormath
Institution Name: University of KwaZulu-Natal
Active Member Count: 7
Allocation Start: 2018-06-11
Allocation End: 2019-01-22
Used Hours: 11302
Project Name: Design of small novel organic compounds as potential drug candidates
Project Shortname: HEAL0835
Discipline Name: Health Sciences
The synthetic and medicinal chemistry research group (SMCRG) led by Prof. R Karpoormath s a prolific and productive research group at the University of KwaZulu-Natal, Westville campus Durban.
The main research theme of this group is target-based drug design against infectious and non-infectious diseases. The research group has published extensively in this field and graduated several Masters and PhD students.
Our research work requires extensive use of computational tools for the design of potential drug-like candidates against TB and cancer. The computational tools or software used are Schrodinger Mestro for docking and virtual screening, Amber for molecular dynamics, Gaussian for energy calculations.
All the projects are progressing satisfactorily and several new projects have been designed, which will commence in 2019.
Principal Investigator: Dr Jean-Baptiste Ramond
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2018-06-12
Allocation End: 2019-02-21
Used Hours: 7501
Project Name: Metagenomics & metaproteomics of Desert soils
Project Shortname: CBBI0951
Discipline Name: Bioinformatics
At the Center for Microbial Ecology and Genomics (CMEG) of the University of Pretoria, we work on large datasets generated by high throughput sequencing technologies that require important informatics capacities.
My research there focuses on using these data to better understand the adaptation of soil microbial communities from arid lands to climate change using meta'omics', ie., meta-genomics, -transcriptomics and -proteomics.
And, for some of the analyses we need to make, the CHPC is our only reliable competent partner with the necessary equipment, i.e., that has important computing capacities.
Since the beginning of our collaboration, the CHPC has been more than useful to our research it is involved in the graduation of 4 students and the publication of more than 5 research articles in the last 18 months.
Principal Investigator: Prof Ray Everson
Institution Name: North-West University
Active Member Count: 2
Allocation Start: 2018-06-12
Allocation End: 2019-01-22
Used Hours: 11031
Project Name: CO2 Capture in Circulating Fluidized Beds
Project Shortname: MECH0866
Discipline Name: Chemical Engineering
High Performance Computing key in SO2 and CO2 Abatement Technologies
Coal-Fired Power Plants are the largest sources of SO2 and CO2 into the atmosphere. Regulatory requirements are forcing big industrial pollutant emitters to implement abatement technologies for cleaning outlet gas from these toxic and climate warming gases. The School of Chemical and Minerals Engineering at the North-West University are working with Industrial Companies in South Africa to improve devices for cleaning pollutants from outlet gases.
An effective method of removing SO2 and CO2 from flue gas originating from the burning of coal is the use of Lime. Fine Lime particles mixed with flue gas is capable of reacting and absorbing these toxic gases. The process of mixing Lime particles with flue gas and allowing the reactions to take place is facilitated in a device called a Circulating Fluidized Bed (CFB). The CFD consist of a riser section in which the particles are introduced to the flue gas and a downcomer where the particles are separated from the clean gas and reintroduced to the flue gas in the riser.
The flow in which the Lime particles interact with the flue gas is called a solid-gas two-phase flow. These two-phase flows are very complex to control especially with the aim of ensuring a uniform particle distribution through the flue gas, which will ensure the most efficient reaction. Computational Fluid Dynamics (CFD) is used to model this kind of complex two-phase flows to better understand and to predict efficiencies of the process. Due to the big size of industrial CFBs very power computers are needed to solve two-phase flows using CFD. World wide the research in gas-solid two-phase flows of plant sized equipment relies heavily on the availability of super computers. This is where the Super Computer facility of CHPC plays a critical role to enable these kinds of flow simulations. The software available on CHPC for two-phase flow applications include OpenFOAM, STARCCM+, MFIX and NEPTUNE_CFD. Current activities include the simulation of the first plant scale Flue Gas Desulfurization unit operating with dry Lime particles in a CFB to be commissioned in South Africa end of 2018.
Principal Investigator: Prof Kevern Cochrane
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2018-06-13
Allocation End: 2019-02-06
Used Hours: 41676
Project Name: Fisheries management in the southern Benguela system under climate change scenarios
Project Shortname: ENVI0908
Discipline Name: Environmental Sciences
Our research group is based at the Department of Ichthyology and Fisheries Science, Rhodes University. Our collaborators include researchers from different South African Universities and from international universities and research institutes. The work we are doing explores optimal management approaches to reduce vulnerability of fisheries in the Southern Benguela to future changes, using the Atlantis modelling framework, amongst other objectives. This model has been used to evaluate future trends in abundance of important fisheries resources under climate change, as well as the robustness of indicators under environmental variability and climate change. Progress to date has been good and further work focusing on the likely effects of climate change on future trends in upwelling and primary production will continue.
Principal Investigator: Prof Francois Engelbrecht
Institution Name: University of the Witwatersrand
Active Member Count: 14
Allocation Start: 2018-06-13
Allocation End: 2019-02-21
Used Hours: 5101876
Project Name: Development of the first African-based earth system model VRESM and its projections of future climate change over Africa
Project Shortname: ERTH0859
Discipline Name: Earth Sciences
New African-based Earth System Model
The first African-based Earth System Model (ESM) is under development at the Council for Scientific and Industrial Research (CSIR) in South Africa, through collaboration with the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Australia and South Africa's Centre for High Performance Computing (CHPC). The new ESM is unique in the sense that it is being developed in Africa and through the lens of African and Southern Hemisphere climate processes. That is, the reliable simulation of climate issues critical to Africa, such as the occurrence of drought in in response to El Niño events, wide-spread flooding over Mozambique due to landfalling tropical cyclones and increased occurrences of heat-waves under global warming are key issues in the development of the new model. The model development process is also focussed on the Southern Ocean's role in regulating southern African climate, as well as the global climate through the absorption of carbon dioxide in the ocean. The development and application of an Earth System Model is a computationally extensive endeavour, and was impossible to undertake in South Africa before the Lengau cluster of the CHPC became available in 2018. The CSIR-CHPC partnership towards development of the new model has in 2018 led to the most detailed set of projections of future climate change over southern Africa obtained to date. These simulations have provided new insight into the plausible impacts of climate change in South Africa, including how the frequencies of droughts, heat-waves and landfalling tropical cyclones may change over the next few decades. These projections were key in informing South Africa's Third National Communication on Climate Change, which was published in 2018 under the science leadership of the CSIR. Moreover, the research papers based on the projections have directly informed the Special Report on Global Warming of 1.5 ºC of the Intergovernmental Panel on Climate Change (IPCC). The CSIR and CHPC are now set to make Africa's first contributions to the international Coupled Model Intercomparioson Project Phase Six (CMIP6) of the World Climate Research Programme in 2019.
Principal Investigator: Dr Rhiyaad Mohamed
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2018-06-15
Allocation End: 2019-02-06
Used Hours: 258971
Project Name: Advanced materials for oxygen evolution reaction
Project Shortname: MATS1123
Discipline Name: Chemical Engineering
Hydrogen is seen as an integral part of the sustainable energy future. Through fuel cell and electrolyser technologies, energy storage and conversion will be possible. This will resolve some of the more critical challenges faced by most renewable energy sources. Co-hosted by the University of Cape Town and operating under the Catalysis Institute, HySA Catalysis (Hydrogen South Africa Catalysis), part of a flagship programme funded by the Department of Science and Technology, aims to find efficient and market ready catalyst technologies for both hydrogen fuel cells and water electrolysers. The former has been an age-old activity with a strong internal knowledge base. On the other hand, water electrolyser research is a new venture with many unresolved and unknown challenges. The Electrolyser Research Group is a new, young and dedicated group in the area of water electrolysis within HySA Catalysis.
We aim to take advantage of both experimental techniques and fundamental principles to predict and design new and better catalysts. Our research is broken down into two main categories, catalyst design and electrode membrane assembly development for commercialisation. Computational resources provided by CHPC's Lengau supercomputer enables us to perform quantum-chemical calculations to understand material properties. Whilst traditionally, unsupported iridium oxide has been used as an electrolyser catalyst, the scarcity and cost of iridium is a good justification to pursue research in supported iridium catalysts—these catalysts will of course require durable and conductive supports. Since some of these materials have never been synthesised before it is critical to methodically predict stable and electrically conductive material for use in water electrolysers. Based on chemical intuition we have identified a class of materials, doped oxides, which may possess excellent electrochemical properties. We have identified doped tin oxide and titanium dioxide as potential catalysts supports—our computational studies have now given us electronic properties of doped tin oxide.
Principal Investigator: Dr Rian Pierneef
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2018-06-19
Allocation End: 2019-03-08
Used Hours: 298975
Project Name: Bioinformatic and Computational Biology analyses of organisms
Project Shortname: CBBI1124
Discipline Name: Bioinformatics
The research group "Bioinformatic and Computational Biology analyses of organisms" is interested in any and all data analysis of biological origin. It is based at the Agricultural Research Council's (ARC) Biotechnology Platform (BTP). The BTP is a cutting edge research facility, housing numerous state of the art sequencing systems. These sequencing systems produce a myriad of biological data types and structures which require skilled analysis and sufficient computational resources. This project aims to answer various biological questions using the most recent data producing technologies. This includes, but is not limited to, analysis within the food production sector and the environmental landscape. The CHPC is of critical value to this project as it contains the needed computational support and the availability all currently used software programs. The CHPC enables this research project to make strides within the research community with results forthcoming out of this project being advantageous to the population at large.
Principal Investigator: Prof Johan W. Joubert
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2018-06-19
Allocation End: 2019-01-22
Used Hours: 808846
Project Name: Mobility modelling using vehicle telematics
Project Shortname: MECH0803
Discipline Name: Other
Government (all spheres) is tasked with the challenge of deciding where to invest in infrastructure (for housing/transport/economic development etc). The real hard part is to balance two questions. Firstly, "who gets the benefit of infrastructure?" and, secondly, "who PAYS for those benefits?".
In our research programme we develop agent-based transport models that are able to depict and imitate the complex, multi-modal and large-scale transport scenarios in a South African context. Each individual - from the Metrorail commuter, to the private car owner, to the minibus taxi driver, to the commercial vehicle delivering your goodies at the Woolies Foods - are represented in such a transport model. The goal of our ongoing research is to assist government and industry make better informed, evidence-based decisions about the intended, and unintended consequences of specific transport interventions.
Since every individual is modelled the computational burden is substantial and the CHPC is invaluable as it allows us to overcome the data preparation and simulation challenges of executing the large-scale, MATSim models.
Principal Investigator: Dr Fabio Cinti
Institution Name: NITHEP
Active Member Count: 4
Allocation Start: 2018-06-20
Allocation End: 2019-02-06
Used Hours: 42603
Project Name: Quantum Monte Carlo for ultra-cold atoms
Project Shortname: PHYS0892
Discipline Name: Physics
Quasi-crystal phases are considered intriguing structures that Nature presents, being largely investigated in materials science. From a theoretical prospective, recently, the interest on the subject is not only involving the pursuit of models capable of describing novel quasicrystals on metallic alloys, self-organised supramolecular micelles and liquid crystals, but also of how possible quantum effects might alter the physics of such quasicrystalline symmetries.
Here, making large use of advanced computational methods, we studied cluster quasi-crystals and cluster crystals where quantum fluctuations are taken into account. Most interestingly, the bosonic model considered displays that the onset of a zero-point motion as well as of the quantum statistics at finite temperature produce an interesting new physics, including a clear stabilisation of quasicrystals into striped and periodic cluster crystals, or the emergence of quantum quasi-crystal phases. CHPC has been a fundamental facilities for simulating such a structure which have potential for future applications in the field of quantum computing.
Principal Investigator: Dr Mervlyn Moodley
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2018-06-22
Allocation End: 2019-01-29
Used Hours: 27267
Project Name: Computational studies of corrosion in transformers
Project Shortname: MATS1120
Discipline Name: Physics
The Quantum Simulations Group (a subgroup of the Quantum Research Group) based at the University of KwaZulu-Natal has undertaken research, from a microscopic perspective, on the corrosion mechanisms involved in the failure of transformers. This failure has been linked to the interaction of copper sulphide with the copper windings in the transformer. The copper sulphide is a product of copper particles that react with the corrosive sulphur within the transformer oil and thereafter deposits on the vacant sites of the copper windings. Density functional theory (DFT) techniques are used in various fields of study and have proved most effective in handling interactions between molecules and surfaces. In this research DFT techniques are used to understand the interaction of copper sulphide on copper surfaces to obtain energetic, electronic and thermodynamic properties of the system. The understanding of the failures on a microscopic level would help in creating a model to prevent further failures and to track current failures caused by corrosion. The failure of transformers affect both power utility and financial sectors due to the high cost in repairing or replacing these failed transformers. This research relies heavily on the CHPC due to the extensive computational resources required to run DFT simulations of our complex model. The CHPC provides the Materials Studio Software (to run the DFT simulations) on the Lengau Cluster which has substantially increased the accuracy of our results and significantly reduced computational time. This project has thus far produced results pertaining to the copper sulphide interaction with the copper surface. CHPC resources are still required for us to fully understand the method of corrosion and the interaction of additives in the transformer oil, together with simulations focusing on the computation of remedial processes to prevent further transformer failures.
Principal Investigator: Dr Gurthwin Bosman
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2018-06-22
Allocation End: 2019-02-20
Used Hours: 62276
Project Name: Quantum computations for photoinduced reactions
Project Shortname: CHEM1126
Discipline Name: Physics
The research group is one of the arms of the Laser Research Institute in the Department of Physics of Stellenbosch University. Laser Research Institute of the Stellenbosch University, boasts of ongoing formidable research projects in the fields of ultrafast science, spectroscopy and laser diagnostics, laser development, trapped ion quantum control and bio-photonics and imaging, with a number of laboratories housing ultra-modern equipment. Our research group is focussed on ultrafast transient absorption spectroscopy on chemical compounds ranging from simple molecules to polymers. Experimental set ups for ultrafast transient absorption spectroscopy have been thoroughly developed over the years by different masters, doctoral and postdoctoral students. The research projects conducted in the ultrafast laboratory had produced masters' and doctoral theses, as well as peer reviewed publications.
Scientific observation being made by experiments in our research group need to be properly understood and interpreted for proper communication to the general community. Therefore, a level of theoretical simulation which will allow deeper insights is needed. Part of these theoretical simulation is the density functional calculation, a theory well accepted to interpret molecular and/or structural dynamics we observe experimentally. The calculations can take forever if run on a single computer. This is where the Centre for High Performance Computing (CHPC) comes in.
Centre for High Performance Computing (CHPC) offers a wide range theoretical coding and simulation with the advantage of supercomputing on parallel computers. This enables users' jobs submission to run on a faster scale. Our research group is privileged to have access to these supercomputing capabilities and the provision of simulation software for our calculations.
We are running series of density functional calculation ranging from simple molecules to polymers using Gaussian 09 that is provided by CHPC.
Principal Investigator: Dr Genevieve Thompson
Institution Name: Agricultural Research Council
Active Member Count: 5
Allocation Start: 2018-06-26
Allocation End: 2019-03-08
Used Hours: 29798
Project Name: Crop genomics
Project Shortname: CBBI1127
Discipline Name: Earth Sciences
Agricultural Research Council Biotechnology Platform research team, employs a range of genomic technologies to improve cultivar production, biofuel production and plant health of a range of agricultural crops in South Africa. The research includes work on key food security crops for both commercial and subsistence farmers, including maize, wheat and sorghum. The outputs of the research will contribute to food security in South Africa, with specific impacts on disease management in maize (MLND) and wheat (RWA).
Principal Investigator: Prof Peter Teske
Institution Name: University of Johannesburg
Active Member Count: 3
Allocation Start: 2018-06-27
Allocation End: 2019-03-01
Used Hours: 457036
Project Name: Coevolution of mangroves and mangrove-associated crabs
Project Shortname: CBBI0979
Discipline Name: Bioinformatics
The Centre for Ecological Genomics and Wildlife Conservation is a research group based at the University of Johannesburg, which mostly uses CHPC resources to analyse very large genetic datasets generated using next-generation sequencing technology. Main themes evolve the evolution of new species, population genetic relationships between species, and the reconstruction of various gene regions, including complete mitochondrial genomes. The data generated are useful to improve the management particularly of marine resources, and presently include a study of the stock structure of South Africa's second most important exploited fish (sardine) and raggedtooth sharks. The group is becoming ever more proficient with the analysis of such data on lengau, and in addition to analysing partial genomic data as before, we are planning to tackle complete animal and plant genomes next.
Principal Investigator: Dr Phillip Nyawere
Institution Name: Kabarak University, Nakuru, Kenya
Active Member Count: 3
Allocation Start: 2018-06-28
Allocation End: 2019-02-06
Used Hours: 162249
Project Name: Barium Floride and Perovskites
Project Shortname: MATS0996
Discipline Name: Physics
Barium Floride and Perovskites is a group led by Dr. P.W.O. Nyawere of Rongo University Kenya. I am a material scientist that worked on computer simulation of properties of BaF2.
The current work is a continuation of what I did for my doctoral degree and it involves doping of BaF2 with lanthanum to study the improvement on its electronic properties. These properties are key in understanding the operation of long life batteries.
We have also some work on Gadolinium perovskite which is superconducting material suitable for use a a conductor in many areas including but not limited to computer cables, TV cables etc. Study of superconductors is a crucial research area currently and breakthrough is slowly being realized.
Use of materials simulation is an alternative way of understanding specific heat jump of this material which for now may not be achieved experimentally. With this knowledge, experimenter can be directed on the best doping proportion necessary to attain application.
We have simulated these materials successfully and much progress is there now. BaF2;La is at 90% completed while Gadolinium is at 30% completed.
Our calculations are done on supercell structures that are dealing with up to 96 atoms. This is a huge crystal that cannot be done on simple PCs. The speed of CHPC has been good and our results are accessible any where with network.
Principal Investigator: Prof Gerrit Basson
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2018-06-28
Allocation End: 2019-01-29
Used Hours: 597874
Project Name: CFD modelling of Hydraulic Structures in Rivers
Project Shortname: MECH0985
Discipline Name: Computational Mechanics
The Institute for Water & Environmental Engineering Stellenbosch University has 3 doctoral students and 1 post-doctoral student who are investigating CFD modelling of hydraulic structures, turbulent vortex structures and sediment transport in rivers. In particular, ANSYS Fluent simulations are run remotely on the CHPC to help develop new user-defined functions for the prediction of bridge pier scour, to optimize bottom-outlet design for sediment flushing at hydropower plants, to investigate the fluid-induced vibration of piano key weirs and to optimize the design of vortex settling basins for small rural pump stations. The simulations are too computationally intensive for standard computers and the CHPC is capable of offering the required computing power to dramatically reduce the modelling time from weeks to a few days and thereby help solve complex civil engineering problems. The CHPC equips South African researchers with the tools necessary to contribute to research on an international platform. Articles at international conferences and peer-reviewed journals are in the process of being written and published while the doctoral students at IWEESU expect to complete their studies and graduate in 2019.
Principal Investigator: Prof Mahmoud soliman
Institution Name: University of KwaZulu-Natal
Active Member Count: 31
Allocation Start: 2018-06-28
Allocation End: 2019-01-29
Used Hours: 5855324
Project Name: Drug Design, development and modelling
Project Shortname: HEAL0790
Discipline Name: Health Sciences
The research scope of the Molecular Bio-Computation and Drug Design Research Lab covers a wide range of computational and molecular modeling research areas with main focus on biological systems and drug design approaches. Main interest is related to design and study of biologically and therapeutically oriented targets by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We show keen interest in diseases of global burden and evident prevalence within the south African populace such as HIV/AIDS, Tuberculosis and Cancer. The computational resources provided by CHPC is employed in performing the molecular dynamic calculations and the corresponding post molecular dynamic simulation analysis
Principal Investigator: Dr Babatunde J. Abiodun
Institution Name: University of Cape Town
Active Member Count: 15
Allocation Start: 2018-06-29
Allocation End: 2019-01-29
Used Hours: 1852478
Project Name: CSAG-Atmospheric Modelling
Project Shortname: ERTH0904
Discipline Name: Earth Sciences
The Climate System Analysis Group (CSAG) Atmospheric Modelling project consists of CSAG researchers and students working on model development and applications. Our group is a unique research group within Africa (CSAG http://www.csag.uct.ac.za/). We are a mix of specialties who put the needs of developing nation users at the forefront of everything we do. As a result, we seek to apply our core research to meet the knowledge needs of responding to climate variability and change. In the project, we develop, evaluate, and apply of dynamic and statistical climate models over Africa. Climate models are powerful tools for understanding the complexity of our earth climate system. We use various form of climate model, ranging from uniform-grid Global Climate Models (GCMs), Regional Climate Models (RCMs) and adaptive-grid GCMs (VGCM) that has capability to increase its grid resolution locally over a region of interest. Given the complexity and computational demand of these models we rely on high performance computers like those at the Meraka CHPC to our models. Our research goal is to understand the dynamics of climate extremes (i.e. droughts, extreme rainfall, heatwaves, and pollution episodes) and the impacts of vegetation changes on regional climate.
The highlights of our past research, carried-out using the Meraka CHPC resources, include: development and application of a VGCM for studying rainfall producing systems in West Africa (Abiodun et al, 2010) and tropical cyclone over the South-West Indian Ocean (Maoyi et al., 2017); application of RCMs in studying the transport of atmospheric NOx and HNO3 over Cape Town (Abiodun et al., 2014), extreme rainfall events over Western Cape (Abiodun et al., 2014), potential impacts of climate change on extreme precipitation over four African coastal cities (Abiodun., 2017), and future projection of droughts over major river basins in Southern Africa at specific global warming levels (Abiodun et al., 2018). The project has graduated more than 22 postgraduate students in last five years, and currently support 13 postgraduate students who are working towards graduating this year or next year.
Principal Investigator: Dr Joseph Mutemi
Institution Name: University of Nairobi
Active Member Count: 3
Allocation Start: 2018-07-03
Allocation End: 2019-01-29
Used Hours: 87742
Project Name: Numerical weather and climate modeling, prediction, forecasting and change projections for Africa and sub regions
Project Shortname: ERTH1131
Discipline Name: Earth Sciences
The ERTH1131 research group is using CHPC resources in modeling climate patterns with the aim of improved representation of climate processes in order to enhance prediction skill over East Africa. Livelihoods over East Africa are hugely dependent on seasonal rainfall and therefore improved early warning will immensely benefit the society. The group has made several accomplishments, given the nature of international scientific conferences where their results have been presented. Several publications are in draft form and will be polished and submitted for journal publication.
Principal Investigator: Prof Karl Rumbold
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2018-07-03
Allocation End: 2019-03-01
Used Hours: 9736
Project Name: Next Generation Bioprospecting
Project Shortname: CBBI1130
Discipline Name: Bioinformatics
The Industrial Microbiology and Biotechnology Laboratory has 10 research members, headed by Prof. Karl Rumbold. We are actively involved in growing Industrial Biotechnology in Africa by
: Influence and stimulate African policy making
: Support the Bio-economy
: Understand Sub-Saharan African biosphere diversity
: Functionalize biodiversity for industrial applications
: Participate in X-omics research
: Promote Synthetic Biology
Principal Investigator: Dr Daniel Cunnama
Institution Name: South African Astronomical Observatory
Active Member Count: 2
Allocation Start: 2018-07-05
Allocation End: 2019-02-14
Used Hours: 93918
Project Name: Mocking Astrophysics: Cluster Comparison Project
Project Shortname: ASTR1132
Discipline Name: Astrophysics
This work will form part of the The Three Hundred project, an endeavour to model 324 large galaxy clusters with full-physics hydrodynamical re-simulations. The aim is to ultimately compare differences to observations for fundamental galaxy cluster properties and scaling relations.
Multiple codes have been used, the particular code being used on the CHPC is a new code developed by Shuiyao Huang, called GadgetPESPH.
Principal Investigator: Dr Uljana Hesse
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2018-07-10
Allocation End: 2019-03-08
Used Hours: 207760
Project Name: Medicinal Plant Genomics
Project Shortname: CBBI1133
Discipline Name: Bioinformatics
My name is Dr Uljana Hesse, I work as Senior Lecturer at the Department of Biotechnology at the University of the Western Cape, Cape Town, South Africa. My research focuses on studying the genomic background of rooibos (Aspalathus linearis), an endemic South African plant best known as a beverage - rooibos tea. Health-promoting properties of rooibos (e.g. antidiabetic and cardioprotective activities) have been scientifically linked to a diverse range of phenolic compounds produced by this plant. With my research, I want to promote our knowledge on the genetic background of medicinal compound biosynthesis in rooibos, and identify genomic markers for important agronomical traits, such as drought, pest and insect resistance, which can support targeted plant selection and breeding programs. I have established a research team, which currently comprises six students. Currently, our work focuses mostly on 1) the establishment of procedures for plant genome and transcriptome research (including plant collection, biochemical screening, genome size determination, RNA/DNA extraction and exhaustive biocomputational data analysis), and 2) the development of computational tools for targeted identification of plant genes involved in medicinal compound production. So far, we have sequenced and analyzed eight rooibos transcriptomes, and are in the process of assembling the rooibos genome using Illumina sequencing data (95% genome coverage). The genome sequencing data analysis is being conducted at CHPC. A first draft genome has now been assembled and analysis of the assembly is underway.
Principal Investigator: Prof Tony Ford
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2018-07-12
Allocation End: 2019-08-02
Used Hours: 50668
Project Name: Computational studies of the properties of molecular complexes
Project Shortname: CHEM1134
Discipline Name: Chemistry
This research group is headed by Emeritus Professor Tony Ford, of the School of Chemistry and Physics at the University of KwaZulu-Natal. The group is interested in the properties of a wide range of molecular complexes, usually containing one acidic and one basic molecule, with the intention of determining what factors are responsible for the stability of a particular complex. These properties include their molecular structures and vibrational spectra, and the ways in which the distribution of electronic charge is perturbed in the formation of the complex. A knowledge of the determinants of the outcomes of the interactions between any pair of molecules as they come together to form a complex is invaluable in predicting the course of a variety of chemical reactions. These reactions may be of the kinds involved in the search for more and more efficient drugs, for example, and would be of great benefit to the pharmaceutical industry. Other potentially useful reactions might be those used in the fabrication of batteries, with applicability in the energy production industry. The regular procedure involves a number of steps, each performed using the standard Gaussian 16 software. An initial guess at the structure of a target complex is proposed, and an input file constructed requesting the program to search for an energy minimum, within chosen convergence limits. If a successful optimization has been achieved, the resulting structure is subjected to a test of its validity in terms of its vibrational spectrum, and the structure is accepted if certain criteria have been met. Along with information on the resulting structure and its spectrum, which may be verified by comparison with experimental data, where available, the Gaussian program also outputs important information on the distribution of electronic charge within the complex, and the ways in which the charges of the individual atoms in the interacting molecules are perturbed on complexation. The Gaussian 16 program contains many thousands of lines of code, and it would not be practicable to use without access to a high performance computing facility. The project is now mature, and has spawned a number of sub-projects in its lifetime. It has the potential to be a valid project for several more years to come.
Principal Investigator: Prof Thirumala Govender
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2018-07-13
Allocation End: 2019-01-22
Used Hours: 17680
Project Name: IN SILICO EVALUATION OF NANO DRUG DELIVERY SYSTEMS
Project Shortname: MATS0816
Discipline Name: Material Science
The Novel Drug Delivery Unit (NDDU) at University of KwaZulu-Natal is led by Professor Thirumala Govender, a Professor of Pharmaceutics, Head of the UKZN NanoHealth Pillar and Evaluator on the Medicine Control Council of South Africa. The NDDU currently focuses on developing advanced medicine formulations to overcome antibiotic resistance. Antibiotic resistance, considered a global crisis currently, affects the development of human society and has high cost implications to government in terms of finances and resources.
Our group has designed various types of novel pharmaceutical materials as well as advanced and new generation "smart" nano drug delivery systems such as nanomicelles, nanoplexes, polymersomes etc. with superior architectural designs which have been prepared by our team and have shown superior activity against sensitive and resistant bacteria. The group philosophy is to use a multidisciplinary integrated approach that will minimize the cost of research and maximize therapeutic outcomes.
Hence the facilities provided by CHPC allows our group to integrate molecular modeling with our research that involves extensive in vitro and invivo animal evaluation of our novel medicines, and is being recognized locally and internationally for excellence.
Principal Investigator: Dr Dominic Stratford
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2018-07-19
Allocation End: 2019-02-06
Used Hours: 10043
Project Name: Application of deformation-based models in paleoanthropology
Project Shortname: CSCI0984
Discipline Name: Imaging
As members of the Sterkfontein Research team, we are investigating 3-million-year-old fossil specimens from the caves and quarries at Sterkfontein, 50 km northwest of Johannesburg. Because it is one of the richest fossil complex site in Africa, this fossil assemblage is critical to challenge long-standing questions in human evolution. Who were our ancestors? Where and when did they live? Did they look like us? Did they walk on two legs, as humans do today? In addition to basic descriptions and traditional metrical analyses, recent incorporation and validation of computer-based techniques for reconstructing and comparing morphological pattern have substantially improved the quality of data delivered by fossil remains. In our project, we use high-resolution imaging techniques (e.g., microtomographic-based scanner) to non-invasively explore the fossil specimens and apply 3D modelling techniques to comparatively describe the anatomy of our ancestors. In that perspective, the access to a supercomputer through the CHPC resources is essential for running our analyses and provide new evidence of human evolution in South Africa.
Principal Investigator: Dr Bubacarr Bah
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 6
Allocation Start: 2018-07-23
Allocation End: 2019-02-07
Used Hours: 210404
Project Name: Large Scale Computations in Data Science
Project Shortname: CSCI0972
Discipline Name: Applied and Computational Mathematics
The research group is the AIMS Data Science group. We work on understanding the mathematical foundations of deep learning; applications of deep learning to health, energy, etc; and the development of deep learning software. On the CHPC we train our models for the applications and also test run our algorithms (software). Deep learning applications have tremendous potentials in solving problems in health, energy, etc. With the availability of the CHPC facility to the group, we are making significant progress in our projects.
Principal Investigator: Dr Mohammad Moghimi Ardekani
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2018-07-26
Allocation End: 2019-01-22
Used Hours: 157262
Project Name: R&D in Solar Energy in particular Concentrating Solar Power Research
Project Shortname: MECH1137
Discipline Name: Computational Mechanics
Dr. Moghimi Ardekani Research group in Mechanical Engineering Department of University of Pretoria is working on Concentrating Solar Power and thermal Energy Storage to engineer and optimize the cost of related technologies and make them available in South Africa.
Solar energy and thermal storage is one of the top renewable energy resources which would be able to resolve the power shortage issue in South Africa.
In that Regard, CHPC is quiet helpful in engineering and numerical simulation of this study and could hugely save the unnecessary trial and error process of experimental studies if the CHPC and numerical modelling were not available.
The project progress is quiet satisfactory and based on the research finding the group has started a collaboration with Imperial College London.
Principal Investigator: Prof Linky Makgahlela
Institution Name: Agricultural Research Council
Active Member Count: 3
Allocation Start: 2018-07-27
Allocation End: 2019-03-08
Used Hours: 2546
Project Name: Beef and Dairy Genomics
Project Shortname: CBBI1138
Discipline Name: Bioinformatics
Beef and Dairy genomics team forms part of the Animal breeding and Genetics unit led by Professor ML Makgahlela at the Agricultural Research Council – Animal Production. It comprises of both researchers and post graduate students. The team works along the two large consortiums in South Africa; the Beef Genomics Program and the Dairy Genomics Program respectively and works towards achieving the goal of generating large genomic data for the South African beef and dairy industry in order to fully implement genomic selection in the future and have the two industries compete at a global level. The work done by the team includes working with commercial and small holder beef and dairy breeders towards collecting a large number of samples for processing, curating and analysing generated genomic data. Globally, breeding programs are moving towards the use of genomic technologies to improve and speed up genetic gain and production. Introduction of these technologies to most developing countries is very important as these will contribute towards the improvement of breeding programs. In addition to this is the prospect of training experts in the field of genomics, young scientist that will come up with new ideas geared towards expanding the South African breeding industry. Upon request, breeders provide us with hair and semen samples and from these genomic data is generated by the Agricultural Research Council Biotechnology platform. Genomic data for thousands of animals is very large thus cannot be stored in normal computers nor can it be analyzed in there; thus CHPC provides the platform to store and analyze this data without any challenges.
Principal Investigator: Prof Don Cowan
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2018-07-30
Allocation End: 2019-03-08
Used Hours: 49170
Project Name: Meta-omics of extreme environments
Project Shortname: CBBI0932
Discipline Name: Bioinformatics
We are working in the area of microbial ecology at the Centre for Microbial Ecology and Genomics at the University of Pretoria. We are interested in understanding the taxonomic and functional potentials of microbes in various extreme temperature soils. The study will assist us to model the factors affecting climate change and environmental microbiota. We apply unculturable and culturable techniques to understand the microbial ecology of extreme environments. More specifically the analysis of total DNA and RNA from the environmental samples. We have obtained very interesting findings supporting the important role and key microbial taxa involved in the process of biogeochemical cycling in the hot and cold desert soils.
Principal Investigator: Dr Kenneth Allen
Institution Name: Greenplan
Active Member Count: 1
Allocation Start: 2018-08-01
Allocation End: 2019-01-28
Used Hours: 13210
Project Name: CFD with Fire Dynamics Simulator (FDS)
Project Shortname: INDY1139
Discipline Name: Other
N/A - commercial, not a research group
The work is being done to determine the effectiveness & suitability of a smoke / ventilation system in a large building basement. Due to the scale of the model and type of analysis, it is not possible to do it without high performance computing.
Principal Investigator: Dr Dirk Swanevelder
Institution Name: Agricultural Research Council
Active Member Count: 1
Allocation Start: 2018-08-01
Allocation End: 2019-03-01
Used Hours: 8789
Project Name: Crop Genomics
Project Shortname: CBBI1141
Discipline Name: Bioinformatics
Sunflower is one of South Africa's major oilseed crops and is grown in most areas of the summer rainfall production region. A fast growth rate and relative drought tolerance allow the crop to be planted later in the summer season when rains are delayed. This enables producers to still produce a viable profitable cropping under challenging weather conditions.
The ARC's Sunflower Genomics group focuses on improving sunflower as a crop. This specific project investigates key sunflower trait development on a molecular level over time. The traits investigated play a role in the profitability of the crop and its by-products. Comparison of transcriptomic data from lines with the desired traits to those without these allows us to investigate these key economic traits as they develop in commercial and non-commercial viable accessions. We believe that this would enable us to not only identify the key role playing genes in the development of these traits, but also the expression levels of these role players required to make these traits commercially viable and the required expressional timing to obtained the desired product/traits in the crop.
The CHPC's large capacity allows us to analyse and compare the transcriptome datasets of the different developmental time periods within and between the different accessions under investigation. The CHPC is central to the analyses of the large transcriptome datasets generated during our investigation. The high-throughput nature of next generation sequence data generated in the project requires the computing resources provided by the CHPC to process the data in a timeous fashion. This will allow us to determine the relevant biological answers we're seeking and help improving the crop. The Project is progressing slowly as a result of the dataset size but we're envisioning finalising computing in the next 6 months.
Principal Investigator: Prof Thuto Mosuang
Institution Name: University of Limpopo
Active Member Count: 7
Allocation Start: 2018-08-03
Allocation End: 2019-01-30
Used Hours: 10925
Project Name: Computational studies of various ultra-hard materials
Project Shortname: MATS0875
Discipline Name: Material Science
The sensors and advanced materials research group is a small developing research group which is housed in the Department of Physics of the University of Limpopo. In this research group existing and new materials are being probed for sensing of various gases. Discovered sensing materials can be converted to sensing devices which can be used for domestic, health, mining and manufacturing industries. Computational modelling is an essential part of our research, as prediction of materials properties is cost effective compared to experimental measurements. The CHPC is a valuable component of our research. Through the CHPC structural, dynamic, electronic, and optical properties of materials can be predicted with ease.
Principal Investigator: Prof Alan Christoffels
Institution Name: University of Western Cape
Active Member Count: 3
Allocation Start: 2018-08-06
Allocation End: 2019-03-01
Used Hours: 302095
Project Name: Bioinformatics and Public Health
Project Shortname: CBBI0819
Discipline Name: Bioinformatics
TB drug resistance – when the bacteria become resistant to at least one anti-TB drug – is a growing problem across the world. Current treatments that include more than one drug known as combination therapy have become inadequate because the bacteria have devised ways to survive even when antibiotics are used. An estimated 3.5% of new cases and 18% of previously treated cases of TB are drug resistant. There is therefore still a need to identify alternative drugs. But the drug discovery process is fairly lengthy (10 to 15 years). This timeline can be shortened with the aid of computers.
In an effort to find new ways of overcoming the problem, we have , together with the school of pharmacy at the University of the Western Cape used a number of computer strategies to identify alternative drugs. The results were published recently in the Plos One Journal.
Principal Investigator: Dr Leigh Johnson
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2018-08-07
Allocation End: 2019-03-01
Used Hours: 236432
Project Name: MicroCOSM: Microsimulation for the Control of South African Morbidity and Mortality
Project Shortname: HEAL1049
Discipline Name: Health Sciences
The MicroCOSM project, based at the Centre for Infectious Disease Epidemiology and Research at the University of Cape Town, is a project to simulate the spread of infectious diseases, as well as the incidence of non-infectious diseases, in the South African population. By simulating the social and biological factors that contribute to disease transmission, we can better understand which sub-populations need to be targeted for special interventions. We can also evaluate the impact that various prevention and treatment programmes have had in South Africa to date, and evaluate the potential impact of new programmes. This simulation involves generating nationally representative samples of 20,000-40,000 South Africans and tracking them over their life course. Because this involves many individual-level calculations, the model requires substantial computing power, and the CHPC is therefore critical to the conduct of these simulations. We have recently published a paper about interactions between human papillomavirus and HIV. Because both viruses are sexually transmitted, it is difficult to establish the extent to which their co-occurrence represents a biological interaction. Our study shows that previously-published findings on the co-occurrence of these two viruses could be due entirely to their common risk factor (risky sex) and is not necessarily attributable to biological interactions between the two viruses.
Principal Investigator: Dr Geoff Nitschke
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2018-08-07
Allocation End: 2019-03-09
Used Hours: 808943
Project Name: Evolving Complexity
Project Shortname: CSCI1142
Discipline Name: Computer Science
The project is a computational simulation of a multi-robot system, where the design of the robots (body-brain) couplings are automatically designed by new specialised machine learning algorithms. The applications are in collective (team) robotics, where robots in groups must cooperate to solve difficult tasks in hazardous
or remote environments (for example toxic waste gathering and removal).
The research is run under the purview of the evolving computation research group at the CS department at UCT. Geoff Nitschke is the research project PI and director of the group.
The simulation (robot design) experiments are computationally intensive and thus rely on the resources of CHPC to be done in a timely manner. The project is on track to finish in early 2020.
Principal Investigator: Prof Stephan Heyns
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2018-08-08
Allocation End: 2019-02-04
Used Hours: 109433
Project Name: Computational investigations in asset integrity mangement
Project Shortname: MECH1145
Discipline Name: Computational Mechanics
With this particular aspect of the project only running now for less than 6 months we are not ready for a press release as yet on the CHPC aspect of the project. We should be in that position after the next six months.
Principal Investigator: Prof Philip Machanick
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2018-08-10
Allocation End: 2020-04-01
Used Hours: 9420
Project Name: Motif quality assessment
Project Shortname: CBBI0922
Discipline Name: Bioinformatics
We are a small group who collaborate between South Africa and Kenya. Philip Machanick is the Principal Investigator and Caleb Kibet does much of the investigation.
Studying transcription factor binding is an important part of understanding regulation of transcription, a key biological process.
In this work we explore methods of predicting transcription factor binding sites by improving models of sites. A motif is a numerical model of how a transcription factor binds, giving the probability that a given DNA base is in a given position in a binding site. A DNA base can be thought of as a letter in a 4-letter alphabet, A, C, G or T. A transcription factor binding site is usually a fixed length on DNA, and the exact "letter" in each position determines whether a transcription factor is likely to bind in that position.
Transcription factors have an affinity for a particular pattern in the DNA. That pattern can vary and can be hard to determine experimentally. A motif represents this pattern and, since there are many ways of identifying motifs with different sources of error, it is hard to know what the best motif is.
If we are able to predict transcription factor binding sites efficiently, this is a powerful tool for understanding issues like developmental problems and diseases with a genetic component like cancer.
In this work, we discover comparative methods of determining the quality of motifs and present them in a web server that is easy to use for the biologist. We are able to use CHPC facilities to explore a wide range of techniques efficiently before combining the final results in a simplified interface un our web server.
In the initial stage of the project, we have developed methods and a web server; we now need to apply these methods to solving biology problems.
Principal Investigator: Prof Ozlem Tastan Bishop
Institution Name: Rhodes University
Active Member Count: 18
Allocation Start: 2018-08-12
Allocation End: 2019-02-28
Used Hours: 6814537
Project Name: Structural Bioinformatics for Drug Discovery
Project Shortname: CBBI0867
Discipline Name: Bioinformatics
Research Unit in Bioinformatics (RUBi) at Rhodes University is specialized in structural bioinformatics research. Structural bioinformatics focuses on the identification and analysis of structure, dynamics and interaction of biological macromolecules in 3D space. While doing so, it aims to make connections between sequence – structure and function of macromolecules. Information on structure is particularly important as you can derive enormous amounts of information.
RUBi's main interest is drug discovery. Computer aided drug design technology has greatly revolutionised the drug research and development process. Traditional computational drug discovery approach includes large scale structure based and/or ligand based in silico docking combined with molecular dynamics and binding free energy calculations. All these computationally expensive calculations require to use HPC facilities.
In the last few years, RUBi has been developing some novel protocols by merging computational chemistry, structural bioinformatics and biophysics approaches and combining with traditional methods. These combined approaches also require HPC facilities. We expect that our protocols will advance our and others research. We have already been testing the combined approaches in different cases and a number of hit compounds identified; including identification of South African natural compounds as hits to cancer, malaria, trypanosoma and HIV.
Principal Investigator: Dr Caroline Kwawu
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 0
Allocation Start: 2018-08-14
Allocation End: 2019-02-10
Used Hours: 290111
Project Name: Renewable Energy Materials
Project Shortname: MATS1146
Discipline Name: Material Science
Renewable energy materials is a research being undertaken by students in the Department of Chemistry, Kwame Nkrumah University of Science and Technology. The Centre for High Performance Computing (CHPC), South Africa, provides computing resources and access to software that makes the research possible. The aim of the research is to model new materials that convert solar energy to fuels and electricity. This work is peculiar and urgent to reduce the over reliance on fossil fuels which pose the problem of Climate Change. This computational group also collaborates with an experimental group to understand their findings and to better tune materials by doping and surface alterations. We employ the Density Functional Theory (quantum) method which is efficient in studying electronic structure to elucidate surface reaction mechanisms, and properties of materials. This research is important to the migration of Ghana from a carbon dioxide emitting economy to a mitigating economy. As Ghana currently produces much green house gases from biomass combustion, due to its cost. This allows Ghana to also contribute to the SDGs (Sustainable Development Goals) of finding renewable, sustainable energy for all.
Principal Investigator: Dr Willem Gerber
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2018-08-14
Allocation End: 2019-02-10
Used Hours: 198027
Project Name: Computational investigation of transition state metal catalysis
Project Shortname: CHEM1061
Discipline Name: Chemistry
The main focus of the Gerber group is the elucidation of inorganic reaction mechanisms that range from ligand exchange, redox processes and catalysis cycles amongst others. To this end we continuously develop software for modelling macroscopic reaction kinetics and associated equilibria coupled with the use of existing quantum computational chemistry packages to understand the results at the molecular level. As high quality analytical data is required for thermodynamic and kinetic modeling we actively develop new or improve on existing analytical techniques (NMR, hyphenated separation techniques) specifically for the platinum group metals (PGM's) present in aqueous or organic solvents.
Principal Investigator: Dr Richard Walls
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2018-08-15
Allocation End: 2019-02-11
Used Hours: 41875
Project Name: Fire Engineering Research
Project Shortname: MECH1148
Discipline Name: Computational Mechanics
When protecting the 1 billion people who live in informal settlements from fire: (a) Should you paint the dwellings walls with protective paint (as currently being done)? (b) How big could our next disaster be? (c) How does fire spread from one dwelling to another, and (d) what is a safe safety distance between dwellings?
These are the sort of questions the Fire Engineering Research Unit at Stellenbosch Universuty (FireSUN) are trying to answer. Following full-scale fire tests on informal settlement dwellings computational analyses of the fire behaviour is now occurring to provide a deep insight into the fire physics that govern what would, or would not, work to improve fire safety.
Principal Investigator: Dr Benjamin Lamptey
Institution Name: University of Ghana
Active Member Count: 7
Allocation Start: 2018-08-16
Allocation End: 2019-02-12
Used Hours: 16085
Project Name: Weather, Climate and Water
Project Shortname: ERTH0955
Discipline Name: Earth Sciences
The group comprises Earth scientists working on Weather, Climate and Water with a special interest in modeling (atmospheric and application modeling such as hydrological, agricultural, etc.) for both operations and research.
The Weather Research and Forecasting (WRF) model is to be used for operational Weather Forecasting over West Africa as part of a European Union funded through the African Development Bank (AfDB) project, called Satellite and Weather Information for Disaster Resilience in Africa (SAWIDRA). The CHPC system was used to run test simulations (called benchmarking) to obtain the technical specifications that were used as input to the bid document to purchase a computing system to be used for the SAWIDRA West Africa operational modeling .
In another initiative, effort are on the way to test the WRF model on the CHPC system for very high resolution simulations (called convection permitting resolutions) over the Ghana region for (a) Numerical Weather Prediction and (b) sub-seasonal prediction in research mode. The target sectors for the high resolution simulations are agriculture, energy, marine, oil and gas, the National Disaster Management Organization and the general public.
Additionally, work is in progress regarding adopting a conceptual hydrological model (a process called calibrating the model), GR5J, for use over the Komadugu-Yobe part of the Lake Chad Basin, West Africa. The calibration is being done using multi-objective optimization techniques on the daily runoff generated by the model. The use of the multi-objective optimization techniques is to investigate the extent to which errors propagated can be addressed. The two-phase calibration process is done for 1973-2013 and 1980-2010 separately to ascertain the robustness of the calibration process.
Principal Investigator: Prof Liliana Mammino
Institution Name: University of Venda
Active Member Count: 3
Allocation Start: 2018-08-16
Allocation End: 2019-03-01
Used Hours: 815433
Project Name: computational study of biologically active molecules of natural origin
Project Shortname: CHEM0959
Discipline Name: Chemistry
WHO?
Computational chemists, Department of Chemistry, University of Venda.
The group is composed by:
*** Prof. Liliana Mammino, PI
*** Ms. Mireille Bilonda, PhD student, currently finalising calculations to be able to submit publications on the last topics of her project (will graduate in May 2019)
*** Mr Thembani Vukeya, M.Sc. student, currently starting the second year of his project.
WHAT? and WHY?
As computational chemists, we study molecules, to find their properties such as energy, preferred geometries. etc. This information is important for a better understanding of the properties of substances.
We focus on biologically active molecules, i.e., molecules that have an effect on the human body and can be potentially interesting for the development of new drugs.
Mireille Bilonda focuses on the study of molecules with antimalarial activity identified in plants used in African traditional medicine.
Thembani Vukeya focuses on the study of molecules with potential or proved activity for the treatment of diabetes.
Liliana Mammino is working on acylphloroglucinols with different types of properties.
HOW?
In order to find the properties of molecules, we use calculations.
The results have better quality if more powerful computational methods are used. More sophisticated computational methods require a lot of computer time. Furthermore, the computer time depends on the number of atoms in a molecule. Most biologically active molecules are not small, so, the necessary computer time can be quite long if calculations were performed using normal PCs. Before starting using CHPC, I had calculations that require months (months for one calculation) on desktop PCs. Using CHCP enables us enormous time-saving, which makes our research much more efficient, both in terms of productivity within a certain time period (leading to the possibility of publishing more articles) and in terms of research questions that we can undertake.
Principal Investigator: Prof Dan Stein
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2018-08-17
Allocation End: 2019-02-13
Used Hours: 5709
Project Name: ENIGMA
Project Shortname: HEAL1147
Discipline Name: Imaging
Our group participates in the world's largest brain imaging consortium, ENIGMA. ENIGMA has produced multiple publications on brain alterations in mental and neurological disorders.
Principal Investigator: Prof Thulani Makhalanyane
Institution Name: Stellenbosch University
Active Member Count: 7
Allocation Start: 2018-08-17
Allocation End: 2019-03-01
Used Hours: 8482
Project Name: Metagenomics of extreme environments
Project Shortname: CBBI1023
Discipline Name: Bioinformatics
During the past year, we have made significant progress with our studies on the microbial ecology of extreme environments.
In one of the studies, published in the high impact factor journal Microbiome, we provide new insights regarding Antibiotic resistance genes (ARGs). We showed that extreme Antarctic soils appear to harbour ARGs contrary to previous expectations.
In our marine studies, we have provided the first analyses of phylogenetic data (including functional processes) along the water column.
We have made significant progress in several project. In 2018, three postgraduate students graduated (1 D and 2 MSc). We anticipate two graduations (1 D and 1M) in September 2019.
Principal Investigator: Prof Hendrik Vermeulen
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2018-08-17
Allocation End: 2019-02-13
Used Hours: 181418
Project Name: Short-term Forecasting Modelling of Wind Power Profiles and High Wind Speed Shutdown Events
Project Shortname: MECH1150
Discipline Name: Electrical Engineering
The Centre for Renewable and Sustainable Energy Solutions (CRSES) at Stellenbosch University is currently engaged in the development of sophisticated wind speed forecasting techniques for wind farm applications. The proliferation of wind energy requires that advanced forecasting tools exist with which to predict the resulting power fluctuations on the National Grid. Failure to do so directly impacts on the ability of the System Operator to schedule Generation reserves to meet near-future demand levels, resulting in an increase in both the cost of operation as well as a risk to the security of supply. Poor forecasting of short-term wind power requires that the System Operator employ corrective action in the sense that customers can be shedded, or reserve generation is dispatched if it is available. Employing conventional stations to meet the generation short-fall is inefficient, costly, increases failure rates, and reduces the required maintenance interval.
The effective forecasting of wind speeds at a wind farm requires that the atmospheric state be predicted using numerical equations. These simulations, which typically employ the Weather Research and Forecasting (WRF) model, are highly computationally intensive and require parallel computing power to produce timeous forecasts. With the aid of the CHPC, the beginnings of a multi-model forecasting tool have been established. By generating multiple models, the initial tests indicate a reduction in the forecasting error to notable levels when utilizing post-processing tools. It is envisioned that further research in this topic will result in significant improvements in current forecasting results.
Principal Investigator: Dr Chris Lennard
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2018-08-19
Allocation End: 2019-02-15
Used Hours: 74337
Project Name: Wind Atlas for South Africa
Project Shortname: ERTH0909
Discipline Name: Earth Sciences
The Wind Atlas for South Africa project (WASA) is a collaboration between the Danish Technological University and the University of Cape Town, CSIR and SAWS that is developing a wind energy resource map across the entire country. The current WASA resource map covers only parts of the Northern, Eastern and Western Cape and is being expanded in two phases to include (1) KZN and the southern Free state then (2) the remainder of the country. UCT is responsible for the creation of the course scale wind resource map using a regional climate model during phase 2 and 3 of the project. As the simulations are computationally very expensive these are being run on the CHPC infrastructure. The phase 2 map will be produced during 2019-2020 and the final, country-wide map during 2020.
Principal Investigator: Dr Njabulo Gumede
Institution Name: Walter Sisulu University
Active Member Count: 1
Allocation Start: 2018-08-21
Allocation End: 2019-02-17
Used Hours: 64708
Project Name: Computer-Aided drug design for cancer therapy
Project Shortname: CHEM1058
Discipline Name: Chemistry
Njabulo Gumede is a Senior Lecturer from Mangosuthu University of Technology (MUT). MUT currently do not have postgraduate degrees for chemistry in their PQM. However, he is a co-supervisor of one MSc student for the University of Limpopo. Njabulo's research work deals with the design of new molecular entities for prostate and breast cancer. He designs his drugs using software packages that utilizes HPC resources such as CPU's and GPU's.
Principal Investigator: Prof Orde Munro
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2018-08-22
Allocation End: 2019-02-18
Used Hours: 66982
Project Name: Bioinorganic Chemistry
Project Shortname: CHEM1065
Discipline Name: Chemistry
Metallodrug Inhibitors for Human Topoisomerase II
Human topoisomerase II (topo II) is an essential enzyme found in the nuclei within our cells. It maintains the topology of our DNA (in unison with other topoisomerases) to allow processes such as mitosis (cell division) and DNA replication to occur. Specifically, topo II decatenates entangled DNA by cutting the double-stranded helix, enabling a distant or daughter strand of the DNA to move through the break, and then resealing the break so that the double helix is returned to full functionality. Topo II is essential during mitosis because it enables chromosomal DNA to separate into daughter copies. Inhibitors of topo II thwart cell division and are excellent anticancer agents. Notable anticancer drugs that work by inhibiting topo II are doxorubicin and etoposide.
In this project, we are calculating the binding affinities of existing and rationally-designed novel metal-organic compounds based on Au(III) to human topo II using molecular docking, molecular dynamics, and quantum mechanics simulations. We aim to discover high-affinity topo II inhibitors using these computational methods. The "hit compounds" have the correct shape, charge, and functionality to block a key step in topo II's catalytic cycle and are expected to be next generation anticancer drug candidates. Hit compounds elucidated in these molecular simulations are then suitable for chemical synthesis, in vitro screening, biophysical affinity studies, and in vivo testing.
The study is being conducted by Dr. Zeynab Fakhar (post-doctoral fellow) and Prof. Orde Munro (SARChI Chair of Bioinorganic Chemistry) at the Molecular Sciences Institute, WITS University. The simulations are multifaceted and the enzyme-drug-DNA target complexes are large, necessitating the use of the parallel computing facilities of the CHPC. The study employs computational platforms that parallelize the simulations over thousands of GPUs (graphic processor units) to shorten the time taken to acquire the requisite data.
Principal Investigator: Dr Marde Helbig
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2018-08-27
Allocation End: 2019-04-19
Used Hours: 440774
Project Name: Solving Multi-objective optimization problems using CI algorithms
Project Shortname: CSCI0874
Discipline Name: Computer Science
The Computational Intelligence Research Group (CIRG) at the University of Pretoria focusses on using computational intelligence algorithms to solve a variety of problems.
This project focusses on solving optimisation problems that have more than two objectives and where at least two objectives are in conflict with one another. Furthermore, the objectives and/or constraints change over time. These types of problems can be applied in a wide range of applications areas such as production plants (scheduling the jobs at the plant), delivery services (vehicle routing optimization), costing (electricity costing optimization), water treatment (optimizing the treatment of water based on what the water will be used for), and stock market (portfolio optimization or prediction of stock movement).
When developing algorithms to solve these kinds of problems they must be evaluated on benchmark functions against other algorithms. Furthermore, performance measures have to be calculated for the various algorithms and the data has to be statistically analysed. CHPC resources are used to run these simulations to obtain the data, which is required to write publications.
Principal Investigator: Prof Robin Emsley
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2018-08-29
Allocation End: 2019-03-08
Used Hours: 80953
Project Name: EONCKS
Project Shortname: CBBI1064
Discipline Name: Health Sciences
The Schizophrenia Research Unit in the Department of Psychiatry at Stellenbosch University is currently working on a large First Episode Schizophrenia dataset that was recruited between 2007 and 2018. While a number of papers have been published by the group, additional analyses are still underway and we expect to publish a number of papers in 2019 with the neuroimaging data that was processed using the Lengau cluster of CHPC. Use of these facilities has allowed us to greatly improve upon our neuroimaging processing pipelines and has reduced the time required by half. In 2017 we processed the baseline neuroimaging data and we expect a number of papers reporting on these findings to be published in 2019. In 2018 we processed more than 200 MRI scans that are part of the 1 year and 2 year follow-up aspects of the study. The longitudinal data will be analysed and submitted for publication in 2019. The Schizophrenia Research Unit has been working with the CHPC for a number of years and with each passing year we have seen improvements in the resources provided by the CHPC and in our ability to utilise these resources more efficiently. We look forward to many more years of collaboration.
Principal Investigator: Dr David Pearton
Institution Name: Oceanographic Research Institute (ORI)
Active Member Count: 4
Allocation Start: 2018-08-29
Allocation End: 2019-02-25
Used Hours: 3866
Project Name: Responses of South African Coral Reefs to Climate Change
Project Shortname: CBBI1072
Discipline Name: Environmental Sciences
The Coral reef team at ORI is using cutting edge techniques to study and protect the precious coral reefs on South Africa's east coast. These unique ecosystems are of great economic and social importance but are under threat from local and global stressors including pollution and climate change. We are using the CHPC to build complex 3D modles of the reefs in order to monitor changes and explore the relationship between the underlying structure of the reef and the organisms that inhabit it. We are employing cutting edge genetic techniques that allow us to determine in detail the responses of corals to climate change and to explore population connectivity and the effectiveness of Marine Protected Areas.
Principal Investigator: Dr Parvesh Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 8
Allocation Start: 2018-08-29
Allocation End: 2019-02-25
Used Hours: 17519
Project Name: Molecular dynamics and docking studies of organic compounds
Project Shortname: CHEM0795
Discipline Name: Chemistry
My research group at UKZN is using CHPC computer facilities to investigate drug-protein interactions and optimization of organic scaffolds and their metal complexes. Our aim is to search potential drug molecules with potent activity against bacterial, diabetes and cancer infections. The CHPC computing facility has proven to be very useful to collect very useful information within a shorter period of time. Running these jobs on normal computers either would have taken months to finish or would die in middle. With this supercomputing facility in our hand, we not only managed to run complex calculations but obtained constructive scientific explanations for our experimental results. Consequently, we managed to this compiled data in reputed chemistry journals. Moreover, my post graduate students has learnt different computational tools that are being used in drug design and drug discovery field. I am highly grateful to chpc for providing us this wonderful facility.
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 0
Allocation Start: 2018-08-31
Allocation End: 2019-03-08
Used Hours: 4733059
Project Name: Structural, electronic, magnetic properties and anisotropy energy in some metallic and non-metallic heterostructures
Project Shortname: MATS0988
Discipline Name: Material Science
The focus of the research is on the design and simulations of materials having novel electronic, optical, transport and magnetic properties with potential applications in high-capacity data storage, catalysis and renewable energy. We employ density-functional theory (DFT) to probe atomic level properties of nanomaterials of interest, ranging from metallic heterostructures, metallic-oxide on surfaces, organic molecules on surfaces, rare-earth transition-metal compounds, and two-dimensional (2D) materials such as graphene and silicene, among others. The last two decade have witnessed the discovery of several 2D materials, and have opened new possibilities to further miniaturization of existing electronic and magnetic devices. Therefore, fundamental understanding of properties of these materials systems is necessary to support experimental research and to aid technological applications. The numerical implementation of DFT is computationally intensive, requiring several computational hours, large data storage and memory requirements, beyond the capacity of ordinary table top computers.. Therefore, high-capacity computer clusters such as the one provided by the Center for High Performance Computing (CHPC) is sine qua non to the research. The research which is ongoing, involves Dr. Abdulrafiu Raji of the University of South Africa (UNISA) and Dr. Malonda Boungou of Marien Ngouabi University, Republic of Congo. Nine postgraduate students are involved in various aspects of the work. At the moment, two Masters students have completed their studies and are continuing to doctorate. The research, as well as the CHPC, has enabled collaboration between South Africa based academic and colleagues in Congo, Mexico and Italy. A research paper [i.e. B. R. Malonda-Boungou, S. Meza-Aguilar, A. Debernardi and A. T. Raji, Computational Condensed Matter, 19, e00368 (2019)] have just been published, while others manuscripts are at various stages of completion.
Principal Investigator: Prof Mario Santos
Institution Name: University of Western Cape
Active Member Count: 17
Allocation Start: 2018-08-31
Allocation End: 2019-02-27
Used Hours: 566691
Project Name: Cosmology with Radio Telescopes
Project Shortname: ASTR0945
Discipline Name: Astrophysics
The Centre for Radio Cosmology (CRC) at UWC aims to fully explore the use of the next generation of radio telescopes for measurements in cosmology, in particular with MeerKAT and SKA. CRC staff is closely involved in the South African and international SKA projects. About 10 postdoctoral researchers and 10 PhD/MSc students are doing their research within the CRC. Our work at the CHPC is mostly focused on running simulations of signals we expect to observe with MeerKAT/SKA and test how well radio telescopes can constrain certain cosmological models. This is a crucial component in the process to use these telescopes for cosmology since we need to understand the signals we are observing. The project include simulations of the hydrogen emission from the early universe, simulations of the contaminants, simulations of the telescope itself and analysis of the constraining power of such telescopes on cosmological models.
Principal Investigator: Dr Jaco Badenhorst
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 4
Allocation Start: 2018-09-04
Allocation End: 2019-03-03
Used Hours: 44482
Project Name: Automatic transcription of broadcast data
Project Shortname: CSIR0978
Discipline Name: Other
The Human Language Technology (HLT) Research Group at the CSIR Meraka Institute develop speech and language-related technologies for the South African context to enhance access to information and communication. Given the multilingual nature of South Africa, HLTs can make information and services accessible to a larger proportion of the South African population in a sustainable way, by reaching people in remote locations, people who are not necessarily trained in using technology, or people who are not fluent in English. HLTs can also provide access to information to people with disabilities. HLT can support language diversity and providing of information in multiple languages in an affordable and equitable fashion. The development of all 11 official languages is a national priority, which requires significant attention to HLT in all of these languages. HLT can be of significant economic importance – both by empowering citizens of the country to work more productively, and by forming the core of an exportable set of technologies (since such technologies are currently not available to most of the developing world). The HLT Research Group operates in a vibrant environment consisting of researchers, developers, project managers and students from backgrounds as diverse as engineering, linguistics and sociology. We conduct basic and applied research into projects related to the following areas of research: automatic speech recognition, text-to-speech synthesis, natural language processing, machine translation, human language analytics, text and speech resource development, speech and language technology system design and implementation, and usability and user experience evaluation of speech and language technology.
Principal Investigator: Mr Muaaz Bhamjee
Institution Name: University of Johannesburg
Active Member Count: 3
Allocation Start: 2018-09-05
Allocation End: 2019-03-04
Used Hours: 73674
Project Name: Modelling of Multiphase Flow in Process Equipment
Project Shortname: MECH0837
Discipline Name: Computational Mechanics
The research group is from the Department of Mechanical Engineering Science at the University of Johannesburg. The primary area of interest in the research is the use of coupled computational fluid dynamics and computational granular dynamics models to investigate the complex multiphase interaction in process equipment. The models are
based on multiple continuum and meso-scopic based approaches which are couple with models such as the Discrete Element Method, Immersed Boundary Method and Eulerian Dense Discrete Phase Models. Both commercial and open-source software has been used in the research. Primarily the research has been focused on
hydrocyclones. However, the research is moving onto fluidised beds, spiral concentrators, highly concentrated slurry flows and gas cyclones. The models are benchmarked accuracy) against experimental measurements as well as for computational efficiency. Accurate and computationally efficient modelling of such phenomena is vital to the design of hydrocyclones which is crucial to the mining industry. The research group has produced numerous publications and has supported the research of four post-graduate students. Research into the computational efficiency of the models is continuing with the aid of the Centre for High Performance Computing (CHPC) facilities. Due to the complex physics and fidelity required in the problems tackled by the research group large computational resources are required. The CHPC provides a computational platform that is vital to the ongoing work and success of the research group.
Principal Investigator: Dr Adeniyi ogunlaja
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 3
Allocation Start: 2018-09-12
Allocation End: 2019-03-11
Used Hours: 1013
Project Name: Chemistry and Material Science
Project Shortname: MATS1070
Discipline Name: Chemistry
Dr Adeniyi Ogunlaja (Research group -Analytical/Inorganic) at Nelson Mandela University.
Project description: The combustion of nitrogen compounds in fuel remains a serious challenge due to its negative impact on public health and environments. Herein, an effective pyridine imprinted polymer (poly aniline-co-DVB) was developed for the selective adsorption of pyridine, a basic nitrogen compound in fuels. The imprinted poly aniline-co-DVB was synthesized via the crosslinked polymerization of vinyl aniline and divinylbenzene in the presence of pyridine. Poly aniline-co-DVB worked as an adsorbent because of the electronic properties and hydrogen bonding interaction it offered. The adsorption performance of the imprinted poly aniline-co-DVB was determined. The synthesised imprinted poly aniline-co-DVB can be successfully applied for the removal of pyridine (30.2 mg/g) in model fuel. This work provides practical application for the removal of pyridine, a nitrogen compound in fuel. The use of DFT study assisted with the design of the material responsible for the selective removal of pyridine as the possibility of hydrogen bonding between adsorbent and analyte was determined via DFT calculations (article has been submitted and it is under review).
CHPC provides the platform and software to carry out basic calculations such as optimization of equilibrium structures, NBO, hydrogen–bonding energy, and HOMO-LUMO calculations.
We are currently making use of computational tools offered by CHPC in most of our study during material design. These studies are progressing well.
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 1
Allocation Start: 2018-09-14
Allocation End: 2019-03-13
Used Hours: 323957
Project Name: Magnetocaloric effect in selected metallic nanoclusters on two-dimensional (2D) substrates, and in selected rare-earths.
Project Shortname: MATS1156
Discipline Name: Material Science
The principal investigator in the research programme is Dr. Abdulrafiu Tunde Raji, of the College of Graduate Studies of the University of South Africa (UNISA). The project investigate magnetocaloric effect (MCE) in metallic nanostructures deposited on various two-dimensional (2D) substrates, such as graphene, silicene, and transition-metal dichalcogenides. Magnetocaloric effect is a property of magnetic materials which could be exploited for refrigeration purposes. The conventional refrigerator system is based on often environmentally unfriendly compression and evaporation of gas. However, magnetic refrigeration systems is based on magnetising and demagnetising a magnetic material. Compared to conventional refrigeration system, magnetic refrigeration is an energy efficient and environmentally friendly technology with the following advantages: the operation of magnetic refrigeration does not involve the use of hazardous chemicals, greenhouse gases, or similar ozone-depleting chemicals; magnetic refrigeration is more efficient when compared with the conventional refrigerator system; magnetic refrigeration is less noisy and less bulky and can be built in more compact form. Furthermore, the phenomenon of magnetic refrigeration has potential for specialized applications as ultrathin refrigerating and air-conditioning system, as well as in cooling nanoelectronic devices, including any system where nanoscale cooling is envisaged. These possible applications motivate this research, that is, to characterize nanocomposite consisting of nanocluster of metallic and intermetallic atoms on 2D materials substrates, for the magnetocaloric effect. 2D material, such as graphene, for example, has good mechanical stability and thus can serves as substrate on which the nanocluster can be deposited.
The research programme is computational and it employs density functional theory (DFT) as the computational method. Performing DFT calculations requires high speed computing and high-capacity data storage resources, i.e. supercomputing systems, which the CHPC provides. The continuous availability of CHPC computing resources is absolutely necessary for the research.
Principal Investigator: Dr Michelle Gordon
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2018-08-29
Allocation End: 2019-04-04
Used Hours: 224637
Project Name: Structural Implications of Mutations in HIV-1
Project Shortname: CBBI0928
Discipline Name: Bioinformatics
Our research group is based at the Nelson R Mandela Medical School at the University of KwaZulu-Natal and focusses on the effects of mutations that cause antiretroviral drug resistance on the structure of HIV-1 proteins. The drugs that patients take as part of their treatment against HIV-1 can stop working because the virus is always changing (mutating). We are looking at how these mutations also change the structure of the virus. To do this, we make a structural model of the affected viral protein using specialised software that uses a lot of computational power. By using the CHPC, I am able to access their high powered server, as well as the software for performing the molecular modelling, mainly the AMBER software suite. With the information gained from this analysis, we can design new drugs that can work against these mutated viruses and improve patient management. The project is ongoing with 2 PhD students currently using the CHPC and a further 3 PhD students to access the service in the next few months.
Principal Investigator: Prof Josua Meyer
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2018-09-17
Allocation End: 2019-03-16
Used Hours: 211894
Project Name: Fundamentals of forced and mixed convection in heat exchangers
Project Shortname: MECH1094
Discipline Name: Computational Mechanics
In-tube condensation is widely seen in many industries such as desalination, power plants and air conditioning. Thoroughly understanding of the condensation phenomenon would lead to better design of the systems which consequently causes the improvement of system efficiency. Although in majority of applications the circular tubes are used, there are some particular cases, like in air-cooled steam condensers, in which non-circular tubes such as rectangular tubes and flattened tubes are utilized. It has been proved that the thermal efficiency of such tubes are better as compared to the conventional circular tubes under specific operating conditions.
This work is being done by the Clean Energy Research Group (CERG) at the University of Pretoria. This group is involved in experimental and numerical heat transfer research focused on clean energy applications. CERG, falling under the Department of Mechanical and Aeronautical Engineering at the University of Pretoria, has a number of world class experimental facilities focused on heat transfer, balanced by a Computational Fluid Dynamics (CFD) division. The Group members have developed, designed and built five unique, state of-the-art experimental set-ups, which are being used for leading-edge heat transfer research.
Due to lack of water resources in South Africa, the research works on the optimizing and performance enhancement of systems working with water as the working fluid should be greatly developed. Such activities will definitely lead to lower energy and water consumptions within the country in the future.
It is the purpose of this research work to numerically investigate the effect of inclination on condensation of steam inside a long flattened channel. Thoroughly understanding of this problem via numerical simulations would assist in proper design of ACCs with low cost and time compared to experimentations.
At the moment, some research paper is going to be prepared.
Principal Investigator: Dr Linke Potgieter
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2018-09-17
Allocation End: 2019-09-11
Used Hours: 6918
Project Name: Decision support for integrated pest management
Project Shortname: CSCI1155
Discipline Name: Applied and Computational Mathematics
In our research group, Surgor, at Stellenbosch University, one of our research focus areas include agro-ecological modelling and simulation for decision support in integrated pest management. In this project, we investigated the concept of refuge areas in crops expressing genes from the bacterium Bacillus Thuringiensis (Bt). These crops produce a protein toxic to members of the order Lepidoptera and is a popular alternative to sprayed insecticides. Although these Bt crops are considered to be an effective pest control method, reckless usage adds environmental pressure on the pest population to develop resistance to the toxin over time. One method of limiting the rate of resistance development is to keep small portions of the cultivated land planted with the non-GMO crop which then acts as a refuge area for the pest, limiting its exposure to the toxin and removing the pressure to develop resistance. Strains of Bt sugarcane for the South African market that should limit the damage caused by the stalk borer moth, Eldana Saccharina Walker are being developed, and a prerequisite to releasing such a product is a recommendation on the size and layout of the refuge areas to be planted, as an area too small may not curb the rate of resistance development enough, but an area too large may not be economically viable for the end user. A simulation-based model was developed to test the effect of differently sized and shaped refuge areas. Individual moths are modelled as agents on an underlying sugarcane field. The model is computationally expensive, however, to reduce the complexity of the model, the field is divided into a series of smaller cells that can interact with each other, which allows us to model the impact of a severe infestation on an area the size of an average sugarcane farm, particularly when running several simulation runs in parallel on a cluster. The project is nearly finished, and a journal article is expected during 2020. Another aspect of the project that is still to be completed is the inclusion of sterile insect releases with Bt sugarcane. We will commence with this part of the project towards the end of 2019.
Principal Investigator: Prof Daniel Joubert
Institution Name: University of the Witwatersrand
Active Member Count: 19
Allocation Start: 2018-09-18
Allocation End: 2019-03-17
Used Hours: 6117630
Project Name: Energy Materials: Numerical explorations
Project Shortname: MATS0800
Discipline Name: Physics
Imagine designing a material atom by atom. Imagine analysing the properties of tomorrow's novel materials
before they exist. Computational materials science plays an important role at every of level of the design
and engineering of new materials. The rapid advances in computer processing power and memory has
given virtual, fundamental, materials design a boost. The first problem faced in designing a virtual material,
a material that has not yet been made, is to find the stable configurations in which the atoms in the mix will
settle into. The designer must find the configuration of electrons and nuclei, the building blocks of atoms,
which result from the interactions among a number of particles that, even for a small piece of material,
exceeds the number of particles of sand on all the beaches in the world. This daunting task has a simple
solution. Instead of finding the configuration of the real material, the problem is solved for a fictitious
material where the constituent particles do not interact. All that is necessary is to find the particle density
distribution of the fictitious material, which by design, is the same as that of the real material. A Noble prize
was awarded for this idea to the chemists Walter Kohn and John Pople in 1998.
A group of postgraduate students at the University of the Witwatersrand use the computer power at the
national Centre for High Performance Computing to conduct virtual experiments on existing and novel
materials to examine their potential as energy harvesters. They examine the potential of a selection of
materials that can be used as cheap components in solar cells, materials that can generate electricity from
waste heat and materials that can be used to split water molecules to extract hydrogen for energy
production.
Principal Investigator: Prof Martin Hill
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2018-09-20
Allocation End: 2019-03-19
Used Hours: 360353
Project Name: Biological Control
Project Shortname: CBBI1076
Discipline Name: Environmental Sciences
The Centre for Biological Control mainly focuses on the biological control of invasive weeds and significant crop pests. This project, however, is a study of the systematics of the Hymenopteran family Chalcididae in the Afrotropical region. This study forms part of a greater study by the CBGP in Montpellier, France, on the world phylogeny of the family. The work is a combination of morphological and genetic work and all analyses on the genetics of this family has been done using the computational abilities of the CHPC. The project is in its final year.
Principal Investigator: Prof Alexander Quandt
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2018-09-21
Allocation End: 2019-03-20
Used Hours: 313362
Project Name: First principles simulations of renewable energy devices
Project Shortname: MATS0882
Discipline Name: Material Science
We are a computational materials science group in the School of Physics at Wits University with a special research focus on renewable energy devices, as well as on the study of fundamental light-matter interactions. We collaborate with a number of experimental groups in Physics, Chemistry and Engineering, and the goal of these collaborations is to develop novel types of batteries, supercapacitors and solar cells.
We currently use CHPC facilities to study the formation and the physical/chemical properties of electrostatic double layers at the electrode surfaces in batteries and supercapacitors. To this end we use ab initio methods based on density functional theory, rather than molecular dynamics simulations. Ab initio methods are a very resource intensive numerical approach, which has not been studied very much in the literature up to now. But by simulating some of the fundamental electrochemical processes at the electrodes on an atomistic level without any adjustable parameters, we hope that we will get a much better understanding of important electrochemical concepts like capacitance and pseudo-capacitance. Such knowledge is crucial for the improvement of commercially available batteries and supercapacitors, and for the development of novel types of electrochemical storage systems.
Recently we have extended our studies to reverse osmosis processes, where we simulate the passage of water through porous graphite oxide membranes, and develop a multi-scale model to predict realistic volumetric flows.
Principal Investigator: Dr Samuel Iwarere
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2018-09-25
Allocation End: 2019-03-24
Used Hours: 6212
Project Name: Understanding Plasma-Liquid Interaction
Project Shortname: MECH1107
Discipline Name: Chemical Engineering
The research is being carried out under the guidance of the Thermodynamics Research Unit based in the School of Chemical Engineering at the University of KwaZulu-Natal. The understanding of plasma-liquid interactions is of prime importance in the context of environmental remediation and wastewater treatment applications. Plasma treatment of wastewater involves complex chemical and physical phenomena, which makes the comprehensive modelling of phenomena such as gas phase reaction, turbulence and heat transfer a difficult task. In order to gain insight into the complex processes associated with the use of plasma wastewater treatment, Computational Fluid Dynamics (CFD) will be used to study the relevant chemistry and fluid dynamic effects at the plasma-liquid interface. The Centre for High Performance Computing (CHPC) allows for calculation within realistic time frames, allowing the researchers to determine the accuracy of the unsteady state simulations encountered in plasma physics. Simulation of the plasma arc is in the early stages with problems being encountered with the definition of the electromagnetism.
Principal Investigator: Prof Eric K. K. Abavare
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 3
Allocation Start: 2018-09-26
Allocation End: 2019-03-25
Used Hours: 202741
Project Name: Atomic and Electronic structures of semiconductor interface systems
Project Shortname: MATS1159
Discipline Name: Physics
We belong to the Frontier Science Group (FSG) in the Department of Physics, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana. We investigate atomistic and electronic properties of light materials using quantum mechanical approach based on first principles calculations in the framework of density functional theory.
Our researches basically focus on the study of interface materials. All electronic devices and related components in atomic level are interfaced. We study these interfacial morphologies and how they affect the overall performance of device applications.
Experimentally, several important semiconductor materials are growth based, as a consequence complete understanding of how these growth are achieved are certainly important for device design and application.
Specifically, our interested lies with interface of silicon carbide (SiC) growth on silicon (Si) and similarly gallium nitride (GaN) on silicon for power electronic materials. These materials are important for power applications and especially crucial in hostile environment. Nevertheless, they exist in small crystal sizes and to obtain large size for device application, researchers are employing all techniques to grow them on silicon since silicon technology is well established and could be easily integrated. The key issue, which troubles the perfect layer-by-layer matching growth, is the lattice mismatch existing between the materials themselves with silicon.
By careful special crystal orientation, the materials involves above could be made to match and perfect growth achieved, which means large crystal sizes could be formed. However, the matching mechanism is not well understood and this needs computational approaches for clarification and here CHPC comes to fore in this search. The CHPC is an indispensable tool to help our group pushes the frontiers of this area for mankind in our quest for the pursuit of scientific achievement and better life through technology.
So far, our initial preliminary investigation of SiC/Si interfaces is promising…
Principal Investigator: Prof Jeanet Conradie
Institution Name: University of the Free State
Active Member Count: 3
Allocation Start: 2018-09-26
Allocation End: 2019-03-25
Used Hours: 1078199
Project Name: Computational chemistry of transition metal complexes
Project Shortname: CHEM0947
Discipline Name: Chemistry
Computational chemistry calculations metal ions containing six water molecules, namely hexaaquachromium(II), hexaaquacopper(II) and hexaaquanickel(II), explained why all the Ni-O(H2O) bonds are equal in hexaaquanickel(II), but in both hexaaquachromium(II) and hexaaquacopper(II) two of the metal-O(H2O) bonds are either longer (called elongation (z-out) Jahn-Teller distortion) or shorter (called compression (z-in) Jahn-Teller distortion) than the other four metal-O(H2O) bonds. It was calculated and visually shown that the electron density difference between M-O bonds determines type of Jahn-Teller distortion
Principal Investigator: Dr Kevin Lobb
Institution Name: Rhodes University
Active Member Count: 13
Allocation Start: 2018-09-26
Allocation End: 2019-03-25
Used Hours: 355447
Project Name: Computational Mechanistic Chemistry and Drug Discovery
Project Shortname: CHEM0802
Discipline Name: Chemistry
The recent usage of the cluster has been through two postdoctoral students, three doctoral and two masters students.
Use has been revolving around several areas, in particular exploration of cardioprotective agents. After a heart attack, the sudden reoxygenation of tissue may cause further damage, and we are exploring how cyclic peptides may be used to mediate or prevent this damage.
To do this, exploration as to the conformation, or how the cardioprotective agents fold is a difficult problem we deal with.
Other work has explored the neurodegenerative disease Alzheimer's disease, and whether South African derived natural products could be used in its treatment.
Principal Investigator: Prof Beatriz Garcia de la Torre
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2018-09-27
Allocation End: 2019-03-26
Used Hours: 50240
Project Name: Peptide Chemistry
Project Shortname: CHEM1090
Discipline Name: Chemistry
Our research involve study of new peptides, their structure, interactions, properties, electronic requirements and dynamics using ab initio calculations and MD calculations and their applications in drug delivery and study physical properties like magnetism etc. We pursue Green peptide synthesis reactions using Materials Studio.
Principal Investigator: Prof Mwadham Kabanda
Institution Name: University of Venda
Active Member Count: 2
Allocation Start: 2018-09-30
Allocation End: 2019-03-29
Used Hours: 80545
Project Name: Reaction mechanism for atmospheric relevant molecules
Project Shortname: CHEM1161
Discipline Name: Chemistry
The research group consist of Prof MM Kabanda and his MSc student Otukile KP. They are members of the North-West University institution. The research work that they conduct is concerned with the computational study of reaction mechanism for biologically relevant molecules. The molecules that are investigated are polyphenolic in nature with known antioxidant activities. The research is being done as part of MSc project for Ms Otukile KP. It is understood that the results of the research will have positive impact on the understanding of the reaction mechanism for the class of compounds being investigated. The computation of reaction mechanisms involving biologically active molecules requires a significant amount of computational power such that personal computers may not be able to provide significant results within the stipulated time. It is for this reason that the group relies on CHPC. Preliminary results of the study have been presented at an international conference
1. Kgalaletso P. Otukile, Mwadham M. Kabanda. A theoretical study on the reaction of phloroglucinol with •OH. QSCP-XXIII, September 23-29, 2018, Kruger national park area, South Africa
2. Kgalaletso P. Otukile, Liliana Mammino, Mwadham M. Kabanda. A theoretical study on the hydrogen atom transfer mechanism in 2-mercaptobenzothiazole by •OH. QSCP-XXIII, September 23-29, 2018, Kruger national park area, South Africa
The student is in her second year of MSc and is looking forward to utilising CHCP to complete her work this year.
Principal Investigator: Dr Evans Benecha
Institution Name: University of South Africa
Active Member Count: 7
Allocation Start: 2018-09-28
Allocation End: 2019-03-27
Used Hours: 817412
Project Name: Defect engineering in novel 2-D materials
Project Shortname: MATS1025
Discipline Name: Physics
The research programme titled "Defect engineering in novel 2-D materials" focuses on investigation of the
properties of defects in single layered materials - usually one atom thick. The group spearheading this research
is headed Dr Evans Benecha and it consists of senior researchers, postdocs and graduate students from the
University of South Africa. Single atom layered materials possess interesting properties as opposed to many
atom thick materials. For example, graphene – which is a single layer of carbon atoms –enables electrons to flow
much faster than silicon, is the world's strongest material, harder than diamond, yet lightweight and flexible.
This unique combination of superior properties makes graphene a credible material for new technologies in a wide
range of fields. Some of the envisaged applications of this class of single atom layered materials
include making of medical implants, solar cells, stronger sports equipment, and batteries; just to name a few.
However, the properties of these materials are not well understood for these applications to be realized. Dr
Benecha and his group's approach towards understanding these materials involves use of large computational
resources, and therefore access to the CHPC computing facility has significantly reduced the time needed to generate
and analyze data. The results from this project will not only assist in the current understanding of the role of
defects in these materials, but will also help to reveal potential new functionalities.
Principal Investigator: Dr Eric Maluta
Institution Name: University of Venda
Active Member Count: 9
Allocation Start: 2018-09-28
Allocation End: 2019-04-05
Used Hours: 599427
Project Name: Energy Material Modeling in the Application of different Photovoltaic Technologies
Project Shortname: MATS0827
Discipline Name: Physics
The Department of Physics at the University of Venda is working on the simulation of different materials for their application in renewable energy. Currently we are working on the material for application in solar cells. Our main aim is to look on the economical issues of this material with an objective of developing a cost effective solar cell in future. Apart from the development of new technology, we are building capacity of the rural students on the postgraduate studies and skill development. The CHPC is a gateway for the department of Physics of the University of Venda as an institution situated in the rural area to produce researchers and to publish research work. There is a growing number of students research work from honours to the PhD level. Several student will be getting their masters and PhD degree through this initiatives.
Principal Investigator: Dr Abu Abrahams
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 3
Allocation Start: 2018-09-27
Allocation End: 2019-03-26
Used Hours: 559208
Project Name: Synthesis and characterisation of lanthanide complexes with Di-(2-picolyl)amine and its derivatives
Project Shortname: CHEM0844
Discipline Name: Chemistry
No changes from previous submission:
Who: Rare earth coordination chemistry research group of Nelson Mandela University
What and why: The study of chemical and structural properties of the inorganic complexes with rare earth elements in order to identify trends in reactivity and identify potential applications in the fields of catalysis, medicine (diagnostic, anti-bacterial) and luminescence. Specifically complexes of rare earth elements with the ligand bis(2-pyridylmethyl)amine are being investigated due to this class of complexes displaying applications in the fields of catalysis, nuclear waste processing and medicine (solution structure elucidation). Increased utilisation of rare earth elements could also support the local economy, since rare earth elements may also be mined in South Africa.
How: The CHPC provides access to advanced computational resources which allows for the extraction of information from modelled systems of novel compounds, which may allow for the prediction of experimentally-determined properties. The latter process of physical experimentation are often time-consuming and expensive, whereas computational modelling may be performed on multiple systems simultaneously and may provide information of sufficient accuracy to inform the user of the most beneficial course of action to take when performing any physical experiments. In addition, modelling may also provide answers to fundamental questions which we may not yet be able to observe physically. In addition, advanced computational chemistry software packages (such as Gaussian 9/16 and ORCA) allow users with limited knowledge theoretical physics and computer programming to find answers to their chemical problems.
The experimental structures and composition of several monomeric- and dimeric- complexes containing the rare earth elements: Y, La, Nd, Dy, Ho and Lu, and preliminary geometry optimisations are well on their way to completion. An incremental refinement strategy implementing larger basis sets has proven feasible and will be carried out next.
Principal Investigator: Prof Richard Tia
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 21
Allocation Start: 2018-10-03
Allocation End: 2019-04-01
Used Hours: 710269
Project Name: Computational Chemistry and Materials Science
Project Shortname: CHEM1044
Discipline Name: Chemistry
We have not yet obtained results that can form the basis of a press release but with the progress made in the our work, especially the work pertaining to the conversion and utilization of carbon dioxide, it should be possible to make a press release in the near future. With increasing interest of the scientific community and government agencies on the mitigation of rising carbon dioxide levels and the attractiveness of using carbon dioxide as a feed-stock for industrial processes, this work might be very suitable for a press release as and when we get interesting results.
Our research activities fall under two broad areas, namely;
1. Molecular modeling - Exploring the mechanisms of organic, inorganic and organometallic reactions.
These studies afford important molecular-level mechanistic details of industrially-relevant chemical reactions that are difficult, if not impossible, to obtain experimentally. Molecular level understanding enable chemical reactions to be guided quickly and efficiently along desirable pathways, with the effect of producing the right product with minimal energy consumption and minimal environmental impact. A key aspect of this work is the development of homogeneous transition metal catalysts for the depolymerization of lignin, an abundant natural resource, for fuel.
2. Materials modeling
The atomic- and molecular-level mechanistic insight gained from these studies are useful for the design of novel catalysts for the conversion of CO2 and other green-house gases as well as stranded gases from the petroleum refining into useful fuels. This addresses the problem of global warming as well as providing an environmentally friendly alternative sources of fuel.
The research objectives described here are very computationally-demanding and using the CHPC resources is highly beneficial. Without that, we would not be able to carry out some of these calculations.
Principal Investigator: Mr Adebayo Azeez Adeniyi
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2018-10-03
Allocation End: 2019-04-01
Used Hours: 681099
Project Name: Drug Discovery Research Using Quantum and Molecular Dynamic Simulation
Project Shortname: CHEM0958
Discipline Name: Chemistry
This research group is identified as "Drug Discovery Research Using Quantum and Molecular Dynamic Simulation". We are making use of quantum software like Gaussian and Games and also molecular dynamic packages like Amber. We have applied quantum packages to study the chemical and spectroscopic properties of small molecules of which we have been able to reproduced some of the experimental results.
We have also been focusing on designing anticholesterase drugs that have the potential of addressing the problem of Alzheimer's disease (AD) which is known to be the major cause of dementia among the elderly.
We have made some significant progress in this research using CHPC facilities which has resulted into three research articles published in peer review journals and one oral presentation at international conference.
Without the CHPC facilities, it would be very difficult to make such kind of progress in application of computer codes to study catalogs of small compound and big molecules like protein.
Principal Investigator: Dr Rose Modiba
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 5
Allocation Start: 2018-10-03
Allocation End: 2019-04-01
Used Hours: 120755
Project Name: Computational modelling of light metals
Project Shortname: MATS1097
Discipline Name: Material Science
Light metal computational research group at CSIR lead by Dr R Modiba used the CHCP facilities to do the computational investigation of the Ti-based shape memory alloys for aerospace and biomedical applications using the CASTEP code. We determined the stability of our materials and compared with the available experimental results which compared to within 3%. The work was presented at local conferences. The other work is on the Ti surfaces, wherein the interaction of halogens on different surfaces of the bulk Ti was investigated. The CHCP resources help us to do all this calculations within a short period of time. The student who started his PhD in 2018, has made great progress and managed to write two thesis chapters based on the results obtained.
Principal Investigator: Mr Theo Fischer
Institution Name: eScience
Active Member Count: 3
Allocation Start: 2018-10-09
Allocation End: 2019-04-07
Used Hours: 223371
Project Name: Acid Deposition
Project Shortname: ERTH0851
Discipline Name: Earth Sciences
EScience Associates, in funding from the WRC, have been using the CHPC to run the Weather, Research and Forecast model coupled with its Chemistry module to run 50 years of emissions over the highveld to determine the impacts of acid deposition on the Vaal Catchment. The output from this model is run through a seperate hydrological model to determine the impacts.
Principal Investigator: Dr Pedro Monteiro
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 11
Allocation Start: 2018-10-09
Allocation End: 2019-05-16
Used Hours: 9473043
Project Name: Southern Ocean Carbon - Climate Observatory SOCCO
Project Shortname: ERTH0834
Discipline Name: Earth Sciences
SOCCO is a CSIR-led and DST co-funded programme that uses the comparative geographical advantage that South Africa has in the Southern Hemisphere to contribute to the global research challenge of understanding the role of the Southern Ocean in global and regional climate. The SOCCO research niche is to explore the role played by fine scale ocean dynamics in improving the climate sensitivity of ocean and coupled numerical models with a special focus in understanding the Southern Ocean's role in the Carbon - Climate links.
To address the scales of dynamics in the ocean, we primarily use the coupled NEMO-PISCES model in a hierarchy of resolutions from 200km, 100km, 50km 10km and 2 km - using the models as experimental platforms. The finer the resolution, the greater the number processes that contribute to ocean-atmosphere carbon exchange. This understanding contributes to reducing model biases in process models and climate projections as well as the development of the CSIR Variable Resolution Earth Systems Model (VR-ESM).
This work advances research in global climate change based on the importance of feedbacks of the Southern Ocean dynamics on the carbon-climate system. Additionally, VR-ESM will be used to explore how the climate sensitivities of the Southern Ocean evolve over the 21st century as well as being South Africa's first submission to the 6th Assessment Report of the IPCC. VR-ESM will be the basis for the medium to long term climate projections in Africa which will then support societal needs in health, water resource planning, agriculture, biodiversity management and more broadly in economic development in the region.
From regional, forced ocean models to fully-coupled earth system models comprising of interacting ocean, ice, atmosphere, land, ocean biogeochemical models, numerical modelling of earth system components require massively parallel computing resources. The size and complexity of these models are such, that for SOCCO's work, the CHPC is indispensable for the resources and service it provides. Through the resources provided by the CHPC, we have developed a hierarchy of models to use as experimental platforms to answer our research questions and support student theses, developed methodology to address model biases and analyse large model output and furthermore address sampling of the real ocean.
Principal Investigator: Mr Randall Paton
Institution Name: University of the Witwatersrand
Active Member Count: 10
Allocation Start: 2018-10-09
Allocation End: 2019-04-07
Used Hours: 469823
Project Name: Compressible Gas Dynamics
Project Shortname: MECH0847
Discipline Name: Other
The Flow Research Unit group utilising the CHPC is currently exploring the effects of straight-line and general acceleration on various aerodynamic properties through high-performance computing. This research has applications in current technologies, such as missiles and unmanned aerial platforms, as well as in emerging future technologies, such as ramjet optimisation for the return of atmospheric, supersonic, commercial flight. Since the geometries involved are sometimes complex, and the loads experienced as a result of arbitrary acceleration are computationally expensive to compute, it is simply not practically feasible to model most of these systems without high-performance computing. The use of the CHPC is therefore essential to developing young South Africans to be capable to participate and excel in the development of these future technologies. The current research group consists of several Masters and two PhD students from a mixture of ethnic backgrounds and sexes. Each research project is progressing well towards on-time completion, which would be impossible without the incredible time-saving that the use of the CHPC affords the students.
Principal Investigator: Dr Adam Skelton
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2018-10-10
Allocation End: 2019-04-08
Used Hours: 326697
Project Name: Molecular modelling of biomolecules and materials
Project Shortname: CHEM0798
Discipline Name: Chemistry
I am Dr. Adam Skelton and I work at the College of Health Science university of KwaZulu-Natal. I work on understanding the behaviour of biological and material systems on the molecular level. A particlar interest is in using molecular simulation to direct the rationale design of functionalized nanoparticles for a range of applications such as drug delivery, water treatment and catalysis. In particular, drug delivery is the use of nanoparticles to carry antiviral or antibacterial drugs into parts of the body that are difficult for conventional drugs to reach. Drug-delivery is, therefore, of huge importance in South Africa, especially in the battle against HIV and Tubercolosis. The research requires running a series of computar simulations, which may take hours at a time. CHPC has had a great impact since it provides me with the facilities to perform such simulations. Since the project started, my group has published more than 15 papers in international journals and has provided deep insight into biological and material systems on the molecular level.
Principal Investigator: Prof Kevin Naidoo
Institution Name: University of Cape Town
Active Member Count: 8
Allocation Start: 2018-10-10
Allocation End: 2019-04-18
Used Hours: 1498149
Project Name: Reaction Dynamics of Complex Systems
Project Shortname: CHEM0840
Discipline Name: Chemistry
The students supervised by Prof. Kevin J. Naidoo are active in two areas: Informatics research in including 1) machine learning methods development and Bioinformatics analysis and code development and 2) computer simulation methods development and applications to chemical glycobiology. We have developed unsupervised machine learning code capabale of discovering subclassess within a cancer type. The method was shown to be superior to current methods in correctly classifying cancer tissue samples. Our simulation codes have been used to develop breast cancer therapeutics. We are testing these models in our wet laboratories.
Principal Investigator: Prof Eric van Steen
Institution Name: University of Cape Town
Active Member Count: 6
Allocation Start: 2018-10-10
Allocation End: 2019-04-08
Used Hours: 272638
Project Name: Lateral interactions on surfaces
Project Shortname: CHEM0780
Discipline Name: Chemistry
Most chemical processes involve catalysts, which accelerate chemical transformations taking place on the surface of the catalytic active material. Their performance is typically understood in terms of the classical Langmuir adsorption behaviour. An improved understanding of these catalysts can be obtained by including the interactions between the various adsorbed species. Our work aims to incorporate these interactions into models decribing catalysts in e.g. fuel cell applications and the production of synthetic fuels.
Principal Investigator: Prof Abu Yaya
Institution Name: University of Ghana
Active Member Count: 5
Allocation Start: 2018-10-12
Allocation End: 2019-04-19
Used Hours: 725513
Project Name: DFT modeling of weak interactions; a case study for Carbon nanosystems
Project Shortname: MATS0990
Discipline Name: Material Science
This research team is made up of members from the University of Ghana and the University of Agriculture, Abeokuta, Nigeria. The work involves the use of computer models for the understanding of how the human DNA are arrange (known as pi-pi stacking) and also how materials bond together to form stronger materials which are used for building and electronics applications. Without a computer with large memories which are known as clusters, it will not be possible to understand this behaviour. Eventhough this can be done by experiment, this will take years to really understand but with computer models, it will be faster, just days or weeks. Therefore computer modelling is used as a microscope in order to understand the real picture of a situation or problem. Our project tries to understand interactions which play a crucial role in arrangements of DNA, proteins, and the stacking of polymers (plastics) This is important in understanding genetic disorders and other life threatening diseases that are linked to DNA and proteins. Secondly, we are also able to understand how materials mix together to form stronger materials which are used for applications such as aeroplanes, cars, flats screen televisions, mobile phones and buildings or civil structures (High-rise buildings) Thankfully, with the resources available at CHPC, we are able to understand and shed light on these complex interactions that mimic nature.
Principal Investigator: Prof Catharine Esterhuysen
Institution Name: Stellenbosch University
Active Member Count: 11
Allocation Start: 2018-10-10
Allocation End: 2019-04-19
Used Hours: 808381
Project Name: Computational chemistry analysis of intermolecular interactions
Project Shortname: CHEM0789
Discipline Name: Chemistry
The focus of the Computational Supramolecular Chemistry group at Stellenbosch University is on understanding the fundamentally important role that intermolecular interactions play in the properties of solid materials. For instance, molecules are taken up into porous materials as a result of the interactions between these species, while the manner in which they interact has an influence on the sorption ability of the porous material. Calculations performed using the CHPC's computational facility have allowed us to explain the role that intermolecular interactions play in the unusual sorption properties of various porous compounds. We have also been able to establish methodologies for determining the behaviour of radicals and polymorphism in a variety of compounds, including cage compounds. We are slowly moving toward the goal of explaining catalytic and biological processes through understanding the role of intermolecular interactions in the mechanism in order to predict improved catalysts and biologically active compounds.
Principal Investigator: Dr Kiprono Kiptiemoi Korir
Institution Name: Moi University, Eldoret, Kenya
Active Member Count: 3
Allocation Start: 2018-10-11
Allocation End: 2019-04-09
Used Hours: 559581
Project Name: Thermal characterization of MoS2 nanostructures: an ab initio study
Project Shortname: MATS0868
Discipline Name: Material Science
This group draws it's members from Moi University, Computational Material Science Group (CMSG), in addition we have a collaborator Slimane Haffad from University of Beijaia- Algeria. Our research activities focus mainly on nanomaterials for energy and related applications, gas sensing, and CO2 capture and storage. We also work on prediction and characterization of ultra-hard materials.
Since the discovery of nanomaterials in the early 1990, various noble applications of these wonder materials have been demonstrated in various fields. However, the process of development of devices addressing major problems ailing the society, such as, energy and pollution has been rather slow due to existing problem related to scaling and stability amongst others. Therefore, an in depth study of these group of materials is needed to establish better understanding that may lead to development of new principles, characterization techniques and methods, which may lead to breakthroughs in addressing some of the bottle-necks currently associated with nanomaterials.
In this work, graphene and nanomaterials of ZnO and MoS2 are simulated via approaches grounded on principles of quantum and classical mechanics, which have been shown to accurately predict material properties. These predictive approaches requires huge computational effort as it entails solving mathematical formulas, such as Schrödinger and Newtonian equations. For this reason, availability of the state of the art High Performance Computing facility, such as CHPC is a critical component for implementation of this work. Solving Schrödinger and Newtonian equations can yield various properties of interest such as structural, mechanical, electronic and optical properties that are essential for comprehensive characterization of these systems. For example, in our recent work, we have shown that TiO2/ZnO/TiO2 nanofilm configurations yields a superior photocatalytic and photovoltaic system and our input parameters may be of importance to experimentalist. Our work on hardness characterization parameters of NbC and NbN yielded interesting results that may be of great significance in the development of low cost ultra-hard devices.
Principal Investigator: Prof Warren du Plessis
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2018-10-10
Allocation End: 2019-04-08
Used Hours: 239812
Project Name: Electronic Warfare (EW) Technologies
Project Shortname: MECH0989
Discipline Name: Electrical Engineering
Proff. du Plessis and Jacobs of the Department of Electrical, Electronic and Computer Engineering at the University of Pretoria have proposed a method to interpolate radar cross section (RCS) simulations. The proposed approach holds the potential to significantly reduce the number of simulations required to characterise the RCS of a target without compromising the accuracy of the result.
Principal Investigator: Prof Cornie van Sittert
Institution Name: North-West University
Active Member Count: 20
Allocation Start: 2018-10-11
Allocation End: 2019-04-09
Used Hours: 5273656
Project Name: Computational Chemistry within LAMM at NWU (Potchefstroom)
Project Shortname: CHEM0778
Discipline Name: Chemistry
Since the 1880 the main source of energy for South Africa was coal and at present coal provides 77% of South Africa's primary energy needs. However, the electricity comes at a very high cost, namely air pollution and the influence of the air pollution to human health. In 2004 the South African government reformed the legislation with regard to air pollution. In an effort to contribute to the management of air quality new energy sources must be investigated. These new energy sources must be affordable, clean and renewable. Some of these alternative energy sources are fuel cells and batteries. Electricity from fuel cells and batteries are obtainable through the use of electrochemistry, where free energy of spontaneous reactions is transformed into electricity. A potential replacement form of energy is the hybrid sulphur (HyS) cycle. The HyS cycle is a two-step water-splitting process, which could be used for the production of hydrogen. In the HyS cycle, the anode material used is platinum. However, because platinum is a rare and expensive metal, it is not an economical viable option for long term and large scale production of hydrogen. Hence, various attempts to reduce or eliminate the platinum content, while not compromising the process performance has been made. In the order to understand the electrochemistry on the anode and make informed decisions on the type and amount of metal to be used in various platinum alloys, investigations on a fundamental level is needed. These type of investigations could be classified as computational chemistry. The resources needed for these type of investigations, namely various types of hardware and software is of cardinal importance. Although resources are available at NWU, it is not nearly enough to fully support the research covered in the Laboratory of Applied Molecular Modelling (LAMM). So if we as researchers within the LAMM did not have access to the CHPC resources the progress of our research will be much slower.
Principal Investigator: Prof Evans Adei
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 6
Allocation Start: 2018-10-11
Allocation End: 2019-04-09
Used Hours: 546015
Project Name: Materials For Energy and Fine Chemicals
Project Shortname: CHEM1046
Discipline Name: Chemistry
There has not been any development that merits press release in this reporting time.
Principal Investigator: Prof Rebecca Garland
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2018-10-15
Allocation End: 2019-04-13
Used Hours: 109569
Project Name: Simulating atmospheric composition
Project Shortname: ERTH0846
Discipline Name: Earth Sciences
Air pollution can have large negative impacts on human health, agriculture, ecosystems, visibility and climate. In South Africa, although ambient air quality is regulated, many areas are out of compliance with the National Ambient Air Quality Standards. In order to protect human health and mitigate impacts, it is critical to improve air quality. The Constitution provides that everyone has a right to have an environment that is not harmful to their health. The Atmospheric Composition Focus Area (ACFA) in the CSIR Climate Studies, Modelling and Environmental Health Research Group aims to provide the evidence base to quantify the impacts of air quality and to improve air quality. The group uses the CHPC to run an air quality model to simulate urban and regional air quality at high resolution. This chemical transport model simulates the physics and chemistry of the atmosphere. The processes represented within the model are complex, and thus computationally intensive, which makes use of the CHPC facility a necessity. The CSIR ACFA is the only group in South Africa routinely running a chemical transport model to simulate air quality. Using the CHPC resources, the team has been able to simulate the impact of policy interventions on air quality in cities. Additionally, the team has simulated the health risk from air pollution regionally in South Africa. In the past, this has been done using monitoring station data only, which then limits the analysis to only those living directly around the station. The team has also simulated the impact of climate change on air pollution. These simulations use the climate projections for the CSIR's VrESM, which is also run at CHPC, to provide meteorology input into the air quality model. These outputs directly provide the evidence base needed for decision makers to draft and implement policies and interventions to effectively improve air quality as well as understand its impacts, now and into the future.
Principal Investigator: Prof Jaco Dirker
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2018-10-15
Allocation End: 2019-04-13
Used Hours: 253250
Project Name: Heat Transfer Enhancement in Thermal Systems
Project Shortname: MECH1029
Discipline Name: Computational Mechanics
Energy transfer and storage is vital to sustain economic development. In this project, heat energy transfer enhancement is investigated to serve the thermal power industry to enable better usage of renewable energy sources, such as solar energy. It has been found that by making small alterations to the size and geometry of heat storage and transfer components, a significant improvement in their performance can be achieved. With the resources made by the CHPC, it is possible for researchers to discover more optimal operating conditions and geometries.
Principal Investigator: Prof Graham Jackson
Institution Name: University of Cape Town
Active Member Count: 6
Allocation Start: 2018-10-16
Allocation End: 2019-04-14
Used Hours: 2686
Project Name: Insect neuropeptides
Project Shortname: CHEM1101
Discipline Name: Chemistry
The Jackson group in the Department of Chemistry at the University of Cape Town is working on developing new species-specific insecticides. Insect flight is under hormonal control via certain neuropeptides. These bind to receptors which release energy for flight episodes. Using computational techniques the structure of the receptor is being determined and the binding site of the hormone identified. This information is necessary for a search for molecules (insecticides) which will block the receptor and hence prevent insect flight. Currently we are working on the malaria mosquito and the desert locust.
Principal Investigator: Prof Penny Govender
Institution Name: University of Johannesburg
Active Member Count: 15
Allocation Start: 2018-10-16
Allocation End: 2019-04-14
Used Hours: 382562
Project Name: Design of MOFs-based sorbent materials for capturing carbon dioxide
Project Shortname: CHEM0797
Discipline Name: Material Science
Environmental and energy problems are important topics globally due to the fast development of urbanization, huge population increases and industrialization. Recently, water pollution is a major issue in developing countries, particularly in regions where people rely on groundwater for domestic and drinking purposes. Almost 40 % of the world's population is facing water shortage. Most countries depend on the low-efficient power generation from the burning fossil fuels as their source of energy. The burning of fossil fuels normally generates a huge amount of CO2, which induces environmental concerns, such as greenhouse effect. As non-renewable natural resources, fossil fuels cannot be sustainable and depleted shortly in the next century owing to their environmental issues and high consumption rate. This has led to the investigation of photocatalysis as a possible solution to the problem. Despite significant concern and substantial efforts, the design of semiconductor photocatalyst materials that is both efficient and robust enough for water/wastewater treatment and energy production is still lacking. Due to the complexity of the experimental process, it is difficult to know the mechanism and origin of the enhanced photocatalytic performance. The first-principles approach is highly desirable in the area of materials science, particularly for understanding both the photocatalysis of nanomaterials, as well as the subsequent physical and chemical properties. Density functional theory (DFT) calculations was used as the method of clarification as it has already proven its superiority in studying the structural stabilities, electronic properties, work functions, charge transfer, and carrier effective mass of several semiconductor photocatalyst materials due to its reduced computational cost in calculating the electron density rather than the wave function.
Principal Investigator: Prof George Amolo
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 11
Allocation Start: 2018-10-16
Allocation End: 2019-04-14
Used Hours: 941174
Project Name: Properties of Materials for Green Energy Harnessing
Project Shortname: MATS862
Discipline Name: Material Science
MATS862 is Kenyan group whose PI is based in Nairobi but with members from all over Kenya and one member from Congo Brazzaville. MATS862 continues with research work aimed at addressing fundamental studies on focus areas that represent the most basic need of our country, in this case energy materials. This need is not only limited to Kenya but the developing world at large. Our work focuses on fundamental studies of materials that play a role in conversion of energy into applicable use. These involves, thermoelectric, hydrogen, solar energy materials and photocatalysts. Involvement in this research work develops human technical capacity to study existing properties of materials in current use to gain knowledge and skills to handle novel materials that promise higher efficiency or are environmentally friendly. The work is carried out by the state-of-the-art computer simulations but with support from experimental collaborations.
There is continual progress based on peer reviewed publications and student graduation to higher levels.
We are now going into partnership with the applied sciences who are leaning towards 3D printing of fabricated materials and possible devices. This can be seen in the latest call by the Kenya Education Network (KENET) with whom I work as a research associate in computational modeling and materials science (see attached copy of November 2018). There is also general move towards environmental protections and health applications, the latter being linked to the transition towards adoption of cleaner forms of energy sources. The inclusion of these latest aspects address the big 4 agenda fronted by the national government of Kenya as being health and the environment, manufacturing, housing and food security
MATS862 members greatly appreciate the provision of these computational resources of our research work and is thankful to the CHPC as well as the government of the Republic of South Africa.
Principal Investigator: Dr Jenny-Lee Panayides
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 5
Allocation Start: 2018-10-17
Allocation End: 2019-04-23
Used Hours: 105538
Project Name: Lead Discovery & Process Development Programme
Project Shortname: CHEM0934
Discipline Name: Chemistry
Alzheimer's disease is the most common form of dementia. To date, there is no cure for the disease and only symptomatic treatments are available. Using in silico computational and in vitro biological screening techniques, a team from CSIR Biosciences and the University of Pretoria are currently testing thousands of compounds to identify new pharmacophores for development into drugs for the treatment of Alzheimer's disease.
Using the computational resources provided by the CHPC, very large numbers of compounds can be tested with greater accuracy than what is possible with standard computational hardware. Hit compounds identified through this screening effort will be optimised using computer-aided drug design, to improve their effectiveness against a particular target within the human body prior to the expensive and time-consuming synthesis of the compounds for advanced biological screening. During this optimisation process, many aspects will be considered, including the ability of the human body to absorb the compound and possible toxic side-effects. Thus, utilisation of the CHPC resources can potentially accelerate drug development in a significantly more cost-effective manner.
Principal Investigator: Dr Lynndle Square
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2018-10-18
Allocation End: 2019-04-16
Used Hours: 4443
Project Name: Exploring poly(2,5)benzimidazole enhanced with carbon nanotubes for space applications
Project Shortname: MATS1088
Discipline Name: Physics
Thin film or particle growth in Chemical Vapour Deposition (CVD) processes involve the decomposition of gas molecules into reactive species. At the physics department at the University of the Western Cape two techniques for breaking down the starting gases are explored, the traditional CVD process and Plasma-Enhanced Chemical Vapour Deposition (PECVD). These are inherently complex processes and a multidisciplinary approach has been necessary in their study and development. The material modelling component of this project strategically focuses on the degradation of hybrid halide perovskites under the influence of environmental factors. First principle calculations will be used to model the instability of perovskites. The CHPC affords users the opportunity to participate in the multi-disciplinary material modelling category by providing a national license which otherwise would not be affordable to new and up and coming participants in the field. HPC also provides the parallelization process capacity required to investigate these huge and complex calculations. This work would not be possible without these resources.
Principal Investigator: Dr Pieter Levecque
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2018-10-18
Allocation End: 2019-04-30
Used Hours: 135892
Project Name: Non carbon supports for electrocatalyts
Project Shortname: MATS1108
Discipline Name: Material Science
The HySA/Catalysis Centre of Competence in the Department of Chemical Engineering at the University of Cape Town conducts research into new catalysts and components for fuel cells and electrolysers. One main focus is new support materials for catalysts for fuel cells.
MAX phases are a new class of materials that can at the same time show properties of ceramics and metals. This means materials can be prepared that show strong corrosion resistance as well as high conductivity which is the properties needed for a good fuel cell catalyst. The purpose of this study is to find a suitable model for MAX phases and their properties so that we can rapidly screen potential compositions and thereby targeting the lab-based preparation as described above. CHPC facilities help us to do the modelling thereby saving significant lab time and expensive chemicals
Principal Investigator: Prof Gerhard Venter
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2018-10-18
Allocation End: 2019-04-16
Used Hours: 306966
Project Name: Finite Element Analysis and Numerical Design Optimization
Project Shortname: MECH0883
Discipline Name: Computational Mechanics
The Materials, Optimization and Design (MOD) research group is a part of the Department of Mechanical and Mechatronic Engineering Faculty at Stellenbosch University. The research group's members work on a diverse group of projects related to structural analysis and optimization. The fields covered by the group are Finite element analysis, Computational fluid dynamics, numerical design optimization, material characterization for numerical modelling purposes and meta-modelling, etc.
Projects have dealt with or are dealing with:
• inflatable structures (inflatable wings, dunnage bags, etc.)
• morphing wings/hydrofoils
• soft robotics
• large radio astronomy antennas
• artificial heart valves
• composites
• vertical axis wind turbines
• particle swarm optimization
• railway bogies
• mining truck tires
• material testing methods
• high-pressure water supply lines
• heat exchanger header boxes for industrial heat exchangers, etc.
The primary goal of the group is to produce or facilitate advanced engineering design.
Principal Investigator: Dr Quinn Reynolds
Institution Name: Mintek
Active Member Count: 2
Allocation Start: 2018-10-18
Allocation End: 2019-04-16
Used Hours: 7025
Project Name: Computational Modelling of Furnace Phenomena
Project Shortname: MINTEK776
Discipline Name: Applied and Computational Mathematics
The Pyrometallurgy Division at Mintek engages in research, development, and technology transfer in the field of high-temperature metallurgical processing. This supports the beneficiation value chain for South Africa's extensive mineral resources.
In pyrometallurgy, furnaces are used to heat and melt rocky raw materials to temperatures in excess of 1500 degrees Celsius. Once in the molten state, the chemical reactions necessary to extract the valuable metal and mineral products they contain can be performed. The design and operation of such furnaces is an engineering grand challenge, and is greatly improved by the building of fundamental and applied knowledge of their behaviour using large computational models. Mintek's collaboration with the Centre for High Performance Computing continues to be invaluable in helping us push the envelope in pyrometallurgical process modelling.
Development achievements in the past six months have included extensive testing of computational combustion models at massively-parallel scale; this enables more realistic simulation of gas-fired pyrometallurgical processes to optimise their efficiency and limit their environmental impact. In addition, new modelling methods for phase separation problems were developed to bridge the gap between micro- and macro-scale phenomena - it is expected that such models will have great utility in virtual prototyping of furnace product handling processes.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2018-10-19
Allocation End: 2019-04-17
Used Hours: 107469
Project Name: CFD Modelling of Concentrated Solar Power Applications
Project Shortname: MECH0873
Discipline Name: Computational Mechanics
Central tower solar power plants are the most promising concentrated solar with research into new receivers and heat transfer fluids and collectors (heliostats) being ongoing world-wide. Researchers at the University of Pretoria's Clean Energy Research group under the leadership of Prof Ken Craig are using the resources at the CHPC to speed up calculations of both heliostat analysis (involving wind loads and fluid-structure interaction) as well as those required for a new point-focus central receiver design being developed. For heliostats, knowledge has been gained in predicting the peak loads that these reflectors will experience during all orientations and wind conditions. Ongoing work is focused on further reducing the cost of these Computational Fluid Dynamics (CFD) hybrid Large Eddy Simulation (LES):Reynolds-Averaged Navier-Stokes models to make them feasible on smaller-scale computers. This project has been ongoing since 2013 with the involvement of CHPC resources since 2016. The project has already delivered two masters students (Dawie Marais and Joshua Wolmarans). PhD student Pierre Poulain is nearing the end of this investigation into LES modelling of the atmospheric boundary layer. For central receivers, work is ongoing to enhance heat transfer, performed by Prof Ken Craig and new masters student Jesse Quick. Of specific interest here is the use of jet impingement, especially in the transient mode through either passive or active excitation. This phenomenon of heat transfer enhancement, although conceptually simple, it very hard to model accurately, and here the resources of the CHPC are invaluable.
Principal Investigator: Dr Farai Muchadeyi
Institution Name: Agricultural Research Council
Active Member Count: 4
Allocation Start: 2018-10-23
Allocation End: 2019-07-10
Used Hours: 7064
Project Name: Application of Genomics and Population Genetic Tools in Livestock
Project Shortname: CBBI1171
Discipline Name: Other
The Indigenous Livestock Genomics group led by Dr FC Muchadeyi at the Agricultural Research Council Biotechnology Platform, composes of researchers and postgraduate students. Research projects conducted include population genomics to understand and unravel patterns of genetic differentiation, gene flow and genomic regions under natural and artificial selection in indigenous breeds and adaptations to environments and production systems. Additionally, the team has used RNA Seq to understand molecular mechanisms underlying host resistance to this parasite, we used RNA-sequencing technology to compare the transcriptomic response of the sites of the host-parasite interaction in Merino sheep. It also is important as it can provide evidence of pathways underlying resistance and susceptibility both primary and tertiary Haemonchus infections in Merino sheep.
Principal Investigator: Prof Giuseppe Pellicane
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2018-10-24
Allocation End: 2019-04-22
Used Hours: 7058
Project Name: Computational Study of Structure-Property Relationships in polymer blends relevant to OPV devices
Project Shortname: MATS0887
Discipline Name: Physics
Designing novel organic materials for Organic Photovoltaic devices (OPV) relevant to solar cells by a combined experimental and computational effort is as major outcome in the field of renewable, sustainable and non-polluting sources of energies. In fact, solar energy is an inexhaustible and green energy source and organic molecules allow for a cheap device preparation cost and exhibit relative ease of processability: these two factors meet the requirements for industrial production and large scale diffusion of solar energy as a viable and economic energy source. Nevertheless, the study of organic conducting materials is important for achieving a fundamental understanding of charge transport phenomena at the molecular level, which represents a remarkable scientific progress in the physics and chemistry of semiconductor devices.
As a team of researchers, our group is based at UKZN, and we are working on Theoretical and Computational studies of Complex fluids. We are involved in addressing the research questions of this research proposal. A number of publications in scientific journals are obviously expected as a result of this research endeavour, and we already produced a number of them, even if they are still limited to the computer simulation study of simplified models of polymer blends, where we try to understand the effect of the geometry of the polymer on the blend morphology. We are also presenting the research outcomes of the project in international conferences/workshops, that will allow for broadcast of vital research data on solar cells with the international scientific community and will be beneficial to the global progress towards a green and sustainable earth planet. We acknowledge the skilled and resourceful personnel at CHPC, and the generous allocation of computational resources granted to us by them, which are instrumental to fulfill the goals of this project.
Principal Investigator: Dr Chris Barnett
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2018-10-24
Allocation End: 2019-04-22
Used Hours: 393005
Project Name: Analysis of disease related polymers
Project Shortname: CBBI1063
Discipline Name: Bioinformatics
I investigate the shapes, structures, and properties of molecules by using computational modelling techniques. I'm particularly interested in complex sugars (glycans), which are interesting to study because they are involved in intricate molecular recognition processes in cells, for example, playing a role in cell signalling, adhesion, and immunity. Further understanding of these molecules and the complex systems they are involved in may lead to the generation of additional diagnostic markers and inhibitors that can be used to combat disease. The CHPC provides a platform for being able to run large-scale and highly parallel simulations which is a great help in making rapid progress towards solving research questions. The CHPC is also a test bed when carrying out computation on and developing algorithms for large datasets.
Principal Investigator: Dr Gerhard Venter
Institution Name: University of Cape Town
Active Member Count: 8
Allocation Start: 2018-10-24
Allocation End: 2019-04-22
Used Hours: 544855
Project Name: Simulation of Ionic Liquids
Project Shortname: CHEM0791
Discipline Name: Chemistry
Dr Venter's research group is part of the Scientific Computing Research Unit at the University of Cape Town and uses computer simulation to study the chemical and physical properties of biopolymers in a special class of solvents, called "ionic liquids". These simulations provide insight into the intermolecular interactions and chemical behaviour that control the dissolution and subsequent reactivity of these naturally occuring polymers. A better understanding of these processes can lead to the rational design of new, environmentally friendly solvents systems that can dissolve biomass and enhance its reactivity. The dissolution of biomass is the first step in converting naturally occuring polymers to biofuels and other platform chemicals.
High performance computing is required for all research conducted in this group and without the resources and infrastructure provided by the Centre for High Performance Computing (CHPC), the research will not be possible.
Principal Investigator: Prof Juliet Hermes
Institution Name: SAEON
Active Member Count: 2
Allocation Start: 2018-10-25
Allocation End: 2019-04-23
Used Hours: 65688
Project Name: SAEON Coastal and Regional Ocean Modelling Programme
Project Shortname: ERTH1103
Discipline Name: Earth Sciences
The Coastal and Regional Ocean Modelling Programme is a modelling initiative of the South African Environmental Observation Network (SAEON) Egagasini Node based in Cape Town. The aim of this programme is to use ocean models to understand regional and coastal shelf dynamics. The ORCA12 configuration, extending from the Angola gyre, Mozambique channel and including the Southern Ocean is used in this programme. A high resolution grid is used which zooms the coastal region including the St Helena Bay region which is an important nursery ground for fish and also the main generation zone of low oxygen water. The low oxygen generated in the St Helena Bay region result in the formation of greenhouse gases including nitrous oxide which has a global warming potential about 265-310 times higher than that of carbon dioxide. With climate change there is also a need to understand implications for primary production and expansion of low oxygen regions in the ocean. The coupled ocean model in this programme is used to understand these processes and the results obtained can be used to fill knowledge gaps and advance coastal modelling. The coupled NEMO-PISCES configuration has been upgraded to a 12 km resolution and this project relies heavily on the use of the CHPC for tuning and testing the model.
Principal Investigator: Dr Nana Ama Browne Klutse
Institution Name: Ghana Space Science and Technology Institute
Active Member Count: 2
Allocation Start: 2018-10-25
Allocation End: 2019-05-16
Used Hours: 164802
Project Name: Regional Climate modeling over Africa
Project Shortname: ERTH1087
Discipline Name: Earth Sciences
The CHPC is giving opportunities to local and international scientists and the government of South Africa is commended for this effort. We are lucky to have free computing space which is valued thousands of Rands to do climate science research. We are grateful to the CHPC team and the government of South Africa.
Principal Investigator: Dr Aniekan Ukpong
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2018-10-26
Allocation End: 2019-04-24
Used Hours: 226266
Project Name: Theoretical and Computational Condensed Matter and Materials Physics
Project Shortname: MATS0941
Discipline Name: Physics
The theoretical and computational condensed matter and materials physics group at the School of Chemistry and Physics, University of KwaZulu-Natal develops and implements state-of-the-art models for studying complex materials. We take special interest in the rich phenomena involved in the interaction of the electron cloud of atoms, molecules and solids with static and dynamic electric and magnetic fields. Our main tool is quantum mechanics as formulated within density functional theory, and we implement it computationally. Our analyses allow us to gain fundamental insights into complex materials, and their associated physical phenomena, which can also be a predictive guide to experiments.
Our research efforts focus mainly on the electronic structure of heterostructure multilayers, nanoparticles, and ceramic glass composites, and their associated atomic dynamics. We also undertake computations of applied spectroscopic signatures of electron states in a broad range of solid systems.
We study charge and spin transport for the development of topological insulators, metallic and semiconducting properties. We also study the response of electronic systems to applied electric and magnetic fields. Our emphasis is on finding answers to questions that arise from materials research in disparate areas of modern society. Finding suitable answers involve doing calculations that help to reveal how electrons behave in materials that contain a very large number of atoms. Such calculations are impossible to perform on laptops or desktop computers. Our use of high performance computing has allowed us to develop technical capabilities in technology areas such as electronics, energy, water purification and nanomedicine, as well as coal beneficiation.
Particularly, in our spintronics research, we have recently predicted the existence of a new robust phase for transporting electrons, which is suitable for storing information efficiently. This finding may pave the way for a whole new family of energy-efficient magnetic recording devices based on artificially-assembled materials.
Principal Investigator: Prof Felix Spanier
Institution Name: North-West University
Active Member Count: 6
Allocation Start: 2018-10-26
Allocation End: 2019-04-24
Used Hours: 1916080
Project Name: Acceleration and transport of high-energy particles in the universe
Project Shortname: ASTR0804
Discipline Name: Astrophysics
South Africa has moved a bit closer to the stars in the recent years by founding its own space agency SANSA. But there is more to space exploration than just building rockets. One important point is the understanding and possible forecast of space weather - the influence of high energy particles emanating from the Sun. Researchers from the NWU have been doing extensive simulations to understand one aspect of space weather: The transport of cosmic rays in high-frequency turbulence. The Centre for Space Research has a decade long tradition in this kind of study and the youngest generation of researchers could benefit from CHPC's newest acquisition the Lengau cluster. This type of research requires sophisticated and large-scale plasma models, which can only be handled with state-of-the-art supercomputers. CHPC has played a pivotal role in enabling NWU's researchers to get to the next level. Especially the new PhDs Alex Ivascenko and Cedric Schreiner have found new interesting details about the electron transport in the solar wind. They could show that the solar wind behaves vastly different at smallest scales and that this affects the transport of electrons significantly. While this seems like a purely academic scenario, it still has an impact on building satellites and spacecrafts in the long run: Any space equipment has to be shielded against electron impacts and understanding the whereabouts of electrons from the Sun is an important piece of the puzzle. Especially for South Africa as aspiring space nation. Future simulations will try to figure out how particle transport changes with a quiet Sun (weak turbulence) and solar eruptions (strong turbulence). The ultimate goal in any of these simulations is to predict when the Sun will emit large particle fluxes that may harm space equipment. The tools and methods used in this project also have another important role: Understanding plasma simulations and high-performance computing is ever more important for industry.
Principal Investigator: Dr Roelf Du Toit Strauss
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2018-10-26
Allocation End: 2019-04-24
Used Hours: 116283
Project Name: Computational Space Weather
Project Shortname: PHYS0918
Discipline Name: Physics
One of the biggest hurdles faced by manned exploration of space is the high levels of natural radiation present in the solar system. This is not only an important consideration faced by future astronauts on board spacecraft, but also by future colonizers of Mars, and inhabitants of future moon bases and space stations. This important risk is acknowledged by both SpaceX and NASA, and planned bases and spacecraft try to accommodate so-called "space storm shelters", where space dwellers can hide from dangerous radiation levels. At the Centre for Space Research of the North-West University, South Africa, we are doing our part to mitigate these possible harmful effects by developing state-of-the-art numerical models that can simulate and predict the levels of harmful natural radiation. To simulate the intensity of these so-called "cosmic ray" particles, complicated and large-scale numerical models are run on large scale computer clusters, such as the Lengau cluster of the Centre for High Performance Computing (CHPC) in Cape Town, South Africa.
Principal Investigator: Dr Sunita Kruger
Institution Name: University of Johannesburg
Active Member Count: 1
Allocation Start: 2018-10-26
Allocation End: 2019-04-24
Used Hours: 7459
Project Name: Environmental Heat Transfer
Project Shortname: MECH0995
Discipline Name: Computational Mechanics
This research group in the Mechanical Engineering Science Department of the University of Johannesburg is currently focusing on environmental heat transfer. Specifically heat transfer in naturally ventilated greenhouses. Greenhouses are used to protect plants from adverse weather conditions and insects. Ventilation of greenhouses are of vital importance to ensure quality crop production. If temperatures in a greenhouse is too high, poor plant growth may result, and an increased need for frequent watering. A mechanical ventilation system might be required to cool the inside of the greenhouse. Natural ventilation is an alternative option used to ventilate greenhouses. Natural ventilation uses temperature and wind to control the indoor climate of greenhouses. Unfortunately greenhouses are extremely energy intensive. Energy costs are the third highest cost related to greenhouse crop cultivation. Reducing the operating costs of energy associated with greenhouse cultivation may result in a price reduction of greenhouse cultivated crops. Conducting experimental work on ventilation of greenhouses can be costly and cumbersome. Using computational methods such as CFD (Computational Fluid Dynamics) to obtain qualitative and quantitative assessment of greenhouses can reduce costs and time involved. The computer cluster at the Centre for High Performance Computing has been used to conduct the numerical investigation using CFD. Currently research is being conducted on a large commercial greenhouse. Smaller greenhouses containing a single span are also being investigated
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2018-10-26
Allocation End: 2019-04-24
Used Hours: 90216
Project Name: CFD modelling of falling-film bioreactors
Project Shortname: MECH1001
Discipline Name: Computational Mechanics
This project stemmed from a passenger transport initiative of Transnet Engineering, known "in-house" as the MC25. While the project's initial phase would consist of a low to medium speed commuter connecting the business hubs of Gauteng to Polokwane, hereby opening the job-market in order to address the high unemployment rate in the country, Transnet's vision would ultimately be a high-speed rail network connecting South Africa's major cities. The optimisation of this train's nose is to serve as a technology demonstrator for this ultimate future goal. The optimisation goals are drag reduction, a financial consideration, and cross-wind stability, a safety consideration. Given the complex nature of the problem, Transnet joined hands with the University of Pretoria and the CHPC to make this vision a reality. While it is usually aeroplanes that seem to fascinate the public, it is the aerodynamics of high-speed trains that are truly challenging, mainly due to the very "dirty" external flow field surrounding the train due to the presence of the ground, the very thick boundary layer flowing over the train surface and the very long trailing wake. This implies that not only would the computational domain for a train have to be very large, but the flow phenomena that would need to be captured are very complex also. Transnet required the development of in-house expertise in the field of fluids and approached Professor Ken Craig of the University of Pretoria to guide Andrea Beneke's research. Because of the very large and complex nature of the required, cluster computing from the CHPC was a necessity. As proven by the documented masters research, the result of the study is a train nose geometry that is not only optimized for windless conditions, but also optimized to be stable under cross-wind conditions.
Principal Investigator: Prof Gert Kruger
Institution Name: University of KwaZulu-Natal
Active Member Count: 11
Allocation Start: 2018-11-01
Allocation End: 2019-04-30
Used Hours: 241710
Project Name: CPRU molecular modeling
Project Shortname: HEAL0839
Discipline Name: Health Sciences
(Who) The Catalysis and Peptide Research Unit at UKZN (http://cpru.ukzn.ac.za/Homepage.aspx) is currently working on the mechanism of action on the HIV PR with respect to the natural substrates. (What) We use an quantum chemical/molecular mechanics hybrid (Oniom) approach that gives us high level results on the thermodnamics and kinetics of the reaction. Our model enables us to study application of both electronics and sterics to change the bond strenght and binding energies of new potential inhibitors. The same approach is followed for transpeptidases, essential enzymes for the inhibition of TB. (Why) HIV is a major health threat in SA and new drugs is required due to the constant development of drug resistance. Similarly, TB and TB co-infection with HIV is a mojor health issue. (How) Our theoretical studies will allow us to test a computational model that correctly describes the interactions between the respective enzymes and existing drugs. We are improving our computational model to the extent where are now in a position to start proposing new potential drug leads for synthesis. This can only be done with large computational resources provided by the CHPC.
Principal Investigator: Prof Titus Msagati
Institution Name: University of South Africa
Active Member Count: 6
Allocation Start: 2018-11-02
Allocation End: 2019-05-01
Used Hours: 9621
Project Name: Metabolomics, Proteomics and Biochemistry
Project Shortname: CHEM1089
Discipline Name: Chemistry
CHPC is the best and Unique platform for emerging researchers to comply with their bioinformatics needs. Our group form UNISA works with CHPC from last year and it saves our time and gives us quick outputs. Thank you CHPC team.
Principal Investigator: Dr Samson Khene
Institution Name: Rhodes University
Active Member Count: 7
Allocation Start: 2018-11-06
Allocation End: 2019-05-05
Used Hours: 401060
Project Name: Synthesis, Spectroscopy and Nonlinear Optical Properties of Phthalocyanines
Project Shortname: CHEM0975
Discipline Name: Chemistry
Many of today's optical sensors are based on optical materials in which non-linear optics may play a role. Defects in the cable can have an effect of reducing the light (which carries information) in an optical fiber or cable. This phenomenon is also present in a variety of non-linear active materials or molecules. This nonlinear reduction of light phenomenon can be used as a sensing method for detection and correction of signals that are sent in cables. The aim of our research (at Rhodes University in the Chemistry department) is to make and study molecules which will help improve signal transmission using a nonlinear process. This work will not be possible if it was not supported by CHPC facilities.
Principal Investigator: Prof Ignacy Cukrowski
Institution Name: University of Pretoria
Active Member Count: 9
Allocation Start: 2018-11-06
Allocation End: 2019-05-17
Used Hours: 783906
Project Name: Understanding chemistry from QM study of molecular systems
Project Shortname: CHEM0897
Discipline Name: Chemistry
Activities in chemistry (in science in general) can be seen as made of two distinctive approaches: 1) development of new theories and methodologies that should lead to better understanding of concepts and chemical process (reactions) and 2) practical implementation of known chemical processes and performing, in principle, routine operations.
Our research group in the Department of Chemistry, University of Pretoria, that consists of Prof I Cukrowski (the leader), several PhD, MSc and Honours students as well as a postdoctoral Fellow is involved in fundamental studies focused on (a) understanding chemical bonds from the electron density distribution throughout a molecule (there are many kinds of bonds but still there is no clue for an ultimate theory of bond; there are various approximate quantum chemical bonding models that can be used only to answer certain questions about particular type of a bond); to this effect several novel methodologies were developed by our group and they are being tested on numerous molecular systems, and (b) modelling reaction mechanisms (to understand on atomic and molecular fragment level how it works or why it does not work) that might be of significance in the development of new drugs in, e.g. tuberculosis (a highly contagious disease that remains a significant public health problem globally) or Alzheimer disease with reported cases growing rapidly throughout the world.
Although we started modelling of reaction mechanisms only recently, a significant progress has been made and about 8 research papers are already under preparation. Any pioneering theoretical work, such is ours, requires a large number of real-life molecular systems (made of tenth of atoms) that have to be computationally 'processed' under specific conditions. This, in turn, requires expensive computational resources, such as CHPC, with a dedicated staff to assure it is available to research groups 24/7.
Principal Investigator: Dr Nkululeko Emmanuel Damoyi
Institution Name: Mangosuthu University of Technology
Active Member Count: 2
Allocation Start: 2018-11-08
Allocation End: 2019-05-16
Used Hours: 84265
Project Name: Surface Reaction Mechanisms
Project Shortname: CHEM1105
Discipline Name: Chemistry
My present area of research is in Computational Chemistry (CC). Computer technological advances make it possible to do research in CC in order to model chemical reactions and predict chemical reaction properties which are difficult or impossible to determine from normal laboratory experiments. Most of my present research involves utilising CC to predict the likely chemical reaction mechanisms that produce valuable organic compounds from alkanes with use of catalysts and also without catalysts.
Principal Investigator: Prof Jacques Joubert
Institution Name: University of Western Cape
Active Member Count: 3
Allocation Start: 2018-11-08
Allocation End: 2019-05-07
Used Hours: 24212
Project Name: Polycyclic cage compounds as multifunctional neuroprotective agents
Project Shortname: CHEM1173
Discipline Name: Chemistry
The drug design and discovery research unit at UWC, School of Pharmacy has been exploring the structures of unique polycyclic cage compounds with the aid of sophisticated theoretical computational models. This data is of significance as it provides us with information on how to improve the physical and chemical properties of these molecules to further develop them into useful medicines for the potential treatment of Parkinson's Disease and related neurodegenerative disorders. Our process involves the development of lead molecules and then through the use of software available at the CHPC, conduct in-depth theoretical structural analysis. Without the help of the CHPC this work would not be possible. Currently we have published one paper in Crystals (2019, 9, 24) and numerous other papers are in the pipeline to be published in 2019, all of this has been achieved in the short time frame of 6 months.
Currently we have two Professors and one post-doc working on this project. We have used DFT calculations with the Gaussian programme to study the structural features of a number of polycyclic structures. Currently we have published on paper in the journal Crystals (2019, 9, 24), submitted one paper to J.Chem.Cryst. (May 2019) and another paper to Crystals. (May 2019). We were also able to set-up an interantions collaboration with Prof Ali El-Emam (University of Mansoura, Egypt) to explore other polycyclic cage compounds. We expect to publish at least another 5 papers in 2019 on the in-dept structural analysis of polycyclic cage compounds.
Principal Investigator: Mrs Chantel Niebuhr
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2018-11-08
Allocation End: 2019-05-07
Used Hours: 127413
Project Name: Hydrokinetic turbine analysis
Project Shortname: MECH1174
Discipline Name: Other
The University of Pretoria, hydropower research team has been investigating Hydrokinetic hydropower installations within canal systems in South Africa. Installation of such projects would open a window to additional possibilities for rural electrification and increasing sustainable energy sources. However the hydrodynamic behaviour of these devices is difficult to predict and is not well understood. This behaviour is important to allow prediction of damming levels (in case of blockage) and how far apart devices can be placed without affecting each other. Computational Fluid dynamics modelling is used to analyze this behaviour, however due to the intricate wake dynamics a large mesh and powerful solving capabilities are required. The CHPC allows analysis of these systems in a realistic time frame, which would otherwise not be possible.
Principal Investigator: Prof Regina Maphanga
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 6
Allocation Start: 2018-11-12
Allocation End: 2019-06-04
Used Hours: 164514
Project Name: Energy Storage Materials
Project Shortname: MATS0919
Discipline Name: Material Science
The Advanced Mathematical Modelling group of Next Generation Enterprises and Institutions cluster of CSIR uses multiscale methods to develop novel energy storage materials with desired properties and enhanced properties for existing materials. The envisaged outcome of this project is to develop energy storage materials models with improved performance and consistency, which will be cheaper and environmentally benign. The ever-increasing global energy needs and depleting fossil-fuel resources demand the pursuit of sustainable energy alternatives, including renewable sources to replace carbon intensive energy sources. Sustainable and renewable energy is considered to be the most effective way to minimize CO2 emissions. Hence, finding sustainable energy storage technologies is vital for optimally harnessing the renewable energy.
Computational methodologies are very effective in predicting material-structure-property correlations. In this project simulation methods and models based on parallel computing are developed to probe energy materials properties. Centre for High Performance Computing (CHPC) resources are used to develop these parallel computing methods and algorithms for large and complex material models. Thus, CHPC resources provide a platform to simulate the evolution of material properties at a wide range of external conditions that are not accessible experimentally and fast track acquisition of results. The major of aim of this project is to create a predictive, reliable and robust set of models of materials for energy storage across the materials modelling length scale, leading to integrated multi-scale capability.
Principal Investigator: Dr Cornelia Inggs
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2018-11-12
Allocation End: 2019-06-27
Used Hours: 411212
Project Name: Parallel and Distributed Search and Planning Algorithms
Project Shortname: CSCI1175
Discipline Name: Computer Science
Our research group is based at the University of Stellenbosch and consists of Marc Christoph — a student that is currently working towards an MSc. in computer science — and his supervisors, Dr. Steve Kroon and Dr. Cornelia Inggs.
Our work falls under the umbrella of Artificial Intelligence (AI) — a branch of computer science with the fundamental goal of developing algorithms that allow computers to make decisions and reason like humans do. Due to the complex nature of these algorithms, we often need to provide them with a massive amount of computational resources in order to have them simulate, or even surpass, the decision-making ability of humans.
An effective way to increase the computational resources available to an AI algorithm is to increase the number of computers that it runs on. This means that we can have dozens — or even hundreds — of computers simultaneously running the same algorithm with the same goal. Effectively distributing the work across multiple computers in this way has many obstacles, and our research focuses on minimising the impact of these obstacles for Monte-Carlo Tree Search — a recently-developed algorithm that showed promise when it led to the first ever defeat of a human professional Go player with no handicaps.
This research is important because it will provide future AI researchers with a better understanding of the benefits and pitfalls of applying AI algorithms to environments with many machines. This will stimulate AI research and accelerate our journey to the ultimate destination of having computers with a decision-making ability that is indiscernible from, or even superior to, that of humans.
In order to carry out our research, we must compare various approaches to mitigating the aforementioned obstacles in distributing an AI algorithm across multiple computers. We make these comparisons by 'teaching' our implementations of these algorithms to play a board game (Lines of Action in our case) and running matches between them to determine how much they improve when they are provided with more computational resources.
In our experiments, we will need a minimum of 64 machines in order to effectively compare our implementations. This is a massive amount of computing power, and the CHPC is the only resource that will allow us to gather the data we want to within our budget. This year, we ran into some speed bumps with one of our algorithms and that set us back to the point where our initial allocation at the CHPC expired. We are well on our way to solving that issue and the rest of our implementations are working as expected. We believe that the project has progressed significantly since our initial allocation and that we are a maximum of two months away from having all of the data we need.
Principal Investigator: Dr Thabang Ntho
Institution Name: Mintek
Active Member Count: 10
Allocation Start: 2018-11-14
Allocation End: 2019-05-13
Used Hours: 74894
Project Name: Hydrogen Storage Materials and Catalysis
Project Shortname: MATS0799
Discipline Name: Material Science
In the Advanced Materials Division, at Mintek, we use density functional theory (DFT) and other simulation methods mostly to accelerate our research in finding or engineering new catalytic and alloy materials that can address South African needs in a variety of areas including health (shape memory alloys), water purification, energy (fuel cells), etc. The CHPC offers us the tools and platform to focus on our work to rapidly achieve results via the use of the Lengau super-computer. So far virtual experiments (simulations) have allowed us to validate some of our experimental findings while helping us cut down on the number of laboratory experiments needed to reach project scientific aims and objectives.
Principal Investigator: Prof Krishna Bisetty
Institution Name: Durban University of Technology
Active Member Count: 2
Allocation Start: 2018-11-19
Allocation End: 2019-05-18
Used Hours: 260111
Project Name: Computational Modelling & Bioanalytical Chemistry
Project Shortname: CHEM0820
Discipline Name: Chemistry
The Computational Modelling & BioAnalytical Research Group in the Department of Chemistry at DUT focuses on smart biodevice platforms in biosensor technology using computational and experimental methods. This is achieved by incorporating nanostructured electrode materials into electroactive polymers for the design of biosensors for applications in the environmental, food and health sectors. The broader goals are to design, model and fabricate doped smart engineered nanomaterials to improve drug delivery and biosensing systems. High level computational tools such as molecular dynamics simulations, molecular docking and density functional codes available on the chpc are implemented in our research projects. The current research projects undertaken in our group has successfully demonstrated an elegant combination of computational and experimental chemistry in the development of diagnostic biosensors for disease biomarkers, additionally, the use of materials modelling tools enabled the design of novel electrode materials and its applicability of the electrochemical biosensor in the food and beverage industry.
Principal Investigator: Prof Fernando Albericio
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2018-11-16
Allocation End: 2019-05-15
Used Hours: 8965
Project Name: Peptide chemistry and Organic chemistry
Project Shortname: CHEM1102
Discipline Name: Chemistry
We are Peptide Science Group at UKZN Westville campus. The project was brought up with an intend to learn computational chemistry. The project involves synthesis of several organic molecules towards application in oligonucleotide chemistry. With the help of computational tools we aim to predict the reaction mechanism. Since CHPC provides the server which speeds up the calculations and helps in achieving the preliminary results. The project so far had been very promising in predicting the mechanism. We expect to be going ahead with these results for further analysis towards prediction of reaction mechanism.
Principal Investigator: Dr Ndumiso Mhlongo
Institution Name: University of KwaZulu-Natal
Active Member Count: 8
Allocation Start: 2018-11-16
Allocation End: 2019-05-16
Used Hours: 509851
Project Name: Biomolecular Modelling Research Unit
Project Shortname: HEAL1002
Discipline Name: Health Sciences
Biomolecular Modelling Research Unit is located at the University of KwaZulu-Natal, Howard College Campus and headed by Dr Ndumiso N. Mhlongo. This research group employs CHPC resources to conduct molecular dynamics simulations to analyse the dynamical properties of macro-molecules such as folding and allosteric regulations; ligand-receptor interactions; atom-to-atom interactions; protein-protein interaction;virtual screening and molecular docking of active molecules; QSAR etc, for the design and development of inhibitors against diseases and disorders. Through the use of CHPC resources, we have designed potential inhibitors against M. tuberculosis and cancer treatment. These have made contributions to discovery new inhibitors & new knowledge which could directly translate into real health benefits of the society.
Principal Investigator: Dr Hezekiel Kumalo
Institution Name: University of KwaZulu-Natal
Active Member Count: 12
Allocation Start: 2018-11-13
Allocation End: 2019-05-12
Used Hours: 475227
Project Name: Molecular modeling and computer aided drug design
Project Shortname: HEAL1009
Discipline Name: Health Sciences
The group covers a wide range of computational and molecular modeling research areas with main focus on biological systems and drug design approaches. Main interest is related to design and study of biologically and therapeutically oriented targets. This is achieved by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We are involved in projects such Understanding drug resistance mechanisms via different computational tools QM/MM MD simulations Quantitative Structure Activity Relationship (QSAR) Conformational Analysis of biomolecules Bioinformatics tools applications Development Projects Approaches to enhance binding free energy calculations results Developing parameters for biomolecules: on-going projects Software implementations: on-going projects. All the projects that we do in the group contribute to the training of pharmaceutical scientists with specific skills for both the pharmaceutical industry and academia. This has the potential of stimulating the local pharmaceutical industries in South Africa to manufacture pharmaceuticals of quality, excellence and affordability for optimum and cost effective patient health, instead of being dependent on multinational pharmaceutical companies. We are still small yet fast growing group however funding is problem, therefore for the resources at CHPC allows us to generate hypotheses for subsequent experimental testing in a much quicker manner and higher throughput than using experiment alone to generate hypotheses that you'd like to test. It has given us an opportunity to be able explain experimental data we could not explain easily such the binding landscapes of different enzymes and the mechanism of action for different inhibitors
Principal Investigator: Dr Bahareh Honarparvar
Institution Name: University of KwaZulu-Natal
Active Member Count: 13
Allocation Start: 2018-11-13
Allocation End: 2019-05-24
Used Hours: 1106764
Project Name: Computer-aided HIV/TB drug design
Project Shortname: CHEM0808
Discipline Name: Health Sciences
My research lies in the clear and coherent road map towards the application of computational methods to address problems in the biomedical field and drug discovery.
Principal Investigator: Dr Stefan du Plessis
Institution Name: Stellenbosch University
Active Member Count: 7
Allocation Start: 2018-11-16
Allocation End: 2019-05-24
Used Hours: 14013
Project Name: Shared Roots
Project Shortname: HEAL0793
Discipline Name: Health Sciences
Understanding the SHARED ROOTS of Neuropsychiatric Disorders and Modifiable Risk Factors for Cardiovascular Disease.
Shared Roots is a collaborative research project undertaken by researchers from the departments of psychiatry, neurology and genetics at Stellenbosch University and researchers from the South African National Bioinformatics Institute (SANBI). It is a MRC Flagship funded study and the principal investigator on the study is the executive head of the department of psychiatry Professor Soraya Seedat. Dr Stéfan du Plessis is responsible for the neuroimaging component. Our study included participants with posttraumatic stress disorder (PTSD), schizophrenia or Parkinson's disease. It is known that individuals with mental illness as well as other common brain disorders have higher rates of heart disease and stroke than the general population. It is not clear why this is the case. Our study therefore aims to collect information about all the potential factors that can play a role, to better understand the increased risk and enable the development of treatment strategies. To achieve this goal we will combine state-of-the-art research techniques such as genetic evaluations and the latest neuroimaging techniques. This will be combined in analysis with information evaluating the brain disorders, general health and lifestyle factors.
For our neuroimaging component, we scanned over 600 participants using Magnetic Resonance Imaging (MRI). Here we investigate potential brain changes associated with increased metabolic risk. We proceeded to calculate precise measurements of around 70 known brain regions using the MRI scans, which will be compared between cases and healthy controls. Processing takes around 24 hours for each scan. To finish in a timely manner, we used the Centre for High Performance Computing Rosebank, Cape Town, Sun Intel Lengau cluster.
Principal Investigator: Prof Moritz Braun
Institution Name: University of South Africa
Active Member Count: 3
Allocation Start: 2018-11-19
Allocation End: 2019-05-18
Used Hours: 2207628
Project Name: Density Functional studies using a variety of different methods and considering materials of current interest
Project Shortname: MATS0924
Discipline Name: Physics
High performance and computing research group
The use of the CHPC computational resources have opened up the avenue to investigate doped 2D systems and 3D catalytic materials that would otherwise be untenable. Several of the doped 2D materials and pristine 2D materials have profound effect in next generation materials. Also, the understanding of active and reactive 3D materials for catalytic and photocatalytic application was possible using the computational resources at the CHPC. These catalytic materials would have significant effects in the broader knowledge economy.
Principal Investigator: Dr Andre Stander
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2018-11-19
Allocation End: 2019-06-18
Used Hours: 24150
Project Name: In silico estimation of ligand binding energies against cancer- and malaria-associated proteins
Project Shortname: CHEM1055
Discipline Name: Health Sciences
At the Department of Physiology, cutting edge molecular modelling techniques are used to identify anticancer agents capable of targeting more than one cancer-associated protein. The computing resources at the CHPC are central in achieving these goals as it allows for timely in silico high throughput screening (HTS) and free energy calculations. New compounds have been identified through HTS and are currently being validated using free energy calculations which will be followed by in vitro testing.
Principal Investigator: Prof Edet Archibong
Institution Name: University of Namibia
Active Member Count: 4
Allocation Start: 2018-11-19
Allocation End: 2019-05-18
Used Hours: 22964
Project Name: (1) Computational Study of Semiconductor Clusters. (2) Computational Study of Bio-active Molecules Extracted from Plants
Project Shortname: CHEM0969
Discipline Name: Chemistry
The University of Namibia (UNAM) has a Computational Chemistry Research and Teaching Group located in the Department of Chemistry and Biochemistry. Two important research projects are currently being undertaken by the group. One of the projects focuses on the reactions of ozone with compounds that are found in wastewater. And the reason for this project is that Namibia is an arid country in southern Africa with facilities for reclaiming water directly from domestic sewage. Ozonation is one of the processes used to disinfect the waste water and also to eliminate certain harmful organic compounds that are dissolved in water. However, despite its importance in drinking water processing, the mechanism of ozone reaction in water is not completely known and the subject remains an important area for research studies. Computational studies prove to be important in these studies because several of the intermediates in the ozone reactions are short lived and difficult to isolate experimentally. Thus, these intermediates are modeled on computers and their thermodynamic and kinetic stability investigated. The computing facilities provided by CHPC in South Africa (SA) allow our group to study these large chemical systems accurately.
The second project where we use CHPC resources involves how to produce solar cells with improved efficiency. One aspect of this project deals with the design and computation of physicochemical properties of ligands and transition metal complexes that can be used to trap visible light in dye-sensitized-solar-cells (DSSC). Efficiency of the latter partly depends on taylor-made compounds with the ability to scavenge light which is subsequently converted to electricity in the cell. Our group is actively involved in modeling such compounds.
The other aspect of the second project involves doping of metal oxides with the aim of reducing the band gaps with concomitant absorption of light in the visible region. The project also investigates how photophysical properties change with the size of doped and undoped metal oxide clusters.
The projects on increasing efficiency of solar cells is motivated by the fact that Namibia is blessed with abundant sunlight which can be utilized to produce energy at a lower cost.
At present, the postgraduate students involved in the above projects, using CHPC resources, have obtained very good results which will be shared with stakeholders in physics and engineering sections for possible consideration in the design of solar cells.
Principal Investigator: Dr Henry Otunga
Institution Name: Maseno University, Kisumu, Kenya
Active Member Count: 1
Allocation Start: 2018-11-19
Allocation End: 2019-05-18
Used Hours: 4147
Project Name: Computational Study of Hematite Clusters
Project Shortname: MATS0888
Discipline Name: Material Science
Sunlight is the most abundant renewable energy resource and considered to be the ultimate solution to address the global energy problem: The Tetrawatt Challenge. However, the vision of solar energy providing a substantial fraction of global energy infrastructure is still far from being realized. The major challenge is to develop an efficient and cost-effective approach for storing solar energy that can be used on demand on a global scale. Splitting water photoelectrochemically is a promising way in which solar energy can be harvested and stored through photocurrent-driven chemical bond rearrangement leading to the formation of molecular hydrogen (2H2O→2H2+O2, E0=1.23 eV, Standard Hydrogen Electrode, SHE), which can be used directly as fuel or as an intermediate in the production of other fuels.
Hematite (alpha-Fe2O3) has emerged as a candidate photoanode material due to several favorable features: a band gap of about 2.0 eV (which allows for a large fraction of solar spectrum to be absorbed), excellent stability under aqueous environments, and abundance in nature. Converting energy from the Sun to electricity efficiently via photoelectrochemical splitting of water is based on photo-induced charge separation at an interface (semiconductor/water interface) and the mobility of photogenerated carriers (electron-hole pairs). However, in bulk hematite, the separated charges recombine very fast (very short lifetimes of electron-hole pairs) and have very low mobility, hindering the conversion efficieny. These limitations can be dealt with by nanostructuring hematite, by growing ultrathin films of hematite, and by introducing impurity atoms in hematite. In this work, the structure and energetics of various size clusters of Fe2O3 have been investigated using the plane-wave pseudopotential approach to Density Functional Theory (DFT) and ab initio Molecular Dynamics (MD).
These calculations require a significant amount of compute resources in terms of memory and cpu scaling. In this respect, I as a member of the Computational Materials Science Group at The Department of Physics and Materials Science, Maseno University, is grateful to the CHPC for granting me access to their supercomputing facilities and I hope for more collaboration in the future.
Principal Investigator: Prof Tahir Pillay
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2018-11-19
Allocation End: 2019-05-18
Used Hours: 227374
Project Name: Molecular Modelling of ligands and receptors
Project Shortname: HEAL0876
Discipline Name: Health Sciences
Prof Tahir Pillay's research group in the Department of Chemical Technology, University of Pretoria is actively working on the field of pharmcoinformatics applications in the genetic and acquired diseases. We have been using the facility of CHPC since 2014. The research group uses several pharmacoinformatics tools to design computational models followed by screening of small molecular databases and simulations for therapeutic application in several diseases including HIV/AIDS, Tuberculosis, Alzheimer's, Malaria, etc. For this purpose we are extensively using Schrodinger, Amber, Gromacs etc. Therefore, the research work is entirely dependent on pharmacoinformatics tools available in the CHPC server. The department does not have sufficient infrastructure to carry out the research in the current project. Hence, our research group requires access to the CHPC server to fulfil the objectives of the current project. We are very pleased with the services available in the CHPC server and would like to thank the entire team for their efforts and support.
Principal Investigator: Prof Enrico B Lombardi
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2018-11-21
Allocation End: 2019-07-04
Used Hours: 687084
Project Name: Defects in wide-bandgap semiconductors and 2D materials
Project Shortname: MATS1160
Discipline Name: Material Science
The materials research group of Prof Lombardi at the University of South Africa (UNISA) focuses on defects in wide band gap semiconductors and 2 dimensional (2D) materials. This vibrant research group is exploring a range of defects 2D materials which affect their functionality and efficiency, for applications ranging from next generation spintronics devices, to nano-electronic an opto-electronic devices. As in all solid state materials systems, point defects are inevitable, and is particularly important in new chemically grown 2D materials due to the imperfection of the growth process, including, amongst others, 2D chalcogenides. Our group has contributed to the understanding of fundamental defects and defect processes in these 2D materials, predicting the properties of intrinsic point defects and other likely defects, and the conditions under which they are likely to occur. These results provide insight to the physics of defects that are grown via chemical vapour deposition, as well as in electron irradiated materials. These defects are responsible for large variation of electric and optical properties, while they may also act as efficient electron or hole traps, which strongly influence transport and optical properties of semiconductors, in turn strongly impacting their applicability to next generation devices. This research is performed using the state-of-the-art density functional theory, and has made extensive use of CHPC compute resources.
Principal Investigator: Dr Sean February
Institution Name: SKA
Active Member Count: 3
Allocation Start: 2018-11-16
Allocation End: 2019-05-18
Used Hours: 2101
Project Name: MeerKAT Open Time Projects - Feasibility Study
Project Shortname: ASTR1114
Discipline Name: Astrophysics
The South African Radio Astronomy Observatory manages the currently operating 64-dish MeerKAT telescope located in Carnarvon in the Karoo. It is expected that approximately 30% of MeerKAT's observing time will be taken up by smaller research groups who do not necessarily have the computing capacity to carry out the required processing of the data. The aim of this research programme is to conduct ongoing, as needed, feasibility studies for anticipated open-time projects. For ease of software deployment and for scientific reproducibility, we have tested two container technologies: uDocker and Singularity. Initial testing: a typical radio-astronomer's software environment (including the underlying operating system) has been exported locally, transferred to Lengau, and successfully executed on a compute node, in both cases. Future plans include more rigorous benchmarking in the form of typical data reductions, from the initial container export stage all the way to the final science product.
Principal Investigator: Prof Eno Ebenso
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2018-11-22
Allocation End: 2019-05-21
Used Hours: 45366
Project Name: Theoretical Investigations of Corrosion Inhibition Activities of Organic Compounds
Project Shortname: CHEM1176
Discipline Name: Chemistry
Our research group, Materials Science Innovations and Modelling (MaSIM) Research Focus Area is domiciled at the Mafikeng Campus of North-West University.
About 75% of our work is on the design of new corrosion inhibitor solutions to mitigate the rate at which metal (alloys) corrode in various environments. Other works in the group include of electrochemical sensors development and thermodynamics of solutions. Our research works involve quite a volume of computational studies, especially quantum chemical calculations using the Gaussian software and Molecular dynamics simulations using the Materials Studio software. The computational studies are often used to corroborate experimental results in our continuously robust and comprehensive investigations. For instance, the potentials of an organic compound to inhibit corrosion of metal is often dependent on its ability to adsorb on metal surface, which in turns depends on its molecular reactivity. Determining corrosion inhibition mechanism is central in such research, and computational study is an important aspect of the research. For a timely output, conventional personal computer (PC) is not an option in the kind of research we do. Continuous access to software license is also not negotiable. Hence, enrollment of our research group on CHPC resources is very important.
For a quantum chemical calculation that takes an average of 15 days per molecule to complete on a PC (if it does not end up crashing due to insufficient memory, as it's often the case), and an investigation involving at least 4 organic molecules (often, more compounds are considered), an investigator will be highly frustrated without a resource like CHPC.
Since our enrollment on CHPC resources, our project has been progressing satisfactorily and the time spent on a particular project has been reduced due to speedy computations. Hence, we have the opportunity of designing more elaborate projects executable within reasonable space of time.
Principal Investigator: Dr Madison Lasich
Institution Name: Mangosuthu University of Technology
Active Member Count: 8
Allocation Start: 2018-11-23
Allocation End: 2019-05-22
Used Hours: 299777
Project Name: Chem Thermo
Project Shortname: CHEM1028
Discipline Name: Chemical Engineering
The Thermodynamics, Materials and Separations Research Group (TMSRG) at Mangosuthu University of Technology has employed molecular-level simulations to study the interactions between humid air and bentonite clay with a view to potential enhancement of food packaging, as well to beneficiate local bentonite sources. Clathrate hydrates are an ice-like compound consisting of water and a gas species and are of interest with regard to offshore gas exploitation as well as in the context of climate change, since natural gas clathrate hydrate deposits form a large methane sink. The TMSRG has recently examined the limitations of a simplified approach for describing the gas content of common clathrate hydrates.
Principal Investigator: Dr Gebremedhn Gebreyesus Hagoss
Institution Name: University of Ghana
Active Member Count: 1
Allocation Start: 2018-11-23
Allocation End: 2019-08-29
Used Hours: 270865
Project Name: Atomistic simulations and condensed matter
Project Shortname: MATS1031
Discipline Name: Physics
The condensed matter research group at the Physics Department in the University of Ghana is focused on the study of the structural, electronic, magnetic, and optical properties of two- and three-dimensional materials. Computational simulations of the properties of these materials is carried out using Quantum Espresso (http://www.quantum-espresso.org) and ABINIT (https://www.abinit.org/) that are the state-of-the-art open-source computational software package. Our experimental research also covers the synthesis and characterization of these materials. Hence, we verify and validate our computational results against our experimental results.
Our computational work would not be possible without the enhanced computing resources available at the CHPC in South Africa. This is due to the fact that the materials we are studying require calculations on systems that contain comparatively large numbers of atoms. Typically, we do preliminary calculations on our computer cluster here at the University of Ghana. Once the basic results are validated, the actual job is then transferred to the CHPC. The job is monitored at least once a day and the results downloaded when completed.
Our main areas of research are:
1. Electronic, magnetic, structural and optical properties of transition-metal oxides.
Experiments are carried on the the synthesis and characterisation of pure and doped zinc peroxide and zinc oxide for oxygen and carbon-dioxide gas sensors, light-emitting applications, energy generation and storage and other applications. We are also investigating the structural, electronic, optical, and magnetic properties of these materials using the first-principle calculations. Moreover, we are investigating the electronic, magnetic , optical and structural properties of ZrO2.
2. Modeling and Simulation of Perovskite Materials for Energy Applications
Perovskite solar cells (organometal CH3NH3PbX3 and mixed halide CH3NH3PbI2X, (X = Cl, Br, I)) have the best power conversion efficiency. However, there is environmental concern due to the existence of a toxic element, lead (Pb). Hence it is very important to search computationally for the replacement of Pb by environmentally friendly elements. We are investigating all the divalent metals (Co, Cu, Fe, Mg, Mn, Ni, Sn, Sr, and Zn) which could substitute Pb in an organometal and mixed halide perovskite and also investigating the electrical, structural and optical properties of the selected organometal and mixed halide perovskite.
3. Two-dimensional Materials Research
In this project, we focus on the effect of introducing lanthanide atoms and spin orbit coupling effects into monolayer RSe2 and WS2.
Two dimensional materials also promise a wide range of applications, including light-emitting applications, energy generation and storage, wear- and corrosion resistant surfaces, and gas and radiation sensors.
Principal Investigator: Dr George Manyali
Institution Name: Masinde Muliro University of Science and Technology, Kakamega, Kenya
Active Member Count: 9
Allocation Start: 2018-11-23
Allocation End: 2019-05-22
Used Hours: 487537
Project Name: Ab Initio study of Thermoelectric Materials
Project Shortname: MATS0712
Discipline Name: Material Science
The Computational and Theoretical Physics (CTheP) Group at the Department of Physics, Masinde Muliro University of Science and Technology, comprises a team of researchers and students dedicated to the development and application of computational modeling to outstanding problems in materials science. In general, the group seeks a deeper understanding of quantum-mechanical descriptions of interacting electrons and nuclei in order to predict and design properties of materials and devices using density functional theory as a tool for the first-principles simulation. This kind of simulation generates volumes of data which cannot be handled by the common desktop computers. High-performance computing provides the computational environment that includes parallel processing, large memory, and storage of the big data. Therefore, Center for High-Performance Computing facility in Cape Town, South Africa, plays a vital role in providing the resources that aid the discovery of new materials and accelerates its application in the industry, an achievement that would have been in vain with desktop computers. Some specific projects for our group include characterization of already known thermoelectric materials. The information gained from this project is used as identifiers in search for new thermoelectric materials with the tailored figure-of-merit. Such materials are used to enhance the efficiency of thermoelectric generator power system for renewable energy. Such outcomes of our projects have an impact on the livelihood of the rural communities in Kenya, and generally, supports the Agenda Four of the Kenyan economic blueprint that was recently availed by the president of the Republic Kenya.
Principal Investigator: Prof Nicola Mulder
Institution Name: University of Cape Town
Active Member Count: 14
Allocation Start: 2018-11-23
Allocation End: 2019-06-05
Used Hours: 75869
Project Name: H3ABioNet
Project Shortname: CBBI0825
Discipline Name: Bioinformatics
The CHPC has been used for further analysis of genotyping array data in a process called imputation, which increases the number of SNPs per sample based on the non-random association of SNPs along the genome. It has also been used for analyzing microbiome samples of biomedical interest. The data is generated using mass spectrometry and we run a novel pipeline to determine which proteins and different organisms are present in the various samples to compare diseased to normal samples. Finally, we have used CHPC for epidemiological analysis of pneumococcal and Mycobacterium tuberculosis isolates to study disease transmission and drug resistance.
Principal Investigator: Dr John Mack
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2018-11-23
Allocation End: 2019-05-22
Used Hours: 3502
Project Name: Rational design of phthalocyanine, porphyrin and BODIPY dyes
Project Shortname: CHEM0796
Discipline Name: Chemistry
The Institute for Nanotechnology Innovation (INI) at Rhodes University under director Prof. Tebello Nyokong carries out research related to the use of molecular dyes in biomedical applications, such as cancer treatment through photodynamic therapy, the use of antimicrobial photodynamic chemotherapy for treating hospital superbugs and as sensors for ions that are harmful to human health. Other applications of interest include wastewater treatment and the development of optical limiters to protect human vision,such as in aviation safety in protecting pilots from the irresponsible use of laser pointers during runway approaches. It is important to understand trends in the electronic and optical properties that make the molecular dyes suitable for these particular applications. The resources of the Centre for High Performance computing help to facilitate this by making it possible to carry out molecular modelling calculations that can be used to predict how changes to the structures of the molecular dyes will modify their properties. The flexibility that CHPC provides where memory allocations are concerned is often vital. The INI currently has three staff members, twelve PhD, fourteen MSc and four Honours students, and four postdoctoral fellows, and usually publishes over forty peer-reviewed publications per year. This rose to a high of sixty-five in 2017 with ten involving the use of CHPC resources.
Principal Investigator: Prof Johan W. Joubert
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2018-11-26
Allocation End: 2019-05-25
Used Hours: 797652
Project Name: Mobility modelling using vehicle telematics
Project Shortname: MECH0803
Discipline Name: Other
Government (all spheres) is tasked with the challenge of deciding where to invest in infrastructure (for housing/transport/economic development etc). The real hard part is to balance two questions. Firstly, "who gets the benefit of infrastructure?" and, secondly, "who PAYS for those benefits?". In our research programme we develop agent-based transport models that are able to depict and imitate the complex, multi-modal and large-scale transport scenarios in a South African context. Each individual - from the Metrorail commuter, to the private car owner, to the minibus taxi driver, to the commercial vehicle delivering your goodies at the Woolies Foods - are represented in such a transport model. The goal of our ongoing research is to assist government and industry make better informed, evidence-based decisions about the intended, and unintended consequences of specific transport interventions. Since every individual is modelled the computational burden is substantial and the CHPC allows us to overcome the data preparation and simulation challenges of executing the large-scale, MATSim models.
Principal Investigator: Prof Claude Carignan
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2018-11-22
Allocation End: 2019-06-21
Used Hours: 9132
Project Name: Numerical Simulations of Barred Galaxies
Project Shortname: ASTR0961
Discipline Name: Astrophysics
Claude Carignan and his group (Nathan Deg, Toky Randriamampandry) at UCT have used carefully crafted simulations run at CHPC to generate one of the first mass models of NGC 1300. This is a particularly exciting achievement as the orientation of this barred galaxy prevents other methods from successfully modeling this galaxy. Their technique can be applied to a range of barred galaxies that could not be modeled otherwise.
Nathan Deg and Claude Carignan, working with Lawrence Widrow (Queen's University) have developed a new method for generating initial conditions for galaxy simulations. This program, call GalactICS (Galaxy Initial ConditionS) can make equilibrium galaxies with a spherical dark matter halo and bulge, two stellar disks, and a gas disk. Other methods for making such initial conditions generally require some time to relax to equilibrium, while GalactICS begins in equilibrium. This program is useful for studying dynamical processes, like bar formation, modeling real galaxies, controlled merging experiments, etc.
In addition, Claude Carignan and Nathan Deg have been working with Sarah Blyth, Nadine Hank, and Simon Krüger to analyze simulations of merging galaxies. They are attempting to characterize how asymmetric these mergers are, how this asymmetry parameter varies with observational systematics, like the angle the merger is observed at, and what the asymmetry parameter can tell us about the galaxies involved in the merger.
Nathan Deg has also used CHPC to test a new project to develop mock IFU observations from numerical simulations with Mathew Colless and Sree Oh. This work is nearing completion.
Principal Investigator: Dr Ernest Odhiambo
Institution Name: University of Nairobi
Active Member Count: 1
Allocation Start: 2018-11-26
Allocation End: 2019-05-25
Used Hours: 28139
Project Name: Computational Modeling of Heat Containment Systems
Project Shortname: MECH1178
Discipline Name: Computational Mechanics
Computational fluid dynamics (CFD) Simulation Laboratories is housed at the department of Mechanical and Manufacturing Engineering at the University of Nairobi. The University of Nairobi is the leading university in Kenya. The group is headed by Dr. Ernest Odhiambo. Apart from Ernest, who is the lead researcher, the group also consists of postgraduate and undergraduate students. Currently Computational Fluid Dynamics is offered at the masters level only although undergraduate students are offered projects with a CFD theme.
The group mainly focuses on problems involving fluid dynamics, thermodynamics and heat transfer. In fluid dynamics the focus is on numerical simulation of isothermal fluid and structural interaction. While for thermodynamics and heat transfer numerical simulation of varying temperature environments like fire disasters are considered.
In the energy sector, some members of the group are considering more efficient wind turbine technologies by applying novel blade designs. The computational simulation of such designs enables the prediction of performance prior to the manufacture of the turbines.
For the Agriculture sector, we are simulating a greenhouse, with the intention of producing one which is most efficient for the prevailing climatic conditions.
In the health sector, we are modelling the human respiratory system with a view to providing a prognosis of common diseases such as Asthma and other related lung diseases.
In fluid flow industry, we are focusing on simulating flow valves that are more efficient in reducing the overall power consumption of fluid flow networks.
The group also supports the building industry by providing computational fire safety models complementing the prescriptive fire safety standards which often fail in buildings with large and complex spaces like atria.
Currently the work is progressing well, with results obtained matching published data. The use of the CHPC clusters have been a tremendous help in working towards achieving the above objectives.
Principal Investigator: Prof Mark New
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2018-11-27
Allocation End: 2019-05-26
Used Hours: 5481
Project Name: AXA Research Chair Programme: African Climate Risk
Project Shortname: ERTH1180
Discipline Name: Environmental Sciences
Who: AXA Research Chair Programme: African Climate Risk, University of Cape Town
What: Attributing the human influence on climate risks for agricultural insurance
Why: Human influence on climate is changing the risk of weather and climate on society. In agriculture one way of managing risk is through insurance. We seek to estimate how the cost of insurance is changing because of climate change, and develop methods by which this added cost can be quantified, and covered by international climate funds.
How: We use climate model simulations of the recent past that represent a world with and without climate change; these are then used to estimate insurance risk and premiums in these two worlds; the different in risk and cost tells us how human influence on climate is affecting cost (and affordability) of insurance.
Principal Investigator: Prof Chris Meyer
Institution Name: Stellenbosch University
Active Member Count: 7
Allocation Start: 2018-11-29
Allocation End: 2019-05-28
Used Hours: 963314
Project Name: Development of CFD models
Project Shortname: MECH1077
Discipline Name: Computational Mechanics
The Department of Mechanical & Mechatronic Engineering at Stellenbosch University has a long and often illustrious history when it comes to the investigation and improvement of industrial-scale cooling systems, most notably for the power generation industry. The focus of our current research is air-cooled condensers (ACCs) where combinations of axial flow fans and heat exchangers are used to condense the steam in a steam power plant. ACCs are specific to arid regions where water for cooling purposes are scarce or completely unavailable.
The research has two primary focal points: the first is the simulation of large-scale systems where multiple fan units are employed, i.e simulating a complete power plant and secondly the simulation of the detailed operation of the axial flow fans used in these ACCs.
The first focal point is important as it allows the researchers to understand what the performance of ACCs would be under adverse environmental conditions such as high ambient temperatures and wind. The mitigation of the deterioration of ACC performance under these adverse conditions then forms part of the solutions engineered from our research findings.
For the second focal point the research will allow us to design more efficient or fit-to-task fans for ACC applications and also guide solutions towards better fan performance under the adverse environmental conditions listed above.
The computational resources needed for this research is a huge challenge which is most adequately addressed by the CHPC. In short, without the support of the CHPC this research would be either impossible or severely diminished in scope and impact.
There are currently 8 post-graduate students working actively within this research footprint with many of them planning to graduate at the end of 2019. Publication in accredited journals should be possible in early 2020.
Principal Investigator: Dr Thishana Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2018-11-30
Allocation End: 2019-06-06
Used Hours: 190910
Project Name: Combined kinetics,quantum-chemical investigation of reaction mechanisms involving catalysts
Project Shortname: CHEM0821
Discipline Name: Chemistry
The TS Computational Chemistry Research Group (University of Kwazulu-Natal, School of Chemistry and Physics) carries out quantum chemical modelling of homogenously catalysed organic reactions in the inter-domain field of Physical-Organic Chemistry. Computational Chemistry can be classified as 'Green Chemistry' as it is sustainable and does not generate chemical waste. The focus of this research group is primarily on catalytic asymmetric synthesis that have many applications in the pharmaceutical and fine chemical industry. The optimisation of a catalyst offers a good understanding of the factors that are responsible for the rate and selectivity of a reaction. Theoretical calculations, together with experimental kinetic measurements, often can pin down the mechanism. Using this methodology, it is possible to understand, and more importantly, design effective catalysts for a number of asymmetric, catalytic processes. The CHPC provides the facilities: hardware, in the form of the Lengau cluster and software programs such as Gaussian16, amongst many others. Thus far the current project has yielded two publications since 2016.
Principal Investigator: Prof Willem PEROLD
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2018-11-30
Allocation End: 2019-06-27
Used Hours: 36159
Project Name: Simulation of advanced semiconductor materials for the optimisation of photovoltaic devices
Project Shortname: MATS0948
Discipline Name: Electrical Engineering
World energy demand per year is growing very quickly. In contrast, depletion of fossil fuels is predicted by several researches and, moreover, their extraction causes pollution that negatively affects our environment. It has been demonstrated that plasmonic solar cells made by adding metallic nanoparticles into standard solar cells offer a good way to produce low cost, clean and renewable energy. The metallic nanoparticles boost solar cell efficiency via surface plasmons whose properties strongly depend on metallic nanoparticles shape, size, nature and surrounding environment. The metallic nanoparticles characteristics (shape, size, nature) can therefore be manipulated to tune light trapping in solar cells. Our staff here at the Electrical and Electronic Engineering Department, Faculty of Engineering, Stellenbosch University is working to see how light absorbed by silicon based solar cells can be significantly increased by adding silver or aluminium nanoparticles with particular shape and size into silicon layer of the solar cell. Both finite difference time domain (FDTD) based on electromagnetism theory and quantum mechanics methods are used to simulate solar cell absorption. To find the electrical properties (short circuit current, open voltage tension, and fill factor) the Poisson equation and continuity equations for electrons and holes are solved using the free available software named Microvolt. By the help of these simulations we have proposed some plasmonic solar cell designs with higher absorption power and ameliorated efficiency. We demonstrated that spherical shape is closed to the ideal geometry to increase solar cell absorption with metallic nanoparticles.
For a complete description of our solar cell configurations, we have to use both Finite Difference Time Domain (FDTD) and quantum mechanics simulations to determine the electrical properties of the device configurations. These simulations are complex and require huge computational resources, which are not possible on conventional computing platforms. The research would thus not be possible if the CHPC system was not available.
Principal Investigator: Prof Tien-Chien Jen
Institution Name: University of Johannesburg
Active Member Count: 26
Allocation Start: 2018-12-10
Allocation End: 2019-06-20
Used Hours: 2031514
Project Name: Developing an Innovative Metal Matrix Composite Membrane for Hydrogen Purification
Project Shortname: MATS0991
Discipline Name: Material Science
Hydrogen is an excellent energy carrier because of its high enthalpy of combustion with less environmental impact. Hydrogen fuel can be directly used in cars, ships, aircraft, and other transportation equipment. Although there are many problems to be resolved for implementation of hydrogen technology, it is generally believed that hydrogen will become a key energy carrier in this century. Until sufficient quantities of hydrogen can be derived from renewable energy sources, it will have to come from hydrogen separation using existing fuels (e.g., diesel, natural gas) as the feedstock. Hydrogen separation units can generate highly purified hydrogen from the feedstock gas mixtures, however, a certain amount of CO and other chemicals will make it into the hydrogen stream and cause catalyst failure on the fuel cell electrode. This significantly deteriorates the activity of the catalyst layer, particularly for Proton-exchange membrane (PEM) fuel cells. This deterioration greatly reduces the efficiency of power generation and the life cycle of the fuel cell. Overcoming this obstacle is necessary for the wider use of highly efficient fuel cells. The objective of this proposal is to develop a new composite metal membrane (CMM) that can achieve extremely high flux and selectivity of the hydrogen separation and achieve the lifetime goal set by the U.S. department of energy (DOE). To accomplish these goals, a research team formed by the University of Johannesburg (UJ), Council for Scientific and Industrial Research (CSIR) and Hydrogen South Africa (HySA) will combine two major technologies: Electrostatic-Force-Assisted Cold Gas Dynamic Spraying (ECGDS) and Laser-Assisted Manufacturing (LAM) to develop this new type of membrane. The proposed new membrane will eliminate the hydrogen embrittlement, catalyst failure, and avoid the difficulty of forming a defect-free, ultrathin Pd film on the substrate surface. The proposed CMM will exhibit superior reliability and can be produced with a relatively low-cost and scalable process. Note that this project is currently supported by the NRF for 2017-2019.
To achieve the end goal, High Performance Computing is a necessity. This service enable the researchers to analyze, numerically simulate and understand from the fundamental behaviour to the optimization of the product and process. A service such as the Centre for high performance computing (CHPC) provide the capability to achieve higher quality works and findings previously impossible to have been achieved.
Principal Investigator: Dr Calford Otieno
Institution Name: Kisii University, Kisii, Kenya
Active Member Count: 3
Allocation Start: 2018-12-10
Allocation End: 2019-07-24
Used Hours: 15518
Project Name: FIRST PRINCIPLE ELECTRONIC STRUCTURE CALCULATIONS OF EMERGING MATERIALS FOR SOLAR CELL APPLICATIONS.
Project Shortname: MATS1083
Discipline Name: Physics
My research group identifies as the Computational Material and theoretical group(C MTG), We are based at Kisii University Main, Kisii town in Kenya. Our groups essentially studies among other things, Chalcogenides and Perovskites compounds for efficient solar cell conversion. We investigate the effects of doping and pressure with an aim to improving these materials for their industrial applications.
Principal Investigator: Prof Charalampos (Haris) Skokos
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2018-12-11
Allocation End: 2019-06-09
Used Hours: 1009706
Project Name: Chaotic behavior of Hamiltonian systems
Project Shortname: CSCI1007
Discipline Name: Applied and Computational Mathematics
Using modern numerical techniques of Nonlinear Dynamics and Chaos Theory we investigate in a unified mathematical way the behavior of models describing the energy transport in disordered and granular media, as well as the properties of new elastic materials like graphene and molecules like the DNA. This research is performed by members of the 'Nonlinear Dynamics and Chaos Group' in the Department of Mathematics and Applied Mathematics at the University of Cape Town. The performed investigations constitute an innovative combination of Applied Mathematics, Chaos Theory, Hamiltonian Dynamics and Nonlinear Lattice Dynamics. Their outcomes will provide answers to some fundamental questions about the effect of chaos on the energy transport in disordered and granular media, and on the behavior of graphene and DNA. Some of the questions we try to address are: Does the presence of impurities and nonlinearities enhance or suppress the propagation of energy (e.g. heat) in solids, of light in crystals, and of vibrations in granular material? How does the ratio of the different base pairs in DNA chains affect their structural stability and the temperature at which the double-stranded DNA breaks to single-stranded DNA?
Principal Investigator: Prof Nelishia Pillay
Institution Name: University of Pretoria
Active Member Count: 8
Allocation Start: 2018-12-11
Allocation End: 2019-07-25
Used Hours: 72554
Project Name: Nature Inspired Computing Optimization
Project Shortname: CSCI0806
Discipline Name: Computer Science
The NICOG (Nature Inspired Computing Research Group) at the University of KwaZulu-Natal and University of Pretoria is using facilities provided by the CHPC to implement distributed multicore architectures to
implement evolutionary algorithms, search algorithms and evolutionary algorithm hyper-heuristics to solve real-world industry problems such as packing, scheduling, forecasting, data mining, computer security and routing problems.
This research has provided a platform to initiate collaborations with both industry and international institutions working in the areas of optimization and operations research.
One of the areas in which this research has made an impact is educational timetabling. The algorithms developed have been used to find solutions to university course, examination and practical scheduling problems. One of these approaches developed has automated the creation of heuristics, which are usually
derived by humans involving a time consuming process, to solve educational timetabling problems. A second area in which this research has made impact is automated design of machine learning to solve real-world problems such as packing, scheduling, financial forecasting and computer security problems such as network intrusion detection.
Principal Investigator: Prof Phuti Ngoepe
Institution Name: University of Limpopo
Active Member Count: 29
Allocation Start: 2018-12-14
Allocation End: 2019-07-05
Used Hours: 8512294
Project Name: Computational Modelling of Materials: Energy Storage
Project Shortname: MATS0856
Discipline Name: Material Science
Materials Modelling Centre at the University of Limpopo employs high performance computing to study materials. Large-scale atomistic simulations contribute immensely towards nanoscale battery technology particularly in the design and development of fast-charging high energy density energy storage materials. Insights on morphological (shape of nanomaterials), particle size and electrochemistry of these electrode materials will add significant value to growth/development of these highly demanded batteries for use in hybrid electric vehicles (HEVS) and large scale smart grids for renewable energy storage, moving into the much anticipated green technology. Exploring micron sized (millions of atoms) primary particle places us in a space where we can directly contribute to real-life synthesis processes in battery production particularly for Mn-based electrodes which can be produced in SA owing to the availability of resources.The ability to potentially explain the underlying relationship between atomic arrangement and electrochemical behaviours will contribute significantly to the design and performance predictions of the new generation of power sources. The project will assist in accelerating development of cathode production plants in the near future in South Africa. The high performance computing methods are also used to design reagents for extraction of precious metals for less understood, particularly in the platreef. Recently, postgraduate students have won prizes for best presentations at local and international conferences.
Principal Investigator: Prof Josua Meyer
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2018-12-18
Allocation End: 2019-06-16
Used Hours: 518050
Project Name: Fundamentals of forced and mixed convection in heat exchangers
Project Shortname: MECH1094
Discipline Name: Computational Mechanics
In-tube condensation is widely seen in many industries such as desalination, power plants and air conditioning. Thoroughly understanding of the condensation phenomenon would lead to better design of the systems which consequently causes the improvement of system efficiency. Although in majority of applications the circular tubes are used, there are some particular cases, like in air-cooled steam condensers, in which non-circular tubes such as rectangular tubes and flattened tubes are utilized. It has been proved that the thermal efficiency of such tubes are better as compared to the conventional circular tubes under specific operating conditions.
This work is being done by the Clean Energy Research Group (CERG) at the University of Pretoria. This group is involved in experimental and numerical heat transfer research focused on clean energy applications. CERG, falling under the Department of Mechanical and Aeronautical Engineering at the University of Pretoria, has a number of world class experimental facilities focused on heat transfer, balanced by a Computational Fluid Dynamics (CFD) division. The Group members have developed, designed and built five unique, state of-the-art experimental set-ups, which are being used for leading-edge heat transfer research.
Due to lack of water resources in South Africa, the research works on the optimizing and performance enhancement of systems working with water as the working fluid should be greatly developed. Such activities will definitely lead to lower energy and water consumptions within the country in the future.
It is the purpose of this research work to numerically investigate the effect of inclination on condensation of steam inside a long flattened channel. Thoroughly understanding of this problem via numerical simulations would assist in proper design of ACCs with low cost and time compared to experimentation.
At the moment, some research paper is going to be prepared.
Principal Investigator: Prof Zenixole Tshentu
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 7
Allocation Start: 2018-12-14
Allocation End: 2019-06-12
Used Hours: 478750
Project Name: Metal-ligand, anion-cation interactions and protein-ligand studies
Project Shortname: CHEM0864
Discipline Name: Chemistry
The group at NMU Chemistry Department under the leadership of Prof Tshentu is engaged in developing selective chemistry for beneficiation of earth and secondary resources. The work on developing reagents that are selective for precious metals has made gains and continues to produce reliable materials that could have industrial applications. The work on desulfurization and denitrogenation of fuel has contributed to the search for new methods for removal of contaminants from fuel (N and S) and is therefore contributing to upgrading of fuel to a zero sulfur level. The CHPC resources are key to the design of selective chemistry for these two applications.
Principal Investigator: Prof Rasheed Adeleke
Institution Name: North-West University
Active Member Count: 12
Allocation Start: 2018-12-21
Allocation End: 2019-06-19
Used Hours: 8654
Project Name: Environmental and Agricultural Microbiology
Project Shortname: CBBI1183
Discipline Name: Environmental Sciences
Our research programme is affiliated with the unit for Environmental Sciences and Management of the North-West University, Potchefstroom. We undertake microbiology-related studies focused on soil health, and agroecosystems. We aim to generate novel solutions that address critical global issues, including environmental sustainability, green energy and food security. Currently, our research projects utilize state of the art technologies that generates mega DNA and/or RNA sequencing data. Such data can only be analysed using large computer hardware/resources. Thus, we are very reliant on the CHPC's server to execute most of our bioinformatics analysis and/or pipeline. So far, we have made tremendous progress on the different research topic fronts. We have been able to generate insights into the potential recovery of post-coal mining reclamation sites using high-throughput sequence analyses of microbial communities. In addition, we have been able to obtain insights into the contribution of microbial communities to biogas generation using multiple feedstock sources. The number of our research topic and collaboration under the agroecosystem theme continues to expand.
Principal Investigator: Dr Ron Machaka
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 2
Allocation Start: 2019-01-07
Allocation End: 2019-08-20
Used Hours: 127716
Project Name: Prediction of metallic structures
Project Shortname: MATS1186
Discipline Name: Material Science
The Materials Science and Manufacturing Research is led by Ronald Machaka (CSIR and UJ).
We're are working developing titanium-based metal alloys for biomedical applications. In more recent times, we developing new alloys for magnetic applications.
Low-cost titanium-based utensiles for biomedical applications will improve the quality of life of the general public. New and stronger magnetic alloys will find applications in renewable energy harnessing and overall energy security in the Republic.
Computational quantum mechanical modelling methods (and resorces at CHPC) are helping us effectively design and deternine the stability, composition and properties of the new alloys (biomedical/magnetic) that we are working on. Computational quantum mechanical modelling speeds up the development of new materials while lowering the cost of experimentation.
Principal Investigator: Prof Sybrand van der Spuy
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2019-01-08
Allocation End: 2019-07-07
Used Hours: 267961
Project Name: CFD simulation of turbomachinery
Project Shortname: MECH1187
Discipline Name: Computational Mechanics
The modelling of high speed turbomachinery in CFD can be challenging due to the extensive resources required. In this instance the shock-boundary layer interaction in a transonic compressor and blade noise propagation in an axial flow fan were modelled successfully. The use of the CHPC has transformed our ability to do turbomachinery CFD and their support has been superb.
Principal Investigator: Dr Nikhil Agrawal
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2019-01-08
Allocation End: 2019-07-07
Used Hours: 60175
Project Name: Molecular Modeling of proteins using different computational tools
Project Shortname: HEAL1189
Discipline Name: Health Sciences
I am currently an Honorary Research Fellow in the School of Health Sciences at the University of KwaZulu-Natal. My research majorly focuses on enzymes and small peptides. In my research work, I use the MD simulation technique to answer how peptide self-assemble, how potential drug candidates bind with the proteins and inhibit their function. This will help in designing new drug molecules.
Principal Investigator: Dr Katherine de Villiers
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2019-01-14
Allocation End: 2019-07-25
Used Hours: 2063
Project Name: Investigations of drugable targets relevant to antimalarial action
Project Shortname: CHEM0801
Discipline Name: Chemistry
As per previous submission since the details of the project have not changed.
Principal Investigator: Prof Stephan Heyns
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2019-01-15
Allocation End: 2019-08-31
Used Hours: 216567
Project Name: Computational investigations in asset integrity mangement
Project Shortname: MECH1145
Discipline Name: Computational Mechanics
The Centre for Asset Integrity Management at the University of Pretoria focuses on the development of measurement and analysis techniques which can be used to continuously determine the condition of rotating machinery like turbines or large fans. This is important to ensure the early detection of reduced performance of such systems or imminent failures. Most of these measurements are related to the dynamic response of the equipment under consideration, and would typically be acceleration measurements on the rotating parts themselves.
In this study we considered rotating blades and asked the question whether disturbances in the pressure fields around faulty equipment could also serve as fault indicators. If this would be feasible it implies that condition measurements could be made without the complexity of mounting sensors on rotating equipment and transmitting signals from the rotating parts to stationary parts.
To explore this problem we investigated the use of time-dependent fluid dynamics simulations around a rotor blade using URANS CFD with the Open FOAM software package. Pressures were probed at locations in the field of the rotor and compared to results attained in an experimental investigation where good correlation was seen between the results.
The study was then extended to consider the effects of a blade that is slightly out of plane, which is a common fault condition. Comparisons were drawn between the blade in its 'healthy' and 'faulty' configurations. It was observed that the fault could be detected by deviations in the amplitudes of the pressure signals for a single revolution at the probed locations in the field.
It was shown that this is indeed possible under some conditions and could be complementary to some of the existing fault identification techniques, with the advantage of a simpler instrumentation system.
Principal Investigator: Prof Mahmoud soliman
Institution Name: University of KwaZulu-Natal
Active Member Count: 25
Allocation Start: 2019-01-15
Allocation End: 2019-07-14
Used Hours: 2579781
Project Name: Drug Design, development and modelling
Project Shortname: HEAL0790
Discipline Name: Health Sciences
The research scope of the Molecular Bio-Computation and Drug Design Research Lab covers a wide range of computational and molecular modeling research areas with main focus on biological systems and drug design approaches. Main interest is related to design and study of biologically and therapeutically oriented targets by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We show keen interest in diseases of global burden and evident prevalence within the south African populace such as HIV/AIDS, Tuberculosis and Cancer. The computational resources provided by CHPC is employed in performing the molecular dynamic calculations and the corresponding post molecular dynamic simulation analysis.
Principal Investigator: Dr Mohammad Moghimi Ardekani
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2019-01-15
Allocation End: 2019-07-14
Used Hours: 94310
Project Name: R&D in Solar Energy in particular Concentrating Solar Power Research
Project Shortname: MECH1137
Discipline Name: Computational Mechanics
Dr. Moghimi Ardekani Research group in Mechanical Engineering Department of University of Pretoria is working on Concentrating Solar Power and thermal Energy Storage to engineer and optimize the cost of related technologies and make them available in South Africa.
Solar energy and thermal storage is one of the top renewable energy resources which would be able to resolve the power shortage issue in South Africa.
In that Regard, CHPC is quiet helpful in engineering and numerical simulation of this study and could hugely save the unnecessary trial and error process of experimental studies if the CHPC and numerical modelling were not available.
The project progress is quiet satisfactory and based on the research findings the group has prepared three manuscripts for publishing in Top peer reviewed journals in collaboration with Imperial College London, Edinburgh University and Shiraz University
Principal Investigator: Prof Marelie Davel
Institution Name: North-West University
Active Member Count: 0
Allocation Start: 2019-01-21
Allocation End: 2019-07-20
Used Hours: 77062
Project Name: DNN Analysis
Project Shortname: CSCI1191
Discipline Name: Computer Science
The Multilingual Speech Technologies (MuST) research group is associated with the Faculty of Engineering of NWU. It focusses on machine learning and statistical pattern recognition, as well as their application in speech technologies. MuST is a node of the Centre for Artificial Intelligence Research, which is supported by DST and hosted by CSIR.
MuST has a long-standing theoretical interest in generalisation, or how information learned on a training set of samples is transferred to new inputs. The group is particularly interested in how generalisation functions in deep neural networks (DNNs), the latter relating to a branch in computer science that uses statistical methods to help computers "learn" from data. Think image recognition: computer applications able to recognise objects in photos have acquired this capability from studying large sets of photos.
Internationally, DNNs have brought renewed energy and focus to the field of AI, through a series of remarkable breakthroughs in fields as diverse as speech recognition, board games and self-driving cars. In each of these and many other applications, DNN systems have reached previously unknown levels of accuracy, making human-level performance a distinct possibility. Interestingly though, many questions remain with regard to how DNNs achieve such good results, and how best to apply them.
MuST's objective is to find answers to some of these questions and to make meaningful contributions to the international scientific community, including training young scientists to do research well. MuST postgraduate students work alongside researchers to study various theories of generalisation and how factors such as learning algorithms and network structures affect generalisation.
The project commenced in 2018 and 2019 will see the first research outputs, including conference papers and a master's dissertation. The programme currently comprises of two research professors, 2 PhD students and 8 Master's students.
Principal Investigator: Dr Richard Walls
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2019-01-21
Allocation End: 2019-07-20
Used Hours: 11524
Project Name: Fire Engineering Research
Project Shortname: MECH1148
Discipline Name: Computational Mechanics
The Fire Engineering Research Unit at Stellenbosch University (FireSUN) is carrying out research to understand how fires behave in informal settlements. This is being done to answer questions such as: how fast can fires move through settlements? What would products for improving fire safety need to do? How long to people have to escape from their dwellings? How could large-scale fires be modeled to predict what might happen in a large disaster?
To this end the research team has conducted large-scale experiments along with modelling the results using computer models. A number of papers and a PhD thesis has been produced from the work.
Principal Investigator: Dr Mary-Jane Bopape
Institution Name: South African Weather Service
Active Member Count: 12
Allocation Start: 2019-01-22
Allocation End: 2019-07-21
Used Hours: 395148
Project Name: Very Short Range Forecasting
Project Shortname: ERTH1022
Discipline Name: Earth Sciences
The research programme focuses on the use of Numerical Weather Prediction models for research purposes. Results from the study contribute towards the operational decisions at the South African Weather Service which is expected to produce operational forecasts on a daily basis and a number of times a day. The current HPC resources are such that no research can be performed, and the use of the CHPC cluster helps SAWS deliver on some strategic decisions. SAWS is also participating in the model development framework where more intercomparisons will be required, and some testing of model physics and dynamics is going to be necessary.
Principal Investigator: Prof Kevern Cochrane
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2019-01-22
Allocation End: 2019-07-21
Used Hours: 41942
Project Name: Fisheries management in the southern Benguela system under climate change scenarios
Project Shortname: ENVI0908
Discipline Name: Environmental Sciences
Our research group is based at the Department of Ichthyology and Fisheries Science, Rhodes University. Our collaborators include researchers from different South African Universities and from international universities and research institutes. Among several objectives, our work explores optimal management approaches to reduce vulnerability of fisheries in the Southern Benguela to future changes, using the Atlantis modelling framework. This model has been used to evaluate future trends in abundance of important fisheries resources under climate change, as well as the robustness of indicators under environmental variability and climate change. Progress to date has been good and further work focusing on the likely effects of climate change on future trends in upwelling and primary production will continue.
Principal Investigator: Dr Fabio Cinti
Institution Name: NITHEP
Active Member Count: 4
Allocation Start: 2019-01-22
Allocation End: 2019-10-15
Used Hours: 23666
Project Name: Quantum Monte Carlo for ultra-cold atoms
Project Shortname: PHYS0892
Discipline Name: Physics
Quasicrystal phases remain among the most intriguing structures that have been ever discovered, being also largely investigated in physics, chemistry and, above all, materials science. From a theoretical prospective, recently, the interest on the subject is not only involving the pursuit of models capable of describing novel quasicrystals on metallic alloys, self-organised supramolecular micelles and liquid crystals, but also of how possible quantum effects might alter the physics of such quasicrystalline symmetries.
This talk presents a thorough study of quasicrystals and cluster crystals where quantum fluctuations are taken into account. Surprisingly, the bosonic model displays that the onset of a zero-point motion at finite temperature produces an interesting new physics, including a clear stabilisation of quasicrystals into striped and periodic cluster crystals, or the emergence of quantum quasicrystal phases.
Principal Investigator: Dr Melanie Rademeyer
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2019-01-22
Allocation End: 2019-07-21
Used Hours: 6497
Project Name: Properties of organic-inorganic hybrids
Project Shortname: MATS0823
Discipline Name: Material Science
The Material Science Research Group at the University of Pretoria, lead by Prof Melanie Rademeyer, focuses, among others, on the computation of the magnetic properties of organic-inorganic hybrid materials. Magnetic materials are important materials due to their potential technological applications, and organic-inorganic hybrid materials offer a unique opportunity in terms of the material design approach followed.
The successful calculation of the magnetic properties of these materials will allow for the identification of hybrid materials with promising magnetic properties. The materials identified via the computational method will then be synthesised in the laboratory and their magnetic properties measured experimentally via SQUID magnetometry.
The computational method involves the use of the single crystal structure of the material, as well as quantum mechanical and statistical thermodynamic calculations.
Significant progress has been made, with the magnetic properties of a number of organic-inorganic hybrid compounds having been calculated successfully employing the resources offered by the CHPC.
Principal Investigator: Dr Rhiyaad Mohamed
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2018-01-23
Allocation End: 2018-07-22
Used Hours: 35656
Project Name: Advanced materials for oxygen evolution reaction
Project Shortname: MATS1123
Discipline Name: Chemical Engineering
Hydrogen is seen as an integral part of the sustainable energy future. Through fuel cell and electrolyser technologies, energy storage and conversion will be possible. This will resolve some of the more critical challenges faced by most renewable energy sources. Co-hosted by the University of Cape Town and operating under the Catalysis Institute, HySA Catalysis (Hydrogen South Africa Catalysis), part of a flagship programme funded by the Department of Science and Technology, aims to find efficient and market ready catalyst technologies for both hydrogen fuel cells and water electrolysers. The former has been an age-old activity with a strong internal knowledge base. On the other hand, water electrolyser research is a new venture with many unresolved and unknown challenges. The Electrolyser Research Group is a new, young and dedicated group in the area of water electrolysis within HySA Catalysis.
We aim to take advantage of both experimental techniques and fundamental principles to predict and design new and better catalysts. Our research is broken down into two main categories, catalyst design and electrode membrane assembly development for commercialisation. Computational resources provided by CHPC's Lengau supercomputer enables us to perform quantum-chemical calculations to understand material properties. Whilst traditionally, unsupported iridium oxide has been used as an electrolyser catalyst, the scarcity and cost of iridium is a good justification to pursue research in supported iridium catalysts—these catalysts will of course require durable and conductive supports. Since some of these materials have never been synthesised before it is critical to methodically predict stable and electrically conductive material for use in water electrolysers. Based on chemical intuition we have identified a class of materials, doped oxides, which may possess excellent electrochemical properties. We have identified doped tin oxide and titanium dioxide as potential catalysts supports—our computational studies have now given us electronic properties of doped tin oxide.
We are pleased to have an opportunity to share our current findings at the International Society of Electrochemistry Annual Meeting (4 - 9 August 2019) in Durban, South Africa.
Principal Investigator: Prof Gerrit Basson
Institution Name: Stellenbosch University
Active Member Count: 5
Allocation Start: 2019-01-29
Allocation End: 2019-07-28
Used Hours: 2108104
Project Name: CFD modelling of Hydraulic Structures in Rivers
Project Shortname: MECH0985
Discipline Name: Computational Mechanics
The Institute for Water & Environmental Engineering Stellenbosch University has 2 Masters students, 2 Doctoral students and 1 Post-Doctoral student who are investigating CFD modelling of hydraulic structures with complex vortices and sedimentation. Key aspects of the research are related to the improved prediction of bridge pier scour, to investigate the fluid-induced vibration of piano key weirs, to optimize the design of vortex settling basins for small rural pump stations and to optimize sand trap and bottom-outlet designs for sediment flushing for SA's WRC guidelines for hydropower plants. The simulations are too computationally intensive for standard computers and the CHPC assists in the research by allowing the students to more extensively explore the hydraulic behaviour of these structures.
Principal Investigator: Dr Rhiyaad Mohamed
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2019-01-23
Allocation End: 2019-07-22
Used Hours: 474555
Project Name: Advanced materials for oxygen evolution reaction
Project Shortname: MATS1123
Discipline Name: Chemical Engineering
Hydrogen is seen as an integral part of the sustainable energy future. Through fuel cell and electrolyser technologies, energy storage and conversion will be possible. This will resolve some of the more critical challenges faced by most renewable energy sources. Co-hosted by the University of Cape Town and operating under the Catalysis Institute, HySA Catalysis (Hydrogen South Africa Catalysis), part of a flagship programme funded by the Department of Science and Technology, aims to find efficient and market ready catalyst technologies for both hydrogen fuel cells and water electrolysers. The former has been an age-old activity with a strong internal knowledge base. On the other hand, water electrolyser research is a new venture with many unresolved and unknown challenges. The Electrolyser Research Group is a new, young and dedicated group in the area of water electrolysis within HySA Catalysis.
We aim to take advantage of both experimental techniques and fundamental principles to predict and design new and better catalysts. Our research is broken down into two main categories, catalyst design and electrode membrane assembly development for commercialisation. Computational resources provided by CHPC's Lengau supercomputer enables us to perform quantum-chemical calculations to understand material properties. Whilst traditionally, unsupported iridium oxide has been used as an electrolyser catalyst, the scarcity and cost of iridium is a good justification to pursue research in supported iridium catalysts—these catalysts will of course require durable and conductive supports. Since some of these materials have never been synthesised before it is critical to methodically predict stable and electrically conductive material for use in water electrolysers. Based on chemical intuition we have identified a class of materials, doped oxides, which may possess excellent electrochemical properties. We have identified doped tin oxide and titanium dioxide as potential catalysts supports—our computational studies have now given us electronic properties of doped tin oxide.
We are pleased to have an opportunity to share our current findings at the International Society of Electrochemistry Annual Meeting (4 - 9 August 2019) in Durban, South Africa.
Principal Investigator: Prof Thuto Mosuang
Institution Name: University of Limpopo
Active Member Count: 7
Allocation Start: 2019-01-28
Allocation End: 2019-08-08
Used Hours: 2068
Project Name: Computational studies of various ultra-hard materials
Project Shortname: MATS0875
Discipline Name: Material Science
The Sensors and Advance materials research group is housed in the Department of Physics, University of Limpopo. In this group full potential all-electron density functional theory exciting code and the classical molecular dynamics dl_poly code are utilised to predict and analyse various properties of carbides, nitrides, and oxide materials. The aim is to identify outstanding properties gas sensing properties of these materials. Computational studies through the CHPC enables us to economically compare results with experimentally observed results. In this way optimum operating gas sensors can be developed.
Principal Investigator: Dr Phillip Nyawere
Institution Name: Kabarak University, Nakuru, Kenya
Active Member Count: 4
Allocation Start: 2019-01-28
Allocation End: 2019-08-13
Used Hours: 92743
Project Name: Barium Floride and Perovskites
Project Shortname: MATS0996
Discipline Name: Physics
Barium flouride and perovskite group is based in Kenya and is a combination of Rongo University, Kisii University, Kenyatta University and Kabarak University. This is Condensed Matter Physics using computer simulation as a tool. The students comprise of Masters in Physics and PhD.
This work is of interest since it is looking at energy solution problem by characterizing crystals of different types to understand their properties and application relationships. For better solar panels, most of the energy absorbed should be converted to power and this has been a challenge to silicon solar cells. We seek to understand the mechanisms.
For perovskites of interest, we are looking at the transition temperature of Gadolinium cuprate. Elevated temperature for superconductors is a big challenge and an area of research that has attracted many scholars. Superconductor wastes no energy and so if Gadolinium would prove to be one, then a milestone will have been attained.
With doping, properties of a material do change. To do doping, a large crystal is necessary for position the dopant at different positions. Such a cell is called a super cell and as such cannot be simulated in a personal computer. This place necessity of using a high speed computer which has been provided by CHPC. Since these projects are student based, it would have put a lot of burden on the students to seek funding so as to maintain their simulations.
The first of my two students are making very nice progress and I expect to graduate them mid 2020 and end of 2020. They have also become of support to just beginning Masters students by showing them how to use the CHPC and on general Physics. We are all grateful for this great resource.
Principal Investigator: Dr Bubacarr Bah
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 8
Allocation Start: 2019-01-29
Allocation End: 2019-07-28
Used Hours: 51962
Project Name: Large Scale Computations in Data Science
Project Shortname: CSCI0972
Discipline Name: Applied and Computational Mathematics
The Data Science Research Group at the African Institute for Mathematical Sciences (AIMS) South Africa.
We conduct Data Science research with applications in ecology, finance, energy, and health. We run Machine Learning algorithms to prediction a quantity of interest like a stock price, identification of individual animals from images, or diseases from images in financial, ecological, or health applications respectively. We are also interested in the theory of Deep Learning, in which case we run simulations as proofs of concepts for theoretical results.
All of the above require enormous computing power, which CHPC provides us. There is no doubt that all these problems are of great importance to society, hence the justification for the use of CHPC as a public resource.
Thanks to CHPC the group is making significant progress in these projects. The finance and ecology projects led to the completion of MSc theses. The others are also progressing well and are mostly PhD projects.
Principal Investigator: Mr Jean Pitot
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2019-01-30
Allocation End: 2019-07-29
Used Hours: 46678
Project Name: SAFFIRE Programme
Project Shortname: MECH1121
Discipline Name: Computational Mechanics
The University of KwaZulu-Natal's Aerospace Systems Research Group (ASReG) is at the forefront of rocket propulsion research in academia, both in South Africa and Africa as a whole. Located at the University's Discipline of Mechanical Engineering, ASReG primarily conducts research in the areas of liquid and hybrid rocket propulsion, as well sounding rocket development. The SAFFIRE Programme aims to develop South Africa's first fully-integrated liquid rocket engine, which is being designed for use in a small satellite launch vehicle. The long-term intention of the Programme is for the engine to enable the indigenous development of a South African space launch capability. To meet its developmental goals, the Programme requires the simulation of complex computational models to predict the fluid dynamic, thermochemical and structural performance of various engine components. These simulations are typically very computationally-expensive, and require extensive computational resources to run within a reasonable time frame. The CHPC offers the only realistic means of obtaining access to such resources. The Programme is progressing well, and 2020 will see the graduation of two masters students.
Principal Investigator: Dr Malebogo Ngoepe
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2019-01-31
Allocation End: 2019-07-30
Used Hours: 135296
Project Name: PROTEA
Project Shortname: MECH1194
Discipline Name: Computational Mechanics
Our group focuses on studying problems related to biomechanics or the overlap of biomechanics and biochemistry. These are currently applied to the study of thrombosis, hair, myocardial infarction and congenital heart disease. Our use of HPC largely relates to the use of computational fluid dynamics codes to develop interventional planning tools, both for thrombosis and congenital heart disease. Thrombosis is the main underlying condition in a large number of cardiovascular diseases and understanding its progression will be beneficial for management of chronic diseases, which are on the rise. Similarly, understanding congenital heart disease will contribute to long term management of conditions which continue to affect individuals over a lifetime.
Principal Investigator: Prof Veikko Uahengo
Institution Name: University of Namibia
Active Member Count: 10
Allocation Start: 2019-01-31
Allocation End: 2019-08-20
Used Hours: 440078
Project Name: Solar Materials
Project Shortname: MATS1043
Discipline Name: Material Science
The group has been working on Solar materials based metal oxides of zinc and copper, at the University of Namibia (UNAM). The main focus of the research is targeting locally available materials with photocatalytic and other equally important properties, used in the development solar materials. The raw materials such as zinc oxides or sulphides or phosphides and copper oxides are widely applied into harvesting energy, via smart engineering of the band gaps. Thus, locally available resources must be exploited for value addition and also to solve our own problems, for the benefits of our societies. The CHPC has become a powerful intermediator making life easier for researchers, because of the role they play into predicting or simulating the systems that are suitable for certain functionalities, thus suitable in guiding towards experimental work, eliminating those which are neither possible (experimentally) or not good enough for that particular functionality. This saves a lot of money in chemicals and solvents along the way. Thus far, the progress of the projects have ran smoothly and achieved milestones, that could not be possible without this Facility.
Principal Investigator: Dr Dominic Stratford
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2019-01-28
Allocation End: 2019-07-27
Used Hours: 20380
Project Name: Application of deformation-based models in paleoanthropology
Project Shortname: CSCI0984
Discipline Name: Imaging
As members of the Sterkfontein Research team, we are investigating 3-million-year-old fossil specimens from the caves and quarries at Sterkfontein, 50 km northwest of Johannesburg. Because it is one of the richest fossil complex site in Africa, this fossil assemblage is critical to challenge long-standing questions in human evolution. Who were our ancestors? Where and when did they live? Did they look like us? Did they walk on two legs, as humans do today? In addition to basic descriptions and traditional metrical analyses, recent incorporation and validation of computer-based techniques for reconstructing and comparing morphological pattern have substantially improved the quality of data delivered by fossil remains. In our project, we use high-resolution imaging techniques (e.g., microtomographic-based scanner) to non-invasively explore the fossil specimens and apply 3D modelling techniques to comparatively describe the anatomy of our ancestors. In that perspective, the access to a supercomputer through the CHPC resources is essential for running our analyses and provide new evidence of human evolution in South Africa.
Principal Investigator: Prof Eric K. K. Abavare
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 3
Allocation Start: 2019-02-04
Allocation End: 2019-08-03
Used Hours: 797007
Project Name: Atomic and Electronic structures of semiconductor interface systems
Project Shortname: MATS1159
Discipline Name: Physics
Our group is Frontier Science Group (FSG) in the Department of Physics, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana. We investigate atomistic and electronic properties of light materials using quantum mechanical approaches based on first principles calculations in the framework of density functional theory.
Our researchers basically focus on the study of interface materials. All electronic devices and related components in atomic level are interfaced. We study these interfacial morphologies and how they affect the overall performance of device applications.
Experimentally, several important semiconductor materials are growth based, as a consequence complete understanding of how these epitaxial growth are achieved are certainly important for device design and application.
The project work seeks to make new contribution to the semiconductor research in understanding the electronic and atomistic properties of silicon carbide interfacing with silicon that results in layer-by-layer growth.
There have been a lot of reports on the experimental front, the epilayer growth of these two materials in spite of their large lattice mismatch of approximately 20%. However, with special alignment between them, the mismatch can reduce drastically to about 1.5% due the two materials similar inherent symmetry relationship. However, there is no sound theoretical understanding clarifying the interface morphology and the electronic structure, and as a consequence this project seeks to unravel the mystery.
The possibility of solving these scientific interfaces problems hinges very much on the application of high performance computers, which makes the CHPC resources increasingly invaluable to our research. It is on the basis of this our group completely acknowledges the kind help for the use of their CHPC in South Africa.
Principal Investigator: Dr Caroline Kwawu
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 10
Allocation Start: 2019-02-04
Allocation End: 2019-08-03
Used Hours: 301272
Project Name: Renewable Energy Materials
Project Shortname: MATS1146
Discipline Name: Material Science
Renewable materials research group is a research team dedicated at contributing to design more efficient catalyst materials for renewable energy production. The focus is currently on fuel cell cathode materials like graphene, photoelectrolysers for CO2 and water reduction to fuels and corrosion science on metal alloys. Density functional theory implemented in quantum espresso enables the modelling of chemical properties and reaction mechanisms and computer clusters required for these simulations is provided by the centre for high performance computing (CHPC). We have made strides and further studies will lead to the design of new materials for the efficient conversion of solar or chemical energy to electricity to solve the problem of power scarcity.
Principal Investigator: Prof Mmantsae Diale
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2019-02-05
Allocation End: 2019-10-11
Used Hours: 334606
Project Name: Electronic Structure of hematite and surface doped hematite
Project Shortname: MATS0944
Discipline Name: Physics
Institution: University of Pretoria
Reseach group: Clean and Green energy
Project title: Electronic structure of hematite and surface doped hematite for water splitting
The current methods of energy production from fossil fuels has a number of draw backs such as global warming and climate change. Therefore, there is need to shift to better methods of energy production. The production of hydrogen fuel from water using solar energy by the process known as Photoelectrochemical (PEC) water splitting is a promising route. Hematite (α-Fe2O3) has been identified as a better semiconductor (SC) material for PEC process owing to its various advantages over other SCs for example a suitable gap of 2 eV; which absorbs in the visible section of the electromagnetic radiation. In addition, it is also cheap, non-toxic, abundant in the earth's crust and inert to chemical corrosion in the pH range. However, α-Fe2O3, has a number of drawbacks, such as rapid carrier recombination and low electrical conductivity, among others. Therefore in this project we intend to address some of the challenges of hematite through surface doping. Doping plays a major role in the improvement of various properties of a material such as electrical conductivity as well as narrowing the band gap. Our study is based on density functional theory (DFT) which is a theoretical computational method implemented within quantum espresso software package. Therefore, we heavily rely on the higher performance computers from CHPC to effectively execute our project.
We are glad to report that so far we have two publications and won an award from an international conference for our work. We are currently working on our third project and so still need the resources from CHPC.
Furthermore, the new developments in 2019 is the pre-award of the SUNRISE EU program where Dr Braun, our collaborator has introduced us to the Flagship. In this project, we have hosted the Swiss-SA public lecture at UP, presented by Dr Braun on 29 July 2019. The lecture was attended by the UP senior management, Prof Stephanie Burton, the deputy head of mission in the Swiss embassy, South Africa, Ms Veronique Haller and the DSTI deputy director general, Mr Dann du Toit. The attendees were able to understand the importance of renewable energy to mitigate the climate change. The DST and University of Pretoria supported the SUNRISE project with letters of support.
Principal Investigator: Dr Babatunde J. Abiodun
Institution Name: University of Cape Town
Active Member Count: 16
Allocation Start: 2019-02-06
Allocation End: 2019-08-20
Used Hours: 2084527
Project Name: CSAG-Atmospheric Modelling
Project Shortname: ERTH0904
Discipline Name: Earth Sciences
The Climate System Analysis Group (CSAG) Atmospheric Modelling project consists of CSAG researchers and students working on model development and applications. Our group is a unique research group within Africa (CSAG http://www.csag.uct.ac.za/). We are a mix of specialties who put the needs of developing nation users at the forefront of everything we do. As a result, we seek to apply our core research to meet the knowledge needs of responding to climate variability and change. In the project, we develop, evaluate, and apply of dynamic and statistical climate models over Africa. Climate models are powerful tools for understanding the complexity of our earth climate system. We use various form of climate model, ranging from uniform-grid Global Climate Models (GCMs), Regional Climate Models (RCMs) and adaptive-grid GCMs (VGCM) that has capability to increase its grid resolution locally over a region of interest. Given the complexity and computational demand of these models we rely on high performance Computers like those at the Meraka CHPC to our models. Our research goal is to understand the dynamics of climate extremes (i.e. droughts, extreme rainfall, heatwaves, and pollution episodes) and the impacts of vegetation changes on regional climate.
The highlights of our past research, carried-out using the Meraka CHPC resources, include: development and application of a VGCM for studying rainfall producing systems in West Africa (Abiodun et al, 2010) and tropical cyclone over the South-West Indian Ocean (Maoyi et al., 2017); application of RCMs in studying the transport of atmospheric NOx and HNO3 over Cape Town (Abiodun et al., 2014), extreme rainfall events over Western Cape (Abiodun et al., 2014), and potential impacts of climate change on extreme precipitation over four African coastal cities (Abiodun., 2017). The project, which has graduated more than 22 postgraduate students in last five years, it is currently support 8 postgraduate students who are working towards graduating this year or next year.
Principal Investigator: Dr Md Ataul Islam
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2019-02-07
Allocation End: 2019-08-06
Used Hours: 154825
Project Name: DR. MA Islam
Project Shortname: CBBI1198
Discipline Name: Bioinformatics
MA Islam's research group is working on the field of pharmcoinformatics applications in the acquired and infectious diseases. Facilities provided by the CHPC are used by this group since February 2019. This research group is using several pharmacoinformatics tools to design computational models followed by the screening of small molecular databases and simulations for the therapeutic application in several diseases Tuberculosis, Alzheimer's, Malaria, Chagas etc. In this purpose we extensively are using Schrodinger, Amber, Gromacs etc. Therefore, the research work entirely dependent on pharmacoinformatics tools available in the CHPC server. Hence, our research group completely in need of the access of CHPC server to fulfill the objectives of the current project. On behalf of the research group I would like to thank CHPC entire team for their efforts and support.
Principal Investigator: Prof Richard Tia
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 20
Allocation Start: 2019-02-07
Allocation End: 2019-08-06
Used Hours: 1542984
Project Name: Computational Chemistry and Materials Science
Project Shortname: CHEM1044
Discipline Name: Chemistry
We have not yet obtained results that can form the basis of a press release but with the progress made in the our work, especially the work pertaining to the conversion and utilization of carbon dioxide, it should be possible to make a press release in the near future. With increasing interest of the scientific community and government agencies on the mitigation of rising carbon dioxide levels and the attractiveness of using carbon dioxide as a feed-stock for industrial processes, this work might be very suitable for a press release as and when we get interesting results.
Our research activities fall under two broad areas, namely;
1. Molecular modeling - Exploring the mechanisms of organic, inorganic and organometallic reactions.
These studies afford important molecular-level mechanistic details of industrially-relevant chemical reactions that are difficult, if not impossible, to obtain experimentally. Molecular level understanding enable chemical reactions to be guided quickly and efficiently along desirable pathways, with the effect of producing the right product with minimal energy consumption and minimal environmental impact. A key aspect of this work is the development of homogeneous transition metal catalysts for the depolymerization of lignin, an abundant natural resource, for fuel.
2. Materials modeling
The atomic- and molecular-level mechanistic insight gained from these studies are useful for the design of novel catalysts for the conversion of CO2 and other green-house gases as well as stranded gases from the petroleum refining into useful fuels. This addresses the problem of global warming as well as providing an environmentally friendly alternative sources of fuel.
The research objectives described here are very computationally-demanding and using the CHPC resources is highly beneficial. Without that, we would not be able to carry out some of these calculations.
Principal Investigator: Prof Orde Munro
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2019-02-08
Allocation End: 2019-08-07
Used Hours: 56420
Project Name: Bioinorganic Chemistry
Project Shortname: CHEM1065
Discipline Name: Chemistry
BIOINORGANIC RESEARCH GROUP – WITS UNIVERSITY
The Bioinorganic Research Group at WITS University is led by Prof. Orde Munro, who is currently the SARChI Chair of Bioinorganic Chemistry. At present, the WITS group comprises two post-doctoral research fellows (Drs. Catherine Slabber and Zeynab Fakhar), two PhD students, and four MSc students.
NATURE OF OUR WORK
The work involves the design, synthesis, and testing of novel metallodrug candidates for chemotherapy. The compounds incorporate ligands that can facilitate and control the interaction of the metal ion with biomolecules such as DNA and/or proteins. Molecular simulations are used not only to design compounds with desirable biological behaviour, but also to gain fundamental insights on their mechanisms of action and electronic structures. We are particularly interested in exploiting and controlling the reactivity of both endogenous and non-natural metal ions to kill drug-resistant pathogenic bacteria such as TB (Mycobacteria) and cancer cells.
WHY WE USE SIMULATIONS
Modern drug discovery uses in silico methods for a number of reasons, including screening large libraries of compounds for binding efficacy to enzyme targets. The enzyme targets are crucial proteins for the survival and replication of cancer cells, bacteria and viruses. Screening many thousands of compounds using computer programs is an efficient way to select a handful of compounds that can ostensibly bind to the enzyme target of interest because they have the correct shape and functional groups. The small library so generated may then be synthesized in the laboratory and tested against the pathogen of interest and the putative enzyme target. In this way, computational methods shorten the time required to find promising new compounds for further testing and development as the medicines of tomorrow. Finally, computer simulations offer important three dimensional details about how drug-like compounds inhibit their enzyme targets, thereby guiding optimization of the compound's structure for enhanced target affinity and, in principle, improved in vivo efficacy.
Principal Investigator: Dr Lucy Kiruri
Institution Name: Kenyatta University, Nairobi, Kenya
Active Member Count: 5
Allocation Start: 2019-02-08
Allocation End: 2019-08-29
Used Hours: 1011593
Project Name: KU Computational Chemistry Research Group
Project Shortname: CHEM1032
Discipline Name: Chemistry
Our research group is CHEM1032. All members are from Kenyatta University, Chemistry and Physics department. Our research interest encompasses both classical dynamics which involve solving the Newtonians equation and quantum mechanical approach. We employ ab initio methods and density functional theory (DFT) to study structures, energetics, catalytic chemical reactions and organometallics. For instance, Abraham is doing his MSc in chemistry and working on theoretical calculations of tetra-pyrenyl porphyrins and their metal analogues. These systems have interesting applications as photosensitizers in Photodynamic antimicrobial chemotherapy (PACT) to inactivate pathogens in water. Clean drinking water has been termed as scarce globally and therefore, this work looks into solving the problem of water pollution.
Molecular dynamics has also been extensively used by some members. An interesting project by Wycliffe who is in his 3rd year PhD level and also a STEP student with the International Center for Theoretical Physics (ICTP) is carrying out a study on the conformational transitions in odorant binding proteins that are important on how malaria is transmitted. The understanding of the conformational heterogeneity is important since malaria is a sub-Saharan Africa key problem and many deaths have been reported to be caused by it.
At Kenyatta University, we lack supercomputer or good workstations to run these jobs. The organometallic work involves the presence of a transition metal and this takes long-computing hours. Molecular dynamics on the other hand, involves simulation in aqueous media which involves atoms in their thousands. This work can only be done using a supercomputer. The CHPC Lengau cluster has been invaluable to my students who have been able to accomplish their dreams in computing.
Principal Investigator: Dr Njabulo Gumede
Institution Name: Walter Sisulu University
Active Member Count: 1
Allocation Start: 2019-02-10
Allocation End: 2019-08-09
Used Hours: 142233
Project Name: Computer-Aided drug design for cancer therapy
Project Shortname: CHEM1058
Discipline Name: Chemistry
The computer Aided Drug design group at MUT is still it early stages. The aim is to design new chemical entities with different chemical scaffolds with good safety and efficacy for prostate and breast cancer. I am an academic at Mangosuthu University of Technology. I completed my PhD in 2016. I have 2 patents under review in national phases. I use CHPC resources because they provide free access to schrodinger license and the cluster. I normally perform simple calculations for docking in my laptop, then intensive calculations that requires a linux cluster like MD simulations are performed on the CHPC platforms remotely. I also purchase licenses for FEP+ web services for more advanced Free energy perturbation methods.
Principal Investigator: Dr Joseph Mutemi
Institution Name: University of Nairobi
Active Member Count: 2
Allocation Start: 2019-02-11
Allocation End: 2019-08-10
Used Hours: 21983
Project Name: Numerical weather and climate modeling, prediction, forecasting and change projections for Africa and sub regions
Project Shortname: ERTH1131
Discipline Name: Earth Sciences
The ERTH1131 research group is using CHPC resources in modeling climate patterns with the aim of improved representation of climate processes in order to enhance prediction skill over East Africa. The focus for improved predictability is to enhance early warning ability of the climate community, in order to deliver reliable information that can promote resilience-building at community, national and regional levels.
Focus is currently on high-impact weather, such as rain storms and tropical cyclones. Ongoing work has been presented in several international conferences, in form of posters and presentations.
Principal Investigator: Prof Charalampos (Haris) Skokos
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2019-02-11
Allocation End: 2019-08-10
Used Hours: 3852084
Project Name: Chaotic behavior of Hamiltonian systems
Project Shortname: CSCI1007
Discipline Name: Applied and Computational Mathematics
Using modern numerical techniques of Nonlinear Dynamics and Chaos Theory we investigate in a unified mathematical way the behavior of models describing the energy transport in disordered and granular media, as well as the properties of new elastic materials like graphene and molecules like the DNA. This research is performed by members of the 'Nonlinear Dynamics and Chaos Group' in the Department of Mathematics and Applied Mathematics at the University of Cape Town. The performed investigations constitute an innovative combination of Applied Mathematics, Chaos Theory, Hamiltonian Dynamics and Nonlinear Lattice Dynamics. Their outcomes will provide answers to some fundamental questions about the effect of chaos on the energy transport in disordered and granular media, and on the behavior of graphene and DNA. Some of the questions we try to address are: Does the presence of impurities and nonlinearities enhance or suppress the propagation of energy (e.g. heat) in solids, of light in crystals, and of vibrations in granular material? How does the ratio of the different base pairs in DNA chains affect their structural stability and the temperature at which the double-stranded DNA breaks to single-stranded DNA?
Principal Investigator: Dr Willem Gerber
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2019-02-12
Allocation End: 2019-08-11
Used Hours: 59149
Project Name: Computational investigation of transition state metal catalysis
Project Shortname: CHEM1061
Discipline Name: Chemistry
The research group of Dr WJ Gerber was founded in 2010 at the Department of Chemistry and Polymer Science at Stellenbosch University. The main aim of this research group is to use computational chemistry at various levels of theory to elucidate inorganic reaction kinetics (ligand exchange/oxidative addition and reductive elimination/general redox reactions), mechanism and thermodynamics. With an understanding of these interrelated topics pertaining to transition metal complex reactions more efficient catalyst can be designed and better optimize separation/purification of platinum group metals pertinent to the mining industry. To achieve these goals requires relatively large computational resources as generously supplied by the CHPC in the past couple of years which greatly assist with the progress of several research projects.
Principal Investigator: Prof Felix Spanier
Institution Name: North-West University
Active Member Count: 5
Allocation Start: 2019-02-18
Allocation End: 2019-08-17
Used Hours: 100214
Project Name: Acceleration and transport of high-energy particles in the universe
Project Shortname: ASTR0804
Discipline Name: Astrophysics
South Africa has moved a bit closer to the stars in the recent years by founding its own space agency SANSA. But there is more to space exploration than just building rockets. One important point is the understanding and possible forecast of space weather - the influence of high energy particles emanating from the Sun.
Researchers from the NWU have been doing extensive simulations to understand one aspect of space weather: The transport of cosmic rays in high-frequency turbulence. The Centre for Space Research has a decade long tradition in this kind of study and the youngest generation of researchers could benefit from CHPC's newest acquisition the Lengau cluster.
This type of research requires sophisticated and large-scale plasma models, which can only be handled with state-of-the-art supercomputers. CHPC has played a pivotal role in enabling NWU's researchers to get to the next level. Especially the new PhDs Alex Ivascenko and Cedric Schreiner have found new interesting details about the electron transport in the solar wind. They could show that the solar wind behaves vastly different at smallest scales and that this affects the transport of electrons significantly.
While this seems like a purely academic scenario, it still has an impact on building satellites and spacecrafts in the long run: Any space equipment has to be shielded against electron impacts and understanding the whereabouts of electrons from the Sun is an important piece of the puzzle. Especially for South Africa as aspiring space nation.
Future simulations will try to figure out how particle transport changes with a quiet Sun (weak turbulence) and solar eruptions (strong turbulence). The ultimate goal in any of these simulations is to predict when the Sun will emit large particle fluxes that may harm space equipment.
The tools and methods used in this project also have another important role: Understanding plasma simulations and high-performance computing is ever more important for industrial purposes. And teaching these skills to young students will make a difference.
Principal Investigator: Mr Muaaz Bhamjee
Institution Name: University of Johannesburg
Active Member Count: 5
Allocation Start: 2019-02-19
Allocation End: 2019-08-18
Used Hours: 6934
Project Name: Modelling of Multiphase Flow in Process Equipment
Project Shortname: MECH0837
Discipline Name: Computational Mechanics
The research group is from the Department of Mechanical Engineering Science at the University of Johannesburg. The primary area of interest in the research is the use of coupled computational fluid dynamics and computational granular dynamics models to investigate the complex multiphase interaction in process equipment. The models are
based on multiple continuum and meso-scopic based approaches which are couple with models such as the Discrete Element Method, Immersed Boundary Method and Eulerian Dense Discrete Phase Models. Both commercial and open-source software has been used in the research. Primarily the research has been focused on
hydrocyclones. However, the research is moving onto fluidised beds, spiral concentrators, highly concentrated slurry flows and gas cyclones. The models are benchmarked accuracy) against experimental measurements as well as for computational efficiency. Accurate and computationally efficient modelling of such phenomena is vital to the design of hydrocyclones which is crucial to the mining industry. The research group has produced numerous publications and has supported the research of four post-graduate students. Research into the computational efficiency of the models is continuing with the aid of the Centre for High Performance Computing (CHPC) facilities. Due to the complex physics and fidelity required in the problems tackled by the research group large computational resources are required. The CHPC provides a computational platform that is vital to the ongoing work and success of the research group.
Principal Investigator: Prof Francois Engelbrecht
Institution Name: University of the Witwatersrand
Active Member Count: 13
Allocation Start: 2019-02-20
Allocation End: 2019-08-19
Used Hours: 738054
Project Name: Development of the first African-based earth system model VRESM and its projections of future climate change over Africa
Project Shortname: ERTH0859
Discipline Name: Earth Sciences
The first African-based Earth System Model (ESM) is under development at the Council for Scientific and Industrial Research (CSIR) in South Africa, through collaboration with the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Australia and South Africa's Centre for High Performance Computing (CHPC). The new ESM is unique in the sense that it is being developed in Africa and through the lens of African and Southern Hemisphere climate processes. That is, the reliable simulation of climate issues critical to Africa, such as the occurrence of drought in in response to El Niño events, wide-spread flooding over Mozambique due to landfalling tropical cyclones and increased occurrences of heat-waves under global warming are key issues in the development of the new model. The model development process is also focussed on the Southern Ocean's role in regulating southern African climate, as well as the global climate through the absorption of carbon dioxide in the ocean. The development and application of an Earth System Model is a computationally extensive endeavour, and was impossible to undertake in South Africa before the Lengau cluster of the CHPC became available in 2018. The CSIR-CHPC partnership towards development of the new model has in 2018 led to the most detailed set of projections of future climate change over southern Africa obtained to date. These simulations have provided new insight into the plausible impacts of climate change in South Africa, including how the frequencies of droughts, heat-waves and landfalling tropical cyclones may change over the next few decades. These projections were key in informing South Africa's Third National Communication on Climate Change, which was published in 2018 under the science leadership of the CSIR. Moreover, the research papers based on the projections have directly informed the Special Report on Global Warming of 1.5 ºC of the Intergovernmental Panel on Climate Change (IPCC).
Principal Investigator: Prof Hendrik Vermeulen
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2019-02-20
Allocation End: 2020-05-21
Used Hours: 37857
Project Name: Short-term Forecasting Modelling of Wind Power Profiles and High Wind Speed Shutdown Events
Project Shortname: MECH1150
Discipline Name: Electrical Engineering
The Centre for Renewable and Sustainable Energy Solutions (CRSES) at Stellenbosch University is currently engaged in the development of sophisticated wind speed forecasting techniques for wind farm applications. The rapid expansion of the South African renewable generation portfolio has necessitated a review of grid management procedures. The increasing penetration of wind energy, in particular, requires the investment in costly flexible generation sources to maintain the frequency stability of the national grid. Reliable forecasting models allow for an informed, cost-effective approach to the scheduling and dispatch of available generation resources to mitigate risk to the stability of the national grid. The utilisation of numerical weather prediction models has been proven to be fundamental to the development of accurate wind speed forecasting models. These numerical weather simulations, which typically employ the Weather Research and Forecasting (WRF) model, are highly computationally intensive and require parallel computing power to produce timeous forecasts. With the aid of the CHPC, the beginnings of a multi-model forecasting tool have been established. Further work targets the development of probabilistic wind farm power prediction models to assist with decision-making processes. It is envisioned that further research into this topic will yield significant improvements in current forecasting practices.
Principal Investigator: Ms Robyn Jacob
Institution Name: SA Sugercane Research Institute
Active Member Count: 3
Allocation Start: 2019-02-25
Allocation End: 2019-08-29
Used Hours: 10847
Project Name: Saccharum Genomics
Project Shortname: CBBI0956
Discipline Name: Bioinformatics
Crops expressing genes from the bacterium Bacillus Thuringiensis (Bt) produces a protein toxic to members of the order Lepidoptera and is a popular alternative to sprayed insecticides. Although these Bt crops are considered to be an effective pest control method, reckless usage adds environmental pressure on the pest population to develop resistance to the toxin over time. One method of limiting the rate of resistance development is to keep small portions of the cultivated land planted with the non-GMO crop which then acts as a refuge area for the pest, limiting its exposure to the toxin and removing the pressure to develop resistance. Strains of Bt sugarcane for the South African market that should limit the damage caused by the stalk borer moth, Eldana Saccharina Walker are being developed, and a prerequisite to releasing such a product is a recommendation on the size and layout of the refuge areas to be planted, as an area too small may not curb the rate of resistance development enough, but an area too large may not be economically viable for the end user. The CHPC was used to produce a simulation-based model where individual moths are modelled as agents on an underlying sugarcane field. Use of the CHPC resources allowed many simulations per parameter to be run in parallel, which drastically cut down on the time required to get results ensuring the timely completion of this project.
Principal Investigator: Dr David Pearton
Institution Name: Oceanographic Research Institute (ORI)
Active Member Count: 7
Allocation Start: 2019-02-25
Allocation End: 2019-08-24
Used Hours: 7018
Project Name: Responses of South African Coral Reefs to Climate Change
Project Shortname: CBBI1072
Discipline Name: Environmental Sciences
The reef team of the Oceanographic Research Institute, part of the South African Association for Marine Biological Research, is dedicated to preserving and understanding the incredibly rich and important reef ecosystems of the amazing South African coasts. These critical ecosystems provide food and livelihoods to millions of people across the globes but are under threat from a wide variety of sources, including climate change, ocean acidification, pollution and overfishing. The ORI reef team is using a combination of traditional and cutting edge techniques to better understand the rich biodiversity and ecosystem processes in order to enhance their resilience and safeguard them for future generations. The resources and facilities provided by the CHPC are critical for us to analyse the vast amount of data generated by new techniques including metabarcoding, transcriptomics and RADSeq that allow us to understand both how both ecosystems and individual organism interact with each other and the environment and to environmental change.
Principal Investigator: Prof Juliet Pulliam
Institution Name: Stellenbosch University
Active Member Count: 10
Allocation Start: 2019-02-25
Allocation End: 2019-08-24
Used Hours: 67135
Project Name: South African Centre for Epidemiological Modelling and Analysis
Project Shortname: CBBI1106
Discipline Name: Other
The South African Centre for Epidemiological Modelling & Analysis (SACEMA) is a national research centre established under the Centre of Excellence programme of the Department of Science and Technology and the National Research Foundation, and based at Stellenbosch University. Our core mission is to improve health in South Africa and across the continent through model-based analysis. Trained in mathematics, biology, physics, economics, statistics, and epidemiology, our researchers bridge disciplines to understand disease dynamics and improve real-world outcomes. Example SACEMA projects that have relied on the CHPC include development of methods to infer transmission patterns of HIV transmission and to estimate the rate of occurrence of HIV infections. The latter project was published in the journal PLoS ONE.
Principal Investigator: Prof Ozlem Tastan Bishop
Institution Name: Rhodes University
Active Member Count: 13
Allocation Start: 2019-02-25
Allocation End: 2019-08-24
Used Hours: 3490431
Project Name: Structural Bioinformatics for Drug Discovery
Project Shortname: CBBI0867
Discipline Name: Bioinformatics
Research Unit in Bioinformatics (RUBi) at Rhodes University is specialized in structural bioinformatics research. Structural bioinformatics focuses on the identification and analysis of structure, dynamics and interaction of biological macromolecules in 3D space. While doing so, it aims to make connections between sequence – structure and function of macromolecules. Information on structure is particularly important as you can derive enormous amounts of information.
RUBi's main research interest is early drug discovery. Computer aided drug design technology has greatly revolutionised the drug research and development process. Traditional computational drug discovery approach includes large scale structure based and/or ligand based in silico docking combined with molecular dynamics and binding free energy calculations. All these computationally expensive calculations require to use HPC facilities.
In the last few years, RUBi has been developing some novel protocols by merging computational chemistry, structural bioinformatics and biophysics approaches and combining with traditional methods. These combined approaches also require HPC facilities. We expect that our protocols will advance our and others research. We have already been testing the combined approaches in different cases and a number of hit compounds identified; including identification of South African natural compounds as hits to cancer, malaria, trypanosoma and HIV.
Principal Investigator: Prof Peter Teske
Institution Name: University of Johannesburg
Active Member Count: 2
Allocation Start: 2019-02-25
Allocation End: 2019-08-24
Used Hours: 304717
Project Name: Coevolution of mangroves and mangrove-associated crabs
Project Shortname: CBBI0979
Discipline Name: Bioinformatics
Who?
Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg
What?
Analysis of DNA and RNA data from a large portion of animal genomes.
Why?
To improve the management of commercially exploited species, optimise conservation efforts aimed at saving endangered species from extinction, improving the management of exploited species and understand evolutionary relationships in nature.
How?
Genomic data sets generated using massive parallel sequencing technology results can only be assembled by means of supercomputers. Using CHPC, we are able to assemble a huge number of short reads into a meaningful sequence that reflects their order in the animal genome.
Progress?
CHPC and the valuable expertise it has gathered in one place allows our small lab to punch well above its weight. We are presently the only group at our university to routinely use next-generation sequencing technology (i.e., technology that falls into the biological component of the 4th industrial revolution), and in addition to using it for genomics, we now also conduct metabarcoding and transcriptomic research. Several of our recent papers have received considerable international media attention, with one being among the top 10 most downloaded ecology articles in Scientific Reports (5771 downloads). All current postgraduate students use next-generation sequencing technology in their research, which considerably improves their employment prospects. Moreover, we have become sought-after collaborators in South Africa, with numerous research groups wishing to benefit from our expertise. None of this would be possible without CHPC, as our own university lacks the technology for this kind of research.
Principal Investigator: Prof Hasani Chauke
Institution Name: University of Limpopo
Active Member Count: 8
Allocation Start: 2019-02-25
Allocation End: 2019-09-10
Used Hours: 432222
Project Name: Computational Modelling of Minerals, Metals and Alloys
Project Shortname: MATS1047
Discipline Name: Material Science
Professor Hasani Chauke is the primary investigator (PI) under the minerals and alloy development programme (MATS1047), he is based at the Materials Modelling Centre (MMC), University of Limpopo. The centre is a research unit focusing on computational modelling studies of various materials properties, including energy storage, mineral processing and alloy development. The work employ first-principles quantum mechanical approaches and molecular dynamics based methods, which employs various academic and commercial software's with different types of interfaces. The computer interfaces and licenses are linked to local servers (MMC) and also benefit from the Centre for High Performance Computing (CHPC). The CHPC provides platform to run large scale simulations, since the type of calculations requires high level computational power. The CHPC thus allowing calculations to run at a much less computational time. Most of the work carried are project at Honours (mini projects), Masters (MSc) and Doctoral (PhD) studies. The research projects under MATS1047 are progressing well in with regard to jobs submission, queuing and running.
Principal Investigator: Prof Francois Engelbrecht
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2019-02-26
Allocation End: 2019-08-25
Used Hours: 483691
Project Name: WITS Climate Modelling
Project Shortname: ERTH1200
Discipline Name: Earth Sciences
The Global Change Institute (GCI) of the University of the Witwatersrand focuses on projecting climate change over Africa and on understanding the socio-economic-environmental risks posed to Africa by climate change. The GCI's work in climate change adaptation is underpinned by a state-of-the art regional climate modelling capbility that is based at and runs on the Lengau cluster of the CHPC. The GCI uses this capability to generate detailed projections of future climate change over southern Africa and elsewhere over the African continent. On the research front, the GCI in collaboration with the CSIR and CSIRO in Australia is developing the first African-based Earth System model, which is to participate in the Coupled Model Intercomparison Project Phase Six (CMIP6) of the World Climate Research Programme (WCRP) in 2020. The CMIP6 climate simulations support Assessment Report Six (AR6) of the Intergovernmental Panel on Climate Change (IPCC). Prof. Francois Engelbrecht, Professor of Climatology of the Wits GCI is one of the Lead Authors of the Report. He also serves on the Working Group of Numerical Experimentation (WGNE) of the WCRP, where he regularly reports on progress with the development of the first African-based Earh System Model on the CHPC Lengau cluster. Particular highlights for the second semester of 2019 include the publication of two papers with Prof. Engelbrecht as co-author, in which the CHPC support is recognised in terms of the projections of future climate change used by these papers to develop climate services for the southern African region. A second highlight is the establishment of a new climate modelling group at the Wits GCI, with a strong HCD programme in computational climatology.
Principal Investigator: Dr Gurthwin Bosman
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2019-02-26
Allocation End: 2019-08-25
Used Hours: 152730
Project Name: Quantum computations for photoinduced reactions
Project Shortname: CHEM1126
Discipline Name: Physics
The research group is one of the arms of the Laser Research Institute in the Department of Physics of Stellenbosch University. Laser Research Institute boasts research projects in the fields of ultrafast science, spectroscopy and laser diagnostics, laser development, trapped ion quantum control and biophotonics and imaging, with a number of laboratories housing ultra-modern equipment. Our research group is focussed on ultrafast transient absorption spectroscopy on chemical compounds ranging from simple molecules to polymers. Experimental setups for ultrafast transient absorption spectroscopy have been thoroughly developed over the years by different masters, doctoral and postdoctoral students. The research projects conducted in the ultrafast laboratory had produced masters' and doctoral theses, as well as peer-reviewed publications. Scientific observations being made by experiments in our research group need to be properly understood and interpreted for proper communication to the general community. Therefore, a level of theoretical simulation which will allow deeper insights is needed. We use density functional calculation, a theory well accepted to interpret molecular and/or structural dynamics that we observe experimentally. The calculations can take forever if run on a single computer. This is where the Centre for High-Performance Computing (CHPC) comes in. Centre for High-Performance Computing (CHPC) offers a wide range of theoretical coding and simulation with the advantage of supercomputing on parallel computers. This enables users' jobs submission to run on a faster scale. Our research group is privileged to have access to these supercomputing capabilities and the provision of simulation software for our calculations. We are running a series of density functional calculation ranging from simple molecules to polymers using Gaussian 09 that is provided by CHPC. Currently, we are investigating UV photoprotective compounds and their stabilizers. Initial DFT results agree well with experimental data and afford us the ability to postulate possible reaction schemes.
Principal Investigator: Prof Karl Rumbold
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2019-02-28
Allocation End: 2019-08-27
Used Hours: 4948
Project Name: Next Generation Bioprospecting
Project Shortname: CBBI1130
Discipline Name: Bioinformatics
Next-generation bioprospecting is high-throughput, data accelerated discovery of active biomolecules. The Industrial Microbiology and Biotechnology Laboratory is a leading entity in the development and application of tools and knowledge in this research field. Using data generated in the field, we have successfully identified new pathways which produce secondary metabolites. The availability of computing power is vital in the integration and analysis of gathered data.
Principal Investigator: Prof Robin Emsley
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2019-02-28
Allocation End: 2019-08-27
Used Hours: 287434
Project Name: EONCKS
Project Shortname: CBBI1064
Discipline Name: Health Sciences
The Schizophrenia Research Unit of the Department of Psychiatry, Stellenbosch University utilises high performance computing in the processing of magnetic resonance neuroimaging data. The overall aim of the unit is to contribute information on differences and similarities in brain morphology and connectivity and its role in the pathophysiology of schizophrenia spectrum disorders. Most importantly, use of high performance computing has significantly decreased the time required to process and segment out the different anatomical regions of the brain with greater sensitivity and specificity. The Schizophrenia Research Unit is therefore able to address pertinent research questions through an effective use of computational and human resources. The unit's capacity building capability is also greatly improved and adds to the development of scarce skills in the field of psychiatric research in South Africa.
Principal Investigator: Dr Dirk Swanevelder
Institution Name: Agricultural Research Council
Active Member Count: 2
Allocation Start: 2019-02-28
Allocation End: 2019-09-18
Used Hours: 8550
Project Name: Crop Genomics
Project Shortname: CBBI1141
Discipline Name: Bioinformatics
Sunflower is one of South Africa's major oilseed crops and is grown in most areas of the summer rainfall production regions. A fast growth rate and relative drought tolerance allow the crop to be planted later in the summer season when rains are delayed. This enables producers to still produce a viable profitable cropping under challenging weather conditions. The ARC's Sunflower Genomics group focuses on improving sunflower. This specific project investigates key sunflower trait development on a molecular level over time. The traits investigated play a role in the profitability of the crop and its by-products. Comparison of transcriptomic data from lines with the desired traits to those without these allows us to investigate these key economic traits as they develop in commercial and non-commercial viable accessions. We believe that this would enable us to not only identify the key role playing genes in the development of these traits, but also the expression levels of these role players required to make these traits commercially viable and the required expressional timing to obtained the desired product/traits in the crop. The CHPC's large capacity allows us to analyse and compare the transcriptome datasets of the different developmental time periods within and between the different accessions under investigation. The CHPC is central to the analyses of the large transcriptome datasets generated during our investigation. The high-throughput nature of next generation sequence data generated in the project requires the computing resources provided by the CHPC to process the data in a timeous fashion. This will allow us to determine the relevant biological answers we're seeking and help improving the crop. The large data set requires substantial time to analyses with completion envisioned soon. The CHPC is also used for a SNP discovery project on 200 plants using the ddRAD protocol.
Principal Investigator: Dr Vuyani Moses
Institution Name: Rhodes University
Active Member Count: 17
Allocation Start: 2019-02-28
Allocation End: 2019-08-27
Used Hours: 1039038
Project Name: Bioinformatics and Computational Chemistry Applications
Project Shortname: CBBI1122
Discipline Name: Bioinformatics
We are a newly created research group which falls under the Rhodes University Research Unit in Bioinformatics (RUBi). Our interests are using computational techniques to solve biological problems such as drug discovery and biofuel production.
In our research group we use the CHPC resources to perform Molecular docking in-order to identify natural compounds with the potential to inhibit a wide variety of drugs targets from various diseases such as HIV and Malaria. To validate these potential compounds, Molecular Dynamics (MD) simulations are performed. Due to complex nature of these calculations, they tend to be quite computationally expensive. As result we are heavily reliant on the CHPC for the computational power required for such calculations.
The CHPC has been an integral part of our research as most of our work is 100 % computational. Therefore our students are highly reliant on the facilities and resources offered by the CHPC to complete their research projects in due time. MSc Students which were enrolled in our one year MSc programme have successfully gone through the examination process and will be graduating next year. Of these students, most are still with us pursuing PhD degrees with research projects which are still heavily reliant on the CHPC.
As a result, access the CHPC cluster is crucial to the proper functioning of our research programme.
Principal Investigator: Dr Adeniyi ogunlaja
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 4
Allocation Start: 2019-02-28
Allocation End: 2019-08-27
Used Hours: 17325
Project Name: Chemistry and Material Science
Project Shortname: MATS1070
Discipline Name: Chemistry
Refractory polyaromatic hydrocarbons found in fuels such as dibenzothiophene, quinoline and its alkylated derivatives emits nitrous oxides and sulfur oxides to the environment when combusted, thereby reducing air quality. Desulfurization by means of oxidative desulfurization and adsorptive denitrogenation has been proposed to complement the hydrodesulfurization (HDS) and hydrodenitrogenation (HDN) processes, currently employed to remove sulfur and nitrogen compounds in fuels. At Nelson Mandela University analytical and inorganic chemistry research group, we design materials that can selectively remove these sulfur and nitrogen compounds. Molecular modelling based upon the density functional theory (DFT) was employed to understand the mode of adsorption (interaction) between synthesised materials and the various compounds to be removed from fuels. Computational study assists with the understanding of the electronic and thermodynamic properties of synthesised materials prior to application. It also gives an insight as to the specific properties to be targeted when designing adsorbents for environmental clean-up. So far, progress has been made around the design and adsorption of some toxic molecules in fuels. HPC assist our group to build models that could be employed in explaining complex phenomena. It has also enabled us to ask big questions around activity of our materials and to test for possible answers computationally. CHPC has created the platform for where researchers like me could assess the HPC and has also assisted me and my students with solving problems some computation problems.
Principal Investigator: Prof Alan Christoffels
Institution Name: University of Western Cape
Active Member Count: 3
Allocation Start: 2019-02-28
Allocation End: 2019-10-09
Used Hours: 283788
Project Name: Bioinformatics and Public Health
Project Shortname: CBBI0819
Discipline Name: Bioinformatics
Bioinformatics occupies the space between biology and computing and aims to answer questions in biology using analytical and computing methodology. At the South African National Bioinformatics Institute (SANBI), our research focus is on methods to store, retrieve and analyze genetic information that spans both communicable and non-communicable diseases. In the context of Public Health, that is a need to interrogate genetic information (DNA) from both hosts (human) and pathogens (bacterial or viruses) to understand susceptibility to diseases and ultimately to track infection trends in real time.
The ever-increasing volume of data being generated in the public domain places a strain on in-house computing resources. While the computing facility at SANBI-UWC is adequate for initial R&D, these resources are inadequate to complete projects timeously. The nature of the bioinformatics workflows that require CHPC resources can be grouped into (1) high throughput computing resources that are needed to describe the 1000s of genetic messages in a genome, versus (2) high performance computing resources that is needed to model a drug-protein interaction environment - these simulations require days/weeks of dedicated compute time.
We have leveraged the CHPC facility in the context of infectious disease research with a view to analyze genetic variation in bacterial genomes, and to identify drug targets in pathogen genomes. Our publications for the past 6 months have focused on modeling drug targets for M.tuberculosis and finding potentially new drugs against multi-drug resistant Mycobacterium tuberculosis.
Principal Investigator: Prof Fourie Joubert
Institution Name: University of Pretoria
Active Member Count: 30
Allocation Start: 2019-02-28
Allocation End: 2019-09-06
Used Hours: 103026
Project Name: NGS Bioinformatics
Project Shortname: CBBI0905
Discipline Name: Bioinformatics
Together with the Avocado genome consortium, we have embarked on a project to sequence the Avocado genome. We anticipate to create a molecular toolbox using the genome sequence data that will be utilised to unravel genetics underpinning complex traits such as disease tolerance. In addition, we are using high throughput sequencing data to identify markers of disease resistance in Avocado.
Avocado is one of the major tropical fruits exhibiting the fastest average annual growth rates among internationally traded food commodities. In recent years, Avocados have gained popularity due to their nutritional profile, coupled with the numerous health benefits that it possesses in comparison to other fleshy fruits. One of the most significant threat to Avocado production is Phytophthora root rot caused by the pathogen Phytophthora cinnamomi. Control and management of Phytophthora root rot spread remains a challenging endeavour. A better understanding of P. cinnamomi molecular or cellular make-up during infection will lead to novel targets for precise and viable control measures while, understanding Avocado defense responses to pathogen attack will lead to development of root stocks that do not succumb to infection. The results generated by these studies have provided a catalogue of potential pathogenicity factors of P.cinnamomi and defense-related genes in Avocado. These defense-related genes will be invaluable for future identification of markers for improved rootstock breeding and screening.
The Avocado research project activities that make use of CHPC resources involve
(i) assembly of the root transcriptome of Avocado. This data is being used by the Avocado genome consortium to identify protein-coding regions of the draft Avocado genome.
(ii) Functional assignment of the draft Avocado genome sequence peptide sequences.
Principal Investigator: Prof Rosemary Dorrington
Institution Name: Rhodes University
Active Member Count: 6
Allocation Start: 2019-02-28
Allocation End: 2019-10-09
Used Hours: 10312
Project Name: Marine Natural Products Research
Project Shortname: CBBI0963
Discipline Name: Bioinformatics
Marine Natural Products Research Group, Department of Biochemistry and Microbiology, Rhodes University
The Marine Natural Products Research Platform covers the broad field of marine biodiscovery, focusing on the potential of bioactive secondary metabolites produced by marine organisms endemic to the Agulhas Bioregion as lead compounds for drug discovery. Overview and aims More than half of new pharmaceutical drugs on the market or in clinical trials are natural products and their derivatives and the majority of these are now coming from marine macrofauna and their associated microbiomes. The Maine Natural Produces research programme is active across the broad field of marine biodiscovery, focusing on exploring the potential of marine invertebrates and their associated microorganisms as sources of novel bioactive small molecules. Research projects include: (1) Biodiversity mapping of benthic habitats in the Agulhas bioregion, focusing on invertebrates, ascidians, soft corals and their associated microbiota; (2) Isolation and characterization of bioactive secondary metabolites of marine organisms; (3) screening marine natural product libraries for anti-viral, anti-cancer and antibacterial activity and (4) elucidating the metabolic pathways that result in the production of lead compounds to pave the way for engineering recombinant systems for their production for the pharmaceutical industry. Associated projects focus on the application of high throughput metagenomic and analytical chemistry technologies to map patterns and processes in marine ecosystems to provide tools for sustainable development of our ocean economy. All of these research activities require access to high performance computing facilities to curate, process and analyse large Next Generation Sequencing (NGS) datasets. Primarily, we have used the CHPC facilities to analyse NGS amplicon library data to characterise the microbial communities of both marine and terrestrial systems.
Principal Investigator: Prof Paulette Bloomer
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2019-02-28
Allocation End: 2019-09-13
Used Hours: 53681
Project Name: Molecular Ecology and Evolution Programme
Project Shortname: CBBI1030
Discipline Name: Bioinformatics
The Molecular Ecology and Evolution Programme (MEEP) is a research group in the Division of Genetics, Department of Biochemistry, Genetics and Microbiology at the University of Pretoria. We investigate the evolutionary history and current genetic diversity of many vertebrate species (marine and terrestrial), using genetics and genomics tools, and try to link the patterns we see with ecological and human-mediated events. We currently have two projects (Cape buffalo and bowhead whales) that make use of the CHPC resources, with additional projects in the pipeline.
Genomics of Cape Buffalo is a hot topic, and is of interest to the general public and wildlife ranchers in particular. Cape buffalo are bred on private game ranchers for a one or a few economically important traits, such as horn length and body size. The effects of this artificial selection, as well as breeding South African buffalo with East African buffalo, is unknown. We can use genomics to evaluate the risks and benefits of these practices for the short and long term (evolutionary) conservation prospects of the species
The genetic work on the bowhead whale uses empirical and simulation data to investigate the effects that different Nearctic human cultures exploiting the whale had on the abundance of the population. This means that genetic data may have more resolution than previously thought and is sufficient to detect subtle changes in population size in relation to exploitation and climate change. This is of great importance as there are many applications. We believe that the work will have sufficient impact to be of interest to the general public in South Africa and internationally.
Principal Investigator: Prof Bettine van Vuuren
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2019-02-28
Allocation End: 2019-10-09
Used Hours: 1956
Project Name: Biocomplexity on sub-Antarctic islands
Project Shortname: CBBI1153
Discipline Name: Bioinformatics
- We are a research group at the Centre of Ecological Genomics and Wildlife Conservation based at the University of Johannesburg, South Africa.
- We are conservation geneticists and are interested in studying spatial and temporal genetic patterns in multiple organisms (plants, invertebrates, microbes) on sub-Antarctic islands, with a special focus on Marion Island. We aim to investigate genetic patterns and structure in the context of environmental changes (for example, climate change). We intend on using our study species as proxies for monitoring global change and its impact on biodiversity as a whole.
- We are well aware of the concept of environmental change (such as climate change, which is more pronounced in the sub-Antarctic region). As conservation geneticists, we will investigate the impact that change has on biodiversity. Understanding genetic patterns is crucial, and our results will bring about far-reaching implications for the development of conservation management programs for Marion Island and on a global scale too.
- To do this, we will be generating next-generation sequencing (NGS) data using various approaches. We will use the CHPC cluster to generate our NGS data, and phylogenetic and population genetic analyses. The above mentioned data is exceptionally large, and therefore we will not be able to conduct our research without the CHPC resources since no other platforms can handle these large datasets.
- We have assembled and annotated the mitogenome of three springtail species, and have also compared the genetic structure of plant species from two sub-Antarctic islands. These have all been published in peer review journals. We are in the process of writing two publications that will investigate the spatial and temporal genetic patterns of several species on Marion Island. In the near future, we hope to publish at least 5 additional articles.
We are happy with the progress we have made thus far and thank the CHPC for this (the CHPC has been acknowledged in the publications).
Principal Investigator: Dr Rian Pierneef
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2019-02-28
Allocation End: 2019-09-11
Used Hours: 25764
Project Name: Bioinformatic and Computational Biology analyses of organisms
Project Shortname: CBBI1124
Discipline Name: Bioinformatics
The research group "Bioinformatic and Computational Biology analyses of organisms" is interested in any and all data analysis of biological origin. It is based at the Agricultural Research Council's (ARC) Biotechnology Platform (BTP). The BTP is a cutting edge research facility, housing numerous state of the art sequencing systems. These sequencing systems produce a myriad of biological data types and structures which require skilled analysis and sufficient computational resources. This project aims to answer various biological questions using the most recent data producing technologies. This includes, but is not limited to, analysis within the food production sector and the environmental landscape. The CHPC is of critical value to this project as it contains the needed computational support and the availability all currently used software programs. The CHPC enables this research project to make strides within the research community with results forthcoming out of this project being advantageous to the population at large.
Principal Investigator: Dr Uljana Hesse
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2019-02-28
Allocation End: 2019-08-27
Used Hours: 66104
Project Name: Medicinal Plant Genomics
Project Shortname: CBBI1133
Discipline Name: Bioinformatics
Knowledge on the genomic background of rooibos, an endemic South African medicinal plant, can help to identify biosynthetic pathways involved in the production of medicinal compounds; and genes associated with biotic and abiotic stress resistance of the plant. The rooibos genome has been sequenced by the research team of Dr Uljana Hesse, Department of Biotechnology, University of the Western Cape. The genome assembly is conducted at CHPC, which provides the extensive computational resources essential for plant genome assembly. Currently, one MSc student is involved in bench-marking biocomputational procedures for genome assembly and evaluation of genome characteristics towards establishing a computational pipeline for high-throughput plant genome assembly and annotation.
Principal Investigator: Dr Ruben Cloete
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2019-02-28
Allocation End: 2019-08-27
Used Hours: 25306
Project Name: HIV-1C integrase drug resistance
Project Shortname: CBBI1154
Discipline Name: Bioinformatics
The laboratory group of Dr Ruben Cloete is based at the South African National Bioinformatics Institute, University of the Western Cape. The work in my group is primarily focussed on molecular modelling and drug design. Here we focus on protein structure prediction, molecular docking and simulation studies of protein-drug, protein-protein systems. Our research efforts is in understanding HIV-1 drug resistance, identifying novel drugs to treat drug resistant Tuberculosis and the prioritization of novel genes associated with Parkinson's disease in South African families. This work has led to the identification of new drugs to treat Tuberculosis. Furthermore, ongoing work might also contribute to the understanding of the development of Parkinson's disease and the better management of HIV-1 infected individuals within South Africa. For this to become a reality requires the use of structural computational methods to understands the movement of the molecular machinery of the cell called proteins. For this large computing resources are required to run large protein systems. Currently we are in the process of submitting several protein structures to the CHPC for simulation analysis. We may even require more resources.
Principal Investigator: Dr Leigh Johnson
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2019-02-28
Allocation End: 2019-08-27
Used Hours: 219030
Project Name: MicroCOSM: Microsimulation for the Control of South African Morbidity and Mortality
Project Shortname: HEAL1049
Discipline Name: Health Sciences
The MicroCOSM project, based at the Centre for Infectious Disease Epidemiology and Research at the University of Cape Town, is a project to simulate the spread of infectious diseases, as well as the incidence of non-infectious diseases, in the South African population. By simulating the social and biological factors that contribute to disease transmission, we can better understand which sub-populations need to be targeted for special interventions. We can also evaluate the impact that various prevention and treatment programmes have had in South Africa to date, and evaluate the potential impact of new programmes. This simulation involves generating nationally representative samples of 20,000-40,000 South Africans and tracking them over their life course. Because this involves many individual-level calculations, the model requires substantial computing power, and the CHPC is therefore critical to the conduct of these simulations. We have recently published two papers about interactions between human papillomavirus (HPV) and HIV, and the impact of HPV vaccination.
Principal Investigator: Prof Carlos Bezuidenhout
Institution Name: North-West University
Active Member Count: 13
Allocation Start: 2019-02-28
Allocation End: 2019-09-23
Used Hours: 87439
Project Name: Metagenomics studies of Microbes
Project Shortname: CBBI0890
Discipline Name: Other
Researchers in the Aquatic and Terrestrial Microbiology research group at the North-West University in Potchefstroom are using the CHPC facility to analyse large data sets. The programme involves amongst others: Whole genome mapping of bacteria for horizontal gene transfer; Whole genome mapping of a novel Xanthomonas plant pathogen; Mapping of plasmids; Microbiome analysis of agricultural soils; Microbiome analysis of water and sediment Environmental metagenomics of drinking water production facilities; Transcriptome analysis of Bt Resistant Busseola fusca. The research focus on water and food security and safety. These are important issues and obtaining local data is critical. Whereas large data sets could be generated quite routinely it is the data mining and analysis that requires sufficient computing capacity, such as that provided by the CHPC. Several papers had been published or are in the final draft stage. Having this capacity also provide this research group (CBB10890 – Metagenomics studies of Microbes) with competitive advantage in applications for funding.
Principal Investigator: Prof Thulani Makhalanyane
Institution Name: Stellenbosch University
Active Member Count: 6
Allocation Start: 2019-02-28
Allocation End: 2019-08-27
Used Hours: 4185
Project Name: Metagenomics of extreme environments
Project Shortname: CBBI1023
Discipline Name: Bioinformatics
The Marine microbial ecology group at the University of Pretoria have initiated a series of projects aimed at elucidating the microbiomes of environmentally extreme habitats. As a consequence, several large scale metagenomic datasets have been generated and sequenced. We are currently using the resources at the CHPC to assess these datasets with a range of diverse research questions. For instance, a core question relates to the prevalence of antibiotic resistance across pristine environments.
Principal Investigator: Prof Liliana Mammino
Institution Name: University of Venda
Active Member Count: 4
Allocation Start: 2019-03-01
Allocation End: 2019-09-06
Used Hours: 543789
Project Name: computational study of biologically active molecules of natural origin
Project Shortname: CHEM0959
Discipline Name: Chemistry
WHO? One professor (Liliana Mammino), and her postgraduate students doing computational chemistry research in the School of Mathematical and Natural Sciences at the University of Venda (UNIVEN).
WHAT? We are studying various molecules of natural origin having biological activities, to compute their molecular properties.
WHY? Because the more we know about the properties of molecules, the more we can understand about their activities or use the information to predict the properties of new molecules. This is very important for drug design. In turn, the design of new, effective drugs to treat diseases is important because of its significance for people's health.
HOW? We use specialised software to compute the molecular properties and then we analyse and compare the results. The availability of CHPC enables us to make calculations that will take too long otherwise, thus enabling us to obtain many more results in a shorter time, including results that we would never be able to obtain on PCs because of the size of some of the molecular structures that we are considering.
HOW IS THE PROJECT PROGRESSING? It is progressing according to plans, and we are quite satisfied with the results obtained so far. Whenever we obtain new results, other research questions come to light, which makes the project more and more interesting.
We are also publication-oriented, that is, we publish our results in international journals, making sure that each publication contains enough information to have up-to-standard quality. Furthermore, we present our results in an international conference before finalising an article for publication, to have interesting feedback from the conference participants. This is particularly important in a situation like ours, with only one expert present in the group.
Principal Investigator: Dr Jaco Badenhorst
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 2
Allocation Start: 2019-02-28
Allocation End: 2019-09-11
Used Hours: 28425
Project Name: Automatic transcription of broadcast data
Project Shortname: CSIR0978
Discipline Name: Other
The Human Technologies (HT) Research Group at the CSIR Next Generation Enterprises and Institutions Cluster develop speech and language-related technologies for the South African context to enhance access to information and communication. Given the multilingual nature of South Africa, human language technologies (HLTs) can make information and services accessible to a larger proportion of the South African population in a sustainable way, by reaching people in remote locations, people who are not necessarily trained in using technology, or people who are not fluent in English. HLTs can also provide access to information to people with disabilities. HLT can support language diversity and providing of information in multiple languages in an affordable and equitable fashion. The development of all 11 official languages is a national priority, which requires significant attention to HLT in all of these languages. HLT can be of significant economic importance – both by empowering citizens of the country to work more productively, and by forming the core of an exportable set of technologies (since such technologies are currently not available to most of the developing world). The HT Research Group operates in a vibrant environment consisting of researchers, developers, project managers and students from backgrounds as diverse as engineering, linguistics and sociology. We conduct basic and applied research into projects related to the following areas of research: automatic speech recognition, text-to-speech synthesis, natural language processing, machine translation, human language analytics, text and speech resource development, speech and language technology system design and implementation, and usability and user experience evaluation of speech and language technology.
Principal Investigator: Prof Evans Adei
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 7
Allocation Start: 2019-03-04
Allocation End: 2019-09-05
Used Hours: 800584
Project Name: Materials For Energy and Fine Chemicals
Project Shortname: CHEM1046
Discipline Name: Chemistry
Three KNUST Kumasi Ghana students are involved in a Royal Society-DFID sponsored collaborative research and training that aims to train a cadre of African scientists in the use of state-of the-art computer modelling and advanced experimental techniques to design, develop new materials for solar cells and energy storage devices and the production of low-carbon sustainable fuels or chemical feedstock.
The initiative seeks to foster a sustainable research networks between research groups/Laboratories in the sub-Saharan Africa (University of Botswana, University of Namibia and KNUST Kumasi Ghana) and the UK (University of Cardiff) in order to strengthen research and training capacity in sub-Saharan African institution higher education through skills transfer between partner organizations of the research consortia.
The 800,000 CPU hrs allocated by CHPC to to our research group over this review period has appreciably increased our students' productivity. With our limited HPC resource here at KNUST Kumasi Ghana and our increasing undergraduate research students in addition to our postgraduate students the CHPC resources have been of immense help to us. It is our hope that CHPC will continue to support us with HPC resources in the short and medium terms to enable us to use more realistic models in our calculations. Our undergraduates have really taken advantage of the CHPC resources; Grace Arhin, one of them has recently published a paper emanating from her research work in the Journal of Molecular Graphics and Modelling, https://doi.org/10.1016/j.jmgm.2019.08.004. One of our students' Elliot Menkah graduated with a Ph.D. this year; he also earned a Master's in High performance computing degree from the joint ICTP-SISSA programme last year. Elliot is likely to take up a postDoc position here at KNUST Kumasi in the 2019/2020 academic year and
the addition will enhance our high performance computing human resource capacity as an Institution. The research work of two of our students on the Royal Society - DFID programme is progressing steadily and expect them to graduate for the Ph.D.programme next year. The CHPC will certainly be duly acknowledged in publications emanating from our research work and relevant reports.
Principal Investigator: Dr Chris Stevens
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2019-03-04
Allocation End: 2019-08-31
Used Hours: 16942
Project Name: Cauchy Characteristic Matching, and Other Uses of the Characteristic Method in Numerical Relativity
Project Shortname: ASTR1202
Discipline Name: Applied and Computational Mathematics
This work on Cauchy Characteristic Matching (CCM) is being done by Professors Nigel Bishop and Denis Pollney, and myself Dr Chris Stevens, all of Rhodes University.
With the recent detections of black hole and neutron star mergers, fast and accurate numerical simulations of these events are more and more useful. This project aims at implementing a computational method to simulate these systems, CCM, which has never been successfully implemented for these cases before.
Due to the computational strain of performing such a simulation, a HPC facility is required.
Principal Investigator: Dr Kevin Lobb
Institution Name: Rhodes University
Active Member Count: 10
Allocation Start: 2019-03-04
Allocation End: 2019-08-31
Used Hours: 610047
Project Name: Computational Mechanistic Chemistry and Drug Discovery
Project Shortname: CHEM0802
Discipline Name: Chemistry
The generation of virtual chemical libraries aids in drug discovery. In the virtual world you can test uncountably more compounds against various diseases than you could possibly do experimentally. However an issue that further complicates the landscape is the issue of conformation, or how molecules have to fold or twist to be able to work against disease targets. This research has made inroads on how a particular compound, cyclosporine, folds and interacts with targets in the search for reperfusion injury treatments.
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 0
Allocation Start: 2019-03-04
Allocation End: 2019-09-13
Used Hours: 266960
Project Name: Magnetocaloric effect in selected metallic nanoclusters on two-dimensional (2D) substrates, and in selected rare-earths.
Project Shortname: MATS1156
Discipline Name: Material Science
The research study is based at the College of Science, Engineering and Technology of the University of South Africa (UNISA). The study concerns fundamental study and potential applications of two-dimensional (2D) nanomaterials in ultrathin refrigeration, air-conditioning system, and in cooling of nanoelectronic devices or any system where nanoscale cooling is envisaged. Specifically, the research aims to study the phenomenon of magnetocaloric effect (MCE) in metallic nanostructures deposited on various two-dimensional substrates, such as graphene, silicene, and similar 2D materials. Magnetocaloric effect is a property of magnetic materials which could be exploited for refrigeration purposes. While the conventional refrigerator system is based on compression and evaporation of often environmentally unfriendly gases, magnetic refrigeration systems is based on magnetising and demagnetising a magnetic material.
In the last few years, the focus in magnetocaloric research seems to have shifted toward ultrathin materials. Because of plethora of candidate materials that may be investigated as possible candidates for MCE, performing experimental investigations may be time and resources consuming, and thus, computational studies could provide the lead and narrow the range of materials that could be considered for further experimental investigations. Performing ab-initio density-functional theory (DFT) study to determine the properties of candidate material systems is a viable and state-of-the-art approach which can complement experimental efforts. DFT calculations require specialized softwares as well as high-capacity data storage and memory requirements which are often beyond the capability of desktop computers. Thus, the availability of high-performance computing (HPC) facility is absolutely necessary.
The project has progressed to the extent that we have characterized a model systems consisting of small vanadium clusters embedded in 2D silicene for their stability and magnetic properties. This provides us with fundamental understanding of structure-magnetization relationship in vanadium-silicene system which will assist in further work on properties and MCE effect in metal-silicene nanocomposite systems.
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 12
Allocation Start: 2019-03-06
Allocation End: 2019-09-02
Used Hours: 3707955
Project Name: Structural, electronic, magnetic properties and anisotropy energy in some metallic and non-metallic heterostructures
Project Shortname: MATS0988
Discipline Name: Material Science
The focus of the research is on the design and simulations of materials having novel electronic, optical, transport and magnetic properties with potential applications in high-capacity data storage, catalysis and renewable energy. We employ density-functional theory (DFT) to probe atomic level properties of nanomaterials of interest, ranging from metallic heterostructures, metallic-oxide on surfaces, organic molecules on surfaces, rare-earth transition-metal compounds, and two-dimensional (2D) materials such as graphene and silicene. Fundamental understanding of properties of these materials systems is necessary to support experimental research and to aid technological applications. The numerical implementation of DFT is computational intensive, requiring several computational hours, large data storage and memory requirements, beyond the capacity of ordinary table-top computers.. Therefore, high-capacity computer clusters such as the one provided by the Center for High Performance Computing (CHPC) is sine-qua-non to the research. The research which is ongoing, involves Dr. Abdulrafiu Raji of the University of South Africa (UNISA) and Dr. Malonda Boungou of Marien-Ngouabi University, Republic of Congo. Twelve postgraduate students are involved in various aspects of the work. At the moment, two Masters students have completed their studies and are continuing to doctorate. The research, as well as the CHPC, has enabled collaboration between South Africa based academic and colleagues in Congo, Mexico and Italy. A research paper [i.e. B. R. Malonda-Boungou, S. Meza-Aguilar, A. Debernardi and A. T. Raji, Computational Condensed Materials, 19, e00368 (2019)] have just been published. Another paper[ C.L. Malonga Matanou, B.R. Malonda-Boungou, M. N'dollo, M.D. Nkoua Ngavouka, P.S. Moussounda, A.T. Raji and B. M'Passi Mabiala, Journal of Physics and Chemistry of Solids, (2019)] have been accepted and in the production process. In these papers, we explore the stability and magnetic properties of metallic and non-metallic nanostructures, and elucidate the atomic level mechanism underpinning the observed phenomena.
Principal Investigator: Prof Joanna Dames
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2019-03-06
Allocation End: 2019-09-18
Used Hours: 6474
Project Name: Mycorrhizal Interactions
Project Shortname: CBBI0966
Discipline Name: Bioinformatics
The Mycorrhizal Research group is based at Rhodes University, Grahamstown.
Mycorrhizal fungi form a symbiotic relationship with the roots of the majority of plant species. The interaction between these soil fungi, other soil microbes and plants results in many beneficial growth effects making an important contribution to sustainable agriculture, horticulture, and environmental rehabilitation. There are several types of mycorrhizal relationships depending on the fungi and host plants involved. Little is known about the biodiversity of these fungi in South African soils. The use of next-generation sequencing provides an opportunity to unravel this biodiversity in order to better understand factors which impact on the relationship. The CHPC platform has assisted in analysis of biodiversity of fungi in general and mycorrhizal fungi in particular as well as some interactions with soil bacteria.
Principal Investigator: Prof Daniel Joubert
Institution Name: University of the Witwatersrand
Active Member Count: 19
Allocation Start: 2019-03-06
Allocation End: 2019-09-02
Used Hours: 5915333
Project Name: Energy Materials: Numerical explorations
Project Shortname: MATS0800
Discipline Name: Physics
Imagine designing a material atom by atom. Imagine analysing the properties of tomorrow's novel materials before they exist. Computational materials science plays an important role at every of level of the design and engineering of new materials. The rapid advances in computer processing power and memory has given virtual, fundamental, materials design a boost. The first problem faced in designing a virtual material, a material that has not yet been made, is to find the stable configurations in which the atoms in the mix will settle into. The designer must find the configuration of electrons and nuclei, the building blocks of atoms, which result from the interactions among a number of particles that, even for a small piece of material, exceeds the number of particles of sand on all the beaches in the world. This daunting task has a simple solution. Instead of finding the configuration of the real material, the problem is solved for a fictitious material where the constituent particles do not interact. All that is necessary is to find the particle density distribution of the fictitious material, which by design, is the same as that of the real material. A Noble prize was awarded for this idea to the chemists Walter Kohn and John Pople in 1998.
A group of postgraduate students at the University of the Witwatersrand use the computer power at the national Centre for High Performance Computing to conduct virtual experiments on existing and novel materials to examine their potential as energy harvesters. They examine the potential of a selection of materials that can be used as cheap components in solar cells, materials that can generate electricity from waste heat and materials that can be used to split water molecules to extract hydrogen for energy production.
Principal Investigator: Prof Sanushka Naidoo
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2019-03-06
Allocation End: 2019-09-02
Used Hours: 79757
Project Name: Eucalyptus and Pine Pathogen Interactions
Project Shortname: CBBI1057
Discipline Name: Environmental Sciences
The Eucalyptus and Pine Pathogen Interactions research group, from the University of Pretoria, focuses on investigating the molecular interactions of economically important forest tree species with pests and pathogens of interest to the South African forestry industry. One of the most pressing threats to global pine cultivation is the pitch canker fungus, Fusarium circinatum, which can have a devastating effect in both the field and nursery. Many strategies are currently employed to manage F. circinatum in the field and nursery, with limited success. Investigation of the host-pathogen interaction between Pinus spp. and F. circinatum is crucial for development of effective disease management strategies. To this end, RNA-sequencing data was generated for six pine species, with varying levels of resistance, during F. circinatum challenge. As with many non-model organisms, however, investigation of host-pathogen interactions in Pinus spp. is hampered by limited genomic resources. Fortunately, advances in bioinformatics has made it possible to leverage the inherent redundancy in next generation sequencing data to assemble the reference transcriptome. A transcriptome assembly and annotation work-flow was established on the CHPC using data for Pinus pinaster. The CHPC is an essential platform that allows access to the tools needed for the generation of high quality transcriptomes and the analysis of differential gene expression. The established work-flow for P. pinaster is being used to investigate host responses for the remaining species to allow comparison of host responses between species and has also been applied to Pinus nigra challenged with Diplodia pathogens.
Principal Investigator: Dr Gwynneth Matcher
Institution Name: Rhodes University
Active Member Count: 5
Allocation Start: 2019-03-06
Allocation End: 2019-09-02
Used Hours: 4174
Project Name: Microbial Ecology in Antarctic and aquatic ecosystems
Project Shortname: CBBI0952
Discipline Name: Environmental Sciences
My research group, based at Rhodes University (Makhanda), focuses on microbial ecology in Antarctic ecosystems. Antarctic ecosystems are characterised by extreme conditions which impose significant pressures on the ability of fauna and flora to survive. In the majority of these ecosystems, the dominating life form is microbial. Despite the fact that these delicate ecosystems are almost entirely driven my microbiota, almost nothing is known about them. These ecosystems are particularly vulnerable to climate change which alter the biodiversity and functional richness of microbial soil populations resulting in significant impacts on ecosystem functioning as a whole. Furthermore, human impacts threaten the biota present in Antarctica. Due to Antarctica's geographical isolation, lack of indigenous people and harsh climate, the misconception exists that Antarctica remains a pristine environment. While this certainly holds true for rarely visited sites, increasing human presence has dramatically exacerbated the anthropogenic impact on the biodiversity. The introduction of non-indigenous microorganisms into these delicate ecosystems has several serious and long-standing ramifications including the extinction of endemic species due to dominance by invasive species. Assessing anthropogenic impacts is thus of critical importance and research to this end will inform future environmental protection policies in Antarctica. Metagenomics, which is utilised to assess the microbial populations in this project, involves sequencing and analysis of the total genetic material in a given environment. This allows for identification of species present as well as providing information of the impact of environmental drivers. The computational analyses are conducted on the CHPC cluster. To date, this project has investigated the effect of invasive Sagina plants on soil microbiota on Marion Island as well as proving detailed microbial profiles from several nunataks in Dronning Maudland which had never been characterised before. While the anthropogenic impacts on Marion Island were clearly evident, the inland nunataks investigated in this study appear to be more vulnerable to climate change.
Principal Investigator: Prof Christine Lochner
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2019-03-06
Allocation End: 2019-09-13
Used Hours: 6148
Project Name: Compulsivity-Impulsivity
Project Shortname: HEAL0907
Discipline Name: Imaging
A key criticism of the Diagnostic and Statistical Manual of Mental Disorders (DSM) is that although it is useful for research and in the practice, its criteria are based upon the description of superficial behavioural signs and symptoms but lacks a biological footing. Recent years have witnessed increasing attempts to address inclusion of biological data that may be similar across disorders. So instead of focusing on behavioural symptomatology only, the current trend is to consider 'neurocognitive endophenotypes', such as compulsivity and impulsivity, that may be derived from neuroimaging data instead of using behavioural data only, and using them 'transdiagnostically', to identify commonalities across disorders. With this project we aim to explore these proposed endophenotypes further by focusing on three psychiatric disorders with apparent compulsive / impulsive features (i.e. obsessive-compulsive disorder, gambling disorder and substance use disorder). Findings may contribute to our understanding of the underpinnings of disorders with such characteristics, and may also render data that are useful in treatment.
The project renders an opportunity for different units - i.e. from Stellenbosch University (e.g. MRC Unit on Risk and Resilience in Mental Disorders, the Department of Psychiatry), the University of Cape Town (the Department of Psychiatry and Mental Health) and the Cape Universities Brain Imaging Centre (CUBIC) to collaborate. The research team thus includes basic scientists, neuroimaging experts, researchers with M-degrees in Research Psychology, a clinical psychologist, a general practitioner and a psychiatrist.
The work is crucially important in establishing expertise in South African neuroimaging, and specifically with regards to structural imaging, diffusion tensor imaging (DTI), magnetic resonance spectroscopy (MRS) and functional MRI in psychiatric disorders.
CHPC creates a user-friendly platform for creating the scripts required to run the Tortoise and other methods used for analysis of MRI data. The project is funded by the National Research Foundation of SA.
Principal Investigator: Prof Mario Santos
Institution Name: University of Western Cape
Active Member Count: 19
Allocation Start: 2019-03-06
Allocation End: 2019-09-02
Used Hours: 968789
Project Name: Cosmology with Radio Telescopes
Project Shortname: ASTR0945
Discipline Name: Astrophysics
The Centre for Radio Cosmology (CRC) at UWC aims to fully explore the use of the next generation of radio telescopes for measurements in cosmology, in particular with MeerKAT and SKA. CRC staff is closely involved in the South African and international SKA projects. About 10 postdoctoral researchers and 10 PhD/MSc students are doing their research within the CRC. Our work at the CHPC is mostly focused on running simulations of signals we expect to observe with MeerKAT/SKA and test how well radio telescopes can constrain certain cosmological models. This is a crucial component in the process to use these telescopes for cosmology since we need to understand the signals we are observing. The project include simulations of the hydrogen emission from the early universe, simulations of the contaminants, simulations of the telescope itself and analysis of the constraining power of such telescopes on cosmological models.
Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 4
Allocation Start: 2019-03-07
Allocation End: 2019-09-18
Used Hours: 48706
Project Name: African Multi-Omics Data Science
Project Shortname: CBBI1039
Discipline Name: Bioinformatics
CBBI1039: UCT Applied Genomics (AGe) is a training programme, running from the University of Cape Town, South Africa. This research programme is fundamentally aiming 1) to provide postgraduate students with the knowledge skills and bioinformatics tools they need to understand the models of medical population genetics and of computational molecular biology; 2) to enable graduate students at the University of Cape Town, across the country and African continent to be able to relate the models and data of statistical genetics to the constraints of inheritance and the molecular mechanisms of genetic data, including DNA sequence data, next generation sequences and to develop the skills to work with these massive data sets. 3) to solicit the assistance of CHPC, South Africa, Cape Town in training the trainers along this proposed programme to efficiently use the resources and master the portable bash servers (PBS) and the implementation of large scale genomic project under CHPC's resources. The accumulation of experimental DNA data in Biology and new high throughput experiments are growing rapidly and give a huge number of data difficult to manage, to store and to analyse this existing and future dispersed information. Therefore, high-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring the field of bioinformatics to use high-performance computing resources and carry out data management and analysis tasks on large scale. Today, the use of HPC has increased our training portfolio to meet the international standard with respect to large scale genomic era in training and increasing data analysis skills of our students and other trainees across the continent. This programme has developed several genomic-based, Bioinformatics, programming courses that address the African training needs around large-scale genomic data in order to meet the international standard required in this field.
Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 21
Allocation Start: 2019-03-07
Allocation End: 2019-09-18
Used Hours: 1333458
Project Name: Computational and statistical methodologies for human and environmental health prediction
Project Shortname: CBBI0818
Discipline Name: Bioinformatics
Computational and statistical methodologies for human and environmental health prediction research programme (CBBI0818) is running from the University of Cape Town, South Africa. This research programme is fundamentally aiming 1) to determinate the environment and genetic variation that cause human species to look different, having difference in allergy, drug responses and treatment. 2) to identify and quantify the pattern of inheritance of the observed trait, drug response and treatment variation among human. These are addressed through the design of machine intelligence and artificial intelligent methodologies and statistical approaches to analysis DNA data of thousands affected/unaffected subjects within a geographical region. In doing so, this programme will contribute to human health by increasing understanding of the genetic and environmental underpinnings of complex traits (or diseases), drug/treatment responses and drug/dosage responses and forecasting individual's health and traits such as the weather is forecasting today. The accumulation of experimental DNA data in Biology and new high throughput experiments are growing rapidly and give a huge number of data difficult to manage, to store and to analyse this existing and future dispersed information. As really DNA data become more and more available and big, better the health prediction is, therefore there is a critical need for national life and long -term storage and robust fast accessible memories.
Today, the use of HPC has critically increased our researcher portfolio to meet the international standard with respect to large scale genomic era. This programme has already developed a number of genomic-based software tools that address African genetic variation challenges and provided advanced trainings around parallel programming with respect to large-scale genomic data to African postgraduate students/researchers.
Principal Investigator: Prof Gerard Tromp
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2019-03-07
Allocation End: 2019-09-18
Used Hours: 45164
Project Name: South African Tuberculosis Bioinformatics Initiative
Project Shortname: CBBI0999
Discipline Name: Bioinformatics
The CHPC is an extremely valuable computational resource for teasing apart how the human body reacts to tuberculosis. We use it to analyse gene expression of human cells to identify pathways that increases our understanding of the disease process and could lead to new approaches for treatment of TB. This work would not be possible without the CHPC.
Principal Investigator: Dr Samuel Iwarere
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2019-03-07
Allocation End: 2019-09-03
Used Hours: 22975
Project Name: Understanding Plasma-Liquid Interaction
Project Shortname: MECH1107
Discipline Name: Chemical Engineering
The research is being carried out under the guidance of the Dr. Samuel Iwarere based in the School of Chemical Engineering at the University of KwaZulu-Natal. The understanding of plasma-liquid interactions is of prime importance in the context of environmental remediation and wastewater treatment applications. Plasma treatment of wastewater involves complex chemical and physical phenomena, which makes the comprehensive modelling of phenomena such as gas phase reaction, turbulence and heat transfer a difficult task. In order to gain insight into the complex processes associated with the use of plasma wastewater treatment, Computational Fluid Dynamics (CFD) will be used to study the relevant chemistry and fluid dynamic effects at the plasma-liquid interface. The Centre for High Performance Computing (CHPC) allows for calculation within realistic time frames, allowing the researchers to determine the accuracy of the unsteady state simulations encountered in plasma physics. Simulation of the plasma arc is in the early stages with problems being encountered with the definition of the electromagnetism.
Principal Investigator: Mrs Chantel Niebuhr
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2019-03-11
Allocation End: 2019-09-07
Used Hours: 241110
Project Name: Hydrokinetic turbine analysis
Project Shortname: MECH1174
Discipline Name: Other
The Hydropower research group at the University of Pretoria has ventured into the use of CFD modelling to develop simplified wake and damming models for the installation of hydrokinetic turbines within canal systems. After completing the first modern hydrokinetic installation in South Africa it was noted that for further development, the hydrodynamics must be well understood, and easily predictable. Due to this validated CFD models were developed in Siemens STAR-CCM+ simcenter to allow analysis of the damming and wake effect or varying installation conditions to define the hydrodynamic boundaries and allow prediction of these effects for any installation initial feasibility study. Due to the turbulent nature of the wake, complex and large models are necessary. The CHPC has allowed solving of these meshes which would otherwise require extremely long solution time, and may not be feasible or possible in the study time frame. This study allows UP to be competitive, if not ahead, of many leading research institutions due to the solving possibilities allowed by the CHPC, and will allow generation of models which will be used world wide for inland hydrokinetic development.
Principal Investigator: Prof Beatriz Garcia de la Torre
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2019-03-11
Allocation End: 2019-09-07
Used Hours: 265739
Project Name: Peptide Chemistry
Project Shortname: CHEM1090
Discipline Name: Chemistry
Peptide science lab at UKZN, Westville works on discovery of new peptides and their therapeutic applications. The current work calculations carried out in chpc is the interaction of peptides with metal ions and their therapeutic application as drugs for bacterial infection. All the abinitio calculation for this project has been done in chpc cluster and the manuscript for this project is under preparation.
Principal Investigator: Prof Gert Kruger
Institution Name: University of KwaZulu-Natal
Active Member Count: 11
Allocation Start: 2019-03-13
Allocation End: 2019-09-09
Used Hours: 564839
Project Name: CPRU molecular modeling
Project Shortname: HEAL0839
Discipline Name: Health Sciences
(Who) The Catalysis and Peptide Research Unit at UKZN (http://cpru.ukzn.ac.za/Homepage.aspx) is currently working on the mechanism of action on both HIV PR and TB (transpeptidases) with respect to the natural substrates.
(What) We use an quantum chemical/molecular mechanics hybrid (Oniom) approach that gives us high level results on the thermodnamics and kinetics of the reaction. Our model enables us to study application of both electronics and sterics to change the bond strenght and binding energies of new potential inhibitors.
The same approach is followed for transpeptidases, essential enzymes for the inhibition of TB.
(Why) HIV is a major health threat in SA and new drugs is required due to the constant development of drug resistance. Similarly, TB and TB co-infection with HIV is a mojor health issue.
(How) Our theoretical studies will allow us to test a computational model that correctly describes the interactions between the respective enzymes and existing drugs. We are improving our computational model to the extent where are now in a position to start proposing new potential drug leads for synthesis. This can only be done with large computational resources provided by the CHPC. We are also expressing the enzymes inhouse for verification of our computational results.
Principal Investigator: Dr Jaap Hoffmann
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2019-03-14
Allocation End: 2019-09-10
Used Hours: 13169
Project Name: Flow through porous media
Project Shortname: MECH1116
Discipline Name: Computational Mechanics
We are investigating the flow and heat transfer in anisotropic packed beds of crushed rock. In the past, packed beds were modelled assuming isotropic resistance and spherical particles. In order to extract the resistance tensor, flow in the interstitial volumes are modelled for a range flow directions. Numerical work, using ANSYS Fluent is supported by experiments. Proper prediction of the three dimensional flow is essential for proper design of packed beds, as found in reactors, thermal energy storage, ground water flow, etc. The project is about 20 % complete, and progress in the next year may be accelerated if new students enrolled for it.
Principal Investigator: Dr Lelanie Smith
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2019-03-14
Allocation End: 2019-09-10
Used Hours: 255352
Project Name: Aeronautical Research
Project Shortname: MECH1118
Discipline Name: Other
The Aeronautical engineering group at the University of Pretoria, is focused on novel aircraft configurations. Dr L Smith specifically looks at these configurations and the physics that make them fuel efficient using CFD. In application studies of this work, passenger aircraft are considered and the size and complexity associated with the domain and flow physics when solving these problems are quite time consuming. Even before expanding to design exploration and optimisation models. The CHPC is an incredible resource to truly make this process achievable. Currently we have 2 Master students preparing to use it and one PhD student in 2020.
Principal Investigator: Prof Mwadham Kabanda
Institution Name: University of Venda
Active Member Count: 2
Allocation Start: 2019-03-18
Allocation End: 2019-09-14
Used Hours: 234012
Project Name: Reaction mechanism for atmospheric relevant molecules
Project Shortname: CHEM1161
Discipline Name: Chemistry
The research group is lead by Prof MM Kabanda who is an employee of the North-West University. The research activities involve studying the reaction mechanisms of biologically relevant molecules using computational methodologies with the aim of understanding the different reaction pathways for a given reaction of interest. The research activities conducted are largely meant for postgraduate students who persue computational chemistry studies at the North-West University with the aim of obtaining an MSc or PhD degree in computational chemistry. This justifies the utilisation of public resources. Moreover, the availability of computational power at CHPC allows the study, which otherwise would be demanding, to proceed in a smooth manner. Currently within a period of one year, two publications have been obtained, the student has attended international conferences to present the findings and she is expected to graduate in the year 2020, thanks to the contributions to her study by the CHPC computational power, which is provided for free for academic programs.
Principal Investigator: Prof Jeanet Conradie
Institution Name: University of the Free State
Active Member Count: 4
Allocation Start: 2019-03-18
Allocation End: 2019-09-14
Used Hours: 805734
Project Name: Computational chemistry of transition metal complexes
Project Shortname: CHEM0947
Discipline Name: Chemistry
Solvent molecules are forming groups called molecular clusters. The molecules in each molecular cluster are linked together by hydrogen bonds. For a given cluster size (i.e. a certain amount of molecules linked together), the structure of the cluster is related to its hydrogen bond network. This hydrogen bondnetwork establishes the difference between the possible isomers of the cluster. Understanding the hydrogen bondnetworks of molecular clusters will improve the understanding of the behaviour of solutions. In the work reported, we investigated the hydrogen bondnetworks in water clusters and ethanol clusters using different levels of computational chemistry theory. We also studied solvated ferrous ion clusters in ammonia. Small to large sized clusters and different patterns of hydrogen bonding networks, forming different isomers, have been investigated.
Principal Investigator: Dr Rose Modiba
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 6
Allocation Start: 2019-03-18
Allocation End: 2019-09-14
Used Hours: 231476
Project Name: Computational modelling of light metals
Project Shortname: MATS1097
Discipline Name: Material Science
The light metals at CSIR who are working on the stability of the materials when alloyed with other transition metals would like to thank CHPC for allowing us to use their facilities. The systematic search for novel materials is hardly achievable only via experimental discovery due to the very large combinatorial space spanned by the crystal structures and chemical compositions for compounds. This difficulty is also connected with eventually high and unstable costs of raw materials on the world market and the time-consuming procedures of synthesis and characterization. It is of great importance for the theoretical search for materials to gain detailed insight into the most relevant physical mechanisms which determine the intrinsic properties of the materials. The CHCP is a very good platform for anyone who would like to do simulation on their materials. Thank you CHPC for the workshops provided to equip us with the most relevant and recent technologies to be able to understand our materials.
Principal Investigator: Dr Krishna Govender
Institution Name: University of Johannesburg
Active Member Count: 6
Allocation Start: 2019-03-19
Allocation End: 2019-09-15
Used Hours: 309106
Project Name: Computational approaches to design novel anticancer agents
Project Shortname: CHEM0792
Discipline Name: Chemistry
With the introduction of Graphical Processing Units (cards that were at one stage used primarily for computer gaming) to the cluster we are now able to have individuals conduct their science in much shorter time frames.
The researchers that benefit most from this resource include those from domains such as Chemistry, Bioinformatics and Computer Science.
It has been proven with this research programme that researchers can get their work done up to 30 times faster then on the normal computational cluster offered by the CHPC.
It is hoped that this will then result in more publications and ground breaking research being able to be achieved within shorter periods of time.
Principal Investigator: Dr EUSTINA BATISAI
Institution Name: University of Venda
Active Member Count: 1
Allocation Start: 2019-03-20
Allocation End: 2019-09-16
Used Hours: 46414
Project Name: Predicting formation of co-crystals and pharmaceutical co-crystals
Project Shortname: CHEM1206
Discipline Name: Chemistry
The UnivenCrystEng group is located within the Chemistry Department at the University of Venda. The group's research interests include supramolecular chemistry and crystal engineering. In particular, studying structure-property relationships in co-crystals and pharmaceutical co-crystals. Active pharmaceutical ingredients are usually plagued with poor physicochemical properties such as solubility and dissolution. One way to improve their properties is to crystallize the active pharmaceutical ingredients with a benign compound in a process known as co-crystallization. The resulting compound is known as a pharmaceutical co-crystal and usually exhibits improved physical and chemical properties compared to those of the active pharmaceutical ingredient. The aim this project is to predict the formation of co-crystals and pharmaceutical co-crystals using computational methods. This is achieved by calculating the interaction energies between the co-former and the API. The CHPC is needed for these calculation as the molecules are big and calculations can take several days when being conducted on normal computer.
To date, interaction energies of up five (5) co-crystals have been obtained and results analysis is currently underway.
Principal Investigator: Prof Warren du Plessis
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2019-03-22
Allocation End: 2019-09-18
Used Hours: 232034
Project Name: Electronic Warfare (EW) Technologies
Project Shortname: MECH0989
Discipline Name: Electrical Engineering
RCS simulation data for simple targets have been generated using CHPC facilities. These data have been used to support Proff du Plessis and Jacobs of the University of Pretoria's research into innovative methods to reduce the number of simulation points required to obtain accurate RCS results. Earlier results considering only the RCS frequency response are in the process of being expanded to consider the effect of angle.
Principal Investigator: Mr Adebayo Azeez Adeniyi
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2019-03-25
Allocation End: 2019-09-21
Used Hours: 227421
Project Name: Drug Discovery Research Using Quantum and Molecular Dynamic Simulation
Project Shortname: CHEM0958
Discipline Name: Chemistry
The primary focus of our group is centered around "Drug Discovery Research Using Quantum and Molecular Dynamic Simulation". In recent time, based on the pressing need of the society and global challenges, we have included study on polymer and molecular electrochemistry. Our research use theoretical modelling to give rational insight into identified propblem which can help in the experimental design that will address the problem. CHPC is an important facility to our research group, we make usse of the facilities and the softwares like quantum packages like Gaussian, Games and Newchem; also used molecular dynamic packages like Amber and Lammps. We have applied quantum packages to study the chemical and spectroscopic properties of small molecules of which we have been able to reproduced some of the experimental results.
We have also been focusing on designing anticholesterase drugs that have the potential of addressing the problem of Alzheimer's disease (AD) which is known to be the major cause of dementia among the elderly.
The evidence of our progress with the last six month in obvious from our two publication within the period and also one international conference presentation.
It is obvious that our research progress and achievement revolve around the service of CHPC and many of our research output wold not have been possible in the absence of CHPC facilities.
Principal Investigator: Dr Abu Abrahams
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 3
Allocation Start: 2019-03-26
Allocation End: 2019-09-22
Used Hours: 1675308
Project Name: Synthesis and characterisation of lanthanide complexes with Di-(2-picolyl)amine and its derivatives
Project Shortname: CHEM0844
Discipline Name: Chemistry
No changes from previous submission:
Who: Rare earth coordination chemistry research group of Nelson Mandela University
What and why: The study of chemical and structural properties of the inorganic complexes with rare earth elements in order to identify trends in reactivity and identify potential applications in the fields of catalysis, medicine (diagnostic, anti-bacterial) and luminescence. Specifically complexes of rare earth elements with the ligand bis(2-pyridylmethyl)amine are being investigated due to this class of complexes displaying applications in the fields of catalysis, nuclear waste processing and medicine (solution structure elucidation). Increased utilisation of rare earth elements could also support the local economy, since rare earth elements may also be mined in South Africa.
How: The CHPC provides access to advanced computational resources which allows for the extraction of information from modelled systems of novel compounds, which may allow for the prediction of experimentally-determined properties. The latter process of physical experimentation are often time-consuming and expensive, whereas computational modelling may be performed on multiple systems simultaneously and may provide information of sufficient accuracy to inform the user of the most beneficial course of action to take when performing any physical experiments. In addition, modelling may also provide answers to fundamental questions which we may not yet be able to observe physically. In addition, advanced computational chemistry software packages (such as Gaussian 9/16 and ORCA) allow users with limited knowledge theoretical physics and computer programming to find answers to their chemical problems.
The experimental structures and composition of several monomeric- and dimeric- complexes containing the rare earth elements: Y, La, Nd, Dy, Ho and Lu, and preliminary geometry optimisations are well on their way to completion. An incremental refinement strategy implementing larger basis sets has proven feasible and will be carried out next.
Principal Investigator: Dr Samson Khene
Institution Name: Rhodes University
Active Member Count: 7
Allocation Start: 2019-03-26
Allocation End: 2019-10-09
Used Hours: 133569
Project Name: Synthesis, Spectroscopy and Nonlinear Optical Properties of Phthalocyanines
Project Shortname: CHEM0975
Discipline Name: Chemistry
Many of today's optical sensors are based on optical materials in which non-linear optics may play a role. Defects in the cable can have an effect of reducing the light (which carries information) in an optical fiber or cable. This phenomenon is also present in a variety of non-linear active materials or molecules. This nonlinear reduction of light phenomenon can be used as a sensing method for detection and correction of signals that are sent in cables. The aim of our research (at Rhodes University in the Chemistry department) is to make and study molecules which will help improve signal transmission using a nonlinear process and optical limiting for protection of photo sensors. This work will not be possible if it was not supported by CHPC facilities.
Principal Investigator: Dr Evans Benecha
Institution Name: University of South Africa
Active Member Count: 7
Allocation Start: 2019-03-27
Allocation End: 2019-09-27
Used Hours: 912452
Project Name: Defect engineering in novel 2-D materials
Project Shortname: MATS1025
Discipline Name: Physics
The research programme titled "Defect engineering in novel 2-D materials" focuses on investigation of the properties of defects in single layered materials - usually one atom thick. The group spearheading this research is Dr Evans Benecha and it consists of senior researchers, postdocs and graduate students from the University of South Africa. Single atom layered materials possess interesting properties as opposed to many atom thick materials. For example, graphene – which comprises a single layer of carbon atoms –enables electrons to flow much faster than silicon, is the world's strongest material, harder than diamond, yet lightweight and flexible. This unique combination of superior properties makes it a credible material for new technologies in a wide range of fields. Some of the envisaged applications of graphene as well as other single atom layered materials include making of medical implants, solar cells, stronger sports equipment, and batteries; just to name a few.
However, the properties of these materials are not well understood for these applications to be realized. Dr Benecha and his group's approach towards understanding these materials involves use of large computational resources, and access to the CHPC computing facility has significantly reduced the time needed to generate and analyze data. The results from this project will not only assist in the current understanding of the role of defects in these materials, but will also help to reveal potential new functionalities.
Principal Investigator: Dr Melaku Tesfaye Yigiletu
Institution Name: South African Weather Service
Active Member Count: 2
Allocation Start: 2019-03-28
Allocation End: 2019-09-24
Used Hours: 211742
Project Name: South African Weather Service Air Quality Modelling and Forecasting (SAWS–AQMF)
Project Shortname: ERTH0912
Discipline Name: Earth Sciences
The blanket of air which surrounds the planet earth is known as the Earth's atmosphere; it helps protect the Earth and allows life to exist. Though trace gases and atmospheric aerosols comprise a small proportion of the Earth's atmosphere mixture; they are primarily accountable for some of the most significant physico-chemical characteristics of the Earth's atmosphere; and in turn, play a substantial role in our climate system. The presence of aerosols and trace gases in the Earth's atmosphere with undesirable amount is regarded as atmospheric pollution. As the air pollutant concentration increases, the quality (cleanness) of the air we breathe will be degraded. This air quality deterioration has several direct and indirect impacts. The South African Weather Service (SAWS) Air Quality Modelling and Forecasting (AQMF) group has developed a research program which principally aim to dealing with the air quality degradation impacts on: human health, Earth-atmosphere system, ecological processes as well as human socio-economic activities. The SAWS-AQMF research activities fundamentally deal with climate-chemistry coupled modelling systems. Such models are computationally highly demanding; hence the CHPC platform is crucial for the achievement of the group research programme. The SAWS-AQMF currently is involved in a number of national/international research projects that deals with: (a) the quantification of air pollution related national burden of diseases (this project is at its final stage); (b) WMO initiated international project on inter-comparison of coupled climate-chemistry model performance in Africa (this project is progressing well); (c) AQMP development programme for the Mpumalanga province (this project is progressing well).
Principal Investigator: Dr Quinn Reynolds
Institution Name: Mintek
Active Member Count: 3
Allocation Start: 2019-03-28
Allocation End: 2019-09-24
Used Hours: 67494
Project Name: Computational Modelling of Furnace Phenomena
Project Shortname: MINTEK776
Discipline Name: Applied and Computational Mathematics
Smelting furnaces operate by heating raw materials such as ores and metals to temperatures at which they become molten, typically over 1500 degrees Celsius. Once in the molten state it's easier to do chemical conversions which are impossible at room temperature, and this simple fact facilitates the mass production of many of the products that our industrial society relies on - steel, steel additives like chromium and manganese, aerospace alloys, precious metals, and many others.
Getting the products out of a smelting furnace requires a process called tapping, which involves opening a hole in the side of the vessel and allowing some of the molten materials inside to drain out. This is no game - tapping is difficult and dangerous, and still requires skilled human operators rather than automated machinery. By using advanced computational modelling methods to create virtual prototypes and digital twins, Mintek is advancing the state of the art in the design and optimisation of tapping systems to make furnaces of the future safer and more efficient.
Principal Investigator: Prof Ben Mans
Institution Name: Agricultural Research Council
Active Member Count: 2
Allocation Start: 2019-03-28
Allocation End: 2019-10-09
Used Hours: 4312
Project Name: Theileria parva genomics
Project Shortname: CBBI0994
Discipline Name: Bioinformatics
Our group perform research on the epidemiology of theileriosis, a disease caused by a parasite called Theileria parva. The disease, affecting cattle, is endemic in some parts of KwaZulu-Natal, Limpopo and Mpumalanga. The work that Ms. Maboko is undertaking, is to determine the different strains of T. parva circulating in South Africa, determine if historical strains of T. parva are still present, determine the genetic source of differences in the behavior of the parasites of those found in South Africa and other African countries. Determining the genetic source involves obtaining the whole DNA content of the parasite, using computer softwares like Fastqc, BWA, samtools, bedtools, Picard, vcftools and SNPeff found in the CHPC to look for differences in the DNA of the different parasite strains. When these DNA differences are found, they can be used to determine if they are specific for parasites found in the same country or host. This will aid in determining whether the current disease control measures are still effective or need to be amended in order to mitigate the risk imposed by different strains should they be found. The project has progressed well since we started using their resources and a manuscript is being prepared on the work done.
Principal Investigator: Prof Walter Meyer
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2019-04-01
Allocation End: 2019-10-10
Used Hours: 350925
Project Name: Dynamics of primary radiation induced defects in semiconductors
Project Shortname: MATS0860
Discipline Name: Physics
Semiconductors used in electronic devices play a crucial role in almost all current technology, ranging from power generation (in solar cells) to power switching and conversion to smart phones, computers and satellite communications. In order to function, the semiconductors require a highly perfect crystal lattice with impurity atoms placed at exact locations in the device. Any unwanted impurities and crystal defects may degrade performance and cause devices to malfunction. These defects may be caused during manufacturing processes but also by harsh environments, e.g. space. On the other hand, some defects also have properties that may be exploited in promising future technology including spintronics and quantum computing. In summary, defects in semiconductors play an important role in both current and future technology.
The aim of the Electronic Materials Group in the Physics Department of the University of Pretoria is to understand the properties of defects on a fundamental level. In order to achieve this deep understanding, both experimental and theoretical techniques are used. Thanks to the power of modern computers, a technique called "Density Functional Theory", or DFT for short, may be used to calculate the expected properties of a specific defect. These properties may be compared to experimental results to test the validity of the theoretical assumptions. The results can lead us to build better models of how defects in semiconductors influence device performance, how devices can be engineered to reduce their susceptibility to defects and to find properties of defects which may make them useful in technologies such as spintronics and quantum computing.
The main disadvantage of DFT is that it requires a very large number of calculations, which have only recently become feasible for computers to perform within a reasonable time. The research currently uses the high performance computer at the CHPC and a free scientific programme Quantum-ESPRESSO to calculate the properties of these defects.
The first step is to perform these calculations on simple defects in well-known materials such as silicon, in order to test the applicability of the theory. Currently the calculations are progressing well and the results are promising. Once we have shown the reliability of these results, we will continue to investigate more complicated defects as well as novel materials.
Principal Investigator: Dr Michael Owen
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2019-04-01
Allocation End: 2019-09-28
Used Hours: 16335
Project Name: Industrial heat exchanger simulation and analysis
Project Shortname: MECH1210
Discipline Name: Computational Mechanics
The Thermofluids Division at Stellenbosch University's Department of Mechanical and Mechatronic Engineering has a long history of research in industrial heat exchangers and has conducted pioneering work in the field of dry cooling for large thermal power plants in particular.
Research in this field continues with a focus on understanding and improving the performance of these water conserving cooling systems under a variety of ambient conditions (including strong winds). Work of this nature benefits greatly from the CHPC which allows us to investigate an unprecedented number of scenarios in a short amount of time using computational fluid dynamics (CFD) and parallel computing.
Dry cooling is a key technology for South Africa's energy sector since thermal energy production (coal, nuclear, combined cycle gas and solar thermal) is typically a water intensive process which South Africa can ill afford considering the arid nature of our country. Ensuring robust operation of dry cooling systems can contribute significantly to the sustainability of South Africa's energy production.
Principal Investigator: Dr Adam Skelton
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2019-04-02
Allocation End: 2019-09-29
Used Hours: 27586
Project Name: Molecular modelling of biomolecules and materials
Project Shortname: CHEM0798
Discipline Name: Chemistry
I am Dr. Adam Skelton and I work at the College of Health Science university of KwaZulu-Natal. I work on understanding the behaviour of biological and material systems on the molecular level. A particlar interest is in using molecular simulation to direct the rationale design of functionalized nanoparticles for a range of applications such as drug delivery, water treatment and catalysis. In particular, drug delivery is the use of nanoparticles to carry antiviral or antibacterial drugs into parts of the body that are difficult for conventional drugs to reach. Drug-delivery is, therefore, of huge importance in South Africa, especially in the battle against HIV and Tubercolosis. The research requires running a series of computar simulations, which may take hours at a time. CHPC has had a great impact since it provides me with the facilities to perform such simulations. Since the project started, my group has published more than 15 papers in international journals and has provided deep insight into biological and material systems on the molecular level.
Principal Investigator: Prof Cornie van Sittert
Institution Name: North-West University
Active Member Count: 21
Allocation Start: 2019-04-02
Allocation End: 2019-10-11
Used Hours: 4656327
Project Name: Computational Chemistry within LAMM at NWU (Potchefstroom)
Project Shortname: CHEM0778
Discipline Name: Chemistry
Since the 1880 the main source of energy for South Africa was coal and at present coal provides 77% of South Africa's primary energy needs. However, the electricity comes at a very high cost, namely air pollution and the influence of the air pollution to human health. In 2004 the South African government reformed the legislation with regard to air pollution. In an effort to contribute to the management of air quality new energy sources must be investigated. These new energy sources must be affordable, clean and renewable. Some of these alternative energy sources are fuel cells and batteries. Electricity from fuel cells and batteries are obtainable through the use of electrochemistry, where free energy of spontaneous reactions is transformed into electricity. A potential replacement form of energy is the hybrid sulphur (HyS) cycle. The HyS cycle is a two-step water-splitting process, which could be used for the production of hydrogen. In the HyS cycle, the anode material used is platinum. However, because platinum is a rare and expensive metal, it is not an economically viable option for long term and large scale production of hydrogen. Hence, various attempts to reduce or eliminate the platinum content, while not compromising the process performance has been made. In the order to understand the electrochemistry on the anode and make informed decisions on the type and amount of metal to be used in various platinum alloys, investigations on a fundamental level is needed. These type of investigations could be classified as computational chemistry. The resources needed for these type of investigations, namely various types of hardware and software is of cardinal importance. Although resources are available at NWU, it is not nearly enough to fully support the research covered in the Laboratory of Applied Molecular Modelling (LAMM). So if we as researchers within the LAMM did not have access to the CHPC resources the progress of our research will be much slower.
Principal Investigator: Prof Eric van Steen
Institution Name: University of Cape Town
Active Member Count: 9
Allocation Start: 2019-04-02
Allocation End: 2019-09-29
Used Hours: 852597
Project Name: Lateral interactions on surfaces
Project Shortname: CHEM0780
Discipline Name: Chemistry
The understanding of catalytic reactions is based on the century-old postulates by Langmuir. Modern computational tools allow a deeper probing of these postulates. Recently, we could show that interaction between adsorbed molecules on a surface play a crucial role in the understanding of reactivity of surfaces as a catalyst.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2019-04-04
Allocation End: 2019-10-01
Used Hours: 26476
Project Name: SANAP CFD
Project Shortname: MECH1196
Discipline Name: Earth Sciences
The sub-Antarctic is one of the windiest regions in the world, with the biotic and abiotic conditions of the sub-Antarctic islands thought to be strongly affected by wind patterns. However, for these isolated terrestrial ecosystems we have a very poor understanding of within-island variation in wind speed and direction, and of how variation in wind patterns impact biotic communities. As a result, despite clear recent changes in broad-scale wind patterns in the sub-Antarctic, we have little quantitative basis for predicting the impacts that climate change-related shifts in wind speed and direction have on the biota of these islands. Computational Fluid Dynamics (CFD) models being developed in this project will provide a robust methodology for estimating wind patterns, and have previously proved successful in understanding fine-scale air flow patterns in this system. The island-scale CFD model will be validated using wind measurement stations that have been erected in 2018 and 2019 as part of this SANAP program.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2019-04-04
Allocation End: 2019-10-01
Used Hours: 418892
Project Name: CFD Modelling of Concentrated Solar Power Applications
Project Shortname: MECH0873
Discipline Name: Computational Mechanics
Central tower solar power plants are the most promising concentrated solar with research into new receivers and heat transfer fluids and collectors (heliostats) being ongoing world-wide. Researchers at the University of Pretoria's Clean Energy Research group under the leadership of Prof Ken Craig are using the resources at the CHPC to speed up calculations of both heliostat analysis (involving wind loads and fluid-structure interaction) as well as those required for a new point-focus central receiver design being developed. For heliostats, knowledge has been gained in predicting the peak loads that these reflectors will experience during all orientations and wind conditions. Ongoing work is focused on further reducing the cost of these Computational Fluid Dynamics (CFD) hybrid Large Eddy Simulation (LES):Reynolds-Averaged Navier-Stokes models to make them feasible on smaller-scale computers. This project has been ongoing since 2013 with the involvement of CHPC resources since 2016. The project has already delivered two masters students (Dawie Marais and Joshua Wolmarans) with Jesse Quick nearing completion. PhD student Pierre Poulain is also nearing the end of this investigation into LES modelling of the atmospheric boundary layer. For central receivers, work is ongoing to enhance heat transfer. Of specific interest here is the use of jet impingement, especially in the transient mode through either passive or active excitation. This phenomenon of heat transfer enhancement, although conceptually simple, it very hard to model accurately, and here the resources of the CHPC are invaluable, especially as LES is required to model the transient and 3D nature of swirling jet, the focus of the work of Jesse Quick.
Principal Investigator: Dr Sunita Kruger
Institution Name: University of Johannesburg
Active Member Count: 1
Allocation Start: 2019-04-04
Allocation End: 2019-10-01
Used Hours: 4832
Project Name: Environmental Heat Transfer
Project Shortname: MECH0995
Discipline Name: Computational Mechanics
This research group in the Mechanical Engineering Science Department of the University of Johannesburg is currently focusing on environmental heat transfer. Specifically heat transfer in naturally ventilated greenhouses. Greenhouses are used to protect plants from adverse weather conditions and insects. Ventilation of greenhouses are of vital importance to ensure quality crop production. If temperatures in a greenhouse is too high, poor plant growth may result, and an increased need for frequent watering. A mechanical ventilation system might be required to cool the inside of the greenhouse. Natural ventilation is an alternative option used to ventilate greenhouses. Natural ventilation uses temperature and wind to control the indoor climate of greenhouses. Unfortunately greenhouses are extremely energy intensive. Energy costs are the third highest cost related to greenhouse crop cultivation. Reducing the operating costs of energy associated with greenhouse cultivation may result in a price reduction of greenhouse cultivated crops. Conducting experimental work on ventilation of greenhouses can be costly and cumbersome. Using computational methods such as CFD (Computational Fluid Dynamics) to obtain qualitative and quantitative assessment of greenhouses can reduce costs and time involved. The computer cluster at the Centre for High Performance Computing has been used to conduct the numerical investigation using CFD. Currently research is being conducted on a large commercial greenhouse. Smaller greenhouses containing a single span are also being investigated.
Principal Investigator: Dr Danie J Ludick
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2019-04-05
Allocation End: 2019-10-02
Used Hours: 44190
Project Name: High Performance Computing (HPC) Postgrad Course 813
Project Shortname: CSCI1214
Discipline Name: Computer Science
The CHPC played a central role in our postgraduate course on High-Performance Computing at Stellenbosch University. The course helped our students to realise the benefits of applying parallel programming strategies to accelerate scientific software efforts. Thank you CHPC for helping us to open up the world of high-performance computing to our students.
Principal Investigator: Prof Andries Engelbrecht
Institution Name: Stellenbosch University
Active Member Count: 11
Allocation Start: 2019-04-08
Allocation End: 2019-05-05
Used Hours: 79490
Project Name: Computational Intelligence for Optimization
Project Shortname: CSCI0886
Discipline Name: Computer Science
The Computational Intelligence and Data Science research group in the Department of Industrial Engineering and the Computer Science Division, Stellenbosch University has developed new swarm-inspired optimization algorithms to solve problems with two or more sub-objectives. New approaches have been developed to further improve the efficiency of these swarm-based optimization algorithms.
Such optimization algorithms are extremely important in developing new, more efficient approaches to solve real-world problems such as railway scheduling, portfolio optimization, and developing new efficient machine learning and data analytics techniques in the data science space.
Before these algorithms can be applied to real-world problems, it is essential to empirically analyze their performance on extensive benchmark problems. This is where the CHPC plays a crucial role: evaluation on one bechmark problem requires in the order of 750 simulations, producing 5400 data files to be analyzed. With around 60 benchmarks to be evaluated on, this results in a major computational cost. Without the CHPC, it will take months for research outputs to be produced.
Principal Investigator: Dr Kiprono Kiptiemoi Korir
Institution Name: Moi University, Eldoret, Kenya
Active Member Count: 6
Allocation Start: 2019-04-08
Allocation End: 2019-10-05
Used Hours: 42439
Project Name: Thermal characterization of MoS2 nanostructures: an ab initio study
Project Shortname: MATS0868
Discipline Name: Material Science
This research group draws it's members from Moi University, Computational Material Science Group (CMSG), in addition we have collaborators: Slimane Haffad of University of Beijaia- Algeria, and Michele Re Fiorentin of Istituto Italiano di Tecnologia (IIT) Italy. Our research activities focus mainly on materials for energy and ultra-hard industry.
Over the last century, intensive use of carbon based energy sources has lead to increase in atmospheric carbon dioxide gas, which has been attributed to anthropogenic climate change, whose adverse effects on the planet are being felt and projected to worsen, unless drastic CO2 cuts are implemented as proposed in Kyoto protocol. Therefore, development of alternative energy sources with zero carbon foot print is deemed critical for the survival of the planet. While in ultra-hard industry, increased demand for hard materials whose performance are comparable or better than that of diamond but with low cost has necessitated the search for material with superior hardness related properties where 3d, 4d or 5d transition metals incorporated with light elements such as carbon and nitrogen has been identified as potential candidate. However, the process of developing such devices poses major technological challenge and an in depth study of these group of materials is needed to establish better understanding that may lead to development of new principles, characterization techniques and methods, which may lead to breakthroughs in addressing some of the bottle-necks currently associated with these materials.
In this work, graphene, NbC, NbN, ZnO nanowires and 2D MoS2 were studied via approaches grounded on principles of quantum and classical mechanics, which have been shown to accurately predict material properties. These predictive approaches requires huge computational effort as it entails solving mathematical formulas, such as Schrödinger and Newtonian equations. For this reason, availability of the state of the art High Performance Computing facility, such as CHPC is a critical component for implementation of this work. Solving Schrödinger and Newtonian equations can yield various properties of interest such as structural, mechanical, electronic and optical properties that are essential for comprehensive characterization of these systems. For example, in our recent work that is under review, we have shown that presence of anionic vacancies tend to deplete hardness in both NbC and NbN, this finding may be of great significance in the development of low cost ultra-hard devices. Other studies on utilization of ZnO nanowires for water splitting have shown that Ti and V dopants of 4% and 2%, respectively, yielded a staggered bandstructure configuration, which is ideal for Photo-electrocatalyltic (PEC) water splitting and related applications. Therefore, these findings may assist in tuning the properties ZnO nanowires for optimal PEC activity.
Principal Investigator: Dr Eric Maluta
Institution Name: University of Venda
Active Member Count: 12
Allocation Start: 2019-04-09
Allocation End: 2019-10-29
Used Hours: 136315
Project Name: Energy Material Modeling in the Application of different Photovoltaic Technologies
Project Shortname: MATS0827
Discipline Name: Physics
The Department of Physics at the University of Venda is working on the understanding of the properties of different material for application in renewable energy technologies through the density functional theory simulations as performed under the CHPC cluster. The main aim is to reduce the cost of the material used in renewable energy technologies for the future use and mitigate climate change through energy supply. We are also building capacity of the rural students on the postgraduate studies and skill development. The CHPC is a gateway for the department of Physics of the University of Venda as an institution situated in the rural area to produce researchers and to publish research work. There is a growing number of students research work from honours to the PhD level. Several student will be getting their masters and PhD degree through this initiatives.
Principal Investigator: Dr Michelle Gordon
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2019-04-10
Allocation End: 2019-10-07
Used Hours: 291362
Project Name: Structural Implications of Mutations in HIV-1
Project Shortname: CBBI0928
Discipline Name: Bioinformatics
Our research group is based at the Nelson R Mandela Medical School at the University of KwaZulu-Natal and focusses on the effects of mutations that cause antiretroviral drug resistance on the structure of HIV-1 proteins. The drugs that patients take as part of their treatment against HIV-1 can stop working because the virus is always changing (mutating). We are looking at how these mutations also change the structure of the virus. To do this, we make a structural model of the affected viral protein using specialized software that uses a lot of computational power. By using the CHPC, I am able to access their high powered server, as well as the software for performing the molecular modelling. With the information gained from this analysis, we can design new drugs that can work against these mutated viruses and improve patient management. One PhD student has submitted her thesis but will continue with the work post PhD. The second should submit his thesis shortly and 3 new PhD students will be added to the programme.
Principal Investigator: Dr Aniekan Ukpong
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2019-04-10
Allocation End: 2019-10-28
Used Hours: 286598
Project Name: Theoretical and Computational Condensed Matter and Materials Physics
Project Shortname: MATS0941
Discipline Name: Physics
Our work in the Theoretical and Computational Condensed Matter and Materials Physics (TCCMMP) group is focused on spintronics - the type of electronics that is based on the transport of electronic spin instead of charge. Here, we investigated using the spin of an electron and its intrinsic magnetic moment as a means of performing computational activity, such as reading, writing and storing of information.
Quantum well heterostructures, which are used in the memory elements of electronic devices (drones, computers, cell phones, robots, aircraft, satellites etc) as perpendicular magnetic tunnel junctions have really reached their limits in charge-based electronics, and there is significant need for them to be made more energy efficient. However, designing these devices to be energy-efficient, with larger storage capacity than is currently possible, and with the ability to transfer data a lot quicker that presently possible depends on the selection and combination of suitable metals in magnetic tunnel junctions. We have accomplished this design criteria computationally. These metals are separated by an insulating barrier layer, which ensures that electrons can only travel between the two metals by tunnelling through the potential barrier between the two electrically isolated metals. During the tunnelling event, electrons have their spins inverted and filtered so that only those spinning either up or down can get through. When a potential difference is applied to drive the pure spin current, no dissipative energy losses occur leading to energy-efficient and fast-operating devices.
Data generated on the CHPC's Lengau cluster were used to show how the external electric and magnetic fields generated when charge current flows into the scatter region of the tunnel junction can be used to tune or control the ability to store spin-based information in memory elements. We showed that in tunnel junctions that contain iron as the pinned layer and monolayer hexagonal boron nitride (hBN) as the tunnel barrier, the use of cobalt, vanadium or nickel as the free layer allows for precise, atomic-level control of the information storing capacity.
Principal Investigator: Prof Rebecca Garland
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2019-04-11
Allocation End: 2019-10-08
Used Hours: 154300
Project Name: Simulating atmospheric composition
Project Shortname: ERTH0846
Discipline Name: Earth Sciences
Air pollution can have large negative impacts on human health, agriculture, ecosystems, visibility and climate. In South Africa, although ambient air quality is regulated, many areas are out of compliance with the National Ambient Air Quality Standards. In order to protect human health and mitigate impacts, it is critical to improve air quality. The Constitution provides that everyone has a right to have an environment that is not harmful to their health. The air quality researchers in the CSIR Climate and Air Quality Modelling Research Group aims to provide the evidence base to quantify the impacts of air quality and to improve air quality. The group uses the CHPC to run an air quality model to simulate urban and regional air quality at high resolution. This chemical transport model simulates the physics and chemistry of the atmosphere. The processes represented within the model are complex, and thus computationally intensive, which makes use of the CHPC facility a necessity. The CSIR CAQM is the only group in South Africa routinely running a chemical transport model to simulate air quality. Using the CHPC resources, the team has been able to simulate the impact of policy interventions on air quality in cities. Additionally, the team has simulated the health risk from air pollution regionally in South Africa. In the past, this has been done using monitoring station data only, which then limits the analysis to only those living directly around the station. The team has also simulated the impact of climate change on air pollution. These simulations use the climate projections for the CSIR's VrESM, which is also run at CHPC, to provide meteorology input into the air quality model. These outputs directly provide the evidence base needed for decision makers to draft and implement policies and interventions to effectively improve air quality as well as understand its impacts, now and into the future.
Principal Investigator: Prof Catharine Esterhuysen
Institution Name: Stellenbosch University
Active Member Count: 9
Allocation Start: 2019-04-12
Allocation End: 2019-11-07
Used Hours: 390652
Project Name: Computational chemistry analysis of intermolecular interactions
Project Shortname: CHEM0789
Discipline Name: Chemistry
The Computational Supramolecular Chemistry group at Stellenbosch University aims to understand the fundamentally important role that intermolecular interactions play in the properties of solid materials. A particular focus is the uptake of molecules by porous compounds, since the manner in which such species interact has an influence on the sorption ability of the porous material. Calculations performed using the CHPC's computational facility have allowed us to explain the role that intermolecular interactions play in the unusual sorption properties of porous compounds. Of particular interest is the nature of interactions between CO2 and porous frameworks, as this helps guide the design of materials for the sorption and sequestration of CO2.
Principal Investigator: Prof Giuseppe Pellicane
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2019-04-12
Allocation End: 2019-10-28
Used Hours: 287885
Project Name: Computational Study of Structure-Property Relationships in polymer blends relevant to OPV devices
Project Shortname: MATS0887
Discipline Name: Physics
The computational study of polymeric materials relevant to photovoltaic devices is an important endeavour in the field of renewable, sustainable and non-polluting sources of energies. In fact, solar energy is the epithome of green energy sources and polymers allow for a cheap device preparation cost and exhibit relative ease of processability, which paves the way to solar energy as a viable and economic energy source. By the scientific point of view, organic conducting materials are an interesting research niche, that is important to achieve a fundamental understanding of charge transport phenomena at the molecular level. Polymers are also widely used as a potential nano-carrier for drugs in nano-medicine and for pharmaceutical applications. In general, our research group at UKZN is operative in the field of theoretical and computational studies of complex fluids. A number of publications in scientific journals are obviously expected as a result of the research efforts in the framework of this project, and we already produced a number of them. We are also presenting the results of our research endeavour in international conferences/workshops, that will allow for sharing and diffusion of vital knowledge with the international scientific community and will be beneficial to the global progress towards a green and sustainable earth planet. Our gratitude always goes to the skilled and resourceful staff members at CHPC, and to the CHPC itself for the generous allocation of computational resources granted to us by them, which are instrumental to fulfill the goals of this project.
Principal Investigator: Prof Penny Govender
Institution Name: University of Johannesburg
Active Member Count: 16
Allocation Start: 2019-04-12
Allocation End: 2019-10-09
Used Hours: 831994
Project Name: Design of MOFs-based sorbent materials for capturing carbon dioxide
Project Shortname: CHEM0797
Discipline Name: Material Science
The computational chemistry research group at the university of Johannesburg is led by Prof Penny Govender. The research group currently focuses on material science, environmental sciences, reaction mechanisms and medicinal chemistry. The work is being performed both for predictive purposes (where experiments are modelled before being actually carried out in the lab) and for support purposes where computational results supports experimental results. All the simulations done by the group are carried out on the Lengau cluster using software such as Materials Studio, Gaussian, Schrodinger, all provided by the CHPC South Africa.
Principal Investigator: Prof Jacomine Grobler
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2019-04-12
Allocation End: 2019-10-09
Used Hours: 1851
Project Name: Computational intelligence for supply chain optimization
Project Shortname: CSCI1170
Discipline Name: Applied and Computational Mathematics
Due to the rise of e-commerce, consumers can purchase an enormous variety of products and have it delivered to their doorstep anywhere in the world. As a result, last mile deliveries are an important competence for many logistics companies. Unmanned aerial vehicles or delivery drones, is a highly promising technology that can revolutionize the way companies do their last mile deliveries. Drones are a cleaner means of transport, do not require or use road infrastructure, and have positive implications on delivery time and cost. The efficient use of delivery drones, however, require advanced optimization algorithms to allocated deliveries to drones, and schedule these deliveries.
Researchers at the Department of Industrial Engineering at Stellenbosch University are currently working in conjunction with the University of California at Berkeley to develop a drone delivery scheduling algorithm. The development of this algorithm requires significant computational resources and here the collaboration with the Centre for High Performance Computing is critical. Many hours of computer time is required to test different algorithm variations, tune algorithm control parameters and ensure that the algorithm is robust over different data sets and changing input parameters.
Initial results indicate that up to a 30% improvement can be obtained by a delivery drone scheduling system when compared to a traditional road freight delivery service.
Principal Investigator: Prof George Amolo
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 11
Allocation Start: 2019-04-15
Allocation End: 2019-11-04
Used Hours: 4274639
Project Name: Properties of Materials for Green Energy Harnessing
Project Shortname: MATS862
Discipline Name: Material Science
MATS862 is a Kenyan group consisting mainly of young Physicists interested in materials science. This group uses computational modeling in materials science as an important component of decision making from excellent insights to experimental study and predictive capability that can be crucial to productivity.
We study the properties of existing materials used in energy and energy conversion hoping to learn their characteristics with a goal of being able to improve them and suggest new as well as more efficient ones.
Environmentally friendly and affordable energy is key to good living in this modern age. It is therefore necessary to develop more research capacity in this area for benefit of our citizens
Computational modeling has the capability to simulate conditions that can be close as possible to actual processes occurring in nature which may require large numbers of atoms or molecules that cannot be handled by small computers and thus the need for resources as provided by the CHPC.
The project is progressing very well and now with attention now being drawn to the MATS862 group at the national and regional level, with requests for visits from graduate students in Uganda and Tanzania.
Principal Investigator: Mr Theo Fischer
Institution Name: eScience
Active Member Count: 2
Allocation Start: 2019-04-15
Allocation End: 2019-10-31
Used Hours: 71988
Project Name: Acid Deposition
Project Shortname: ERTH0851
Discipline Name: Earth Sciences
The Mpumalanga Highveld region power station SO2 emissions amounted to 2.2 million tons in 2010. This could equate to an increased total dissolved salt (TDS) deposition load of 4.6 million tons. This is 23 times higher than the natural annual average TDS load in the runoff from the entire 38 600 km2 Vaal Dam catchment. Although only a fraction of this salt load falls on the Vaal Dam catchment, outfall of only 4% of the emitted sulphur could double the long-term equilibrium salt export of the catchment. The Weather Research and Forecasting model coupled to Chemistry (WRF-Chem) was used to model emissions of sulphuric acidic precursors, their chemical conversions and their wet and dry deposition over the Highveld region between 1950 and 2050. The daily time step NACLS hydro-salinity model (Herold et al., 2001) was used to simulate daily rainfall-runoff processes and sub-surface storages, along with the TDS and sulphate fluxes and storages in order to model the eventual impact of atmospheric deposition on the salinity of Vaal Dam catchment runoff. The 2017 anthropogenic atmospheric deposition is estimated to contribute 5.9 times more to the Vaal Dam catchment TDS load than the runoff from industrial and mining sources. By 2030 the differential is expected to grow to 7.4 times. The treatment costs attributable to the modelled salinity in the Vaal Dam catchment were calculated as being R950 million per annum by 2017. Thereafter they are expected to peak at R1 516 million by 2033, followed by a remarkably shallow decline to reach R1 123 billion by 2050. The salinity impacts from atmospheric deposition on water quality will remain and continue to impose annual costs of the order of over R1 billion for the next three decades. It is therefore considered essential to account for these impacts in water supply infrastructure planning and system operating rules to minimise these costs.
Principal Investigator: Prof Jaco Dirker
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2019-04-16
Allocation End: 2019-10-13
Used Hours: 117550
Project Name: Heat Transfer Enhancement in Thermal Systems
Project Shortname: MECH1029
Discipline Name: Computational Mechanics
Renewable energy exploration and the responsible usage of existing energy resources are vital for sustainable economic and industrial development. Future energy needs will require continual improvement in energy processing technologies and storage systems. The Clean Energy Research Group at the University of Pretoria aims to contribute to such efforts by conducting both applied and fundamental research using experimental and numerical techniques. One of the group's focus areas is that of large scale thermal energy storage and conversion systems which have lower associated costs than electric energy storage systems. This, however, requires improved heat transfer mechanisms to match demand side energy consumption rates and has led to the need for geometric optimization and innovation in heat exchanger equipment and thermal energy storage modules. This is the driving force behind the exciting investigations supported by the CHPC whereby the effects of heat transfer enhancement due to turbulator inclusion and the augmentation of latent phase change material energy cycling are considered. For this purpose, high performance computing is required to solve complicated and detailed energy transfer, mass transfer, and fluid dynamics equations in the transient domain using computational codes such as those included in commercial simulation packages such as Ansys Fluent. Detailed simulation results of flow eddies and phase transition fronts, as well as design space exploration results will assist in deriving smaller, more efficient energy transfer components which has lower capital and operating costs in both solar renewable energy systems and fossil fuel based systems. Among the early successes include the improvement of local and average heat transfer coefficients by more than 50% which, if implemented, would result in a significant size reduction of heat exchanger equipment.
Principal Investigator: Dr Adeola Joseph Oyenubi
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2019-04-17
Allocation End: 2019-10-14
Used Hours: 235572
Project Name: Optimizing balance in for Impact Evaluation
Project Shortname: ECON1213
Discipline Name: Economics and Finance
This research is conducted by Dr Oyenubi, a lecturer at the University of the Witwatersrand.
Usually policy interventions (like the child support grant programme) require assessment in terms of the impact of the policy on beneficiaries. To do this a researcher must compare the response units under the policy with units that are not under the policy. For this comparison to be valid the two groups should have identical characteristics or covariates. This is achieved by comparing the distribution of covariates using various balance statistics e.g. mean and standardized difference in means.
This work assesses if the performance of different balance statistics vary in terms of their ability to compare the distribution of covariates. The premise is that differences in the performance of balance measures will lead to variation in the estimate of policy impact. With no guidance on the performance of various balance measures it will be difficult to identify the correct impact estimate.
This work will provide guidance to researchers on how to use the various balance measures that are available when estimating the impact of a policy. However doing this require extensive Monte Carlo experiments. This experiments are computationally expensive and without the CHPC the work will be virtually impossible.
The process involves setting up a data generating process that mimics various condition that is encountered in real life impact assessment. In this fictitious world we know what the correct impact estimate is. We then use various method to try and estimate this (known) impact estimate. The idea is that some methods will perform well while others will fail. This knowledge (about what method perform better and under what conditions) can then be used on real life data where we do not know the correct impact estimate.
This particular stage of the project is near competition.
Principal Investigator: Prof Abu Yaya
Institution Name: University of Ghana
Active Member Count: 7
Allocation Start: 2019-04-17
Allocation End: 2019-10-28
Used Hours: 456406
Project Name: DFT modeling of weak interactions; a case study for Carbon nanosystems
Project Shortname: MATS0990
Discipline Name: Material Science
This research team is made up of members from the University of Ghana and the University of Agriculture, Abeokuta, Nigeria.
Mapping up surface interactions that controls drug bindings to DNA is something that has been studied for long time, yet our understanding of drug-DNA interactions in the curing of diseases such as cancer is limited.
This research therefore, involves the use of computer models for the understanding of how the human DNA are arrange (known as pi-pi stacking) and also how materials bond together to form stronger materials which can be used for building and electronics applications.
Without computers with large memories which are known as clusters, it will not be possible to understand this behaviour. Even-though this can be done by experiment, the cost is highly unsustainable and will take several years to really understand the genetic sequence but with computer models, it will be faster, and easier to understand the DNA sequences thereby reducing cost and making allowing value for money experiments to be conducted. Therefore computer modelling is used as a microscope in order to understand the real picture of a situation or problem.
Our project tries to understand interactions which play a crucial role in arrangements of DNA, proteins, and the stacking of polymers (plastics)
This is important in understanding genetic disorders and other life threatening diseases that are linked to DNA and proteins. Secondly, we are also able to understand how materials mix together to form stronger materials which are used for applications such as aeroplanes, cars, flats screen televisions, mobile phones and buildings or civil structures (High-rise buildings)
Thankfully, with the resources available at CHPC (Lengau cluster), we are able to understand these complex interactions in order to formulate proper diagnostic methods that can target diseases in our body.
Principal Investigator: Dr Shankara Radhakrishnan
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2019-04-17
Allocation End: 2019-10-14
Used Hours: 13774
Project Name: Solar energy and CO2 Reduction
Project Shortname: CHEM0869
Discipline Name: Chemistry
We at the Chemistry Department from the University of Pretoria are the renewable energy group and work on Conversion of CO2 to useful chemicals such which in future is expected to replace gasoline and other coal burnt fuel production processes. Thus, the aim is to mitigate the CO2 expelled into the atmosphere along with use of renewable energy to meet electrical demand which at this stage comes from fossil fuels in South Africa. This will also serve in providing solution to the global climate change which is one of the most important national imperative.
Principal Investigator: Dr Pieter Levecque
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2019-04-18
Allocation End: 2019-10-28
Used Hours: 12505
Project Name: Non carbon supports for electrocatalyts
Project Shortname: MATS1108
Discipline Name: Material Science
The HySA/Catalysis Centre of Competence in the Department of Chemical Engineering at the University of Cape Town conducts research into new catalysts and components for fuel cells and electrolysers. One main focus is new support materials for catalysts for fuel cells.
MAX phases are a new class of materials that can at the same time show properties of ceramics and metals. This means materials can be prepared that show strong corrosion resistance as well as high conductivity which is the properties needed for a good fuel cell catalyst. The purpose of this study is to find a suitable model for MAX phases and their properties so that we can rapidly screen potential compositions and thereby targeting the lab-based preparation as described above. CHPC facilities help us to do the modelling thereby saving significant lab time and expensive chemicals
Principal Investigator: Prof Kevin Naidoo
Institution Name: University of Cape Town
Active Member Count: 8
Allocation Start: 2019-04-24
Allocation End: 2019-11-04
Used Hours: 2640041
Project Name: Reaction Dynamics of Complex Systems
Project Shortname: CHEM0840
Discipline Name: Chemistry
Cancer Therapeutics and Diagnostics Only available once patents filed.
Principal Investigator: Prof Andries Engelbrecht
Institution Name: Stellenbosch University
Active Member Count: 13
Allocation Start: 2019-04-24
Allocation End: 2019-10-21
Used Hours: 845652
Project Name: Computational Intelligence for Optimization
Project Shortname: CSCI0886
Discipline Name: Computer Science
Algorithms inspired by a simple model of bird flocking behaviour have been developed to solve complex optimization problems. Approaches have also been developed to gain a better understanding of the complexity of optimization problems, in order to develop approaches to match the best algorithm to solve a given optimization problem, based on the characteristics of the problem. We have also developed machine learning approaches to recognize emotion in humans from video and audio samples.
Principal Investigator: Dr Roelf Du Toit Strauss
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2019-04-24
Allocation End: 2019-11-07
Used Hours: 1670984
Project Name: Computational Space Weather
Project Shortname: PHYS0918
Discipline Name: Physics
One of the biggest hurdles faced by manned exploration of space is the high levels of natural radiation present in the solar system. This is not only an important consideration faced by future astronauts on board spacecraft, but also by future colonizers of Mars, and inhabitants of future moon bases and space stations. This important risk is acknowledged by both SpaceX and NASA, and planned bases and spacecraft try to accommodate so-called "space storm shelters", where space dwellers can hide from dangerous radiation levels. At the Centre for Space Research of the North-West University, South Africa, we are doing our part to mitigate these possible harmful effects by developing state-of-the-art numerical models that can simulate and predict the levels of harmful natural radiation. To simulate the intensity of these so-called "cosmic ray" particles, complicated and large-scale numerical models are run on large scale computer clusters, such as the Lengau cluster of the Centre for High Performance Computing (CHPC) in Cape Town, South Africa.
Principal Investigator: Prof Juliet Hermes
Institution Name: SAEON
Active Member Count: 2
Allocation Start: 2019-04-24
Allocation End: 2019-10-21
Used Hours: 133608
Project Name: SAEON Coastal and Regional Ocean Modelling Programme
Project Shortname: ERTH1103
Discipline Name: Earth Sciences
Coastal and regional oceans are often poorly represented in current global ocean models. This is usually due to use of coarse resolutions in the models subsequently leading to shortcomings in representation of fine scale coastal and regional processes. To improve this regional, high resolution or nested configurations are commonly applied to capture and study these processes. In this programme, high resolution ocean models (NEMO and ROMS) are used to understand physical and biogeochemical processes around the coast of South Africa and adjacent basins. These models contain a suite of useful schemes that need to be tested and used in a regional context. Once configured and tested these models can be used to improve knowledge by taking advantage of available in-situ and satellite data to understand oceanic processes under realistic scenarios.
Principal Investigator: Dr Gerhard Venter
Institution Name: University of Cape Town
Active Member Count: 8
Allocation Start: 2019-04-24
Allocation End: 2019-10-21
Used Hours: 371273
Project Name: Simulation of Ionic Liquids
Project Shortname: CHEM0791
Discipline Name: Chemistry
Dr Venter's research group is part of the Scientific Computing Research Unit at the University of Cape Town and uses computer simulation to study the chemical and physical properties of biopolymers in a special class of solvents, called "ionic liquids". These simulations provide insight into the intermolecular interactions and chemical behaviour that control the dissolution and subsequent reactivity of these naturally occuring polymers. A better understanding of these processes can lead to the rational design of new, environmentally friendly solvents systems that can dissolve biomass and enhance its reactivity. The dissolution of biomass is the first step in converting naturally occuring polymers to biofuels and other platform chemicals.
High performance computing is required for all research conducted in this group and without the resources and infrastructure provided by the Centre for High Performance Computing (CHPC), the research will not be possible.
Principal Investigator: Dr Jenny-Lee Panayides
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 6
Allocation Start: 2019-04-26
Allocation End: 2019-10-23
Used Hours: 83195
Project Name: Lead Discovery & Process Development Programme
Project Shortname: CHEM0934
Discipline Name: Chemistry
Alzheimer's disease is the most common form of dementia. To date, there is no cure for the disease and only symptomatic treatments are available. Using in silico computational and in vitro biological screening techniques, a team from CSIR Biosciences and the University of Pretoria are currently testing thousands of compounds to identify new pharmacophores for development into drugs for the treatment of Alzheimer's disease.
Using the computational resources provided by the CHPC, very large numbers of compounds can be tested with greater accuracy than what is possible with standard computational hardware. Hit compounds identified through this screening effort will be optimised using computer-aided drug design, to improve their effectiveness against a particular target within the human body prior to the expensive and time-consuming synthesis of the compounds for advanced biological screening. During this optimisation process, many aspects will be considered, including the ability of the human body to absorb the compound and possible toxic side-effects. Thus, utilisation of the CHPC resources can potentially accelerate drug development in a significantly more cost-effective manner.
Principal Investigator: Dr William Horowitz
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2019-04-26
Allocation End: 2019-11-07
Used Hours: 11217
Project Name: Probing the Frontiers of Nuclear Physics
Project Shortname: PHYS0974
Discipline Name: Physics
The CHPC provides critical computing power for the research programme of Dr. W. A. Horowitz. The goal of Dr. Horowitz's research is to unlock the secrets of nuclear matter under extreme conditions, for example in the centre of neutron stars or at a trillion degrees. Why a trillion degrees? That's the temperature of the universe a microsecond after the Big Bang, when the fundamental matter making up space was very different from what we experience every day. Instead of the usual protons and neutrons that make up normal nuclear matter, something very different is at work. The goal is to understand what exactly makes up this nuclear matter in extreme conditions and also to determine the impact of the dynamics of this matter on the early evolution of the universe. The incredible computing power of the CHPC allows for the world's most precise predictions for the behavior of certain particles known as quarks when the universe is at a trillion degrees. These predictions have been compared with measurements made at the world's premier atom smashers, such as the Large Hadron Collider in Europe, and it was shown that the data do in fact agree with calculations made at the CHPC. As a result, we're learning that the hottest stuff in the universe is still very strongly-coupled, like the most perfect trillion degree soup ever created.
Principal Investigator: Dr Chris Barnett
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2019-04-26
Allocation End: 2019-10-23
Used Hours: 639095
Project Name: Analysis of disease related polymers
Project Shortname: CBBI1063
Discipline Name: Bioinformatics
I investigate the shapes, structures, and properties of molecules by using computational modelling techniques. I'm particularly interested in complex sugars (glycans), which are interesting to study because they are involved in intricate molecular recognition processes in cells, for example, playing a role in cell signalling, adhesion, and immunity. Further understanding of these molecules and the complex systems they are involved in may lead to the generation of additional diagnostic markers and inhibitors that can be used to combat disease. The CHPC provides a platform for being able to run large-scale and highly parallel simulations which is a great help in making rapid progress towards solving research questions. The CHPC is also a test bed when carrying out computation on and developing algorithms for large datasets.
Principal Investigator: Dr ADEDAPO ADEYINKA
Institution Name: University of Johannesburg
Active Member Count: 2
Allocation Start: 2019-04-29
Allocation End: 2019-10-26
Used Hours: 138509
Project Name: Computational Design of Molecules
Project Shortname: CHEM1221
Discipline Name: Chemistry
The Computational Design of Molecules research group is based at the University of Johannesburg. We aim to design new and improved molecules and materials for applications in Catalysis and renewable energy.Since the availability of energy is one of the main challenges of the African continent, being able to achieve our aims as a group will provide clean energy solutions for the continent. We use computational chemistry software to explore the properties of molecules which is responsible for their activity and then use the knowledge gained to design more efficient and improved materials.
Principal Investigator: Dr John Mack
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2019-05-02
Allocation End: 2019-10-29
Used Hours: 4207
Project Name: Rational design of phthalocyanine, porphyrin and BODIPY dyes
Project Shortname: CHEM0796
Discipline Name: Chemistry
The Institute for Nanotechnology Innovation (INI) at Rhodes University under director Prof. Tebello Nyokong carries out research related to the use of molecular dyes in biomedical applications, such as cancer treatment through photodynamic therapy, the use of antimicrobial photodynamic chemotherapy for treating hospital superbugs and as sensors for ions that are harmful to human health.
Other applications of interest include wastewater treatment and the development of optical limiters to protect human vision,such as in aviation safety in protecting pilots from the irresponsible use of laser pointers during runway approaches. It is important to understand trends in the electronic and optical properties that make the molecular dyes suitable for these particular applications. The resources of the Centre for High Performance computing help to facilitate this by making it possible to carry out molecular modelling calculations that can be used to predict how changes to the structures of the molecular dyes will modify their properties. The flexibility that CHPC provides where memory allocations are concerned is often vital.
The INI currently has three staff members, twenty PhD, seven MSc and two Honours students, and three postdoctoral fellows, and usually publishes over forty peer-reviewed publications per year. This rose to a high of sixty-five in 2017 with ten involving the use of CHPC resources.
Principal Investigator: Prof Thomas Harms
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2019-05-02
Allocation End: 2020-10-15
Used Hours: 524948
Project Name: Modelling Inter-relationships of Diesel Properties and Engine Performance
Project Shortname: MECH1222
Discipline Name: Computational Mechanics
There is a global imperative to minimise the impact of fossil fuels on the environment, and while the best solution is to the eliminate their use altogether, this will take a long time, more so in some sectors where alternatives are not commercially available yet. One such sector is long distance goods transport which relies heavily on trucks powered by diesel engines. Technology solutions such as electric propulsion using either batteries or fuel cells to provide the energy required, are developed at a rapid pace, but are not yet market ready and will also require a lot of additional infrastructure before they can make a meaningful impact. There are also solutions which could allow the continued use of internal combustion engines, such as using biofuels or synthetic fuels. For these reasons, understanding the interactions between engines and liquid fuels remains important as ever, and the use of state-of-the art machine learning techniques provides a new lens through which these interactions can be viewed. - A research project is therefore underway in the Mechanical and Mechatronic Engineering Department at Stellenbosch University, which aims to develop a 'digital twin' of a heavy-duty diesel engine which will allow engine-fuel interactions to be investigated in a virtual space, rather then having to resort to costly and time-consuming experimental programmes. Artificial neural network models have been developed which predict the performance and exhaust emissions of a diesel engine, depending on the engine's duty cycle, how the engine's software has been calibrated, and the properties of the fuel that is being used. These models are now being used to enhance the level of understanding of how specific fuel properties impact engine performance and emissions, and how these fuel properties and the engine's software can be co-optimised to give the best system performance. - Neural network models do not contain any prior knowledge of the system that is being modelled, and therefore have to be taught or 'trained' using experimental data, in a process known as supervised learning. The more data used for training the better (more than 4 million data points were used in this project), but this places a large burden on computing resources. Access to the Lengau Cluster at the CSIR's Centre for High Performance Computing (CHPC) has been critical in enabling the development of the neural network models, which is an iterative and inherently time-consuming process. As a result, the quality of the models has been significantly enhanced. The project is nearing completion, and future applications of the methodology developed, such as investigating the performance of advanced biofuels, have already been identified.
Principal Investigator: Prof Fernando Albericio
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2019-05-02
Allocation End: 2019-10-29
Used Hours: 12045
Project Name: Peptide chemistry and Organic chemistry
Project Shortname: CHEM1102
Discipline Name: Chemistry
We are Peptide Science Group at UKZN Westville campus. The project was brought up with an intend to learn computational chemistry. The project involves synthesis of several organic molecules with application in peptides. Since CHPC provides the server which speeds up the calculations and helps in achieving the preliminary results. The project so far had been very promising in predicting the mechanism. We expect to be going ahead with these results for further analysis towards prediction of reaction mechanism.
Principal Investigator: Prof Moritz Braun
Institution Name: University of South Africa
Active Member Count: 3
Allocation Start: 2019-05-03
Allocation End: 2019-10-30
Used Hours: 3010516
Project Name: Density Functional studies using a variety of different methods and considering materials of current interest
Project Shortname: MATS0924
Discipline Name: Physics
Dr Kingsley O. Obodo strongly collaborates with Prof Moritz Braun at the University of South Africa. While Dr K.O. Obodo was at University of South Africa and currently HySA Infrastructure at the North West University, the use of CHPC resources has led to significant understanding of 2D transition metal dichalcogenides and bulk ZnTiO3. Insights on improving the use of monolayer transition metal dichalcogenides was found to occur via the introduction of transition metal atoms. The use of 2D TcS2 for hydrogen evolution reaction was reported with significant insights provided on how to effectively improve the compound. The presence of impurity atoms in ZnTiO3 was found to effectively improve its luminesce properties. The studied materials are important in solar and hydrogen technology.
Principal Investigator: Dr Madison Lasich
Institution Name: Mangosuthu University of Technology
Active Member Count: 9
Allocation Start: 2019-05-04
Allocation End: 2019-10-31
Used Hours: 47512
Project Name: Chem Thermo
Project Shortname: CHEM1028
Discipline Name: Chemical Engineering
Gas hydrates are of interest in industry as a potential energy storage medium and in industrial separation processes, and it is attractive to employ as few parameters as possible when modelling these systems. Dr Lasich and Dr Tumba at the Mangosuthu University of Technology have recently discovered limits to the use of a simplified approach to describing these ice-like compounds via molecular simulations using the facilities of the CHPC. Work is ongoing in studying novel industrial separation systems, with a view to enhanced product recovery, reduced waste generation, and improved energy efficiency.
Principal Investigator: Prof Johan W. Joubert
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2019-05-06
Allocation End: 2019-11-02
Used Hours: 303638
Project Name: Mobility modelling using vehicle telematics
Project Shortname: MECH0803
Discipline Name: Other
Government (all spheres) is tasked with the challenge of deciding where to invest in infrastructure (for housing/transport/economic development etc). The real hard part is to balance two questions. Firstly, "who gets the benefit of infrastructure?" and, secondly, "who PAYS for those benefits?". In our research programme we develop agent-based transport models that are able to depict and imitate the complex, multi-modal and large-scale transport scenarios in a South African context. Each individual - from the Metrorail commuter, to the private car owner, to the minibus taxi driver, to the commercial vehicle delivering your goodies at the Woolies Foods - are represented in such a transport model. The goal of our ongoing research is to assist government and industry make better informed, evidence-based decisions about the intended, and unintended consequences of specific transport interventions. Since every individual is modelled the computational burden is substantial and the CHPC allows us to overcome the data preparation and simulation challenges of executing the large-scale, MATSim models.
Principal Investigator: Prof Krishna Bisetty
Institution Name: Durban University of Technology
Active Member Count: 4
Allocation Start: 2019-05-01
Allocation End: 2019-10-28
Used Hours: 27870
Project Name: Computational Modelling & Bioanalytical Chemistry
Project Shortname: CHEM0820
Discipline Name: Chemistry
We successfully designed electrochemical biosensors for the detection of different analytes with application in food industry, supported by computational tools provided by the CHPC.
Principal Investigator: Dr Ndumiso Mhlongo
Institution Name: University of KwaZulu-Natal
Active Member Count: 11
Allocation Start: 2019-05-08
Allocation End: 2019-11-04
Used Hours: 822512
Project Name: Biomolecular Modelling Research Unit
Project Shortname: HEAL1002
Discipline Name: Health Sciences
Biomolecular Modelling Research Unit is located at the University of KwaZulu-Natal, Howard College Campus and headed by Dr Ndumiso N. Mhlongo. This research group employs CHPC resources to conduct molecular dynamics simulations to analyse the dynamical properties of macro-molecules such as folding and allosteric regulations; ligand-receptor interactions; atom-to-atom interactions; protein-protein interaction;virtual screening and molecular docking of active molecules; QSAR etc, for the design and development of inhibitors against diseases and disorders. Through the use of CHPC resources, we have designed potential inhibitors against M. tuberculosis and cancer treatment. These have made contributions to discovery new inhibitors & new knowledge which could directly translate into real health benefits of the society.
Principal Investigator: Dr Nkululeko Emmanuel Damoyi
Institution Name: Mangosuthu University of Technology
Active Member Count: 3
Allocation Start: 2019-05-09
Allocation End: 2019-11-05
Used Hours: 23041
Project Name: Surface Reaction Mechanisms
Project Shortname: CHEM1105
Discipline Name: Chemistry
My name is Dr Nkululeko Damoyi and I teach Inorganic Chemistry in the department of Chemistry at Mangosuthu University of Technology (MUT). My present research is in Computational Chemistry (CC) and modelling calculations are done through the Centre for High Performance Computing (CHPC) in Cape Town. Research is registered at CHPC under the name: Surface Reaction Mechanisms. Presently there are three members of the group (Ntola P, Ebenezer O and myself). I also supervise some MUT Btech students in small CC research projects although they use their laptops for calculations. Current research output is in a form of two publications in peer-reviewed journals and a third publication is presently being finalized. A large production of alkanes, for example LPG gas, from imported crude oil and mined natural gas and coal exists in South Africa through a variety of industrial processes. The alkanes are used as starting materials for many other industrial organic compounds, such as plastics. However, the production of some of these industrial organic compounds is too costly and there is a high commercial demand for catalytic methods and new catalysts that would bring down the costs of production. Computer technological advances make it possible to do research in CC in order to model chemical reactions and predict chemical reaction properties which are difficult or impossible to determine from normal laboratory experiments. Most of our present research involves utilising CC to predict the likely chemical reaction mechanisms that produce valuable organic compounds from alkanes with use of catalysts and also without catalysts. Through the CHPC we are able to use internet to connect to their cluster computers in order to run the calculations and from the results be able to model the energetics of chemical reactions and predict reaction mechanisms.
Principal Investigator: Prof Ignacy Cukrowski
Institution Name: University of Pretoria
Active Member Count: 8
Allocation Start: 2019-05-09
Allocation End: 2019-11-05
Used Hours: 813823
Project Name: Understanding chemistry from QM study of molecular systems
Project Shortname: CHEM0897
Discipline Name: Chemistry
Activities in chemistry (in science in general) can be seen as made of two distinctive approaches: 1) development of new theories and methodologies that should lead to better understanding of concepts and chemical process (reactions) and 2) practical implementation of known or new methodologies that should lead to routine and highly efficient experimental/computational operations. Our research group in the Department of Chemistry, University of Pretoria (Prof. Ignacy Cukrowski (the leader), Dr. Jurgens de Lange, several PhD, MSc and Honours students as well as a postdoctoral Fellows) is involved in fundamental studies. Our focus is primarily on understanding fundamentals governing inter-atomic and inter-fragment interactions from the electron density distribution throughout a molecule, or molecular system in general. For instance, there are many kinds of chemical bonds but still there is no an ultimate general theory of bonding. Hence, there are various approximate quantum chemical models that are being used to describe and explain just a specific kind of bonding. In our group we prefer to interpret classical chemical bonding, regardless of its kind, as an interaction governed by universal laws of physics. This allows us to expend the concept of interactions from classical 2-atom approach (a chemical bond) to poly-atomic interactions involving fragments of a molecular system. Such approach proved to be very useful in modelling reaction mechanisms (to understand (on atomic and molecular fragment level) how and why new compounds are or are not formed as planned by a synthetic (in)organic chemist. Full understanding of successful and failed synthetic processes is of great importance as it must aid the development of, e.g., new drugs needed for treatment of (i) highly contagious diseases, such as tuberculosis, HIV/AIDS, or (ii) Alzheimer, a disease with reported cases growing rapidly throughout the world. It is important to realize that such theoretical work requires, due to the size of molecular systems under investigations, dedicated and expensive computational facilities, such as CHPC, with a dedicated staff to ensure that research groups can access and make use of computational centre 24/7.
Principal Investigator: Dr Pedro Monteiro
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 13
Allocation Start: 2019-05-10
Allocation End: 2019-11-06
Used Hours: 2530315
Project Name: Southern Ocean Carbon - Climate Observatory SOCCO
Project Shortname: ERTH0834
Discipline Name: Earth Sciences
SOCCO is a CSIR-led and DST co-funded programme that uses the comparative geographical advantage that South Africa has in the Southern Hemisphere to contribute to the global research challenge of understanding the role of the Southern Ocean in global and regional climate. The SOCCO research niche is to explore the role played by fine scale ocean dynamics in improving the climate sensitivity of ocean and coupled numerical models with a special focus in understanding the Southern Ocean's role in the Carbon-Climate links.
To address the scales of dynamics in the ocean, we primarily use the coupled NEMO-PISCES model in a hierarchy of resolutions from 200 km to 2 km - using the models as experimental platforms. The finer the resolution, the greater the number processes that contribute to ocean-atmosphere carbon exchange. This understanding contributes to reducing model biases in process models and climate projections as well as the development of our Earth Systems Model (VR-ESM).
This work advances research in global climate change based on the importance of feedbacks of the Southern Ocean dynamics on the carbon-climate system. Additionally, VR-ESM will be used to explore how the climate sensitivities of the Southern Ocean evolve over the 21st century as well as being South Africa's first submission to the 6th Assessment Report of the IPCC. VR-ESM will be the basis for the medium to long term climate projections in Africa which will then support societal needs in health, water resource planning, agriculture, biodiversity management and more broadly in economic development in the region.
From regional, forced ocean models to fully-coupled earth system models comprising of interacting ocean, ice, atmosphere, land, ocean biogeochemical models, numerical modelling of earth system components require massively parallel computing resources. The size and complexity of these models are such, that for SOCCO's work, the CHPC is indispensable for the resources and service it provides.
Principal Investigator: Dr Nana Ama Browne Klutse
Institution Name: Ghana Space Science and Technology Institute
Active Member Count: 2
Allocation Start: 2019-05-10
Allocation End: 2019-11-06
Used Hours: 1086
Project Name: Regional Climate modeling over Africa
Project Shortname: ERTH1087
Discipline Name: Earth Sciences
West Africa Climate is highly variable and more studies over the region is recommended. The CHPC provides a good platform for climate simulation especially for long period studies.
Principal Investigator: Dr Sean February
Institution Name: SKA
Active Member Count: 3
Allocation Start: 2019-05-15
Allocation End: 2019-11-11
Used Hours: 50959
Project Name: MeerKAT Open Time Projects - Feasibility Study
Project Shortname: ASTR1114
Discipline Name: Astrophysics
The South African Radio Astronomy Observatory manages the currently operating 64-dish MeerKAT telescope located in Carnarvon in the Karoo. It is expected that approximately 30% of MeerKAT's observing time will be taken up by smaller research groups who do not necessarily have the computing capacity to carry out the required processing of the data. The point of this research programme is to provide an avenue for such projects to perform at least a portion of their processing. For ease of software deployment and for scientific reproducibility, we are including the use of the container technology Singularity into our mix. We have progressed beyond our initial testing, and have begun our official benchmarking activities, which considers a typical imaging pipeline using a simulated MeerKAT dataset as input. Current results already suggest that we may use our existing framework to at least start addressing how best to distribute the imaging pipeline in question.
Principal Investigator: Dr Emmanuel Sakala
Institution Name: Council for Geoscience
Active Member Count: 0
Allocation Start: 2019-05-15
Allocation End: 2019-11-11
Used Hours: 10307
Project Name: Application of high performance computing at the Council for Geoscience
Project Shortname: ERTH1227
Discipline Name: Earth Sciences
The primary mandate of the Council for Geoscience (CGS) according to the Geoscience Act is to develop and publish world-class geoscience knowledge products and to render geoscience-related services to the South African public and industry. In order for the CGS to fulfill this mandate and also to advance the geoscience field within South Africa and beyond, the CGS registered a research programme with the Center for High-Performance Computing and is titled "The application of high-performance computing at the Council for Geoscience". This programme was formulated to expand the currently available computing resources at the CGS and the programme involves running high computing packages for geophysical modelling, seismological data processing, geological modelling and any other packages which are currently not optimum for desktop computing. Research and development of the various geoscience fields (geophysics, geology, geochemistry, hydrogeology) are covered in this programme. Currently, the CGS is embarking on training of scientists to get them up to speed in the utilisation of this new technology in their line of work. The ultimate intention of the CGS is to extract value from geoscientific data. These data will be used for predictive mineral mapping, water mapping, pollution characterizations, geohazards modelling and climate change studies.
Principal Investigator: Dr Hezekiel Kumalo
Institution Name: University of KwaZulu-Natal
Active Member Count: 15
Allocation Start: 2019-05-15
Allocation End: 2019-11-11
Used Hours: 628204
Project Name: Molecular modeling and computer aided drug design
Project Shortname: HEAL1009
Discipline Name: Health Sciences
he group covers a wide range of computational and molecular modeling research areas with main focus on biological systems and drug design approaches.
Main interest is related to design and study of biologically and therapeutically oriented targets. This is achieved by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We are involved in projects such Understanding drug resistance mechanisms via different computational tools QM/MM MD simulations Quantitative Structure Activity Relationship (QSAR) Conformational Analysis of biomolecules Bioinformatics tools applications Development Projects Approaches to enhance binding free energy calculations results Developing parameters for biomolecules: on-going projects Software implementations: on-going projects. All the projects that we do in the group contribute to the training of pharmaceutical scientists with specific skills for both the pharmaceutical industry and academia. This has the potential of stimulating the local pharmaceutical industries in South Africa to manufacture pharmaceuticals of quality, excellence and affordability for optimum and cost effective patient health, instead of being dependent on multinational pharmaceutical companies. We are still young group therefore funding is problem, therefore for the resources at HPC allows us to generate hypotheses for subsequent experimental testing in a much quicker manner and higher throughput than using experiment alone to generate hypotheses that you'd like to test. It has h given us an opportunity to be able explain experimental data we could not explain easily such the binding landscapes of different enzymes and the mechanism of action for different inhibitors.
Principal Investigator: Dr Bahareh Honarparvar
Institution Name: University of KwaZulu-Natal
Active Member Count: 12
Allocation Start: 2019-05-15
Allocation End: 2019-11-11
Used Hours: 932638
Project Name: Computer-aided HIV/TB drug design
Project Shortname: CHEM0808
Discipline Name: Health Sciences
The research group are doing drug discovery research using commercial software packages that are installed on CHPC.
Principal Investigator: Dr Thabang Ntho
Institution Name: Mintek
Active Member Count: 10
Allocation Start: 2019-05-17
Allocation End: 2019-11-13
Used Hours: 208324
Project Name: Hydrogen Storage Materials and Catalysis
Project Shortname: MATS0799
Discipline Name: Material Science
In the Advanced Materials Division, at Mintek, we use density functional theory (DFT) and other simulation methods mostly to accelerate our research in finding or engineering new catalytic and alloy materials that can address South African needs in a variety of areas including health (shape memory alloys), water purification, energy (fuel cells), etc. The CHPC offers us the tools and platform to focus on our work to rapidly achieve results via the use of the Lengau super-computer. So far virtual experiments (simulations) have allowed us to validate some of our experimental findings while helping us cut down on the number of laboratory experiments needed to reach project scientific aims and objectives.
Principal Investigator: Dr Winfred Mulwa
Institution Name: Egerton University, Egerton, Kenya
Active Member Count: 8
Allocation Start: 2019-05-17
Allocation End: 2019-11-13
Used Hours: 26070
Project Name: Magnetic Refrigeration
Project Shortname: MATS1181
Discipline Name: Physics
Who: MATS1181 under PI Winfred Mulwa from Egerton University Kenya: Magnetic refrigeration.
What: Magnetization and demagnetization of magnetic materials known as magnetic refrigeration that rely on magnetocaloric effect (MCE). In cooling technology, magnetic refrigeration which depends on magnetocaloric effect is commonly used in refrigerators to achieve exceptionally low temperatures.
Why: . Magnetic refrigeration does not rely on the uses of harmful and ozone-depleting coolant gases.
How: This work is done computationally. We use the Quantum Espresso code (Density Functional Theory). This purely depends on CHPC because all the calculations have to be done in CHPC. Thanks to CHPC.
How is the project progressing: We have achieved our third objective. One more objective to go. The project is as planned.
Principal Investigator: Dr George Manyali
Institution Name: Masinde Muliro University of Science and Technology, Kakamega, Kenya
Active Member Count: 12
Allocation Start: 2019-05-17
Allocation End: 2019-11-13
Used Hours: 398866
Project Name: Ab Initio study of Thermoelectric Materials
Project Shortname: MATS0712
Discipline Name: Material Science
The Computational and Theoretical Physics (CTheP) Group at the Department of Physical Sciences, Kaimosi Friends University College, comprises a team of researchers and students dedicated to the development and application of computational modeling to outstanding problems in materials science. In general, the group seeks a deeper understanding of quantum-mechanical descriptions of interacting electrons and nuclei in order to predict and design properties of materials and devices using density functional theory as a tool for the first-principles simulation. This kind of simulation generates volumes of data which cannot be handled by the common desktop computers. High-performance computing provides the computational environment that includes parallel processing, large memory, and storage of the big data. Therefore, Center for High-Performance Computing facility in Cape Town, South Africa, plays a vital role in providing the resources that aid the discovery of new materials and accelerates its application in the industry, an achievement that would have been in vain with desktop computers. Some specific projects for our group include characterization of already known thermoelectric materials. The information gained from this project is used as identifiers in search for new thermoelectric materials with the tailored figure-of-merit. Such materials are used to enhance the efficiency of thermoelectric generator power system for renewable energy. Such outcomes of our projects have an impact on the livelihood of the rural communities in Kenya, and generally, supports the Agenda Four of the Kenyan economic blueprint that was recently availed by the president of the Republic Kenya.
Principal Investigator: Prof Chris Meyer
Institution Name: Stellenbosch University
Active Member Count: 7
Allocation Start: 2019-05-20
Allocation End: 2019-11-16
Used Hours: 1533433
Project Name: Development of CFD models
Project Shortname: MECH1077
Discipline Name: Computational Mechanics
The research activity is led by Prof CJ Meyer from Stellenbosch University and is focused on developing computational models of industrial thermo- and fluid dynamic processes. There is a specific emphasis on the use of free software under the GNU General Public License. The industrial processes under consideration are those relevant to specific segments of industry in South Africa most notably power generation. Current projects include the simulation of large-scale air-cooled condensers as well as detailed simulations concerning the flow through axial flow fans used in the energy sector. The cohort of students are making excellent progress with 3 students having submitted their work for examination and the rest to dos o shortly. Two of these students will definitely go on to their PhDs with a third a strong possibility.
Principal Investigator: Prof Edet Archibong
Institution Name: University of Namibia
Active Member Count: 4
Allocation Start: 2019-05-20
Allocation End: 2019-11-16
Used Hours: 5194
Project Name: (1) Computational Study of Semiconductor Clusters. (2) Computational Study of Bio-active Molecules Extracted from Plants
Project Shortname: CHEM0969
Discipline Name: Chemistry
The computational chemistry group at the University of Namibia (UNAM), have computationally synthesized the first intermediates that are initially formed when ozone reacts with thiophenol, catechol and resorcinol. These phenols are found in water processed for drinking using ozone. They are also found in the lower layer of the atmosphere (troposphere). The intermediates that we have studied using computational modeling are very important in shedding lights on how ozone interacts with the phenolic compounds found in water and in the atmosphere. Therefore, from environment point of view, the research is very important in order to know some of the chemical processes going on in the atmosphere and in water processed for domestic and commercial uses. The properties of these intermediates have been studied in the gas phase and in water. Our work show that solvent (water) play significant role in the stability of the intermediates and the transition states leading to the formation of the intermediates.
More importantly, the use of computer clusters (Lengau) provided by CHPC in South Africa have facilitated successful study of these systems because they are large and required significant computational resources.
The first stage of the project is virtually completed and the group is moving to the next stage of elucidating other intermediates in the reaction path and also studying the effect of solvents on the reactions.
Principal Investigator: Dr Holliness Nose
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 2
Allocation Start: 2019-05-22
Allocation End: 2019-11-18
Used Hours: 251793
Project Name: Inorganic Computational Chemistry
Project Shortname: CHEM1003
Discipline Name: Chemistry
Our current project involves preparation of photosensitizers for water purification. Water treatment strategies commonly adopted include chlorination, distillation, UV-radiation, boiling and reverse osmosis. While these methods have proved to be effective in water decontamination, they have not been completely efficient in treatment of microbe polluted water. This is attributed to emergence of anti-microbial resistant (AMR) microorganisms such as Methicillin-resistant Staphylococcus aureus and Amphotericin-resistant Candida albican. AMR pathogens find their way into drinking water, causing waterborne diseases. Photodynamic antimicrobial therapy (PACT) provides an alternative and viable method of water disinfections, especially in addressing the anti-microbial resistant bacteria. PACT makes use of a photosensitizer, which when localized in microorganisms can be activated by irradiating it with light of appropriate wavelength to generate a reactive oxygen species (ROS). This ROS is able to destroy or affect biological structures such as cell wall material, nucleic acids, peptides and lipids therefore leading to cytotoxicity. Therefore, this method allows the photosensitizer to bind to the bacterial or fungal cell wall, inhibiting cell growth, with no possibility of recovery or development of resistance against it. My group intends to design and develop the photosensitizers computationally, followed by synthesis of the metal complexes and finally carry-out biological assays to examine their cytotoxicity. This project therefore relies on CHPC heavily as we need to design the photosensitizers theoretically before we go to the laboratory to synthesize them and test their biological activities. This project is intended began on June 1st 2019 and and is currently ongoing. But without the CHPC facilities, we are unable to do this type of research. The project is proceeding on well.
Principal Investigator: Dr Stefan du Plessis
Institution Name: Stellenbosch University
Active Member Count: 9
Allocation Start: 2019-05-20
Allocation End: 2019-11-16
Used Hours: 6369
Project Name: Shared Roots
Project Shortname: HEAL0793
Discipline Name: Health Sciences
Shared Roots is a collaborative research project undertaken by researchers from the departments of psychiatry, neurology and genetics at Stellenbosch University and researchers from the South African National Bioinformatics Institute (SANBI). It is a MRC Flagship funded study and the principal investigator on the study is the executive head of the department of psychiatry Professor Soraya Seedat. Dr Stéfan du Plessis is responsible for the neuroimaging component. Our study included participants with posttraumatic stress disorder (PTSD), schizophrenia or Parkinson's disease. It is known that individuals with mental illness as well as other common brain disorders have higher rates of heart disease and stroke than the general population. It is not clear why this is the case. Our study therefore aims to collect information about all the potential factors that can play a role, to better understand the increased risk and enable the development of treatment strategies. To achieve this goal we will combine state-of-the-art research techniques such as genetic evaluations and the latest neuroimaging techniques. This will be combined in analysis with information evaluating the brain disorders, general health and lifestyle factors.
For our neuroimaging component, we scanned over 600 participants using Magnetic Resonance Imaging (MRI). Here we investigate potential brain changes associated with increased metabolic risk. We proceeded to calculate precise measurements of around 70 known brain regions using the MRI scans, which will be compared between cases and healthy controls. Processing takes around 24 hours for each scan. To finish in a timely manner, we used the Centre for High Performance Computing Rosebank, Cape Town, Sun Intel Lengau cluster.
Principal Investigator: Dr MC du Plessis
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 2
Allocation Start: 2019-05-27
Allocation End: 2019-11-23
Used Hours: 44183
Project Name: ACO Routing for OBS Networks
Project Shortname: CSCI1211
Discipline Name: Computer Science
Optical Burst Switching (OBS) is a next-generation paradigm which holds the promise of improved capacity on fibre optic networks. However, there is a gap for effective, efficient and responsive network resource management algorithms, to ensure that OBS can fulfill it's promise. Research is being done at the Nelson Mandela University, Center for Broadband Communications by postgrad computer science students, Joshua Oladipo and Francois du Plessis, under the supervision of Dr MC du Plessis from the department of computer science and Prof Tim Gibbon from the department of physics to apply the machine learning algorithm known as Ant Colony Optimisation to this problem. CHPC resources are being used to investigate the effectiveness of several algorithm variants. This information is essential for developing a successful OBS routing algorithm.
Principal Investigator: Prof Eno Ebenso
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2019-05-27
Allocation End: 2019-11-23
Used Hours: 93534
Project Name: Theoretical Investigations of Corrosion Inhibition Activities of Organic Compounds
Project Shortname: CHEM1176
Discipline Name: Chemistry
Our research group, Materials Science Innovations and Modelling Research Focus Area is domiciled at the Mafikeng Campus of North-West University.
About 75% of our work is on the design of new corrosion inhibitor solutions to mitigate the rate at which metal (alloys) corrode in various environments. Other works in the group include of electrochemical sensors development and thermodynamics of solutions. Our research works involve quite a volume of computational studies, especially quantum chemical calculations using the Gaussian software and Molecular dynamics simulations using the Materials Studio software. The computational studies are often used to corroborate experimental results in our continuously robust and comprehensive investigations. For instance, the potentials of an organic compound to inhibit corrosion of metal is often dependent on its ability to adsorb on metal surface, which in turns depends on its molecular reactivity. Determining corrosion inhibition mechanism is central in such research, and computational study is an important aspect of the research. For a timely output, conventional personal computer (PC) is not an option in the kind of research we do. Continuous access to software license is also not negotiable. Hence, enrollment of our research group on CHPC resources is very important.
For a quantum chemical calculation that takes an average of 15 days per molecule to complete on a PC (if it does not end up crashing due to insufficient memory, as it's often the case), and an investigation involving at least 4 organic molecules (often, more compounds are considered), an investigator will be highly frustrated without a resource like CHPC.
Since our enrollment on CHPC resources, our project has been progressing satisfactorily and the time spent on a particular project has been reduced due to speedy computations. Hence, we have the opportunity of designing more elaborate projects executable within reasonable space of time.
Principal Investigator: Prof Sybrand van der Spuy
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2019-05-27
Allocation End: 2019-11-23
Used Hours: 666868
Project Name: CFD simulation of turbomachinery
Project Shortname: MECH1187
Discipline Name: Computational Mechanics
The turbomachinery research group of Stellenbosch University focuses on the simulation and testing of cooling fans and gas turbine components. The ability to simulate these components is of importance to both power and defense industries in South Africa. The physical process inside these machines is not only one associated with a large geometry but also includes highly non-linear physics like turbulent flow, heat transfer and combustion. The CHPC enables us to simulate these really large turbomachinery problems. This is an ability that is not only held in high esteem nationally but also internationally.
Principal Investigator: Prof Regina Maphanga
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 6
Allocation Start: 2019-05-23
Allocation End: 2019-11-19
Used Hours: 82863
Project Name: Energy Storage Materials
Project Shortname: MATS0919
Discipline Name: Material Science
The Design and Optimisation group is a group under Operational Intelligence Impact Area in the Next Generation Enterprises and Institutions cluster of CSIR and uses multiscale methods to develop novel energy storage materials with desired properties and enhanced properties for existing materials. The envisaged outcome of this project is to develop energy storage materials models with improved performance and consistency, which will be cheaper and environmentally benign. The ever-increasing global energy needs and depleting fossil-fuel resources demand the pursuit of sustainable energy alternatives, including renewable sources to replace carbon intensive energy sources. Sustainable and renewable energy is considered to be the most effective way to minimize CO2 emissions. Hence, finding sustainable energy storage technologies is vital for optimally harnessing the renewable energy.
Computational methodologies are very effective in predicting material-structure-property correlations. In this project simulation methods and models based on parallel computing are developed to probe energy materials properties. Centre for High Performance Computing (CHPC) resources are used to develop these parallel computing methods and algorithms for large and complex material models. Thus, CHPC resources provide a platform to simulate the evolution of material properties at a wide range of external conditions that are not accessible experimentally and fast track acquisition of results. The major of aim of this project is to create a predictive, reliable and robust set of models of materials for energy storage across the materials modelling length scale, leading to integrated multi-scale capability.
Principal Investigator: Prof Josua Meyer
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2019-05-30
Allocation End: 2019-11-26
Used Hours: 242232
Project Name: Fundamentals of forced and mixed convection in heat exchangers
Project Shortname: MECH1094
Discipline Name: Computational Mechanics
In-tube condensation is widely seen in many industries such as desalination, power plants and air conditioning. Thoroughly understanding of the condensation phenomenon would lead to better design of the systems which consequently causes the improvement of system efficiency. Although in majority of applications the circular tubes are used, there are some particular cases, like in air-cooled steam condensers, in which non-circular tubes such as rectangular tubes and flattened tubes are utilized. It has been proved that the thermal efficiency of such tubes are better as compared to the conventional circular tubes under specific operating conditions.
This work is being done by the Clean Energy Research Group (CERG) at the University of Pretoria. This group is involved in experimental and numerical heat transfer research focused on clean energy applications. CERG, falling under the Department of Mechanical and Aeronautical Engineering at the University of Pretoria, has a number of world class experimental facilities focused on heat transfer, balanced by a Computational Fluid Dynamics (CFD) division. The Group members have developed, designed and built five unique, state of-the-art experimental set-ups, which are being used for leading-edge heat transfer research.
Due to lack of water resources in South Africa, the research works on the optimizing and performance enhancement of systems working with water as the working fluid should be greatly developed. Such activities will definitely lead to lower energy and water consumption within the country in the future.
It is the purpose of this research work to numerically investigate the effect of inclination on condensation of steam inside a long flattened channel. Thoroughly understanding of this problem via numerical simulations would assist in proper design of ACCs with low cost and time compared to experimentation.
At the moment, most of the work has been done, and a research paper is going to be prepared.
Principal Investigator: Prof Jacques Joubert
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2019-06-03
Allocation End: 2020-01-15
Used Hours: 4050
Project Name: Polycyclic cage compounds as multifunctional neuroprotective agents
Project Shortname: CHEM1173
Discipline Name: Chemistry
A number of organic molecules have been studied for their electronic and physical-chemical properties in order to determine their biological relevance. The use of sophisticated softwares provided by the CHPC have shed light on the activities and properties of these molecules. These data obtained will be used in future studies to optimise the potential therapeutic abilities of these molecules.
Principal Investigator: Prof Zenixole Tshentu
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 6
Allocation Start: 2019-06-03
Allocation End: 2019-11-30
Used Hours: 473725
Project Name: Metal-ligand, anion-cation interactions and protein-ligand studies
Project Shortname: CHEM0864
Discipline Name: Chemistry
The group at NMU Chemistry Department under the leadership of Prof Tshentu is engaged in developing selective chemistry for beneficiation of earth and secondary resources. The work on developing reagents that are selective for precious metals has made gains and continues to produce reliable materials that could have industrial applications. The work on desulfurization and denitrogenation of fuel has contributed to the search for new methods for removal of contaminants from fuel (N and S) and is therefore contributing to upgrading of fuel to a zero sulfur level. The CHPC resources are key to the design of selective chemistry for these two applications.
Principal Investigator: Prof Nicola Mulder
Institution Name: University of Cape Town
Active Member Count: 14
Allocation Start: 2019-06-04
Allocation End: 2019-12-01
Used Hours: 46075
Project Name: H3ABioNet
Project Shortname: CBBI0825
Discipline Name: Bioinformatics
The CHPC resources have been used for a few projects related to the analysis of biomedical data. One project is enabling human genotype data to be imputed using a reference panel (collection of existing human genome sequences from different populations). A second project is running the analysis of proteomics data on human microbiome samples. the microbiome is the component of non-human organisms found within different areas of the human body. The other project relate to the analysis of pathogen genomics data, including the malaria parasite and pneumococcal bacterial isolates to study virulence and transmission.
Principal Investigator: Dr Thishana Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2019-06-05
Allocation End: 2019-12-02
Used Hours: 174144
Project Name: Combined kinetics,quantum-chemical investigation of reaction mechanisms involving catalysts
Project Shortname: CHEM0821
Discipline Name: Chemistry
The TS Computational Chemistry Research Group (University of Kwazulu-Natal, School of Chemistry and Physics) carries out quantum chemical modelling of homogenously catalysed organic reactions in the inter-domain field of Physical-Organic Chemistry. Computational Chemistry can be classified as 'Green Chemistry' as it is sustainable and does not generate chemical waste. The focus of this research group is primarily on catalytic asymmetric synthesis that have many applications in the pharmaceutical and fine chemical industry. The optimisation of a catalyst offers a good understanding of the factors that are responsible for the rate and selectivity of a reaction. Theoretical calculations, together with experimental kinetic measurements, often can pin down the mechanism. Using this methodology, it is possible to understand, and more importantly, design effective catalysts for a number of asymmetric, catalytic processes. The CHPC provides the facilities: hardware, in the form of the Lengau cluster and software programs such as Gaussian16, amongst many others. Thus far the current project has yielded three publications in 2019.
Principal Investigator: Prof Tahir Pillay
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2019-06-05
Allocation End: 2020-01-15
Used Hours: 129100
Project Name: Molecular Modelling of ligands and receptors
Project Shortname: HEAL0876
Discipline Name: Health Sciences
Prof Tahir Pillay's research group in the Department of Chemical Pathology, University of Pretoria is actively working on the field of pharmcoinformatics applications in the genetic and acquired diseases. We have been using the facility of CHPC since 2014. The research group uses several pharmacoinformatics tools to design computational models followed by screening of small molecular databases and simulations for therapeutic application in several diseases including HIV/AIDS, Tuberculosis, Alzheimer's, Malaria, etc. For this purpose we are extensively using Schrodinger, Amber, Gromacs etc. Therefore, the research work is entirely dependent on pharmacoinformatics tools available in the CHPC server. The department does not have sufficient infrastructure to carry out the research in the current project. Hence, our research group requires access to the CHPC server to fulfil the objectives of the current project. We are quite happy with the services available in the CHPC server and would like to thank entire team for their efforts and support.
Principal Investigator: Prof Gerhard Venter
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2019-06-06
Allocation End: 2020-02-11
Used Hours: 46391
Project Name: Finite Element Analysis and Numerical Design Optimization
Project Shortname: MECH0883
Discipline Name: Computational Mechanics
We do not have a press release based on the latest work we did yet. Hopefully in future there will be more interesting results that will warrant a press release.
Principal Investigator: Prof Enrico B Lombardi
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2019-06-07
Allocation End: 2019-12-04
Used Hours: 1142340
Project Name: Defects in wide-bandgap semiconductors and 2D materials
Project Shortname: MATS1160
Discipline Name: Material Science
The materials research group of Prof Lombardi at the University of South Africa (UNISA) focuses on defects in wide band gap semiconductors and 2 dimensional (2D) materials, exploring a range of defects which affect the functionality and efficiency of these materials. Applications of these materials range from next generation spintronics devices, to nano-electronic and opto-electronic devices. As in all solid state materials systems, defects are inevitable, and is particularly important in new chemically grown 2D materials due to the imperfection of the growth process, including, amongst others, 2D chalcogenides.
Our group has contributed to the understanding of fundamental defects and defect processes in these 2D materials, predicting the properties of intrinsic point defects and other likely defects, and the conditions under which they are likely to occur. These results provide insight to the physics of defects that are grown via chemical vapour deposition, as well as in electron irradiated materials. These defects are responsible for large variation of electric and optical properties, while they may also act as efficient electron or hole traps, which strongly influence transport and optical properties of semiconductors, in turn strongly impacting their applicability to next generation devices. This research is performed using the state-of-the-art density functional theory, and has made extensive use of CHPC compute resources.
Principal Investigator: Dr Caroline Kwawu
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 11
Allocation Start: 2019-06-18
Allocation End: 2020-03-12
Used Hours: 514125
Project Name: Renewable Energy Materials
Project Shortname: MATS1146
Discipline Name: Material Science
Renewable Energy Materials group members are student of Kwame Nkrumah University of Science and Technology. The group members focuses on the study of materials for chemical processes. We study the reaction mechanisms on heterogeneous surfaces, and also study the effect of defects on the band engineering of semiconductors for CO2 reduction and water reduction. This research is crucial as the world is both confronted with issues of Global warming, energy scarcity and there is the need for alternative cleaner energy sources. This includes green house gas (methane, water, CO2 etc) conversion to mitigate global warming, biomass conversion to fuels and harnessing of solar energy using solar cell materials. We employ electronic density functional theory computational simulations using quantum espresso to investigate the areas mentioned above. Research has led to the 4 draft manuscripts that will be published in 2020. The CHPC has provided computing resources (hardware and software) for our simulations.
Principal Investigator: Prof Tien-Chien Jen
Institution Name: University of Johannesburg
Active Member Count: 21
Allocation Start: 2019-06-19
Allocation End: 2020-03-04
Used Hours: 2288201
Project Name: Developing an Innovative Metal Matrix Composite Membrane for Hydrogen Purification
Project Shortname: MATS0991
Discipline Name: Material Science
Hydrogen is an excellent energy carrier because of its high enthalpy of combustion with less environmental impact. Hydrogen fuel can be directly used in cars, ships, aircraft, and other transportation equipment. Although there are many problems to be resolved for implementation of hydrogen technology, it is generally believed that hydrogen will become a key energy carrier in this century. Until sufficient quantities of hydrogen can be derived from renewable energy sources, it will have to come from hydrogen separation using existing fuels (e.g., diesel, natural gas) as the feedstock. Hydrogen separation units can generate highly purified hydrogen from the feedstock gas mixtures, however, a certain amount of CO and other chemicals will make it into the hydrogen stream and cause catalyst failure on the fuel cell electrode. This significantly deteriorates the activity of the catalyst layer, particularly for Proton-Exchange Membrane (PEM) fuel cells. This deterioration greatly reduces the efficiency of power generation and the life cycle of the fuel cell. Overcoming this obstacle is necessary for the wider use of highly efficient fuel cells. The objective of this mproposal is to develop a new composite metal membrane (CMM) that can achieve extremely high flux and selectivity of the hydrogen separation and achieve the lifetime goal set by the U.S. Department of Energy (DOE). To accomplish these goals, a research team formed by the University of Johannesburg (UJ), Council for Scientific and Industrial Research (CSIR) and Hydrogen South Africa (HySA) will combine two major technologies: Electrostatic-Force-Assisted Cold Gas Dynamic Spraying (ECGDS) and Laser-Assisted Manufacturing (LAM) to develop this new type of membrane. The proposed new membrane will eliminate the hydrogen embrittlement, catalyst failure, and avoid the difficulty of forming a defect-free, ultrathin Pd film on the substrate surface. The proposed CMM will exhibit superior reliability and can be produced with a relatively low-cost and scalable process. Along with the development process, numerous numerical methods are utilized to simulate the material properties and behaviour as well as the optimization fabrication procedure. To accomplish these task HPC services from CHPC plays a crucial role in understanding the numerous unknown phenomena's. This service enables the research to be simulated from feature scale to reactor scale .Note that this project is currently supported by the NRF for 2017-2020
Principal Investigator: Dr Danie J Ludick
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2019-06-19
Allocation End: 2020-01-29
Used Hours: 12093
Project Name: Development of parallelized CEM solvers
Project Shortname: MECH1240
Discipline Name: Electrical Engineering
The Electromagnetics and Microwave, Antenna and Computational Systems Lab (EMACS) group at the Department of Electrical and Electronic Engineering, Stellenbosch University is frequently involved with the numerical analysis of electrically large structures, such as antenna arrays used in radio astronomy applications. The analysis of these structures typically includes a rigorous software simulation phase, which is computationally expensive. The CHPC provided our team with the necessary infrastructure to both simulate real-life computational electromagnetic (CEM) problems, as well as research and develop new parallelisation strategies. One of these algorithms, the Domain Green's Function Method (DGFM) developed by our group targets the fast analysis of sparse antenna arrays, such as the low-frequency aperture array envisioned for the Square Kilometre Array (SKA) radio astronomy project.
Our group is working a novel parallelisation strategy for this algorithm with the help of the computing resources provided by the CHPC. The key strategy of this method was to partition the global array problem into many sub-array problems, each of which is distributed to a compute node. Each of the compute nodes then used shared memory programming paradigms (such as OpenMP) to further speed-up the analysis. Afterwards, the results are gathered so that we have a global solution.
Promising results will be showcased at the European Conference on Antennas and Propagation (EuCAP) conference in Copenhagen, Denmark later this year. This presentation is accompanied by the following international conference proceeding: "A Parallelized Fast Array Analysis Approach" by Mr Tameez Ebrahim and Dr Danie J Ludick. Follow-up work is already in the pipeline which will enable us to simulate even larger, more complex antenna arrays.
Principal Investigator: Dr Md Ataul Islam
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2019-06-20
Allocation End: 2019-12-17
Used Hours: 160659
Project Name: DR. MA Islam
Project Shortname: CBBI1198
Discipline Name: Bioinformatics
MA Islam's research group is working on the field of pharmcoinformatics applications in communicable and non-communicable diseases including tuberculosis, diabetes, Alzheimer's disease, cancer, malaria and common bacterial infections etc. Facilities provided by the CHPC are used by this group since February 2019. This research group is using several pharmacoinformatics tools to design computational models followed by the screening of small molecular databases and simulations for the therapeutic application in several diseases as mentioned earlier. In this purpose we are extensively using Schrodinger, Amber, Gromacs tools etc. Therefore, the research work entirely dependent on pharmacoinformatics tools available in the CHPC server. Hence, our research groups completely in need of the access of CHPC server to fulfill the objectives of the current project. On behalf of the research group I would like to thank CHPC entire team for their efforts and support.
Principal Investigator: Dr Farai Muchadeyi
Institution Name: Agricultural Research Council
Active Member Count: 4
Allocation Start: 2019-06-24
Allocation End: 2020-03-20
Used Hours: 1806
Project Name: Application of Genomics and Population Genetic Tools in Livestock
Project Shortname: CBBI1171
Discipline Name: Other
The Indigenous Livestock Genomics group led by Dr FC Muchadeyi at the Agricultural Research Council Biotechnology Platform, composes of researchers and postgraduate students. Research projects conducted include population genomics to understand and unravel patterns of genetic differentiation, gene flow and genomic regions under natural and artificial selection in indigenous breeds and adaptations to environments and production systems. The team used linkage disequilibrium and haplotype block in village, commercial and indigenous pigs of South Africa for a successful selection programs and genome-wide association study (GWAS) because they provide insights into population genetic history. Additionally, the team has used RNA Seq to understand molecular mechanisms underlying host resistance to this parasite and used RNA-sequencing technology to compare the transcriptomic response of the sites of the host-parasite interaction in Merino sheep. It also is important as it can provide evidence of pathways underlying resistance and susceptibility both primary and tertiary Haemonchus infections in Merino sheep.
Principal Investigator: Dr Benjamin Lamptey
Institution Name: University of Ghana
Active Member Count: 11
Allocation Start: 2019-06-25
Allocation End: 2020-07-14
Used Hours: 113137
Project Name: Weather, Climate and Water
Project Shortname: ERTH0955
Discipline Name: Earth Sciences
This group comprises Earth Scientists including meteorologists from the Ghana Meteorological Agency (GMet). Different works are being done. These include (a) investigating the predictability of extreme events that result in persistent annual flooding in the major cities of Ghana. The goal is to study the characteristics of the weather systems that are responsible for these extreme events; (b) performing sensitivity tests to obtain optimal configurations of the WRF model for weather and seasonal climate predictions over Ghana and West Africa. The WRF model is being used to downscale Global models in these activities.
There are plans to run an ocean model and an air pollution model.
Principal Investigator: Dr Andre Stander
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2019-06-21
Allocation End: 2019-12-18
Used Hours: 120897
Project Name: In silico estimation of ligand binding energies against cancer- and malaria-associated proteins
Project Shortname: CHEM1055
Discipline Name: Health Sciences
Fourth Industrial revolution techniques such as machine-learning methods were applied to improve the prediction of Ki for ligands bound to proteins. This will greatly improve the accuracy of in silico screening campaigns to identify new medicinally relevant compounds.
Principal Investigator: Dr Rhiyaad Mohamed
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2019-06-21
Allocation End: 2020-01-29
Used Hours: 232188
Project Name: Advanced materials for oxygen evolution reaction
Project Shortname: MATS1123
Discipline Name: Chemical Engineering
Hydrogen is seen as an integral part of the sustainable energy future. Through fuel cell and electrolyser technologies, energy storage and conversion will be possible. This will resolve some of the more critical challenges faced by most renewable energy sources. Co-hosted by the University of Cape Town and operating under the Catalysis Institute, HySA Catalysis (Hydrogen South Africa Catalysis), part of a flagship programme funded by the Department of Science and Technology, aims to find efficient and market ready catalyst technologies for both hydrogen fuel cells and water electrolysers. The former has been an age-old activity with a strong internal knowledge base. On the other hand, water electrolyser research is a new venture with many unresolved and unknown challenges. The Electrolyser Research Group is a new, young and dedicated group in the area of water electrolysis within HySA Catalysis.
Using theoretical methods such as density functional theory (DFT), we aim to predict highly conductive and stable OER catalyst support materials. These predictions will then inform our on-going experimental pursuits. This synergistic approach not only improves efficiency but also enables are more detailed understanding of applied materials opening new insights and potentially new applications. CHPC provides computational resources need for performing DFT calculations which are extremely computationally intensive.
We have now completed the investigation of some electronic properties of bulk tin dioxide and doped tin dioxide materials. We plan to extend the list of dopants and are also interested in investigating titanium dioxide and its doped derivatives. Overall, our study will ultimately provide much needed insights into the fundamental properties of these highly sought-after materials.
We were pleased to have an opportunity to share our current findings at the International Society of Electrochemistry Annual Meeting (August 2019) in Durban, South Africa; and with the positive feedback received from international delegates.
Principal Investigator: Dr Gaston Mazandu Kuzamunu
Institution Name: University of Cape Town
Active Member Count: 10
Allocation Start: 2019-06-27
Allocation End: 2020-01-29
Used Hours: 13220
Project Name: Sickle Africa Data Coordinating Center (SADaCC)
Project Shortname: CBBI1243
Discipline Name: Health Sciences
Sickle Cell Disease is the most common monogenic diseases mainly caused by a single-point mutation in the beta-subunit of haemoglobin, the principal oxygen transporter in red blood cells. Because of the protective effect of the sickle cell mutation against malaria, sickle cell disease has the highest incidence and prevalence in tropical regions, particularly in Sub-Saharan African countries, where more than 70% of patients live, affecting approximately 300 000 newborn babies every
year and more than 20 million people globally.
Thus, the Sickle Africa Coordinating Center project at University of Cape Town, Faculty of Health Sciences under the Division of Human Genetics has been set to coordinate different type of sickle cell datasets across Africa: collection and analyses, and tackle issues related to this condition, including phenotype pattern prediction, diagnostics and treatments. Genetics being a key components for this condtions and considering more than 11000 patients that have been identified across Africa (Tanzania, Ghana and Nigeria), genomic datasets are now being carried out predicting and prioritizing in silico mutations leading to optimal therapeutics. This is important, especially with the current trend of gene therapy that is being suggested. With this sample size, which is expected to increase as the project is planning to expand to more African countries, High Performance Computing, such as CHPC is really needed to design scalable pipeline to effectively process these datasets to contribute to overcoming this disease.
Principal Investigator: Dr Nikhil Agrawal
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2019-06-28
Allocation End: 2020-01-15
Used Hours: 76541
Project Name: Molecular Modeling of proteins using different computational tools
Project Shortname: HEAL1189
Discipline Name: Health Sciences
We are based at University of KwaZulu-natal, Durban, South Africa. We majorly work on proteins and peptides and try to understand their structures and their binding with other molecules, e.g. drug, polymers and lipid molecules. Peptides and candidate drug molecules we work on shows activity against several diseases, e.g. bacterial diseases, viral diseases, HIV, TB etc. Since this peptides and candidate drug molecules bind to a disease-causing protein and inhibit its function. So, it is crucial to understand their binding with these proteins. Using CHPC resource, we understand their binding. The generated information will be helpful to design new and efficient drug molecules and peptides against these diseases.
Principal Investigator: Dr Geoff Nitschke
Institution Name: University of Cape Town
Active Member Count: 9
Allocation Start: 2019-07-01
Allocation End: 2019-12-28
Used Hours: 1055595
Project Name: Evolving Complexity
Project Shortname: CSCI1142
Discipline Name: Computer Science
The evolutionary machine learning group at the department of computer science at the University of Cape Town is running evolutionary robotics and deep-learning experiments.
The evolutionary-robotics experiments simulate groups of robots with adapting behaviour, where a global problem-solving collective behaviour emerges from their interactions.
The deep-learning experiments test new machine-learning methods for adapting deep-artificial neural networks for a range of pattern recognition tasks.
Both of these experimental platforms use complex computational architectures and require many computational evaluations per experiment, thus necessitating the use of the high-performance computing cluster.
Principal Investigator: Dr Cornelia Inggs
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2019-07-01
Allocation End: 2020-01-15
Used Hours: 469464
Project Name: Parallel and Distributed Search and Planning Algorithms
Project Shortname: CSCI1175
Discipline Name: Computer Science
Our research group is based at the University of Stellenbosch and consists of Marc Christoph — a student that is currently working towards an MSc. in computer science — and his supervisors, Dr. Steve Kroon and Dr. Cornelia Inggs.
Our work falls under the umbrella of Artificial Intelligence (AI) — a branch of computer science with the fundamental goal of developing algorithms that allow computers to make decisions and reason like humans do. Due to the complex nature of these algorithms, we often need to provide them with a massive amount of computational resources in order to have them simulate, or even surpass, the decision-making ability of humans.
An effective way to increase the computational resources available to an AI algorithm is to increase the number of computers that it runs on. This means that we can have hundreds of computers simultaneously running the same algorithm with the same goal. Effectively distributing the work across multiple computers in this way has many obstacles, and our research focuses on minimising the impact of these obstacles for Monte-Carlo Tree Search — a recently-developed algorithm that showed promise when it led to the first ever defeat of a human professional Go player with no handicaps.
This research is important because it provides future AI researchers with a better understanding of the benefits and pitfalls of applying AI algorithms to environments with many machines, which stimulates AI research and accelerate our journey to the ultimate destination of having computers with a decision-making ability that is indiscernible from, or even superior to, that of humans.
Principal Investigator: Prof Phuti Ngoepe
Institution Name: University of Limpopo
Active Member Count: 30
Allocation Start: 2019-07-05
Allocation End: 2020-02-25
Used Hours: 15380973
Project Name: Computational Modelling of Materials: Energy Storage
Project Shortname: MATS0856
Discipline Name: Material Science
Materials Modelling Centre (MMC), at the University of Limpopo (UL), employs High Performance Computing (HPC) methods to design and predict properties of valuable materials. Firstly, the demand of lithium ion batteries is increasing significantly owing to rapidly expanding automotive and energy storage markets. MMC simulates fabrication of lithium ion battery cathode particles made of nickel, manganese and cobalt, which are similar to those grown in production plant reactors. This is intended to reduce deterioration and breakage of such cathodes during charging and discharging in order to extend distances to be covered by electric vehicles in one charge. The work is conducted to support the production of cathode precursors at a pilot plant hosted by UL and supported by the Department of Science and Technology. Batteries beyond lithium ion, with higher capacity are also being investigated. Secondly, high recoveries of precious group metals from mines with the less understood platreef, particularly in Limpopo province, are not easily achieved. MMC, in collaboration with various research groups, use HPC to simulate the design of near green reagents for better recovery. A proof of concept on how simulations reproduce experimental approaches in such designs has been conducted on known sulphide minerals. The concept is being extended to explore ores with precious metal minerals containing less sulphur, with intention of enhancing their recoveries. Lastly, titanium powder metallurgy facilitates convenient manufacturing of alloys. MMC employs simulations to predict properties of high temperature titanium platinum based shape memory alloys. Furthermore, growth of titanium nanoclusters is modeled and provides valuable insights on titanium growth in a pilot plant at the Council for the Scientific and Industrial Research. Simulations across these three themes, are highly computer intensive and are achievable by use of HPC where UL postgraduate students are main beneficiaries.
Principal Investigator: Prof Josua Meyer
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2019-07-09
Allocation End: 2020-01-29
Used Hours: 1408358
Project Name: Fundamentals of forced and mixed convection in heat exchangers
Project Shortname: MECH1094
Discipline Name: Computational Mechanics
In-tube condensation is widely seen in many industries such as desalination, power plants and air conditioning. Thoroughly understanding of the condensation phenomenon would lead to better design of the systems which consequently causes the improvement of system efficiency. Although in majority of applications the circular tubes are used, there are some particular cases, like in air-cooled steam condensers, in which non-circular tubes such as rectangular tubes and flattened tubes are utilized. It has been proved that the thermal efficiency of such tubes are better as compared to the conventional circular tubes under specific operating conditions.
This work is being done by the Clean Energy Research Group (CERG) at the University of Pretoria. This group is involved in experimental and numerical heat transfer research focused on clean energy applications. CERG, falling under the Department of Mechanical and Aeronautical Engineering at the University of Pretoria, has a number of world class experimental facilities focused on heat transfer, balanced by a Computational Fluid Dynamics (CFD) division. The Group members have developed, designed and built five unique, state of-the-art experimental set-ups, which are being used for leading-edge heat transfer research.
Due to lack of water resources in South Africa, the research works on the optimizing and performance enhancement of systems working with water as the working fluid should be greatly developed. Such activities will definitely lead to lower energy and water consumption within the country in the future.
It is the purpose of this research work to numerically investigate the effect of inclination on condensation of steam inside a long flattened channel. Thoroughly understanding of this problem via numerical simulations would assist in proper design of ACCs with low cost and time compared to experimentation.
At the moment, most of the work has been done, and a research paper is going to be prepared.
Principal Investigator: Prof Richard Tia
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 25
Allocation Start: 2019-07-09
Allocation End: 2020-01-05
Used Hours: 2710889
Project Name: Computational Chemistry and Materials Science
Project Shortname: CHEM1044
Discipline Name: Chemistry
The work being conducted in this research programme involves the development of active and selective catalysts for conversion of greenhouse gases like carbon dioxide into useful fuels and fine chemicals, the depolymerization of lignin, an abundant resource in plant biomass, into value-added chemicals and fuels and studies on the computer-aided synthesis of organic molecules of applications in medicine.
With increasing interest of the scientific community and government agencies on the mitigation of rising carbon dioxide levels and the attractiveness of using carbon dioxide as a feed-stock for industrial processes, this work has direct benefit for humanity.
Our research activities fall under two broad areas, namely;
1. Molecular modeling - Exploring the mechanisms of organic, inorganic and organometallic reactions.
These studies afford important molecular-level mechanistic details of industrially-relevant chemical reactions that are difficult, if not impossible, to obtain experimentally. Molecular level understanding enable chemical reactions to be guided quickly and efficiently along desirable pathways, with the effect of producing the right product with minimal energy consumption and minimal environmental impact. A key aspect of this work is the development of homogeneous transition metal catalysts for the depolymerization of lignin, an abundant natural resource, for fuel.
2. Materials modeling
The atomic- and molecular-level mechanistic insight gained from these studies are useful for the design of novel catalysts for the conversion of CO2 and other green-house gases as well as stranded gases from the petroleum refining into useful fuels. This addresses the problem of global warming as well as providing an environmentally friendly alternative sources of fuel.
The research objectives described here are very computationally-demanding and using the CHPC resources is highly beneficial. Without that, we would not be able to carry out some of these calculations.
Principal Investigator: Dr Michelle Lochner
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 2
Allocation Start: 2019-07-10
Allocation End: 2020-01-29
Used Hours: 40298
Project Name: Machine Learning and Statistics Applied to Astronomical Big Data
Project Shortname: ASTR1246
Discipline Name: Astrophysics
The upcoming Square Kilometre Array telescope will detect a billion galaxies. No human could manually go through the data to find all these galaxies so we at the SARAO data science group, have been developing sophisticated new algorithms to automatically detect sources in astronomical data. The techniques we have developed could be used in any application that requires automatically detecting compact objects in an image where high precision is required.
Principal Investigator: Dr Brigitte Glanzmann
Institution Name: Stellenbosch University
Active Member Count: 14
Allocation Start: 2019-07-10
Allocation End: 2020-01-15
Used Hours: 20751
Project Name: SAMRC Precision Medicine African Genomics Centre
Project Shortname: CBBI1195
Discipline Name: Bioinformatics
The advent and evolution of next generation sequencing (NGS) has considerably impacted genomic research, including precision medicine. High-throughput technology currently allows for the generation of billions of short DNA or RNA sequence reads within a matter of hours. This becomes extremely important in the case of genetic disorders where rapid and inexpensive access to a patient's individual genomic sequence is imperative and enables target variant identification. NGS technologies however lead to the generation of large data sets which require extensive bioinformatic and computational resources. Computational life sciences therefore relies on the implementation of well-structured data analysis pipelines as well as high-performance computing (HPC) for large-scale applications. Here, we report the sequencing of the first six whole human genomes in South Africa and the processing of the data in collaboration with the Centre for High Performance Computing (CHPC). Efficient parallel and distributed implementations of common time-consuming NGS algorithms on modern computational infrastructures are imperative. The latter becomes pivotal as NGS will continue to transcend from research labs to clinical applications in the near future.
Principal Investigator: Prof Nithaya Chetty
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2019-07-11
Allocation End: 2020-04-03
Used Hours: 178674
Project Name: Advanced Computational Resources for members of ASESMA
Project Shortname: MATS1050
Discipline Name: Material Science
Work on two dimensional (2D) materials is now firmly established as an area of excellence at the University of Pretoria. The focus on the past years was mainly on the study of the popular 2D materials such as molybdenum disulphide, graphene and boronetrene. The 2D hexagonal-like transition metal oxides (TMO) materials such as MoO2 is also predicted to be thermodynamically stable, however, a detailed study on the structural, electronic and dynamical properties of these new oxide material is still missing. Therefore, research about these properties is important and could bring them from the laboratory to commercial products. Recently (over the past two years) a 2-dimensional bilayer of zeolite has been experimentally synthesized by scientists in the USA. This is an area of promising new research for computational studies, and worth to be explored. We are mainly interested in the use of these 2D materials for catalysis, filtering of ions (especially in aqueous solution) and storage of ions (for example Li). To achieve these goals, creating complex system such as introducing defects or adatoms will enhance the properties of the MoO2 and the 2D zeolite model. Some of the work have been carried out using CHPC cluster and the preliminary results are promising.
Principal Investigator: Dr Melanie Rademeyer
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2019-07-11
Allocation End: 2020-01-29
Used Hours: 9894
Project Name: Properties of organic-inorganic hybrids
Project Shortname: MATS0823
Discipline Name: Material Science
The Material Science Research Group at the University of Pretoria, lead by Prof Melanie Rademeyer, focuses, among others, on the computation of the magnetic properties of organic-inorganic hybrid materials. Magnetic materials are important materials due to their potential technological applications, and organic-inorganic hybrid materials offer a unique opportunity in terms of the material design approach followed.
The successful calculation of the magnetic properties of these materials will allow for the identification of hybrid materials with promising magnetic properties. The materials identified via the computational method will then be synthesised in the laboratory and their magnetic properties measured experimentally via SQUID magnetometry.
The computational method involves the use of the single crystal structure of the material, as well as quantum mechanical and statistical thermodynamic calculations. Significant progress has been made, with the magnetic properties of a number of organic-inorganic hybrid compounds having been calculated successfully employing the resources offered by the CHPC.
Principal Investigator: Prof Gerrit Basson
Institution Name: Stellenbosch University
Active Member Count: 5
Allocation Start: 2019-07-12
Allocation End: 2020-01-29
Used Hours: 398444
Project Name: CFD modelling of Hydraulic Structures in Rivers
Project Shortname: MECH0985
Discipline Name: Computational Mechanics
The postgraduate students at the Institute for Water & Environmental Engineering Stellenbosch University are using CFD modelling to optimize the design of hydraulic structures. Key aspects of the research are related to addressing sedimentation problems at hydropower plants and abstraction works for SA's WRC guidelines. The simulations are too computationally intensive for standard computers and the CHPC assists in the research by allowing the students to more extensively explore the hydraulic behaviour of these structures within the time constraints of their studies.
Principal Investigator: Prof Nelishia Pillay
Institution Name: University of Pretoria
Active Member Count: 9
Allocation Start: 2019-07-12
Allocation End: 2020-01-30
Used Hours: 717048
Project Name: Nature Inspired Computing Optimization
Project Shortname: CSCI0806
Discipline Name: Computer Science
The NICOG (Nature Inspired Computing Research Group) at the University of KwaZulu-Natal and University of Pretoria is using facilities provided by the CHPC to implement distributed multicore architectures to implement evolutionary algorithms and evolutionary algorithm hyper-heuristics to solve real-world industry problems such as packing, scheduling, forecasting, data mining, computer security and routing problems. This research has provided a platform to initiate collaborations with both industry and international institutions working in the area of operations research.
One of the areas in which this research has made an impact is educational timetabling. The algorithms developed have been used to find solutions to university course, examination and practical scheduling problems. One of these approaches developed has automated the creation of heuristics, which are usually derived by humans involving a time consuming process, to solve educational timetabling problems.
A further area is the automated design of machine learning techniques to solve real-world problems. The aim is to provide off-the-shelf tools that non-experts can use to solve problems in the commercial and health sectors.
Principal Investigator: Dr Morne Du Plessis
Institution Name: National Zoological Gardens of South Africa
Active Member Count: 11
Allocation Start: 2019-07-15
Allocation End: 2020-02-05
Used Hours: 1079
Project Name: Wildlife Comparative Genomics and Bioinformatics
Project Shortname: CBBI0831
Discipline Name: Bioinformatics
Our research group is physically based at the National Zoological Gardens of SANBI, in Pretoria. Our work ranges across various wildlife species and include sequencing and analyses of genomes in order to understand the differences, evaluating the biodiversity of species as well as the abundances of species, engaging in genetic data of forensic importance, and in all of these contexts particularly focusing on the interaction with their environment. The focus of this research is of a national interest as it is forms the basis of the countries foundational biodiversity research, as well as feeding into policy making decisions. The nature of this work, given its large data volumes and complexity, as such, requires access to High Performance computing resources, which is therefore provided to us through the CHPC. The primary use of these resources is therefore implemented to use Bioinformatics as a tool to unravel the complexity of the data we produce and thereby to understand the biological context of this.
Principal Investigator: Prof Mahmoud soliman
Institution Name: University of KwaZulu-Natal
Active Member Count: 24
Allocation Start: 2019-07-15
Allocation End: 2020-01-30
Used Hours: 1461767
Project Name: Drug Design, development and modelling
Project Shortname: HEAL0790
Discipline Name: Health Sciences
The research scope of the Molecular Bio-Computation and Drug Design Research Lab covers a wide range of computational and molecular modeling research areas with main focus on biological systems and drug design approaches. Main interest is related to design and study of biologically and therapeutically oriented targets by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We show keen interest in diseases of global burden and evident prevalence within the south African populace such as HIV/AIDS, Tuberculosis and Cancer. The computational resources provided by CHPC is employed in performing the molecular dynamic calculations and the corresponding post molecular dynamic simulation analysis.
Principal Investigator: Prof Peter Nyasulu
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2019-07-15
Allocation End: 2020-01-15
Used Hours: 34231
Project Name: SimpactSimulation
Project Shortname: CBBI1184
Discipline Name: Applied and Computational Mathematics
SimpactSimulation as identified at CHPC, is a group from the University of Stellenbosch working on a project that simulate heterosexual transmission of HIV and prevention in complex sexual networks. The simulations in this project are implemented through individual based models (IBMs) which allow individuals in the model to behave autonomous for an individual goal; one such is starting or ending a sexual relationship. The great gains in the nature of our work is that our model can be used as experiments in certain cases where it is unethical to perform in the real world.
In our current work, we seek to evaluate the impact of early access to antiretroviral drugs among adults on HIV incidence in young woman. For the model to be realistic we need to mimic the target population summary statistics by carefully calibrate the model. This is very computational intensive process due to the complexity and computational burden associated with large number of model parameters and a large number of target statistics.
However, the availability of CHPC and parallesation capabilities we are able to run model simulation with big enough population that allow huge amount of data storage for surrogates statistics to be computed from and matched to the real world summary statistics.
To-date, we have successfully developed a new calibration procedure which is currently being submitted for publication. The application paper were we customized the Simpact model motivated by the eSwatini stepped wedge community randomized trial termed "MaxART". Therein, the study setting makes it difficult to make inferences about the effect of the study intervention on young people, 15-24 year-old. We anticipate our modelling study findings will inform the Treatment-as-prevention strategy to reduce new HIV infections among young women taking into account age-disparate relationships, HIV viral load, treatment retention on the infected individual among other variables.
Principal Investigator: Dr Mohammad Moghimi Ardekani
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2019-07-16
Allocation End: 2020-02-11
Used Hours: 383456
Project Name: R&D in Solar Energy in particular Concentrating Solar Power Research
Project Shortname: MECH1137
Discipline Name: Computational Mechanics
Dr. Moghimi Ardekani Research group in Mechanical Engineering Department of University of Pretoria is working on Concentrating Solar Power and thermal Energy Storage to engineer and optimize the cost of related technologies and make them available in South Africa.
Solar energy and thermal storage is one of the top renewable energy resources which would be able to resolve the power shortage issue in South Africa.
In that Regard, CHPC is quiet helpful in engineering and numerical simulation of this study and could hugely save the unnecessary trial and error process of experimental studies if the CHPC and numerical modelling were not available.
The project progress is quiet satisfactory and based on the research findings the group has Published three paper in top per reviewed journals and prepared three manuscripts for publishingin collaboration with Imperial College London, Edinburgh University. These collaboration proves that South African researchs are working on leading edge of sciences and their work are internationally acceptable.
Principal Investigator: Dr Malebogo Ngoepe
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2019-07-16
Allocation End: 2020-02-11
Used Hours: 57017
Project Name: PROTEA
Project Shortname: MECH1194
Discipline Name: Computational Mechanics
Our group focuses on studying problems related to biomechanics or the overlap of biomechanics and biochemistry. These are currently applied to the study of thrombosis, hair, myocardial infarction and congenital heart disease. Our use of HPC largely relates to the use of computational fluid dynamics codes to develop interventional planning tools, both for thrombosis and congenital heart disease. Thrombosis is the main underlying condition in a large number of cardiovascular diseases and understanding its progression will be beneficial for management of chronic diseases, which are on the rise. Similarly, understanding congenital heart disease will contribute to long term management of conditions which continue to affect individuals over a lifetime.
Principal Investigator: Prof Eric K. K. Abavare
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 5
Allocation Start: 2019-07-18
Allocation End: 2020-06-25
Used Hours: 15076
Project Name: Atomic and Electronic structures of semiconductor interface systems
Project Shortname: MATS1159
Discipline Name: Physics
Our group is Frontier Science Group (FSG) in the Department of Physics, Kwame Nkrumah University of Science an Technology (KNUST), Kumasi, Ghana. We investigate atomistic and electronic properties of light materials using quantum mechanical approaches based on first principles calculations in the framework of density functional theory.
At the heart of our research is to understand how important semiconductor materials substrate interfaces with each other. All electronic devices are always put on some form of bulk surfaces.
Substrates are required to fabricate important semiconducting device structures like solar cells, light emitting diodes, biopolar transistors and field-effect transistors. These substrates are obtained from bulk crystals. For certain devices namely light-emitting diods and photodetectors, epitaxial layers are grown on underlying substrates to tailor their devices characteristics. These layers are deposited on substrates whose surface normal is slightly misoriented from specific crystallographic directions.
If the substrate surface is clean the top layer may be either reconstructed or not. In unreconstructed surfaces, the atomic arrangement is in registry with that of the bulk except for an interlayer spacing change often referred to as relaxation. The shrinking of the interlayer distance between the first few layer atoms with the respect to subsequent layers in the bulk is rather a dominant phenomenon. When such two surfaces are brought together, interesting atomistic features emerges which are still not clarified but are generally believe to exist from the experimental point of view.
To understand these interfacial characteristics we employ theoretical techniques such as the density functional theory to probe interface structures of important semi-conductor materials of silicon carbide and silicon scientifically written as 3C-SiC(111)/Si 111). Presently our calculation have revealed interesting results which have been submitted in high impact journal under peer reviewing presently.
The possibility of solving these scientific interfaces problems hinges very much on the application of high performance computers, which makes the CHPC resources increasingly invaluable to our research. It is on the basis of this our group completely acknowledges the kind help for the use of their CHPC in South Africa.
Principal Investigator: Dr Abu Abrahams
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 3
Allocation Start: 2019-07-22
Allocation End: 2020-01-18
Used Hours: 1298304
Project Name: Synthesis and characterisation of lanthanide complexes with Di-(2-picolyl)amine and its derivatives
Project Shortname: CHEM0844
Discipline Name: Chemistry
Who: Rare earth coordination chemistry research group of Nelson Mandela University
What and why: The study of chemical and structural properties of the inorganic complexes with rare earth elements in order to identify trends in reactivity and identify potential applications in the fields of catalysis, medicine (diagnostic, anti-bacterial) and luminescence. Specifically complexes of rare earth elements with the ligand bis(2-pyridylmethyl)amine are being investigated due to this class of complexes displaying applications in the fields of catalysis, nuclear waste processing and medicine (solution structure elucidation). Increased utilisation of rare earth elements could also support the local economy, since rare earth elements may also be mined in South Africa.
How: The CHPC provides access to advanced computational resources which allows for the extraction of information from modelled systems of novel compounds, which may allow for the prediction of experimentally-determined properties. The latter process of physical experimentation are often time-consuming and expensive, whereas computational modelling may be performed on multiple systems simultaneously and may provide information of sufficient accuracy to inform the user of the most beneficial course of action to take when performing any physical experiments. In addition, modelling may also provide answers to fundamental questions which we may not yet be able to observe physically. In addition, advanced computational chemistry software packages (such as Gaussian 9/16 and ORCA) allow users with limited knowledge theoretical physics and computer programming to find answers to their chemical problems.
Principal Investigator: Prof Kevern Cochrane
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2019-07-22
Allocation End: 2020-01-18
Used Hours: 7642
Project Name: Fisheries management in the southern Benguela system under climate change scenarios
Project Shortname: ENVI0908
Discipline Name: Environmental Sciences
Our research group is based at the Department of Ichthyology and Fisheries Science, Rhodes University. Our collaborators include researchers from different South African Universities and from international universities and research institutes. Among several objectives, the work we are doing explores optimal management approaches to reduce vulnerability of fisheries in the Southern Benguela to future changes, using the Atlantis modelling framework. This model has been used to evaluate future trends in abundance of important fisheries resources under climate change, as well as the robustness of indicators under environmental variability and climate change. Progress to date has been good and further work focusing on the likely effects of climate change on future trends in upwelling and primary production will continue.
Principal Investigator: Dr Calford Otieno
Institution Name: Kisii University, Kisii, Kenya
Active Member Count: 3
Allocation Start: 2019-07-22
Allocation End: 2020-01-29
Used Hours: 9817
Project Name: FIRST PRINCIPLE ELECTRONIC STRUCTURE CALCULATIONS OF EMERGING MATERIALS FOR SOLAR CELL APPLICATIONS.
Project Shortname: MATS1083
Discipline Name: Physics
Kisii University Computational Condensed matter Group is a computational material modelling group with research areas in; Emerging materials for solar cell applications and energy harvesting, superconducting materials for various industrial and novel oxides for various industrial applications. There is need for clean and renewable energy sources and such research groups as ours seek to study new/emerging materials for energy harvesting and how that energy will be transported with minimal loss. Our research basically employs opensource software to carry out first principle calculations and due to high cost in computing we employ the capability of the CHPC. The research is progressing well and students in Masters of Science and Doctor of Philosophy are due to graduate later this year.
Principal Investigator: Dr Mary-Jane Bopape
Institution Name: South African Weather Service
Active Member Count: 17
Allocation Start: 2019-07-23
Allocation End: 2020-02-12
Used Hours: 52783
Project Name: Very Short Range Forecasting
Project Shortname: ERTH1022
Discipline Name: Earth Sciences
The CHPC is helping us understand the performance of models in simulating high impact weather events. We are testing different physics settings in the models so that we can get better weather simulations over southern Africa. Forecasters use output from models to issue warnings to the public. An improvement in warnings can reduce the impacts of adverse weather events.
Principal Investigator: Dr Bubacarr Bah
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 8
Allocation Start: 2019-07-25
Allocation End: 2020-01-21
Used Hours: 34132
Project Name: Large Scale Computations in Data Science
Project Shortname: CSCI0972
Discipline Name: Applied and Computational Mathematics
The Data Science Research Group at the African Institute for Mathematical Sciences (AIMS) South Africa conducts Data Science research with applications in ecology, finance, energy, and health. We run Machine Learning algorithms to prediction a quantity of interest like a stock price, identification of individual animals from images, or diseases from images in financial, ecological, or health applications respectively. We are also interested in the theory of Deep Learning, in which case we run simulations as proofs of concepts for theoretical results. All of the above require enormous computing power, which CHPC provides us. There is no doubt that all these problems are of great importance to society, hence the justification for the use of CHPC as a public resource. Thanks to CHPC the group is making significant progress in these projects. The finance and ecology projects led to the completion of MSc theses. The others are also progressing well and are mostly PhD projects.
Principal Investigator: Dr Dominic Stratford
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2019-07-25
Allocation End: 2020-01-21
Used Hours: 1631
Project Name: Application of deformation-based models in paleoanthropology
Project Shortname: CSCI0984
Discipline Name: Imaging
As members of the Sterkfontein Research team, we are investigating 3-million-year-old fossil specimens from the caves and quarries at Sterkfontein, 50 km northwest of Johannesburg. Because it is one of the richest fossil complex site in Africa, this fossil assemblage is critical to challenge long-standing questions in human evolution. Who were our ancestors? Where and when did they live? Did they look like us? Did they walk on two legs, as humans do today? In addition to basic descriptions and traditional metrical analyses, recent incorporation and validation of computer-based techniques for reconstructing and comparing morphological pattern have substantially improved the quality of data delivered by fossil remains. In our project, we use high-resolution imaging techniques (e.g., microtomographic-based scanner) to non-invasively explore the fossil specimens and apply 3D modelling techniques to comparatively describe the anatomy of our ancestors. In that perspective, the access to a supercomputer through the CHPC resources is essential for running our analyses and provide new evidence of human evolution in South Africa.
Principal Investigator: Prof Rudolf Laubscher
Institution Name: University of Johannesburg
Active Member Count: 3
Allocation Start: 2019-07-26
Allocation End: 2020-02-11
Used Hours: 32591
Project Name: Numerical modelling of Machining
Project Shortname: MECH1249
Discipline Name: Computational Mechanics
The hole-drilling technique for measuring near-surface residual stresses requires the use of a numerical method, such as the finite element method to determine the surface strain-to-stress calibration coefficient for each drilled hole-depth increment.
This work is run, under the titanium machining research group of Professor RF Laubscher from the Mechanical Engineering Science department of the University of Johannesburg.
Due to the large plastic deformation and temperature gradient generated from machining of a part, it is critical to measure the near-surface residual stresses. These residual stresses can affect the fatigue life of the component, depending on the direction and magnitude thereof.
The incremental hole-drilling technique for the measurement of residual stresses is suited to this application if applied with stringent practices.
The measurement of the residual stresses in machined titanium alloys then assists in the development of a numerical model to "predict" the near-surface residual stresses, which are less expensive and time-consuming than measurement work.
The project is currently behind schedule, due to time constraints as well as "loading shedding".
Principal Investigator: Dr Mervlyn Moodley
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2019-07-29
Allocation End: 2020-02-05
Used Hours: 6584
Project Name: Computational studies of corrosion in transformers
Project Shortname: MATS1120
Discipline Name: Physics
The Computational Studies of Corrosion in Transformers group based at University of Kwazulu-Natal is set to understand the corrosion mechanisms involved in the failure of transformers. The failures of transformers have been linked to the interaction of copper sulphide with copper windings. The copper sulphide is a product of copper particles that react with the corrosive sulphur within the transformer oil. This copper sulphide thereafter deposits on the vacant sites of the copper windings. Density functional theory (DFT) techniques are used in various fields of study and have proved most effective in handling interactions between molecules and surfaces. In this research the DFT techniques are used to understand the interaction of copper sulphide on copper surfaces to obtain energetic, electronic and thermodynamic properties of the system. The understanding of the failures on a computational level would help in creating a model to prevent further failures and to track current failures caused by corrosion. The failures of transformers have also been found to affect both financial and economic sectors due to the high cost in repairing or replacing these failed transformers. This research relies heavily on CHPC resources due to the extensive computational methods needed to understand this complex system. The CHPC provides the Materials Studio Software and a connection to the Lengau Cluster which increases the accuracy of the results and reduces computational time. This project has so far obtained results of the copper sulphide interaction with the copper surface. Upon investigation it was found that more research is required to fully understand the method of corrosion and the interaction of addictives in the transformer oil. The CHPC resources are also needed to compute a remedial process to prevent further transformer failures.
Principal Investigator: Dr Phillip Nyawere
Institution Name: Kabarak University, Nakuru, Kenya
Active Member Count: 4
Allocation Start: 2019-07-29
Allocation End: 2020-04-01
Used Hours: 120988
Project Name: Barium Floride and Perovskites
Project Shortname: MATS0996
Discipline Name: Physics
Barium Flouride and Perovskite MATS0996 is a group of researchers based in Kenya. As lead researcher I am based in Kabarak University, School of Science, Engineering and Technology, Department of Physical and Biological Sciences. This took place after relocation from Rongo University in September 2019. But despite this relocation, the research team remains intact.
As PI, I am researcher with experience in Density Functional Theory where we use different codes such as Quantum Espresso, Yambo, Castep, Siesta etc some of which are implemented in CHPC. This group has both Masters and PhD students based in Kabarak University, Kisii University, Masinde Muliro University of Science and Technology and Kenyatta University. This is academic research team that includes both the MSc and PhD students.
Our research is based on fabrication of new materials that can be applied in efficient battery manufacturing company using Barium Fluoride and doped Barium Fluoride. The perovskites we are studying here are those appropriate for superconducting applications. In this regard we are interesting in fabricating materials that can be used in cables at room temperatures and yet they are superconductors. As for now most of the materials known to be superconducting are doing so at very low temperatures. But through doping we can be able to adjust this to elevated temperatures.
As a computer simulation research, we need to have a powerful computers to enable timely results that are also reliable.
Since we need powerful computational resources to run most of these calculations, CHPC has provided the platform for this.
So far we have accomplished much including students mentor ship and training on research. We have published a number of papers that are listed elsewhere and this has given our team visibility as a strong research team.
We have attended both local and international workshops that have exposed our students very well.
We believe this support from CHPC team is helping us do great work and train students faster than if we were to do it locally. In fact most of these calculations would be impossible without this high speed computer resource.
Furthermore in our local set, high speed computation resources are not available.
We are very grateful to the team and South Africa Republic for availing this resources to us. Also to all sponsors of this resource we pass our appreciation.
My appeal would be that we be given continuous support so that we engage more students yearly. And since this is a continuous process the time limitation can be wavered to allow continuous work.
Principal Investigator: Dr Kevin Lobb
Institution Name: Rhodes University
Active Member Count: 10
Allocation Start: 2019-08-01
Allocation End: 2020-01-28
Used Hours: 400907
Project Name: Computational Mechanistic Chemistry and Drug Discovery
Project Shortname: CHEM0802
Discipline Name: Chemistry
In our research group we have recently been exploring possible agents in the treatment of Alzheimer's disease. In this exploration (using databases of natural products) we have identified key South African compounds that have the potential to destabilize plaques in Alzheimer's Disease.
Principal Investigator: Prof Fanie van Heerden
Institution Name: University of KwaZulu-Natal
Active Member Count: 7
Allocation Start: 2019-07-29
Allocation End: 2020-01-25
Used Hours: 245930
Project Name: Natural Product Chemistry
Project Shortname: CHEM0885
Discipline Name: Chemistry
The natural product chemistry research group in the School of Chemistry and Physics, University of KwaZulu-Natal, is led by Prof Fanie van Heerden, who is a NRF/DST Chair holder. The main project of the group is 'The Chemistry of Indigenous Medicinal Plants'. The group is investigating local medicinal plants to see what the ingredients are and what the biological activity of compounds present is. The activity of drugs and other bioactive compounds can be explained by their interaction with important enzymes. Computational chemistry is an ideal tool to predict what these interactions will be. Therefore, our research group is studying the
interactions between natural products and enzymes by computational methods.
Principal Investigator: Dr Adeola Joseph Oyenubi
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2019-08-01
Allocation End: 2020-01-28
Used Hours: 262450
Project Name: Optimizing balance in for Impact Evaluation
Project Shortname: ECON1213
Discipline Name: Economics and Finance
This research is conducted by Dr Oyenubi, a lecturer at the University of the Witwatersrand.
Usually policy interventions (like the child support grant programme) require assessment in terms of the impact of the policy on beneficiaries. To do this a researcher must compare the response units under the policy with units that are not under the policy. For this comparison to be valid the two groups should have identical characteristics or covariates. This is achieved by comparing the distribution of covariates using various balance statistics e.g. mean and standardized difference in means.
This work assesses if the performance of different balance statistics vary in terms of their ability to compare the distribution of covariates. The premise is that differences in the performance of balance measures will lead to variation in the estimate of policy impact. With no guidance on the performance of various balance measures it will be difficult to identify the correct impact estimate.
This work will provide guidance to researchers on how to use the various balance measures that are available when estimating the impact of a policy. However doing this require extensive Monte Carlo experiments. This experiments are computationally expensive and without the CHPC the work will be virtually impossible.
The process involves setting up a data generating process that mimics various condition that is encountered in real life impact assessment. In this fictitious world we know what the correct impact estimate is. We then use various method to try and estimate this (known) impact estimate. The idea is that some methods will perform well while others will fail. This knowledge (about what method perform better and under what conditions) can then be used on real life data where we do not know the correct impact estimate.
This particular stage of the project is near competition.
Principal Investigator: Prof Tony Ford
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2019-08-01
Allocation End: 2020-01-28
Used Hours: 47774
Project Name: Computational studies of the properties of molecular complexes
Project Shortname: CHEM1134
Discipline Name: Chemistry
This research group is headed by Emeritus Professor Tony Ford, of the School of Chemistry and Physics at the University of KwaZulu-Natal. The group is interested in the properties of a wide range of molecular complexes, usually containing one acidic and one basic molecule, with the intention of determining what factors are responsible for the stability of a particular complex. These properties include their molecular structures and vibrational spectra, and the ways in which the distribution of electronic charge is perturbed in the formation of the complex. A knowledge of the determinants of the outcomes of the interactions between any pair of molecules as they come together to form a complex is invaluable in predicting the course of a variety of chemical reactions. These reactions may be of the kinds involved in the search for more and more efficient drugs, for example, and would be of great benefit to the pharmaceutical industry. Other potentially useful reactions might be those used in the fabrication of batteries, with applicability in the energy production industry. The regular procedure involves a number of steps, each performed using the standard Gaussian 16 software. An initial guess at the structure of a target complex is proposed, and an input file constructed requesting the program to search for an energy minimum, within chosen convergence limits. If a successful optimization has been achieved, the resulting structure is subjected to a test of its validity in terms of its vibrational spectrum, and the structure is accepted if certain criteria have been met. Along with information on the resulting structure and its spectrum, which may be verified by comparison with experimental data, where available, the Gaussian program also outputs important information on the distribution of electronic charge within the complex, and the ways in which the charges of the individual atoms in the interacting molecules are perturbed on complexation. The Gaussian 16 program contains many thousands of lines of code, and it would not be practicable to use without access to a high performance computing facility. The project is now mature, and has spawned a number of sub-projects in its lifetime. It has the potential to be a valid project for several more years to come.
Principal Investigator: Prof Felix Spanier
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2019-08-01
Allocation End: 2020-01-28
Used Hours: 162117
Project Name: Acceleration and transport of high-energy particles in the universe
Project Shortname: ASTR0804
Discipline Name: Astrophysics
Researchers from NWU Centre of Space Research have used CHPC's supercomputers to understand how energetic particles are moving through the solar system.These particles are emitted by the Sun and move outwards and constantly bombarding Earth.
How exactly they move through the solar system is not yet understood and may only be understood by doing extremely large computer simulations.
These energetic particles actually have an impact on everyday life: They produce "Northern lights", can destroy satellites or even disrupt power lines when the Sun emits extreme amounts of energetic particles.
Principal Investigator: Prof Thuto Mosuang
Institution Name: University of Limpopo
Active Member Count: 8
Allocation Start: 2019-08-02
Allocation End: 2020-02-11
Used Hours: 31379
Project Name: Computational studies of various ultra-hard materials
Project Shortname: MATS0875
Discipline Name: Material Science
The Sensors and Advanced materials research group is based in the Department of Physics of the University of Limpopo. The group utilizes both the computational and experimental techniques in quest of suitable gas sensors. The aim is to acquire novel materials who can improve gas sensing for domestic, agricultural, environmental safety, and industrial purposes. Results obtained computationally are often compared with those obtained experimentally then quantified accordingly for community utilisation. The CHPC is quite valuable in the compilation and storage of all the softwares we use in our computational potion of the project.
Principal Investigator: Prof Charalampos (Haris) Skokos
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2019-08-05
Allocation End: 2020-02-01
Used Hours: 750719
Project Name: Chaotic behavior of Hamiltonian systems
Project Shortname: CSCI1007
Discipline Name: Applied and Computational Mathematics
Using modern numerical techniques of Nonlinear Dynamics and Chaos Theory we investigate in a unified mathematical way the behavior of models describing the energy transport in disordered and granular media, as well as the properties of new elastic materials like graphene and molecules like the DNA. This research is performed by members of the 'Nonlinear Dynamics and Chaos Group' in the Department of Mathematics and Applied Mathematics at the University of Cape Town. The performed investigations constitute an innovative combination of Applied Mathematics, Chaos Theory, Hamiltonian Dynamics and Nonlinear Lattice Dynamics. Their outcomes will provide answers to some fundamental questions about the effect of chaos on the energy transport in disordered and granular media, and on the behavior of graphene and DNA. Some of the questions we try to address are: Does the presence of impurities and nonlinearities enhance or suppress the propagation of energy (e.g. heat) in solids, of light in crystals, and of vibrations in granular material? How does the ratio of the different base pairs in DNA chains affect their structural stability and the temperature at which the double-stranded DNA breaks to single-stranded DNA?
Principal Investigator: Prof Jaco Dirker
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2019-08-05
Allocation End: 2020-03-11
Used Hours: 244813
Project Name: Heat Transfer Enhancement in Thermal Systems
Project Shortname: MECH1029
Discipline Name: Computational Mechanics
Renewable energy exploration and the responsible usage of existing energy resources are vital for sustainable economic and industrial development. Future energy needs will require continual improvement in energy processing technologies and storage systems. The Clean Energy Research Group at the University of Pretoria aims to contribute to such efforts by conducting both applied and fundamental research using experimental and numerical techniques. One of the group's focus areas is that of large scale thermal energy storage and conversion systems which have lower associated costs than electric energy storage systems. This, however, requires improved heat transfer mechanisms to match demand side energy consumption rates and has led to the need for geometric optimization and innovation in heat exchanger equipment and thermal energy storage modules. This is the driving force behind the exciting investigations supported by the CHPC whereby the effects of heat transfer enhancement due to turbulator inclusion and the augmentation of latent phase change material energy cycling are considered. For this purpose, high performance computing is required to solve complicated and detailed energy transfer, mass transfer, and fluid dynamics equations in the transient domain using computational codes such as those included in commercial simulation packages such as Ansys Fluent. Detailed simulation results of flow eddies and phase transition fronts, as well as design space exploration results will assist in deriving smaller, more efficient energy transfer components which has lower capital and operating costs in both solar renewable energy systems and traditional energy systems. Among the early successes include the improvement of local and average heat transfer coefficients and the optimization of a latent energy thermal battery to better match the required energy release rate. Current and future work include the study of low-cost thermal energy storage technologies, as well as processes which involve phase change of materials.
Principal Investigator: Dr Leigh Johnson
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2019-08-07
Allocation End: 2020-02-03
Used Hours: 3694
Project Name: MicroCOSM: Microsimulation for the Control of South African Morbidity and Mortality
Project Shortname: HEAL1049
Discipline Name: Health Sciences
The MicroCOSM project, based at the Centre for Infectious Disease Epidemiology and Research at the University of Cape Town, is a project to simulate the spread of infectious diseases, as well as the incidence of non-infectious diseases, in the South African population. By simulating the social and biological factors that contribute to disease transmission, we can better understand which sub-populations need to be targeted for special interventions. We can also evaluate the impact that various prevention and treatment programmes have had in South Africa to date, and evaluate the potential impact of new programmes. This simulation involves generating nationally representative samples of 20,000-40,000 South Africans and tracking them over their life course. Because this involves many individual-level calculations, the model requires substantial computing power, and the CHPC is therefore critical to the conduct of these simulations. We have recently used the model to conduct a study (published in Scientific Reports) on optimal HIV testing strategies in South Africa.
Principal Investigator: Prof Daniel Joubert
Institution Name: University of the Witwatersrand
Active Member Count: 20
Allocation Start: 2019-08-06
Allocation End: 2020-02-11
Used Hours: 4537237
Project Name: Energy Materials: Numerical explorations
Project Shortname: MATS0800
Discipline Name: Physics
Imagine designing a material atom by atom. Imagine analysing the properties of tomorrow's novel materials before they exist. Computational materials science plays an important role at every of level of the design and engineering of new materials. The rapid advances in computer processing power and memory has given virtual, fundamental, materials design a boost. The first problem faced in designing a virtual material, a material that has not yet been made, is to find the stable configurations in which the atoms in the mix will settle into. The designer must find the configuration of electrons and nuclei, the building blocks of atoms, which result from the interactions among a number of particles that, even for a small piece of material, exceeds the number of particles of sand on all the beaches in the world. This daunting task has a simple solution. Instead of finding the configuration of the real material, the problem is solved for a fictitious material where the constituent particles do not interact. All that is necessary is to find the particle density distribution of the fictitious material, which by design, is the same as that of the real material. A Noble prize was awarded for this idea to the chemists Walter Kohn and John Pople in 1998.
A group of postgraduate students at the University of the Witwatersrand use the computer power at the national Centre for High Performance Computing to conduct virtual experiments on existing and novel materials to examine their potential as energy harvesters. They examine the potential of a selection of materials that can be used as cheap components in solar cells, materials that can generate electricity from waste heat and materials that can be used to split water molecules to extract hydrogen for energy production.
Principal Investigator: Prof Peter Teske
Institution Name: University of Johannesburg
Active Member Count: 2
Allocation Start: 2019-08-08
Allocation End: 2020-03-04
Used Hours: 185208
Project Name: Coevolution of mangroves and mangrove-associated crabs
Project Shortname: CBBI0979
Discipline Name: Bioinformatics
Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg.
Analysis of next-generation sequencing datasets (genomics, transcriptomics and eDNA metabarcoding).
Projects relating to the identification of biodiversity and population structure of marine and freshwater animals.
CHPC is used to assemble millions of DNA reads into datasets that can be compared between individuals or to identify species. It is also used for downstream analyses of population structure or evolutionary relationships.
Principal Investigator: Dr Gwynneth Matcher
Institution Name: Rhodes University
Active Member Count: 6
Allocation Start: 2019-08-12
Allocation End: 2020-02-08
Used Hours: 20899
Project Name: Microbial Ecology in Antarctic and aquatic ecosystems
Project Shortname: CBBI0952
Discipline Name: Environmental Sciences
My research group, based at Rhodes University (Makhanda), focuses on microbial ecology in Antarctic ecosystems. Antarctic ecosystems are characterised by extreme conditions which impose significant pressures on the ability of fauna and flora to survive. In the majority of these ecosystems, the dominating life form is microbial. Despite the fact that these delicate ecosystems are almost entirely driven my microbiota, almost nothing is known about them. These ecosystems are particularly vulnerable to climate change which alter the biodiversity and functional richness of microbial soil populations resulting in significant impacts on ecosystem functioning as a whole. Metagenomics, which is utilised to assess the microbial populations in this project, involves sequencing and analysis of the total genetic material in a given environment. This allows for identification of species present as well as providing information of the impact of environmental drivers. The computational analyses are conducted on the CHPC cluster. To date, this project has investigated the effect of invasive Sagina plants on soil microbiota on Marion Island as well as proving detailed microbial profiles from several previously uncharacterised nunataks in Dronning Maudland.
With respect to estuarine ecology, our research focuses on the Swartkop estuary which is impacted by urban and industrial activities and the Sundays Estuary is influenced by agricultural activities. The health of the river is of fundamental importance to sustainable biodiversity. To date, most monitoring has focused on fish assemblages and targeted analysis of algal blooms. This is time-consuming, labor-intensive and requires a comprehensive and extensive knowledge of the relevant species. Also, this approach completely excludes the fauna and flora not evident to the naked eye. Most of the work done to date has involved physical/microscopy identification. This research project focuses more on rapid molecular characterization techniques which will also increase the frequency at which these estuaries can be monitored.
Principal Investigator: Prof Robin Emsley
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2019-08-12
Allocation End: 2020-02-08
Used Hours: 290262
Project Name: EONCKS
Project Shortname: CBBI1064
Discipline Name: Health Sciences
The Schizophrenia Research Unit based in the Department of Psychiatry at Stellenbosch University collected neuroimaging, specifically Magnetic Resonance Imaging, data on 130 patients with a schizophrenia spectrum disorder and a similar number of controls between 2007 and 2017. The purpose of the project was to explore the underlying neurobiological underpinnings of the disorder in order to glean insight on the development of the disorder. The team has published several papers on the topic and continuously strives to remain at the forefront of research by utilising the CHPC resources. This has allowed the Unit to be internationally competitive and make significant contributions to the growing body of research on the neurobiology of schizophrenia spectrum disorders.
Principal Investigator: Dr Uljana Hesse
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2019-08-13
Allocation End: 2020-02-09
Used Hours: 99466
Project Name: Medicinal Plant Genomics
Project Shortname: CBBI1133
Discipline Name: Bioinformatics
Knowledge on the genomic background of rooibos, an endemic South African medicinal plant, can help to identify biosynthetic pathways involved in the production of medicinal compounds; and genes associated with biotic and abiotic stress resistance of the plant. The rooibos genome has been sequenced by the research team of Dr Uljana Hesse, Department of Biotechnology, University of the Western Cape. The genome assembly is conducted at CHPC, which provides the extensive computational resources essential for plant genome assembly. Currently, one MSc student is involved in bench-marking biocomputational procedures for genome assembly and evaluation of genome characteristics towards establishing a computational pipeline for high-throughput plant genome assembly and annotation.
Principal Investigator: Prof Mario Santos
Institution Name: University of Western Cape
Active Member Count: 20
Allocation Start: 2019-08-13
Allocation End: 2020-02-09
Used Hours: 1576764
Project Name: Cosmology with Radio Telescopes
Project Shortname: ASTR0945
Discipline Name: Astrophysics
The Centre for Radio Cosmology (CRC) at UWC aims to fully explore the use of the next generation of radio telescopes for measurements in cosmology, in particular with MeerKAT and SKA. CRC staff is closely involved in the South African and international SKA projects. About 10 postdoctoral researchers and 10 PhD/MSc students are doing their research within the CRC. Our work at the CHPC is mostly focused on running simulations of signals we expect to observe with MeerKAT/SKA and test how well radio telescopes can constrain certain cosmological models. This is a crucial component in the process to use these telescopes for cosmology since we need to understand the signals we are observing. The project include simulations of the hydrogen emission from the early universe, simulations of the contaminants, simulations of the telescope itself and analysis of the constraining power of such telescopes on cosmological models.
Principal Investigator: Prof Oleg Smirnov
Institution Name: Rhodes University
Active Member Count: 6
Allocation Start: 2019-08-13
Allocation End: 2020-02-25
Used Hours: 1100
Project Name: MeerKAT Imaging
Project Shortname: ASTR0967
Discipline Name: Astrophysics
The Radio Astronomy Research Group (RARG) at SARAO has been experimenting with the use of CHPC clusters for novel MeerKAT imaging algorithms. Using a package called dask-ms (based on the open source dask package), Simon Perkins has demonstrated scalable, massively parallel computations for visibility predicition. This is an important achievement for the realization of future, compute-heavy Bayesian processing methods.
Principal Investigator: Prof Eric van Steen
Institution Name: University of Cape Town
Active Member Count: 8
Allocation Start: 2019-08-13
Allocation End: 2020-02-09
Used Hours: 1941452
Project Name: Lateral interactions on surfaces
Project Shortname: CHEM0780
Discipline Name: Chemistry
More than 70% of all materials could not have been produced without a catalyst (and over 90% of all newly developed chemical processes involve a catalyst), preferentially a heterogeneous catalyst. Our understanding of processes taking place on this catalysts have been limited to idealized situation, e.g. present during the ammonia synthesis. However, the majority of industrially relevant processes result in less idealized situations, where adsorbates interact with each other. So far, we have shown that this is important in both the oxygen reduction reaction in fuel cells and in the CO-hydrogenation. This type of work relies primarily on quality input data using high level DFT-calculation for which high performance computing is essential. This type of work will yield a better theoretical understanding of the working of platinum as a catalyst in fuel cells as well has guide researchers to develop novel catalysts for CO and CO2 hydrogenation.
Principal Investigator: Mr Jean Pitot
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2019-08-14
Allocation End: 2020-02-25
Used Hours: 211454
Project Name: SAFFIRE Programme
Project Shortname: MECH1121
Discipline Name: Computational Mechanics
The University of KwaZulu-Natal's Aerospace Systems Research Group (ASReG) is at the forefront of rocket propulsion research in academia, both in South Africa and Africa as a whole. Located at the University's Discipline of Mechanical Engineering, ASReG primarily conducts research in the areas of liquid and hybrid rocket propulsion, as well sounding rocket development. The SAFFIRE Programme aims to develop South Africa's first fully-integrated liquid rocket engine, which is being designed for use in a small satellite launch vehicle. The long-term intention of the Programme is for the engine to enable the indigenous development of a South African space launch capability.
To meet its developmental goals, the Programme requires the simulation of complex computational models to predict the fluid dynamic, thermochemical and structural performance of various engine components. These simulations are typically very computationally-expensive, and require extensive computational resources to run within a reasonable time frame. The CHPC offers the only realistic means of obtaining access to such resources.
The programme is progressing well, and 2020 will see the intake of numerous new postgraduate and undergraduate students. It is anticipated that four of the programme's current postgraduate students will graduate during the course of the year.
Principal Investigator: Prof Prof Abidemi Paul Kappo
Institution Name: University of Johannesburg
Active Member Count: 1
Allocation Start: 2019-08-14
Allocation End: 2020-02-10
Used Hours: 19747
Project Name: Structural bioinformatics of druggable proteins in diseases
Project Shortname: HEAL1252
Discipline Name: Health Sciences
My broad research niche area is in Molecular Biophysics and Structural Biology of biomedically-important proteins. My laboratory uses computational biology (bioinformatics), molecular biology, and mathematical modelling in rational drug discovery and development of diagnostics for communicable (HIV/AIDS) and non-communicable (Diabetes, Obesity, Cancer, Malaria, Schistosomiasis) diseases. Recently, we delved into the synthesis of aptamers in order to develop lateral flow device that can detect HIV during the "window period" since the available testing kits lack the capability to detect the virus during this period. Bioinformatics is used to ascertain the affinity of synthesized HIV-specific aptamers to their cognate HIV protein. Another research area revolves around cancer biology; synthesize cadmium telluride quantum dots, capped with gum arabic and bioconjugated to cancer-specific proteins for in vivo application in humans are investigated using bioinformatics to ascertain the affinity of the cancer proteins for the nanoparticles. More so, my group have been leading the study into Schistosomiasis, which is known to predispose sufferers to cancer of the bladder and other cancer morbidities. The research idea is to developed an alternative drug with better efficacy than the current first-line treatment drug, Praziquantel. Here, we employ bioinformatics in investigating the various dynamical 'shifts' that occur when two proteins are docked together, before molecular dynamics simulations. The rationale behind studying schistosomiasis is due to the fact that there have been widespread drug resistance regarding this disease. Above all, more than 5 million people are infected and KwaZulu-Natal have been identified literature as the 'hotspot' for this disease. We have also used bioinformatics to identified 2 druggable proteins using AMPs via computational biology. Mathematical modelling is further used to model the spread of the disease and will in future serve as the basis for biocontrol measures for Schistosomiasis and other diseases.
Principal Investigator: Dr Lucy Kiruri
Institution Name: Kenyatta University, Nairobi, Kenya
Active Member Count: 6
Allocation Start: 2019-08-16
Allocation End: 2020-04-22
Used Hours: 1442267
Project Name: KU Computational Chemistry Research Group
Project Shortname: CHEM1032
Discipline Name: Chemistry
The group, CHEM1032 is based in Kenyatta University, Chemistry department. It consists of six members. The members of the group are in quantum mechanics and molecular dynamics.
Daniel is a PhD student in Nelson Mandela African Institution of Science & Technology (NM-AIST). He has done part of his PhD research –Solvents effects on host-guest residence time and kinetics: A metadynamics simulation of TouA unbinding from chitosan nanoparticle using the Lengau cluster.
Katana defended his PhD exam. His work entails DFT study of Cationic iron half-sandwich complexes of mixed donor ligands. This involves geometry optimization and frequency calculations with the aim of determining the best coordination site of the mixed donor ligands.
Isaac is a second year Masters student working on re-engineering existing drugs of Mycobacterium tuberculosis by introducing organometallic fragment into their molecular structure and determining drug-likeness computationally. The computations are based on Density Functional Theory (DFT) methods such as B3LYP, CAM-B3LYP, and PBEPBE with the standard Pople's polarized split valence basis set 6-31++G**.
George did some work on chpc using g16. He graduated with an MSc in Chemistry in 2019. He is very grateful to CHPC for giving him an opportunity to compute and learn science.
Lucy has done calculations on Barakol and anhydrobarakol using gaussian16. The work involves geometry optimization and frequency calculations. The project aims to determine the stability of the two molecules. She is preparing a manuscript. She has also done molecular dynamics of herbicide encapsulation by cyclodextrin.
The CHPC is invaluable in fast-tracking our work since we were using core i5 desktop before where calculations would take much longer. Since the start of using the CHPC, we have made much progress on the work.
Principal Investigator: Dr Chris Stevens
Institution Name: Rhodes University
Active Member Count: 3
Allocation Start: 2019-08-16
Allocation End: 2020-02-12
Used Hours: 5367
Project Name: Cauchy Characteristic Matching, and Other Uses of the Characteristic Method in Numerical Relativity
Project Shortname: ASTR1202
Discipline Name: Applied and Computational Mathematics
Professor Nigel Bishop, Associate Professor Denis Pollney and Dr Chris Stevens are working on a new algorithm to numerically simulate coalescing black holes. Currently the simulations take a very long time and this project aims at not only making them run faster, but more accurately as well. These simulations require heavy computing resources and thus we need facilities like the CHPC. The project has passed the first phase of testing and we are now looking at more realistic simulations for the algorithm.
Principal Investigator: Prof Rebecca Garland
Institution Name: University of Pretoria
Active Member Count: 12
Allocation Start: 2019-08-19
Allocation End: 2020-02-15
Used Hours: 1765580
Project Name: Development of the first African-based earth system model VRESM and its projections of future climate change over Africa
Project Shortname: ERTH0859
Discipline Name: Earth Sciences
The first African-based Earth System Model (ESM) is under development at the Council for Scientific and Industrial Research (CSIR) in South Africa, through collaboration with the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Australia and South Africa's Centre for High Performance Computing (CHPC). The new ESM is unique in the sense that it is being developed in Africa and through the lens of African and Southern Hemisphere climate processes. That is, the reliable simulation of climate issues critical to Africa, such as the occurrence of drought in in response to El Niño events, wide-spread flooding over Mozambique due to landfalling tropical cyclones and increased occurrences of heat-waves under global warming are key issues in the development of the new model. The model development process is also focussed on the Southern Ocean's role in regulating southern African climate, as well as the global climate through the absorption of carbon dioxide in the ocean. The development and application of an Earth System Model is a computationally extensive endeavour, and was impossible to undertake in South Africa before the Lengau cluster of the CHPC became available in 2018. The CSIR-CHPC partnership towards development of the new model has in 2018 led to the most detailed set of projections of future climate change over southern Africa obtained to date. These simulations have provided new insight into the plausible impacts of climate change in South Africa, including how the frequencies of droughts, heat-waves and landfalling tropical cyclones may change over the next few decades. These projections were key in informing South Africa's Third National Communication on Climate Change, which was published in 2018 under the science leadership of the CSIR. Moreover, the research papers based on the projections have directly informed the Special Report on Global Warming of 1.5 ºC of the Intergovernmental Panel on Climate Change (IPCC).
Principal Investigator: Dr Ron Machaka
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 2
Allocation Start: 2019-08-19
Allocation End: 2020-02-15
Used Hours: 10424
Project Name: Prediction of metallic structures
Project Shortname: MATS1186
Discipline Name: Material Science
Prof. Ronald Machaka of CSIR (Future Production: Manufacturing Cluster) leads the programme with collaborators from higher education institutions and science councils.
The amount and variety of experimental data in the literature are becoming available at alarming rates. As such, pure experimentalist approaches, trial & error data analysis methods, and traditional platforms can no longer meet the need to rapidly develop new metal products and applied sciences. Therefore, the goal of this programme is to develop computational platforms for studying metal alloys - to best-inform experimental decisions.
The project has posted significant milestones; (1.) a computational platform for studying metal alloys at the atomistic level (DFT level) was developed, using the Material Studio suite, (2.) yet another platform for studying metal alloys was developed in R, using machine learning algorithms, with a specific focus on high entropy alloys, (3) now the work shifts to making the best out of these and handshaking the platforms.
Principal Investigator: Dr Aijaz Ahmad
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2019-08-19
Allocation End: 2020-02-15
Used Hours: 4955
Project Name: Molecular modelling and drug design
Project Shortname: HEAL1257
Discipline Name: Health Sciences
We are based in University of the Witwatersrand in School of Health Sciences and the Department of Clinical Microbiology and Infectious Diseases. Here we are exploring the anti-microbial and anit-viral drugs by targeting various enzymes. We are implementing virtual screening, pharmacophore modeling and molecular dynamic simulation studies to discover these drugs as potential therapeutics in various infectious diseases.
Principal Investigator: Dr Samuel Iwarere
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2019-08-21
Allocation End: 2020-02-25
Used Hours: 42306
Project Name: Understanding Plasma-Liquid Interaction
Project Shortname: MECH1107
Discipline Name: Chemical Engineering
The research is being carried out under the guidance of the Thermodynamics Research Group based in the School of Chemical Engineering at the University of KwaZulu-Natal. The understanding of plasma-liquid interactions is of prime importance in the context of environmental remediation and wastewater treatment applications. Plasma treatment of wastewater involves complex chemical and physical phenomena, which makes the comprehensive modelling of phenomena such as gas phase reaction, turbulence and heat transfer a difficult task. In order to gain insight into the complex processes associated with the use of plasma wastewater treatment, Computational Fluid Dynamics (CFD) will be used to study the relevant chemistry and fluid dynamic effects at the plasma-liquid interface. The Centre for High Performance Computing (CHPC) allows for calculation within realistic time frames, allowing the researchers to determine the accuracy of the unsteady state simulations encountered in plasma physics. Simulation of the plasma arc is progressing well with the researchers working in conjunction with other scientists in the plasma field.
Principal Investigator: Dr Jaap Hoffmann
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2019-08-21
Allocation End: 2020-02-17
Used Hours: 28147
Project Name: Flow through porous media
Project Shortname: MECH1116
Discipline Name: Computational Mechanics
Dr. Jaap Hoffmann from the Department of Mechanical & Mechatronic Engineering and his students are investigating flow and heat transfer in rock bed thermal energy storage. The function of the rock bed is to store surplus solar energy harvested during the day, to produce electricity at night. Rock particles have a distinct long and flat axes, and as a result, they pack in an anisotropic way. As a result, the flow through the bed is also anisotropic. Designers need information on the flow in different directions to make optimal use of the bed's capacity. Here, we used a discrete element modelling/computational fluid dynamics approach to model the flow through the interstitial volumes in the bed. A total of 258 simulations were performed on meshes comprising of about 15 million tetrahedral cells. Simulations run about 30 hours on a 10 CPU, 64 GB desktop. Running on the CHPC reduced wall time to less than 2 hours, using 72 CPU's. The current set of simulations was for a single packing. A statistically stationary result will only emerge after several packings were evaluated. This will be addressed in 2020.
Principal Investigator: Prof Gert Kruger
Institution Name: University of KwaZulu-Natal
Active Member Count: 11
Allocation Start: 2019-08-24
Allocation End: 2020-02-20
Used Hours: 557268
Project Name: CPRU molecular modeling
Project Shortname: HEAL0839
Discipline Name: Health Sciences
(Who) The Catalysis and Peptide Research Unit at UKZN (http://cpru.ukzn.ac.za/Homepage.aspx) is currently working on the mechanism of action on the HIV PR with respect to the natural substrates. (What) We use an quantum chemical/molecular mechanics hybrid (Oniom) approach that gives us high level results on the thermodnamics and kinetics of the reaction. Our model enables us to study application of both electronics and sterics to change the bond strenght and binding energies of new potential inhibitors. The same approach is followed for transpeptidases, essential enzymes for the inhibition of TB. (Why) HIV is a major health threat in SA and new drugs is required due to the constant development of drug resistance. Similarly, TB and TB co-infection with HIV is a mojor health issue. (How) Our theoretical studies will allow us to test a computational model that correctly describes the interactions between the respective enzymes and existing drugs. We are improving our computational model to the extent where are now in a position to make and test new potential drug leads for synthesis. This can only be done with large computational resources provided by the CHPC.
Principal Investigator: Dr Ruben Cloete
Institution Name: University of Western Cape
Active Member Count: 3
Allocation Start: 2019-08-24
Allocation End: 2020-02-20
Used Hours: 378711
Project Name: HIV-1C integrase drug resistance
Project Shortname: CBBI1154
Discipline Name: Bioinformatics
The research group of Dr Ruben Cloete is based at the South African National Bioinformatics Institute, University of the Western Cape. The work in my group is primarily focussed on molecular modelling and drug design. Here we focus on protein structure prediction, molecular docking and simulation studies of protein-drug, protein-protein systems. Our research efforts is in understanding HIV-1 drug resistance, identifying novel drugs to treat drug resistant Tuberculosis and the prioritization of novel genes associated with Parkinson's disease in South African families. This work has led to the identification of new drugs to treat Tuberculosis. Furthermore, ongoing work might also contribute to the understanding of the development of Parkinson's disease and the better management of HIV-1 infected individuals within South Africa. For this to become a reality requires the use of structural computational methods to understands the movement of the molecular machinery of the cell called proteins. For this large computing resources are required to run large protein systems. Currently we are in the process of submitting several protein structures to the CHPC for simulation analysis. We may even require more resources.
Principal Investigator: Dr Gebremedhn Gebreyesus Hagoss
Institution Name: University of Ghana
Active Member Count: 5
Allocation Start: 2019-08-24
Allocation End: 2020-04-22
Used Hours: 582026
Project Name: Atomistic simulations and condensed matter
Project Shortname: MATS1031
Discipline Name: Physics
The condensed matter research group at the Physics Department at the University of Ghana is focused on the study of the structural, electronic, magnetic, and optical properties of 2D and bulk materials. Computational simulations of the properties of these materials are carried out using Quantum Espresso, which is the state-of-the-art open-source computational software package.
Our computational work would not be possible without the enhanced computing resources available at the CHPC in South Africa. Typically, we prepare our input files in our laptops and run our calculations in the CHPC. The job is monitored at least once a day and the results downloaded when completed.
Our main areas of research:
1. Electronic, magnetic, structural and optical properties of transition-metal oxides.
Experiments are carried on the synthesis and characterization of ZnO, ZnO2, and ZrO2 for oxygen and CO2 gas sensors and energy applications. We are also investigating the structural, electronic, optical, and magnetic properties of these materials using the first-principle calculations.
2.Perovskite Materials for energy applications
a) There is lead (Pb) on Perovskite solar cells (organometal CH3NH3PbX3 and mixed halide CH3NH3PbI2X, (X = Cl, Br, I)). Hence it is very important to search computationally for the replacement of Pb by environmentally friendly elements. We are investigating all the divalent metals (Co, Cu, Fe, Mg, Mn, Ni, Sn, Sr, and Zn) which could substitute Pb in an organometal and mixed halide perovskite.
b) In this project, we focus on the investigation of structural, electronic, dielectric, and vibrational properties of low-temperature phase perovskite materials using DFT+U.
3. Two-dimensional Materials Research
In this project, we focus on the effect of introducing lanthanide atoms and spin-orbit coupling effects into monolayer RSe2 and WS2.
Two-dimensional materials also promise a wide range of applications, including light-emitting applications, energy generation and storage, wear- and corrosion-resistant surfaces, and gas and radiation sensors.
Principal Investigator: Prof Veikko Uahengo
Institution Name: University of Namibia
Active Member Count: 6
Allocation Start: 2019-08-24
Allocation End: 2020-03-18
Used Hours: 306907
Project Name: Solar Materials
Project Shortname: MATS1043
Discipline Name: Material Science
The group is working on Solar materials, based at the University of Namibia (UNAM). The group is targeting locally available materials with photocatalytic properties used in the development solar materials. The raw materials such as zinc oxides and copper oxides are used nowadays to harvest energy from the sun, after smart engineering of their band gaps. Abundant in Namibia, these materials are exported in their raw forms without even a single percentage of value addition. Under the circumstances, energy has become critical in our ever fast growing societies with a high dependency on energy for technological advancement. Thus, locally available resources must be optimized to add value in order to contribute to economic growth and benefit our societies. The CHPC has become a powerful intermediator making life easier for researchers, because we use the facility to simulate and predict certain properties of our systems for a desired functionalities, which guides us into the experimental work, by eliminating the undesirables. Thus, assisting us saves a lot of resources in chemicals and solvents along the way, and more importantly the TIME. Thus far, the progress of the projects have ran smoothly and achieved best results, that could not be possible without this Facility.
Principal Investigator: Prof Mwadham Kabanda
Institution Name: University of Venda
Active Member Count: 2
Allocation Start: 2019-08-24
Allocation End: 2020-02-20
Used Hours: 13985
Project Name: Reaction mechanism for atmospheric relevant molecules
Project Shortname: CHEM1161
Discipline Name: Chemistry
The research on the reaction mechanisms of atmospheric relevant molecules from a computational perspective is being done because it allows for better understanding the preferred reactions species that are engaged in the mechanism as well as the corresponding reaction rates. In other words, in the case of competing reactions species, it becomes possible to differentiate which species have high probability to be involved in the mechanism
Principal Investigator: Dr Rose Modiba
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 5
Allocation Start: 2019-08-27
Allocation End: 2020-03-18
Used Hours: 342841
Project Name: Computational modelling of light metals
Project Shortname: MATS1097
Discipline Name: Material Science
We are the Advanced Materials and Engineering group within manufacturing cluster at CSIR. Our group is mainly focused on the Ti and Platinum group metals beneficiation using both experimental and first principle approach. The stability predictions of alloys are done using Materials Studio at CHPC and the results validated using experimental procedures. The modeling approach using CHPC resources helps in minimizing cost and time spend in the lab. Some materials can also be harmful to use in the labs hence modeling comes with such benefits. The work is progressing well wherein students are at the last stage of writing their thesis and some using their results to perform some of the experiments for validation.
Principal Investigator: Prof Evans Adei
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 14
Allocation Start: 2019-08-24
Allocation End: 2020-02-20
Used Hours: 1430342
Project Name: Materials For Energy and Fine Chemicals
Project Shortname: CHEM1046
Discipline Name: Chemistry
There has not been any new development worth reporting since our last feedback.
Principal Investigator: Prof Jeanet Conradie
Institution Name: University of the Free State
Active Member Count: 4
Allocation Start: 2019-08-24
Allocation End: 2020-02-20
Used Hours: 2277076
Project Name: Computational chemistry of transition metal complexes
Project Shortname: CHEM0947
Discipline Name: Chemistry
This project is concerned with the computational chemistry of transition metal complexes, with special focus on the application of computational chemistry in determining the structure and energy of transition metal complexes, transition states and reaction-intermediates. This is reflected in the outputs of my research group during the period of report. The outputs gave a better understanding of experimental observation and of the factors influencing the reactivity of metal complexes, in order to streamline them for use in different applications, for example in catalysis or energy sources (batteries and solar cells).
Principal Investigator: Dr Parvesh Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2019-08-26
Allocation End: 2020-05-21
Used Hours: 5889
Project Name: Molecular dynamics and docking studies of organic compounds
Project Shortname: CHEM0795
Discipline Name: Chemistry
We are using CHPC computer facilities to investigate drug-protein interactions and optimization of organic scaffolds and their metal complexes. Our aim is to search potential drug molecules with potent activity against bacterial, diabetes and cancer infections. The CHPC computing facility has proven to be very useful to collect very useful information within a shorter period of time. Running these jobs on normal computers either would have taken months to finish or would die in middle. With this supercomputing facility in our hand, we not only managed to run complex calculations in a speedy manner but also obtained reasonably good scientific explanations for to support our experimental results. Consequently, we managed to publish the compiled data in reputed chemistry and medicinal chemistry journals. Moreover, my post graduate students have learnt different computational tools that are being used in drug design and drug discovery field.
Principal Investigator: Dr Babatunde J. Abiodun
Institution Name: University of Cape Town
Active Member Count: 17
Allocation Start: 2019-08-27
Allocation End: 2020-03-17
Used Hours: 1157505
Project Name: CSAG-Atmospheric Modelling
Project Shortname: ERTH0904
Discipline Name: Earth Sciences
The highlights of our research during the reporting period include:
(1) Quantification of efficiency of solar radiation management (SRM) in mitigating impacts of climate change in Africa.
(2) Potential impacts of specific global warming levels on extreme rainfall events over southern Africa in CORDEX and NEX‐GDDP ensembles.
(3) Understanding the influence of ENSO patterns on drought over southern Africa.
(4) Understanding the timing of future changes in crop suitability in West Africa
(5) Understanding the transport of PM10 over Cape Town during high pollution episodes
(6) Projecting drought characteristics over East African basins at specific global warming levels.
Principal Investigator: Mr Darren Martin
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2019-08-27
Allocation End: 2020-02-23
Used Hours: 7690
Project Name: New Method for Measuring Telomeres at High Resolution
Project Shortname: CBBI1262
Discipline Name: Bioinformatics
The work we do involves finding a new method for measuring the end caps on chromosomes known as telomeres. These pieces of DNA are responsible for protecting DNA during DNA replication, but get shorter with each round of cellular replication. When telomere length drops below a critical length, the cell enters a state of cell-cycle arrest. It is for this reason that telomeres are viewed as a "molecular clock" that measure the replicative capacity of a group of cells. We using Oxford nanopore sequencing to measure telomere length. This method generates large files of raw data that need to be processed using the CHPC facilities. We conduct our lab work in the department of Integrated Biomedical Sciences, Faculty of Health Sciences, University of Cape Town. Zoe is a registered PhD student in the division of Computational Biology. The project is near completion, and Zoe should be finishing her research in September 2020.
Principal Investigator: Dr Vuyani Moses
Institution Name: Rhodes University
Active Member Count: 17
Allocation Start: 2019-08-27
Allocation End: 2020-03-11
Used Hours: 4099583
Project Name: Bioinformatics and Computational Chemistry Applications
Project Shortname: CBBI1122
Discipline Name: Bioinformatics
We are a newly created research group which falls under the Rhodes University Research Unit in Bioinformatics (RUBi). Our interests are using computational techniques to solve biological problems such as drug discovery and biofuel production. In our research group we use the CHPC resources to perform Molecular docking in-order to identify natural compounds with the potential to inhibit a wide variety of drugs targets from various diseases such as HIV and Malaria. To validate these potential compounds, Molecular Dynamics (MD) simulations are performed. Due to complex nature of these calculations, they tend to be quite computationally expensive. As result we are heavily reliant on the CHPC for the computational power required for such calculations. The CHPC has been an integral part of our research as most of our work is 100 % computational. Therefore our students are highly reliant on the facilities and resources offered by the CHPC to complete their research projects in due time. MSc Students which were enrolled in our one year MSc programme have successfully gone through the examination process and will be graduating next year. Of these students, most are still with us pursuing PhD degrees with research projects which are still heavily reliant on the CHPC. As a result, access the CHPC cluster is crucial to the proper functioning of our research programme.
Principal Investigator: Prof Linky Makgahlela
Institution Name: Agricultural Research Council
Active Member Count: 5
Allocation Start: 2019-08-27
Allocation End: 2020-02-23
Used Hours: 4153
Project Name: Beef and Dairy Genomics
Project Shortname: CBBI1138
Discipline Name: Bioinformatics
Beef and Dairy genomics team forms part of the Animal breeding and Genetics unit led by Professor ML Makgahlela at the Agricultural Research Council – Animal Production. It comprises of both researchers and post graduate students. The team works along the two large consortiums in South Africa; the Beef Genomics Program (BGP) and the Dairy Genomics Program (DGP) and works towards achieving the goal of generating large genomic data for the South African beef and dairy industry in order to fully implement genomic selection in the future and have the two industries compete at a global level. The work done by the team includes working with commercial and small holder beef and dairy breeders towards collecting a large number of samples for processing, curating and analysing generated genomic data. Thus far, the projects carried out by the team have developed strategies that can be used by breed society's. In addition to the strategies are the research findings that have revealed the genomic structure of the South African beef breeds and underlying genetic factors that are associated with adaptation that warrant the need for conserving these important genetics for future use in times of possible drought. The project has further contributed to capacity building by training experts especially in the field of bioinformatics.
Principal Investigator: Prof Juliet Pulliam
Institution Name: Stellenbosch University
Active Member Count: 20
Allocation Start: 2019-08-26
Allocation End: 2020-02-22
Used Hours: 4402
Project Name: South African Centre for Epidemiological Modelling and Analysis
Project Shortname: CBBI1106
Discipline Name: Other
SACEMA is a DSI-NRF Centre of Excellence focused on Epidemiological Modelling and Analysis, hosted at Stellenbosch University. We use computational approaches to address questions of public health relevance to South Africa and the African continent. We use the CHPC primarily to run stochastic simulations and for simulation-based validation of novel inference methods.
Principal Investigator: Dr Adeniyi ogunlaja
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 4
Allocation Start: 2019-08-28
Allocation End: 2020-03-04
Used Hours: 20624
Project Name: Chemistry and Material Science
Project Shortname: MATS1070
Discipline Name: Chemistry
Refractory polyaromatic hydrocarbons found in fuels such as dibenzothiophene, quinoline and its alkylated derivatives emits nitrous oxides and sulfur oxides to the environment when combusted, thereby reducing air quality. Desulfurization by means of oxidative desulfurization and adsorptive denitrogenation has been proposed to complement the hydrodesulfurization (HDS) and hydrodenitrogenation (HDN) processes, currently employed to remove sulfur and nitrogen compounds in fuels. At Nelson Mandela University analytical and inorganic chemistry research group, we design materials that can selectively remove these sulfur and nitrogen compounds. Molecular modelling based upon the density functional theory (DFT) was employed to understand the mode of adsorption (interaction) between synthesised materials and the various compounds to be removed from fuels. Computational study assists with the understanding of the electronic and thermodynamic properties of synthesised materials prior to application. It also gives an insight as to the specific properties to be targeted when designing adsorbents for environmental clean-up. So far, progress has been made around the design and adsorption of some toxic molecules in fuels. HPC assist our group to build models that could be employed in explaining complex phenomena. It has also enabled us to ask big questions around activity of our materials and to test for possible answers computationally. CHPC has created the platform for where researchers like me could assess the HPC and has also assisted me and my students with solving problems some computation problems.
Principal Investigator: Dr Lonnie van Zyl
Institution Name: University of Western Cape
Active Member Count: 1
Allocation Start: 2019-08-29
Allocation End: 2020-02-25
Used Hours: 50004
Project Name: Engineering bacterial pyruvate decarboxylase for increased thermostability
Project Shortname: CBBI1265
Discipline Name: Bioinformatics
Dr. Leonardo van Zyl at the The Institute for Microbial Biotechnology and Metagenomics (IMBM) at the University of the Western Cape is investigating which portions of an enzyme contribute to its stability at high temperatures. The enzyme being investigated is called pyruvate decarboxylase (PDC) that catalyzes the conversion of pyruvate, a central metabolite in bacterial cells, to acetaldehyde. Through the action of a second enzyme called alcohol dehydrogenase, the acetaldehyde is converted to ethanol. This makes the enzymes useful in engineering bacterial strain to enable them to produce ethanol from renewable resources such as plant waste material. Bacteria which grow at high temperatures (60C), called thermophiles, have been identified as possible candidates for ethanol production, as ethanol production at these elevated temperatures has benefits for the process. The PDC enzymes are only found in organisms that grow at moderate temperatures and thus cannot withstand the high temperatures during the fermentation process. This research aims to identify the areas of the protein susceptible to high temperatures and engineer the enzyme to cope with the higher temperature. The protein crystal structures for the least- and most thermostable versions of PDC have been solved, and we can use computer simulations of the movement of these proteins at various temperatures to identify where the structure fails and address it by incorporating chemical bonds that are not so easily broken thereby retaining its functionality. A general thermostabilizing feature has not been identified for all proteins, and there is exists a huge demand for thermostable variants of a wide range of proteins globally. Should this work be successful it may suggest a general workflow for the engineering of thermostable proteins as well as shed new light on thermostabilizing features of proteins. Dr. van Zyl used the CHPC Lengau cluster to perform 250 nanosecond simulations of these medium sized (240000 atoms) protein systems at 25C and 60C to establish how temperature affects these proteins. This work should help South Africa grow its knowledge economy, display the talents of its researchers and possibly help it be a global competitor in the biofuels market through the use of publicly funded computational resources.
Principal Investigator: Dr David Pearton
Institution Name: Oceanographic Research Institute (ORI)
Active Member Count: 6
Allocation Start: 2019-08-29
Allocation End: 2020-02-25
Used Hours: 13770
Project Name: Responses of South African Coral Reefs to Climate Change
Project Shortname: CBBI1072
Discipline Name: Environmental Sciences
The Reef and Estuarine ecology groups of the Oceanographic Research Institute (ORI) have been using cutting edge "omics" approaches to address critical questions in marine conservation in South Africa. Based at uShaka seaworld, ORI is part of the South African Association for Marine Biological Research (SAAMBR). Founded in 1951, SAAMBR is dedicated to the conservation of marine and coastal resources in the Western Indian Ocean.
We have been using the CHPC infrastructure to analyse High Throughput Genetic sequencing data to examine questions of community structure, population connectivity and invasive species in orde to help with the management of our critical marine resources and help in its conservation.
Principal Investigator: Prof Hasani Chauke
Institution Name: University of Limpopo
Active Member Count: 9
Allocation Start: 2019-08-30
Allocation End: 2020-03-18
Used Hours: 305761
Project Name: Computational Modelling of Minerals, Metals and Alloys
Project Shortname: MATS1047
Discipline Name: Material Science
The minerals, metal and alloy development programme (MATS1047), led by Professor Hasani Chauke (primary investigator, PI) is amongst others one of the major strategic research niche at the Materials Modelling Centre (MMC), University of Limpopo. The work employ first-principles quantum mechanical approaches and molecular dynamics based methods, which employs various academic and commercial software's with different types of interfaces. These computers based software's are linked to local servers (MMC) and the Centre for High Performance Computing (CHPC). The CHPC in particular provides platform to run large scale calculations at a more reasonable time. The research projects under MATS1047 are progressing well with regard to jobs submission, queuing and running. The project contributes to human capital development through training of Honours, Masters and Doctoral students.
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 12
Allocation Start: 2019-08-30
Allocation End: 2020-03-25
Used Hours: 3783552
Project Name: Structural, electronic, magnetic properties and anisotropy energy in some metallic and non-metallic heterostructures
Project Shortname: MATS0988
Discipline Name: Material Science
The research work is a collaboration between the Dr. Raji (Physics Department, UNISA, South Africa) and the group of Dr. Brice Rodrigue Malonda (Marien Ngouabi University, Republic of Congo). The focus of the research is numerical studies of electronic, optical, transport and magnetic properties of selected two-dimensional (2D) and three-dimensional (3D) solid materials for potential applications in high-capacity data storage, catalysis and renewable energy. The study employs density-functional theory (DFT) as the numerical method, to probe atomic-level properties of these materials. Our approach is mainly atomic and defect engineering of these solids which involve modifying the properties of the solids through the introduction of external atoms into their otherwise pristine structure. The last two decades have witnessed the discovery of several 2D materials, and have opened new possibilities to further miniaturization of existing electronic and magnetic devices. Therefore, fundamental understanding of properties of these materials systems is necessary to support experimental research and to aid technological applications. One of the aims of our research therefore, is to discover novel materials that can be synthesized in the labouratory for potential technological applications.
The numerical implementation of DFT is computational intensive, requiring several computational hours, large data storage and memory requirements, beyond the capacity of ordinary table-top computers. Therefore, high-capacity computer clusters such as the one provided by the Center for High Performance Computing (CHPC) is sine qua non for the research. There are about twelve postgraduate students working in various aspects of the project. At the moment, four Masters students have completed their studies and two of them are continuing to doctorate. This research, as well as the CHPC, has enabled collaboration between South Africa based academic researcher and colleagues in Congo, Mexico and Italy. There have been research outputs in form of publications, and the scope of the project will guarantee regular postgraduate students training who are able to undertake cutting-edge research and contribute to scientific development.
Principal Investigator: Prof Ozlem Tastan Bishop
Institution Name: Rhodes University
Active Member Count: 20
Allocation Start: 2019-09-02
Allocation End: 2020-02-29
Used Hours: 5339226
Project Name: Structural Bioinformatics for Drug Discovery
Project Shortname: CBBI0867
Discipline Name: Bioinformatics
Research Unit in Bioinformatics (RUBi) at Rhodes University is specialized in structural bioinformatics research. Structural bioinformatics focuses on the identification and analysis of structure, dynamics and interaction of biological macromolecules in 3D space. While doing so, it aims to make connections between sequence – structure and function of macromolecules. Information on structure is particularly important as you can derive enormous amounts of information.
RUBi's main research interest is early drug discovery. Computer aided drug design technology has greatly revolutionised the drug research and development process. Traditional computational drug discovery approach includes large scale structure based and/or ligand based in silico docking combined with molecular dynamics and binding free energy calculations. All these computationally expensive calculations require to use HPC facilities.
In the last few years, RUBi has been developing some novel protocols by merging computational chemistry, structural bioinformatics and biophysics approaches and combining with traditional methods. These combined approaches also require HPC facilities. We expect that our protocols will advance our and others research. We have already been testing the combined approaches in different cases and a number of hit compounds identified; including identification of South African natural compounds as hits to cancer, malaria, trypanosoma and HIV.
Principal Investigator: Mr kirodh Boodhraj
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 2
Allocation Start: 2019-09-02
Allocation End: 2020-02-29
Used Hours: 79694
Project Name: Geospatial modelling regarding satellite imagery, oceans and coastal areas using machine learning, ODC and STAC
Project Shortname: CSIR1266
Discipline Name: Earth Sciences
We discovered that SA port users, ocean industries and recreational ocean users use European/American ocean forecast products. There is not a SA based ocean forecast model available currently and if there is one that exists, it is not widely available.
The goal of this project are as follows:
-Using the Nucleus for the European Modelling of the Ocean (NEMO) model, we can fine tune the model to suit SA conditions. We can then obtain an ocean forecast.
The amount of climate data is huge and it takes time to process the data and then format the data for producing wave forecasts in the local regions of SA. The models needed to produce the forecasts take a long time to run and produce large amounts of data. The port authorities need such wave forecasts in the local regions of SA's ports to determine if port operations are safe or risky.
The goals of this project are as follows:
-The Smiulating Waves Near-Shore (SWAN) model (in the Delft suite of programs) will be used operationally to produce wave forecasts for port operations.
-Running hydrodynamic coastal models using FLOW, which comes with Delft suite, to determine ocean currents near ports to determine if port operations are safe or risky.
Numerical ocean models require input data to produce an output. Our approach to obtaining an ocean forecast, will be to use machine learning to forecast the ocean model input data and then run the ocean model using this data.
The goal of this project are as follows:
-Run machine learning algorithms for large ocean model input data sets to obtain a forecast for them.
Principal Investigator: Dr Gurthwin Bosman
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2019-09-02
Allocation End: 2020-03-18
Used Hours: 116833
Project Name: Quantum computations for photoinduced reactions
Project Shortname: CHEM1126
Discipline Name: Physics
The research group is one of the arms of the Laser Research Institute in the Department of Physics of Stellenbosch University. Laser Research Institute of the Stellenbosch University, boasts of ongoing formidable research projects in the fields of ultrafast science, spectroscopy and laser diagnostics, laser development, trapped ion quantum control and bio-photonics and imaging, with a number of laboratories housing ultra-modern equipment. Our research group is focussed on ultrafast transient absorption spectroscopy on chemical compounds ranging from simple molecules to polymers. Experimental set ups for ultrafast transient absorption spectroscopy have been thoroughly developed over the years by different masters, doctoral and postdoctoral students. The research projects conducted in the ultrafast laboratory had produced masters' and doctoral theses, as well as peer reviewed publications.
Scientific observation being made by experiments in our research group need to be properly understood and interpreted for proper communication to the general community. Therefore, a level of theoretical simulation which will allow deeper insights is needed. Part of these theoretical simulation is the density functional calculation, a theory well accepted to interpret molecular and/or structural dynamics we observe experimentally. The calculations can take forever if run on a single computer. This is where the Centre for High Performance Computing (CHPC) comes in.
Centre for High Performance Computing (CHPC) offers a wide range theoretical coding and simulation with the advantage of supercomputing on parallel computers. This enables users' jobs submission to run on a faster scale. Our research group is privileged to have access to these supercomputing capabilities and the provision of simulation software for our calculations.
We are running series of density functional calculation ranging from simple molecules to polymers using Gaussian 09, ORCA and Maestro that is provided by CHPC.
Principal Investigator: Dr EUSTINA BATISAI
Institution Name: University of Venda
Active Member Count: 1
Allocation Start: 2019-09-02
Allocation End: 2020-02-29
Used Hours: 28261
Project Name: Predicting formation of co-crystals and pharmaceutical co-crystals
Project Shortname: CHEM1206
Discipline Name: Chemistry
The UnivenCrystEng group is located within the Chemistry Department at the University of Venda. The group's research interests include supramolecular chemistry and crystal engineering. In particular, studying structure-property relationships in co-crystals and pharmaceutical co-crystals. Active pharmaceutical ingredients are usually plagued with poor physicochemical properties such as solubility and dissolution. One way to improve their properties is to crystallize the active pharmaceutical ingredients with a benign compound in a process known as co-crystallization. The resulting compound is known as a pharmaceutical co-crystal and usually exhibits improved physical and chemical properties compared to those of the active pharmaceutical ingredient. The aim this project is to predict the formation of co-crystals and pharmaceutical co-crystals using computational methods. This is achieved by calculating the interaction energies between the co-former and the API. The CHPC is needed for these calculation as the molecules are big and calculations can take several days when being conducted on normal computer.
To date, interaction energies of up five (5) co-crystals. The results were analysed and correlated with experimental data. The work will be extended to include structurally similar compounds.
Principal Investigator: Prof Liliana Mammino
Institution Name: University of Venda
Active Member Count: 4
Allocation Start: 2019-09-03
Allocation End: 2020-03-01
Used Hours: 428621
Project Name: computational study of biologically active molecules of natural origin
Project Shortname: CHEM0959
Discipline Name: Chemistry
WHO WE ARE
A computational chemistry research group at the University of Venda (Thohoyandou)
WHAT WE ARE DOING
We do computational studies of biologically active molecules.
During 2019 we considered molecules with antimalarial, antidiabetic, anti-inflammatory and antioxidant activities. Structures that might potentially be useful for drug delivery were also explored.
WHY?
Studying biologically active molecules means investigating the properties of molecules that might be interesting as drugs to treat diseases. We prefer to study molecules of natural origin because they are the most promising, as it is already known that they have specific effects for specific diseases. Computational studies provide information about the properties of molecules, and this information is useful for researchers working on further stages of drug development.
HOW WE WORK
We use programs (software) to calculate the molecules in which we are interested. The outputs give a variety of data, that we analyse and, when enough data on a certain molecule or class of molecules are obtained, we organise them in an article, to share the information with other researchers who might be interested in using them. In most cases, we also present the results at conferences.
The project relies extensively on the CHPC because the same calculations would take at least 100 times more time on a normal computer (PC). The enormous saving of time enabled by the CHPC enables us to obtain results faster, and our project progresses much faster than it would without using the CHPC.
The project is progressing satisfactorily. The number of research outputs (publications, conference papers) associated with it so far can be considered satisfactory. Furthermore, the new questions arising as the project proceeds make it increasingly more interesting. This means that the project has realistic perspectives of interesting developments and growth.
Principal Investigator: Prof Francois Engelbrecht
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2019-09-05
Allocation End: 2020-03-03
Used Hours: 717386
Project Name: WITS Climate Modelling
Project Shortname: ERTH1200
Discipline Name: Earth Sciences
The Global Change Institute (GCI) of the University of the Witwatersrand (Wits) has launched a new academic programme in Earth System Model development. Earth System Models have become the main tools to project future climate change. However, these modelling systems are computationally expensive. In South Africa, the Lengau cluster of the CHPC is the only high-performance computer capable of undertaking the lengthy integrations of ensembles of projections of future climate change. A particular lighthouse of this programme, is the development of the first global ocean model to be developed in Africa and in the Southern Hemisphere, the Wits Planetary Ocean Model (WPOM). Message Passing Interface (MPI) capabilities were added to this code in 2019 through a vibrant research collaboration between the Wits GCI and the CSIRO on Australia. Within South Africa, the CSIR, UCT Oceanography and the University of Venda are important partners in the model development process. Extensive production simulations, aimed at verification of the new coupled ocean-atmosphere modelling system, are currently underway on the Lengau cluster. A major milestone reached in 2019, was the publication of the first paper ever to described detailed downscalings of palaeoclimate over southern Afrcia. The model simulations revealed new insights into glacial climate over southern Africa and provided physical mechanism for the observed east-west gradient in Fynbos diversity stretching from the Eastern to Western Cape in South Africa. The Wits programme in Earth System Model development is associated with an accompanying programme in human capital development, which is largely funded by the Earth System Science Research Programme (ESSRP) of the National Research Foundation (NRF). Over the last year 8 full-time students (1 post-doc, 6 PhDs and one MSc) have joined the programme, an important towards establishing a new cadre of Earth System Modellers living and working in Africa.
Principal Investigator: Mr Adebayo Azeez Adeniyi
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2019-09-05
Allocation End: 2020-03-03
Used Hours: 333778
Project Name: Drug Discovery Research Using Quantum and Molecular Dynamic Simulation
Project Shortname: CHEM0958
Discipline Name: Chemistry
Our main research focus is "Drug Discovery Research Using Bioinformatics, Quantum and Molecular Dynamic Simulation". We are presently working on vaccine development using pathogenic genomes. In recent time, based on the pressing need of the society and global challenges, we have included study on polymer and molecular electrochemistry. Our research use theoretical modelling to give rational insight into identified problems which can help in the experimental designs for possible solutions. CHPC is an important facility to our research group, we make use of the facilities and the softwares like Gaussian, Games and Newchem; also used molecular dynamic packages like Gromacs, Amber and Lammps. We have applied quantum packages to study the chemical and spectroscopic properties of small molecules of which we have been able to reproduced some of the experimental results.
It is obvious that our research progress and achievement revolve around the service of CHPC and many of our research output would not have been possible in without the support from CHPC.
Principal Investigator: Prof Warren du Plessis
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2019-09-05
Allocation End: 2020-03-03
Used Hours: 543692
Project Name: Electronic Warfare (EW) Technologies
Project Shortname: MECH0989
Discipline Name: Electrical Engineering
Exhaustive searches are time-consuming and are thus generally considered naive. However, they are often the only way to ensure that the best possible result to a problem has been obtained, and such optimal results are required to establish trends and benchmarks. The CHPC facilities have been used by Prof. du Plessis of the University of Pretoria to perform exhaustive searches in thinned antenna array research and in support of research into radar ambiguities. This research would not be possible without the CHPC facilities.
Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 18
Allocation Start: 2019-09-06
Allocation End: 2020-03-04
Used Hours: 407327
Project Name: Computational and statistical methodologies for human and environmental health prediction
Project Shortname: CBBI0818
Discipline Name: Bioinformatics
Computational and statistical methodologies for human and environmental health prediction research programme (CBBI0818) is running from the University of Cape Town, South Africa. This research programme is fundamentally aiming 1) to determinate the environment and genetic variation that cause human species to look different, having difference in allergy, drug responses and treatment. 2) to identify and quantify the pattern of inheritance of the observed trait, drug response and treatment variation among human. These are addressed through the design of machine intelligence and artificial intelligent methodologies and statistical approaches to analysis large-scale DNA data of thousands affected/unaffected subjects. In doing so, and the use of CHPC this programme is contributing to human health by increasing understanding of the genetic and environmental underpinnings of complex traits, drug/treatment responses and drug/dosage responses. The accumulation of experimental DNA data in Biology and new high throughput experiments are growing rapidly and give a huge number of data difficult to manage, to store and to analyse this existing and future dispersed information. As really DNA data become more and more available and big, better the health prediction is, therefore there is a critical need for national life and long -term storage and robust fast accessible memories. Up to today, the use of parallel High-Performance Computing at CHPC has critically increased our researcher portfolio to meet the international standard with respect to large scale genomic era. This programme has already developed of genomic-based software tools that address African genetic variation challenges and provided advanced training around parallel programming with respect to large-scale genomic data to African postgraduate students/researchers.
Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 3
Allocation Start: 2019-09-06
Allocation End: 2020-03-04
Used Hours: 1336
Project Name: African Multi-Omics Data Science
Project Shortname: CBBI1039
Discipline Name: Bioinformatics
Computational and statistical methodologies for human and environmental health prediction research programme (CBB1039) is running from the University of Cape Town, South Africa. This teaching and training programme are fundamentally aiming 1) to provide training to students and other research in handling, processing big Biomedical data science. The accumulation of experimental DNA data in Biology and new high throughput experiments are growing rapidly and give a huge number of data difficult to manage, to store and to analyse this existing and future dispersed information. As really DNA data become more and more available and big, better the health prediction is, therefore there is a critical need to teach and train our students in using High Performance Computing. In doing so, this programme will contribute to educate from honours to PhD students in the fundamental of processing large scale genomics data sets and handling computational cost task.
Principal Investigator: Dr Krishna Govender
Institution Name: University of Johannesburg
Active Member Count: 6
Allocation Start: 2019-09-06
Allocation End: 2020-03-04
Used Hours: 234331
Project Name: Computational approaches to design novel anticancer agents
Project Shortname: CHEM0792
Discipline Name: Chemistry
With any HPC centre it is imperative that codes can scale well.
To ensure that this is the case the codes need to be installed correctly and thoroughly tested
The goal of the current programme is to install and test various chemistry/material science and machine learning codes on the system to ensure that they work the way they should and thereby ensure that users make efficient use of the system with highly optimized codes.
Principal Investigator: Dr Jaco Badenhorst
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 3
Allocation Start: 2019-09-06
Allocation End: 2020-03-04
Used Hours: 26403
Project Name: Automatic transcription of broadcast data
Project Shortname: CSIR0978
Discipline Name: Other
The Digital Audio Visual Technology (DAVT) Research Group at the CSIR Nextgen Enterprises and Institutions (NGEI) cluster develop speech and language-related technologies for the South African context to enhance access to information and communication. Given the multilingual nature of South Africa, human language technologies (HLTs) can make information and services accessible to a larger proportion of the South African population in a sustainable way, by reaching people in remote locations, people who are not necessarily trained in using technology, or people who are not fluent in English. HLTs can also provide access to information to people with disabilities. HLT can support language diversity and providing of information in multiple languages in an affordable and equitable fashion. The development of all 11 official languages is a national priority, which requires significant attention to HLT in all of these languages. HLT can be of significant economic importance – both by empowering citizens of the country to work more productively, and by forming the core of an exportable set of technologies (since such technologies are currently not available to most of the developing world).
The HLT Research Group operates in a vibrant environment consisting of researchers, developers, project managers and students from backgrounds as diverse as engineering, linguistics and sociology. We conduct basic and applied research into projects related to the following areas of research: automatic speech recognition, text-to-speech synthesis, natural language processing, machine translation, human language analytics, text and speech resource development, speech and language technology system design and implementation, and usability and user experience evaluation of speech and language technology.
Principal Investigator: Prof Beatriz Garcia de la Torre
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2019-09-07
Allocation End: 2020-03-05
Used Hours: 7965
Project Name: Peptide Chemistry
Project Shortname: CHEM1090
Discipline Name: Chemistry
Our research involve study of new peptides, their structure, interactions, properties, electronic requirements and dynamics using ab initio calculations and MD calculations and their applications in drug delivery and study physical properties like magnetism etc. We pursue Green peptide synthesis reactions using Materials Studio.
Principal Investigator: Dr Rian Pierneef
Institution Name: University of Pretoria
Active Member Count: 8
Allocation Start: 2019-09-06
Allocation End: 2020-03-04
Used Hours: 37666
Project Name: Bioinformatic and Computational Biology analyses of organisms
Project Shortname: CBBI1124
Discipline Name: Bioinformatics
The CHPC is an integral part of research in South Africa and provides the opportunity for researchers to analyze a wealth of information in a single location. The current trend in research is big data. The CHPC allows all researchers to investigate their big data and rapidly analyze large data sets. As the fourth industrial revolution has started, the CHPC is a critical component in the current research and science landscape. The CHPC further aids in the development of human capital by providing an easy to use platform to students and early career researchers.
Principal Investigator: Dr Dirk Swanevelder
Institution Name: Agricultural Research Council
Active Member Count: 3
Allocation Start: 2019-09-06
Allocation End: 2020-03-04
Used Hours: 3962
Project Name: Crop Genomics
Project Shortname: CBBI1141
Discipline Name: Bioinformatics
Sunflower is one of South Africa's major oilseed crops and is grown in most areas of the summer rainfall production regions. A fast growth rate and relative drought tolerance allow the crop to be planted later in the summer season when rains are delayed. This enables producers to still produce a viable profitable cropping under challenging weather conditions. The ARC's Sunflower Genomics group focuses on improving sunflower. This specific project investigates key sunflower trait development on a molecular level over time. The traits investigated play a role in the profitability of the crop and its by-products. Comparison of transcriptomic data from lines with the desired traits to those without these allows us to investigate these key economic traits as they develop in commercial and non-commercial viable accessions. We believe that this would enable us to not only identify the key role playing genes in the development of these traits, but also the expression levels of these role players required to make these traits commercially viable and the required expressional timing to obtained the desired product/traits in the crop. The CHPC's large capacity allows us to analyse and compare the transcriptome datasets of the different developmental time periods within and between the different accessions under investigation. The CHPC is central to the analyses of the large transcriptome datasets generated during our investigation. The high-throughput nature of next generation sequence data generated in the project requires the computing resources provided by the CHPC to process the data in a timeous fashion. This will allow us to determine the relevant biological answers we're seeking and help improving the crop. The large data set requires substantial time to analyses with completion envisioned soon. The CHPC is also used for a SNP discovery project on 200 plants using the ddRAD protocol.
Principal Investigator: Prof Johan W. Joubert
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2019-09-09
Allocation End: 2020-03-07
Used Hours: 131976
Project Name: Mobility modelling using vehicle telematics
Project Shortname: MECH0803
Discipline Name: Other
Government (all spheres) is tasked with the challenge of deciding where to invest in infrastructure (for housing/transport/economic development etc). The real hard part is to balance two questions. Firstly, "who gets the benefit of infrastructure?" and, secondly, "who PAYS for those benefits?". In our research programme we develop agent-based transport models that are able to depict and imitate the complex, multi-modal and large-scale transport scenarios in a South African context. Each individual - from the Metrorail commuter, to the private car owner, to the minibus taxi driver, to the commercial vehicle delivering your goodies at the Woolies Foods - are represented in such a transport model. The goal of our ongoing research is to assist government and industry make better informed, evidence-based decisions about the intended, and unintended consequences of specific transport interventions. Since every individual is modelled the computational burden is substantial and the CHPC allows us to overcome the data preparation and simulation challenges of executing the large-scale, MATSim models.
Principal Investigator: Mr Anban Pillay
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2019-09-10
Allocation End: 2020-03-18
Used Hours: 56439
Project Name: Deep Learning Approaches
Project Shortname: CSCI1078
Discipline Name: Computer Science
The Deep Learning research group belongs to the Centre for Artificial Intelligence Research Node at the University of KwaZulu-Natal. The Centre for Artificial Intelligence Research (CAIR) (CAIR.za.net) is a South African distributed Research Network that conducts foundational, directed and applied research into various aspects of Artificial Intelligence. The research group conducts foundational research in machine learning in general and deep learning in particular. Deep learning projects require substantial computing resources and the CHPC is vital to its success. The projects involve various area of deep learning that include deep reinforcement learning, convolutional and recurrent neural networks. Application areas include image processing, natural language processing and speech recognition. Several students are busy with projects at present.
Principal Investigator: Prof Andries Engelbrecht
Institution Name: Stellenbosch University
Active Member Count: 11
Allocation Start: 2019-09-10
Allocation End: 2020-03-23
Used Hours: 1021470
Project Name: Computational Intelligence for Optimization
Project Shortname: CSCI0886
Discipline Name: Computer Science
The computational intelligence and data science research group at Stellenbosch University develops swarm-inspired optimisation algorithms to solve complex problems, where the search landscapes change over time, and where more than one constrained objective have to be simultaneously satisfied. Before these algorithms can be used, they have to be extensively benchmarked and analysed. Such analyses led to further improvements of the algorithms, that are now ready for real-world application.
Principal Investigator: Prof Gerard Tromp
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2019-09-06
Allocation End: 2020-03-04
Used Hours: 2887
Project Name: South African Tuberculosis Bioinformatics Initiative
Project Shortname: CBBI0999
Discipline Name: Bioinformatics
The South African Tuberculosis Bioinformatics Initiative (SATBBI) has the mandate to support tuberculosis research in South Africa. SATBBI relies on the computational power of the CHPC to achieve this mandate. The CHPC is particularly important for the Big Data analyses in bioinformatics including analysis of next-generation sequencing and epigenomics.
Principal Investigator: Prof Paulette Bloomer
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2019-09-10
Allocation End: 2020-03-08
Used Hours: 47698
Project Name: Molecular Ecology and Evolution Programme
Project Shortname: CBBI1030
Discipline Name: Bioinformatics
The Molecular Ecology and Evolution Programme (MEEP) is a research group in the Division of Genetics, Department of Biochemistry, Genetics and Microbiology at the University of Pretoria. We investigate the evolutionary history and current genetic diversity of many vertebrate species (marine and terrestrial), using genetics and genomics tools, and try to link the patterns we see with ecological and human-mediated events. We currently have two projects (Cape buffalo and bowhead whales) that make use of the CHPC resources, with additional projects in the pipeline.
Genomics of Cape Buffalo is a hot topic and is of interest to the general public and wildlife ranchers in particular. Cape buffalo are bred on private game ranchers for a one or a few economically important traits, such as horn length and body size. The effects of this artificial selection, as well as breeding South African buffalo with East African buffalo, is unknown. We can use genomics to evaluate the risks and benefits of these practices for the short and long term (evolutionary) conservation prospects of the species
The genetic work on the bowhead whale uses empirical and simulation data to investigate the effects that different Nearctic human cultures exploiting the whale had on the abundance of the population. This means that genetic data may have more resolution than previously thought and is sufficient to detect subtle changes in population size in relation to exploitation and climate change. This is of great importance as there are many applications. We believe that the work will have sufficient impact to be of interest to the general public in South Africa and internationally.
The development of a new molecular clock calibration method for tropical reef species makes use of simulations for validation. This calibration enables genetic time to be related to chronological time. This method may then be applied to empirical data to identify driving factors for increases in population size of reef dependent species in the tropics.
Principal Investigator: Prof Carlos Bezuidenhout
Institution Name: North-West University
Active Member Count: 13
Allocation Start: 2019-09-13
Allocation End: 2020-03-11
Used Hours: 89202
Project Name: Metagenomics studies of Microbes
Project Shortname: CBBI0890
Discipline Name: Other
Researchers in the Microbiology research group at the North-West University in Potchefstroom are using the CHPC facility to analyse large data sets. The programme involves amongst others: Whole genome mapping of bacteria for horizontal gene transfer; Whole genome mapping of a novel Xanthomonas plant pathogen; Mapping of plasmids; Microbiome analysis of agricultural soils; Microbiome analysis of water and sediment Environmental metagenomics of drinking water production facilities; Transcriptome analysis of Bt Resistant Busseola fusca. The research focus on water and food security and safety. These are important issues and obtaining local data is critical. Whereas large data sets could be generated quite routinely it is the data mining and analysis that requires sufficient computing capacity, such as that provided by the CHPC. Several papers had been published or are in the final draft stage. Having this capacity also provide this research group (CBB10890 – Metagenomics studies of Microbes) with competitive advantage is applications for funding.
Principal Investigator: Dr Lelanie Smith
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2019-09-16
Allocation End: 2020-03-14
Used Hours: 56149
Project Name: Aeronautical Research
Project Shortname: MECH1118
Discipline Name: Other
The Aeronautical engineering group at the University of Pretoria, focuses on research on novel aircraft configurations. In this context Dr L Smith considers different modelling strategies and approaches to investigate fuselage integrated propulsion and body optimisation.
In application studies of this work, passenger aircraft are considered and the size and complexity associated with the domain and flow physics when solving these problems are quite time consuming. Even before expanding to design exploration and optimisation models.
The CHPC becomes a necessary resource when full scale passenger aircraft modelling is important. Two Master students are currently making use of the CHPC and we hope that as the group grows we will make use of it more.
Principal Investigator: Dr Quinn Reynolds
Institution Name: Mintek
Active Member Count: 3
Allocation Start: 2019-09-11
Allocation End: 2020-03-25
Used Hours: 176617
Project Name: Computational Modelling of Furnace Phenomena
Project Shortname: MINTEK776
Discipline Name: Applied and Computational Mathematics
Pyrometallurgy is the science and technology of processing raw materials into more valuable products using thermal energy. By operating at very high temperatures - typically over 1500 degrees Celsius - smelting furnaces can perform chemical conversions which are impossible at room temperature, and this simple fact facilitates the mass production of many of the world's strategically-important commodities including iron and steel, chromium, manganese, precious metals, and many others.
Mintek makes use of direct-current (DC) electric arc furnace smelters to conduct research into novel pyrometallurgical applications. DC furnaces are some of the most extreme process engineering unit operations in the world, truly grand challenge problems with massively complex physics and chemistry governing their behaviour.
In order to understand that behaviour better, Mintek works with the CHPC leveraging the power of high performance computing to build sophisticated numerical models of the phenomena of interest. These models are then used as the building blocks for virtual prototypes and digital twins of our furnaces, allowing us to experiment safely and cheaply in our ongoing search for the best ways to design and operate future generations of smelters.
Principal Investigator: Mrs Chantel Niebuhr
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2019-09-17
Allocation End: 2020-03-15
Used Hours: 139176
Project Name: Hydrokinetic turbine analysis
Project Shortname: MECH1174
Discipline Name: Other
The University of Pretoria has undertaken research into the hydrodynamic effects around hydrokinetic turbines. This is necessary to allow further development of this type of hydropower in SA infrastructure. The CHPC cluster allows efficient and fast analysis and modelling of results necessary to achieve the conclusions necessary for further installations in SA. The project is progressing well as should be completed by June 2021.
Principal Investigator: Dr Sunita Kruger
Institution Name: University of Johannesburg
Active Member Count: 1
Allocation Start: 2019-09-17
Allocation End: 2020-03-15
Used Hours: 18035
Project Name: Environmental Heat Transfer
Project Shortname: MECH0995
Discipline Name: Computational Mechanics
This research group in the Mechanical Engineering Science Department of the University of Johannesburg is currently focusing on environmental heat transfer. Specifically heat transfer in naturally ventilated greenhouses. Greenhouses are used to protect plants from adverse weather conditions and insects. Ventilation of greenhouses are of vital importance to ensure quality crop production. If temperatures in a greenhouse is too high, poor plant growth may result, and an increased need for frequent watering. A mechanical ventilation system might be required to cool the inside of the greenhouse. Natural ventilation is an alternative option used to ventilate greenhouses. Natural ventilation uses temperature and wind to control the indoor climate of greenhouses. Unfortunately greenhouses are extremely energy intensive. Energy costs are the third highest cost related to greenhouse crop cultivation. Reducing the operating costs of energy associated with greenhouse cultivation may result in a price reduction of greenhouse cultivated crops. Conducting experimental work on ventilation of greenhouses can be costly and cumbersome. Using computational methods such as CFD (Computational Fluid Dynamics) to obtain qualitative and quantitative assessment of greenhouses can reduce costs and time involved. The computer cluster at the Centre for High Performance Computing has been used to conduct the numerical investigation using CFD. Currently research is being conducted on a large commercial greenhouse. Smaller greenhouses containing a single span are also being investigated, as well as rooftop greenhouses in the Johannesburg CBD.
Principal Investigator: Dr Michael Owen
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2019-09-17
Allocation End: 2020-03-15
Used Hours: 4819
Project Name: Industrial heat exchanger simulation and analysis
Project Shortname: MECH1210
Discipline Name: Computational Mechanics
The Thermofluids Division at Stellenbosch University's Department of Mechanical and Mechatronic Engineering has a long history of research in industrial heat exchangers and has conducted pioneering work in the field of dry cooling for large thermal power plants in particular.
Research in this field continues with a focus on understanding and improving the performance of these water conserving cooling systems under a variety of ambient conditions (including strong winds). Work of this nature benefits greatly from the CHPC which allows us to investigate an unprecedented number of scenarios in a short amount of time using computational fluid dynamics (CFD) and parallel computing.
Dry cooling is a key technology for South Africa's energy sector since thermal energy production (coal, nuclear, combined cycle gas and solar thermal) is typically a water intensive process which South Africa can ill afford considering the arid nature of our country. Ensuring robust operation of dry cooling systems can contribute significantly to the sustainability of South Africa's energy production.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2019-09-19
Allocation End: 2020-03-17
Used Hours: 13363
Project Name: SANAP CFD
Project Shortname: MECH1196
Discipline Name: Earth Sciences
The sub-Antarctic is one of the windiest regions in the world, with the biotic and abiotic conditions of the sub-Antarctic islands thought to be strongly affected by wind patterns. However, for these isolated terrestrial ecosystems we have a very poor understanding of within-island variation in wind speed and direction, and of how variation in wind patterns impact biotic communities. As a result, despite clear recent changes in broad-scale wind patterns in the sub-Antarctic, we have little quantitative basis for predicting the impacts that climate change-related shifts in wind speed and direction have on the biota of these islands. Computational Fluid Dynamic (CFD) models provide a robust methodology for estimating wind patterns, and have previously proved successful in understanding fine-scale air flow patterns in this system. However, the application of CFD to island-scale wind simulation is still an under-utilized approach despite recent relevant advances. Therefore, in this project we develop, and then apply, an island-scale CFD model to simulate wind flow patterns across an entire island, testing the potential for this approach to provide accurate insight into spatial variation of wind patterns across the island. The resources at the CHPC help in running large CFD models of the wind patterns on the island for all the predominant wind directions as obtained from the ongoing experimental wind mast study. The CFD results are of interest to botanists and those studying bird behaviour. Another spin-off is to investigate the use of wind power on parts of the island not inhabited by birds in order to replace the current diesel power generation.
Principal Investigator: Prof Fourie Joubert
Institution Name: University of Pretoria
Active Member Count: 35
Allocation Start: 2019-09-20
Allocation End: 2020-03-18
Used Hours: 38954
Project Name: NGS Bioinformatics
Project Shortname: CBBI0905
Discipline Name: Bioinformatics
The computational resources at the CHPC have made it possible for use to undertake research into human health and plant health. It has enabled a better understanding of the immune processes taking place when patients are infected by HIV. It has also helped us understand which processes take place when Avocado trees are infected with pathogens, and when trees are infected with Botryosphaeriaceae. Two publications are being readied for submission, 1 PhD has been obtained and one conference presentation has been given.
Principal Investigator: Dr Adam Skelton
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2019-09-20
Allocation End: 2020-03-18
Used Hours: 8666
Project Name: Molecular modelling of biomolecules and materials
Project Shortname: CHEM0798
Discipline Name: Chemistry
I am Dr. Adam Skelton and I work at the College of Health Science university of KwaZulu-Natal. I work on understanding the behaviour of biological and material systems on the molecular level.
A particlar interest is in using molecular simulation to direct the rationale design of functionalized nanoparticles for a range of applications such as drug delivery, water treatment and catalysis. In particular, drug delivery is the use of nanoparticles to carry antiviral or antibacterial drugs into parts of the body that are difficult for conventional drugs to reach. Drug-delivery is, therefore, of huge importance in South Africa, especially in the battle against HIV and Tubercolosis.
The research requires running a series of computar simulations, which may take hours at a time. CHPC has had a great impact since it provides me with the facilities to perform such simulations.
Since the project started, my group has published more than 15 papers in international journals and has provided deep insight into biological and material systems on the molecular level.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2019-09-20
Allocation End: 2020-03-18
Used Hours: 338676
Project Name: CFD Modelling of Concentrated Solar Power Applications
Project Shortname: MECH0873
Discipline Name: Computational Mechanics
Central tower solar power plants are the most promising concentrated solar with research into new receivers and heat transfer fluids and collectors (heliostats) being ongoing world-wide. Researchers at the University of Pretoria's Clean Energy Research group under the leadership of Prof Ken Craig are using the resources at the CHPC to speed up calculations of both heliostat analysis (involving wind loads and fluid-structure interaction) as well as those required for a new point-focus central receiver design being developed. For heliostats, knowledge has been gained in predicting the peak loads that these reflectors will experience during all orientations and wind conditions. Ongoing work is focused on further reducing the cost of these Computational Fluid Dynamics (CFD) hybrid Large Eddy Simulation (LES):Reynolds-Averaged Navier-Stokes models to make them feasible on smaller-scale computers. This project has been ongoing since 2013 with the involvement of CHPC resources since 2016. The project has already delivered two masters students (Dawie Marais and Joshua Wolmarans) with Jesse Quick and Derwalt Erasmus nearing completion. PhD student Pierre Poulain is also nearing the end of this investigation into LES modelling of the atmospheric boundary layer. For central receivers, work is ongoing to enhance heat transfer. Of specific interest here is the use of jet impingement, especially in the transient mode through either passive or active excitation. This phenomenon of heat transfer enhancement, although conceptually simple, it very hard to model accurately, and here the resources of the CHPC are invaluable, especially as LES is required to model the transient and 3D nature of swirling jet, the focus of the work of Jesse Quick.
Principal Investigator: Dr Samson Khene
Institution Name: Rhodes University
Active Member Count: 7
Allocation Start: 2019-09-23
Allocation End: 2020-03-21
Used Hours: 589180
Project Name: Synthesis, Spectroscopy and Nonlinear Optical Properties of Phthalocyanines
Project Shortname: CHEM0975
Discipline Name: Chemistry
Many of today's optical sensors are based on optical materials in which non-linear optics may play a role. Defects in the cable can have an effect of reducing the light (which carries information) in an optical fiber or cable. This phenomenon is also present in a variety of non-linear active materials or molecules. This nonlinear reduction of light phenomenon can be used as a sensing method for detection and correction of signals that are sent in cables. The aim of our research (at Rhodes University in the Chemistry department) is to make and study molecules which will help improve signal transmission using a nonlinear process. This work will not be possible if it was not supported by CHPC facilities.
Principal Investigator: Dr Chris Lennard
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2019-09-25
Allocation End: 2020-03-23
Used Hours: 2776
Project Name: Wind Atlas for South Africa
Project Shortname: ERTH0909
Discipline Name: Earth Sciences
The Wind Atlas for South Africa project (WASA) is a collaboration between the Danish Technological University and the University of Cape Town, CSIR and SAWS that is developing a wind energy resource map across the entire country. The current WASA resource map covers parts of the Northern, Eastern and Western Cape, KZN and the southern Free state. It is being expanded in Phase 3 to include the remainder of the country. UCT is responsible for the creation of the mesoscale wind resource map using a regional climate model. As the simulations are computationally very expensive these are being run on the CHPC infrastructure. The final country-wide phase 3 map will be produced during 2020 and released late 2020 or early 2021.
Principal Investigator: Dr Stewart Bernard
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 2
Allocation Start: 2019-09-25
Allocation End: 2020-03-23
Used Hours: 13637
Project Name: Marine EO Cubes
Project Shortname: ERTH1271
Discipline Name: Environmental Sciences
Processing and analyses of multi-year marine earth observation data sets in the ocean colour and sea surface temperature domains.
The project use 15 years of satellite data to assess the frequency and potential impact of harmful algal blooms on South Africa's south coast. This synthesis is of high value to the aquaculture industry, regulators and investors, and allows us to see if changing climate is impacting upon coastal ecosystem services.
Principal Investigator: Prof Ben Mans
Institution Name: Agricultural Research Council
Active Member Count: 2
Allocation Start: 2019-09-25
Allocation End: 2020-03-23
Used Hours: 2867
Project Name: Theileria parva genomics
Project Shortname: CBBI0994
Discipline Name: Bioinformatics
Our group researches on the epidemiology of theileriosis, a disease caused by a parasite called Theileria parva. The disease, affecting cattle, is endemic in some parts of KwaZulu-Natal, Limpopo and Mpumalanga. The work that Ms. Maboko is undertaking, is to determine the different strains of T. parva circulating in South Africa, determine if historical strains of T. parva are still present, determine the genetic source of differences in the behavior of the parasites of those found in South Africa and other African countries. Determining the genetic source involves obtaining the whole DNA content of the parasite, using computer softwares like Fastqc, BWA, samtools, bedtools, bcftools, Picard and vcftools found in the CHPC to look for differences in the DNA of the different parasite strains. When these DNA differences are found, they can be used to determine if they are specific for parasites found in the same country or host. This will aid in determining whether the current disease control measures are still effective or need to be amended in order to mitigate the risk imposed by different strains should they be found. The project has progressed well since we started using their resources and a manuscript is being revised on the work done.
Principal Investigator: Prof Bettine van Vuuren
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2019-09-30
Allocation End: 2020-03-28
Used Hours: 6832
Project Name: Biocomplexity on sub-Antarctic islands
Project Shortname: CBBI1153
Discipline Name: Bioinformatics
- We are a research group at the Centre of Ecological Genomics and Wildlife Conservation based at the University of Johannesburg, South Africa.
- We are conservation geneticists and are interested in studying spatial and temporal genetic patterns in multiple organisms (plants, invertebrates, microbes) on sub-Antarctic islands, with a special focus on Marion Island. We aim to investigate genetic patterns and structure in the context of environmental changes (for example, climate change). We intend on using our study species as proxies for monitoring global change and its impact on biodiversity as a whole.
- We are well aware of the concept of environmental change (such as climate change, which is more pronounced in the sub-Antarctic region). As conservation geneticists, we will investigate the impact that change has on biodiversity. Understanding genetic patterns is crucial, and our results will bring about far-reaching implications for the development of conservation management programs for Marion Island and on a global scale too.
- To do this, we will be analysing next-generation sequencing (NGS) data using various approaches. We will use the CHPC cluster to address phylogenetic and population genetic related questions. The above mentioned data is exceptionally large, and therefore we will not be able to conduct our research without the CHPC resources, since no other platforms can handle these large datasets.
- We have assembled and annotated the mitogenome of three springtail species, and have also compared the genetic structure of plant species from two sub-Antarctic islands. These have all been published in peer review journals. Three additional papers have been submitted for publication and in the near future, we hope to publish at least four additional articles.
We are happy with the progress we have made thus far and thank the CHPC for this (the CHPC has been acknowledged in the publications).
Principal Investigator: Dr Gavin Gouws
Institution Name: SAIAB
Active Member Count: 10
Allocation Start: 2019-09-30
Allocation End: 2020-03-28
Used Hours: 6356
Project Name: RADseq studies of aquatic biodiversity
Project Shortname: CBBI1274
Discipline Name: Other
The Marine Fish Research Team in the Aquatic Genomics Research Platform at the National Research Foundation employs a variety of genetic tools to understand the evolution and ecology of marine fishes (and marine invertebrates). We are interested in the relationships between species, populations and individuals, and in the movement and migration of individuals, with a view to informing conservation and management. Over the last year, we have conducted studies examining whether the genetic diversity of commercially-exploited marine fishes have changed over time, as a result of harvesting, and whether an endangered line-fish exists as and should be managed as a single population along the South African coast. For the former, SNP genotype data were generated and analysed using applications on the CHPC, while the latter used the CHPC and it's applications to model patterns of migration and dispersal. This work is to be published shortly, and similar studies are planned involving a number of species.
Principal Investigator: Prof Alan Christoffels
Institution Name: University of Western Cape
Active Member Count: 3
Allocation Start: 2019-09-30
Allocation End: 2020-05-07
Used Hours: 182894
Project Name: Bioinformatics and Public Health
Project Shortname: CBBI0819
Discipline Name: Bioinformatics
As part of our work to develop tools for Public health bioinformatics, we have been supporting the computer-assist screening of potential molecules that can serve as potential therapeutic agents against Tuberculosis. This work is compute intensive and requires the resources based at CHPC. The methods have been extended to Trypanosomiasias and specifically molecules that could be used as repellents against Tsetse Flies.
Principal Investigator: Prof Rosemary Dorrington
Institution Name: Rhodes University
Active Member Count: 9
Allocation Start: 2019-09-30
Allocation End: 2020-04-13
Used Hours: 25537
Project Name: Marine Natural Products Research
Project Shortname: CBBI0963
Discipline Name: Bioinformatics
Marine Natural Products Research Group, Department of Biochemistry and Microbiology, Rhodes University
The Marine Natural Products (MNPs) Research Platform covers the broad field of marine biodiscovery, focusing on the potential of bioactive secondary metabolites produced by marine organisms endemic to the Agulhas Bioregion as lead compounds for drug discovery. More than half of new pharmaceutical drugs on the market or in clinical trials are natural products and their derivatives and the majority of these are now coming from marine macrofauna and their associated microbiomes.
The MNPs research programme is active across the broad field of marine biodiscovery, focusing on exploring the potential of marine invertebrates and their associated microorganisms as sources of novel bioactive small molecules. Research projects include: (1) Biodiversity mapping of benthic habitats in the Agulhas bioregion, focusing on invertebrates, ascidians, soft corals and their associated microbiota; (2) Isolation and characterization of bioactive secondary metabolites of marine organisms; (3) screening marine natural product libraries for anti-viral, anti-cancer and antibacterial activity and (4) elucidating the metabolic pathways that result in the production of lead compounds to pave the way for engineering recombinant systems for their production for the pharmaceutical industry. Associated projects focus on the application of high throughput metagenomic and analytical chemistry technologies to map patterns and processes in marine ecosystems. These "omics" approaches e.g. next generation DNA and RNA sequencing and high resolution tandem mass-spectrometry generate very large and complex datasets, the analysis of which requires the high performance computing capacity provided by the CHPC.
Principal Investigator: Prof Rasheed Adeleke
Institution Name: North-West University
Active Member Count: 12
Allocation Start: 2019-10-03
Allocation End: 2020-03-31
Used Hours: 4920
Project Name: Environmental and Agricultural Microbiology
Project Shortname: CBBI1183
Discipline Name: Environmental Sciences
Our research programme is affiliated with the unit for Environmental Sciences and Management of the North-West University, Potchefstroom. We undertake microbiology-related studies focused on soil health in agroecosystems as well as on the microbial endophytes associated with ready-to-eat vegetables. We aim to generate novel solutions that address critical global issues, including environmental sustainability, green energy and food security. Currently, our research projects utilize state of the art sequencing technologies to decipher the whole genome of novel microorganisms, and to understand the composition and functional repertoire of microbial community in different environments, including soil, water and plants. Such data can only be analysed using large computer hardware/resources. Thus, we are very reliant on the CHPC's server to execute most of our bioinformatics analysis and/or pipeline. So far, we have made tremendous progress on the different research topic fronts. Our research programme currently boasts of several postgraduate students including 10 PhD students and several honours students. The number of our research topic and collaboration under the agroecosystem theme continues to expand.
Principal Investigator: Dr Holliness Nose
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 1
Allocation Start: 2019-10-04
Allocation End: 2020-04-01
Used Hours: 495265
Project Name: Inorganic Computational Chemistry
Project Shortname: CHEM1003
Discipline Name: Chemistry
Our current project involves preparation of photosensitizers for water purification. Water treatment strategies commonly adopted include chlorination, distillation, UV-radiation, boiling and reverse osmosis. While these methods have proved to be effective in water decontamination, they have not been completely efficient in treatment of microbe polluted water. This is attributed to emergence of anti-microbial resistant (AMR) microorganisms such as Methicillin-resistant Staphylococcus aureus and Amphotericin-resistant Candida albican. AMR pathogens find their way into drinking water, causing waterborne diseases. Photodynamic antimicrobial therapy (PACT) provides an alternative and viable method of water disinfections, especially in addressing the anti-microbial resistant bacteria. PACT makes use of a photosensitizer, which when localized in microorganisms can be activated by irradiating it with light of appropriate wavelength to generate a reactive oxygen species (ROS). This ROS is able to destroy or affect biological structures such as cell wall material, nucleic acids, peptides and lipids therefore leading to cytotoxicity. Therefore, this method allows the photosensitizer to bind to the bacterial or fungal cell wall, inhibiting cell growth, with no possibility of recovery or development of resistance against it. My group intends to design and develop the photosensitizers computationally, followed by synthesis of the metal complexes and finally carry-out biological assays to examine their cytotoxicity. This project therefore relies on CHPC heavily as we need to design the photosensitizers theoretically before we go to the laboratory to synthesize them and test their biological activities. This project began on June 1st 2019 and and is currently ongoing. But without the CHPC facilities, we are unable to do this type of research. The project is proceeding on well.
Principal Investigator: Dr ADEDAPO ADEYINKA
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2019-10-05
Allocation End: 2020-04-02
Used Hours: 119282
Project Name: Computational Design of Molecules
Project Shortname: CHEM1221
Discipline Name: Chemistry
The Computational Design of Molecules research group is based at the University of Johannesburg. We aim to design new and improved molecules and materials for applications in Catalysis and renewable
energy. Since the availability of energy is one of the main challenges of the
African continent, being able to achieve our aims as a group will provide clean energy solutions for the continent. We use computational chemistry software to
explore the properties of molecules which is responsible for their activity and then use the knowledge gained to design more efficient and improved
materials.
Principal Investigator: Dr Bradley Frank
Institution Name: SKA
Active Member Count: 4
Allocation Start: 2019-10-07
Allocation End: 2020-04-04
Used Hours: 6061
Project Name: Calibration and Imaging of MeerKAT Data
Project Shortname: ASTR1276
Discipline Name: Astrophysics
We used the Lengau system to do high-quality spectral line imaging of MeerKAT observations. The imaging of interferometric observations is typically computationally expensive, and often requires fine tuning to ensure the scientific productivity of the imaging. The Lengau system has allowed us to use a flexible, yet efficient workflow to quickly and robustly conduct many iterations of interferometric imaging.
Principal Investigator: Dr Michelle Gordon
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2019-10-07
Allocation End: 2020-04-30
Used Hours: 263508
Project Name: Structural Implications of Mutations in HIV-1
Project Shortname: CBBI0928
Discipline Name: Bioinformatics
Our research group is based at the Nelson R Mandela Medical School at the University of KwaZulu-Natal and focusses on the effects of mutations that cause antiretroviral drug resistance on the structure of HIV-1 proteins. The drugs that patients take as part of their treatment against HIV-1 can stop working because the virus is always changing (mutating). We are looking at how these mutations also change the structure of the virus. To do this, we make a structural model of the affected viral protein using specialized software that uses a lot of computational power. By using the CHPC, I am able to access their high powered server, as well as the software for performing the molecular modelling. With the information gained from this analysis, we can design new drugs that can work against these mutated viruses and improve patient management.
To date, one PhD student has graduated but will continue with the work post PhD. The second has submitted his thesis. There are 3 additional PhD students will be/using the service.
Principal Investigator: Dr Fabio Cinti
Institution Name: NITHEP
Active Member Count: 4
Allocation Start: 2019-10-07
Allocation End: 2020-04-22
Used Hours: 10471
Project Name: Quantum Monte Carlo for ultra-cold atoms
Project Shortname: PHYS0892
Discipline Name: Physics
Pattern formation, the ability of the system to spontaneously form spatially ordered structures from an initially disordered configuration, is an example of self-organization, namely the formation of spatial, temporal, spatiotemporal structures or functions in sys- tems composed of few or many components. Pattern formation is ubiquitous in nature. It can be found in several branches of physics including condensed matter, soft matter, and astrophysics as well as in chemistry, biology, mathematics, and computer graphics to mention a few. These studies are particularly important as they represent new opportunities to simulate systems which cannot be easily manipulated. While noteworthy progress has been made in many directions, the research in the subfields of hard matter and soft condensed matter physics has been only weakly connected. Furthermore, while the equilibrium properties have received a lot of attention (using, e.g., tools of statistical physics), the equilibration process appeared to be at least as rich in surprises.
Principal Investigator: Prof Mmantsae Diale
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2019-10-08
Allocation End: 2020-05-27
Used Hours: 218909
Project Name: Electronic Structure of hematite and surface doped hematite
Project Shortname: MATS0944
Discipline Name: Physics
Institution: University of Pretoria
Research group: Clean and Green energy
Project title: Density functional theory study of doped hematite surfaces for water splitting
Photoelectrochemical water splitting using sunlight and appropriate semiconductors is a promising route to solve both the production of clean hydrogen fuel and storage for solar energy. Hematite has been enlisted has a good semiconductor material for water splitting due to its various advantages such a suitable band gap and its high stability in broad pH range. However, it also has few draw backs among them poor conductivity and quick electron-hole recombinations. In this project we intend to improve on the challenges of hematite so as to make it an efficient material for PEC water splitting. Our project is a theoretical one based on DFT calculations and therefore highly depends on the cluster resources from CHPC. We greatly appreciate the support from CHPC.
Principal Investigator: Mr Randall Paton
Institution Name: University of the Witwatersrand
Active Member Count: 10
Allocation Start: 2019-10-09
Allocation End: 2020-04-06
Used Hours: 1573961
Project Name: Compressible Gas Dynamics
Project Shortname: MECH0847
Discipline Name: Other
The Flow Research Unit group utilising the CHPC is currently exploring the effects of straight-line and general acceleration on various aerodynamic properties through high-performance computing, as well as the effect of supersonic engine inlet geometry on performance. This research has applications in current technologies, such as missiles and unmanned aerial platforms, as well as in emerging future technologies, such as ramjet optimisation for the return of atmospheric, supersonic, commercial flight. Since the geometries involved are sometimes complex, and the loads experienced as a result of arbitrary acceleration are computationally expensive to compute, it is simply not practically feasible to model most of these systems without high-performance computing. The use of the CHPC is therefore essential to developing young South Africans to be capable to participate and excel in the development of these future technologies.
The current research group consists of several Masters and one PhD student from a mixture of ethnic backgrounds and sexes. Each research project is progressing well towards on-time completion, and some are already under examination, which would be impossible without the incredible time-saving that the use of the CHPC affords the students. The results of our work are published in prominent international journals. One of our students, Mr Sean Morrow, also won a prize for his work at the 32nd International Symposium on Shock Waves in Singapore in July 2019.
Principal Investigator: Prof Rebecca Garland
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2019-10-09
Allocation End: 2020-04-06
Used Hours: 31259
Project Name: Simulating atmospheric composition
Project Shortname: ERTH0846
Discipline Name: Earth Sciences
Air pollution can have large negative impacts on human health, agriculture, ecosystems, visibility and climate. In South Africa, although ambient air quality is regulated, many areas are out of compliance with the National Ambient Air Quality Standards. In order to protect human health and mitigate impacts, it is critical to improve air quality. The Constitution provides that everyone has a right to have an environment that is not harmful to their health. The Atmospheric Composition Focus Area (ACFA) in the CSIR Climate and Air Quality Modelling research group aims to provide the evidence base to quantify the impacts of air quality and to improve air quality.
The group uses the CHPC to run an air quality model to simulate urban and regional air quality at high resolution. This chemical transport model simulates the physics and chemistry of the atmosphere. The processes represented within the model are complex, and thus computationally intensive, which makes use of the CHPC facility a necessity. The CSIR ACFA is the only group in South Africa routinely running a chemical transport model to simulate air quality for management purposes.
Using the CHPC resources, the team has been able to simulate the impact of policy interventions on air quality in cities. Additionally, the team has simulated the health risk from air pollution regionally in South Africa. In the past, this has been done using monitoring station data only, which then limits the analysis to only those living directly around the station. The team has also simulated the impact of climate change on air pollution. These simulations use the climate projections from the CSIR's CCAM-CABLE, which is also run at CHPC, to provide meteorology input into the air quality model.
These outputs directly provide the evidence base needed for decision makers to draft and implement policies and interventions to effectively improve air quality as well as understand its impacts, now and into the future.
Principal Investigator: Prof Penny Govender
Institution Name: University of Johannesburg
Active Member Count: 16
Allocation Start: 2019-10-10
Allocation End: 2020-04-07
Used Hours: 822489
Project Name: Design of MOFs-based sorbent materials for capturing carbon dioxide
Project Shortname: CHEM0797
Discipline Name: Material Science
The computational chemistry research group at the university of Johannesburg is led by Prof Penny Govender. The research group currently focuses on material science, environmental sciences, reaction mechanisms and medicinal chemistry. The work is being performed both for predictive purposes (where experiments are modelled before being actually carried out in the lab) and for support purposes where computational results supports experimental results. All the simulations done by the group are carried out on the Lengau cluster using software such as Materials Studio, Gaussian, Schrodinger, all provided by the CHPC South Africa.
Principal Investigator: Prof Cornie van Sittert
Institution Name: North-West University
Active Member Count: 20
Allocation Start: 2019-10-10
Allocation End: 2020-04-07
Used Hours: 1917606
Project Name: Computational Chemistry within LAMM at NWU (Potchefstroom)
Project Shortname: CHEM0778
Discipline Name: Chemistry
Since 1880 the main source of energy for South Africa was coal and at present coal provides 77% of South Africa's primary energy needs. However, the electricity comes at a very high cost, namely air pollution and the influence of the air pollution to human health. In 2004 the South African government reformed the legislation with regard to air pollution. In an effort to contribute to the management of air quality new energy sources must be investigated. These new energy sources must be affordable, clean and renewable. Some of these alternative energy sources are fuel cells and batteries. Electricity from fuel cells and batteries are obtainable through the use of electrochemistry, where free energy of spontaneous reactions is transformed into electricity. A potential generator of hydrogen that is needed for fuel cells is the hybrid sulphur (HyS) cycle. The HyS cycle is a two-step water-splitting process. In the HyS cycle, the anode material used is platinum. However, because platinum is a rare and expensive metal, it is not an economically viable option for long term and large scale production of hydrogen. Hence, various attempts to reduce or eliminate the platinum content, while not compromising the process performance has been made. In order to understand the electrochemistry on the anode and make informed decisions on the type and amount of metal to be used in various platinum alloys, investigations on a fundamental level is needed. These type of investigations could be classified as computational chemistry. The resources needed for these type of investigations, namely various types of hardware and software is of cardinal importance. Although resources are available at NWU, it is not nearly enough to fully support the research covered in the Laboratory of Applied Molecular Modelling (LAMM). So if we as researchers within the LAMM did not have access to the CHPC resources the progress of our research will be much slower.
Principal Investigator: Dr Ryno Laubscher
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2019-10-10
Allocation End: 2020-04-07
Used Hours: 74931
Project Name: University of Cape Town Applied Thermal-Fluid Research Unit
Project Shortname: MECH1279
Discipline Name: Computational Mechanics
The Applied Thermofluid Process Modelling (ATProM) group applies the fundamental principles of fluid mechanics, thermodynamics and heat and mass transfer to model industrial processes. To accurately model such processes the governing equations of mass, energy and momentum conservation need to be solved for steady-state and transient operating modes in a computationally inexpensive manner using techniques such as 1D network modelling, computational fluid dynamics and machine learning.
The current research direction of the group pertains to the development of digital twins of energy conversion processes. This entails the generation of large quantities of data using complex simulation models such as three-dimensional models of combustion processes in a boiler or the dynamic response of a gas turbine during fast response periods. The data is then used to build data-driven predictive models, using machine- and deep-learning approaches, which could be deployed to run in near real time along the actual process. These predictive models is then used to perform what-if studies, monitor the performance of the system, optimize system settings and detect possible failures.
Principal Investigator: Prof Mohsen Sharifpur
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2019-10-10
Allocation End: 2020-04-07
Used Hours: 232843
Project Name: Computational Heat transfer
Project Shortname: MECH1073
Discipline Name: Computational Mechanics
Our research group is from the Department of Mechanical and Aeronautical Engineering at the University of Pretoria. The main research field of our research group is related to improve heat transfer systems and investigation on a new generation of heat transfer fluids. Because nowadays energy plays a key role in human being's life, and daily the energy demand is increasing. But to investigating energy using high-performance computing is mandatory, because of its complex equations. CHPC resources are a lot valuable since we couldn't do these runs on our research group machines. These are still in progress: Model development for nano-scale heat transfer, Study and development of a new method for particles in pool boiling with different base fluid and various inclination angles, jet cooling and so on.
Principal Investigator: Dr Eric Maluta
Institution Name: University of Venda
Active Member Count: 12
Allocation Start: 2019-10-11
Allocation End: 2020-04-22
Used Hours: 124960
Project Name: Energy Material Modeling in the Application of different Photovoltaic Technologies
Project Shortname: MATS0827
Discipline Name: Physics
The Department of Physics at the University of Venda is working on the understanding of the properties of different materials for application in renewable energy technologies through the density functional theory simulations as performed under the CHPC cluster. The main aim is to reduce the cost of the material used in renewable energy technologies for the future use and mitigate climate change through energy supply. We are also building capacity of the rural students on the postgraduate studies and skill development. The CHPC is a gateway for the department of Physics of the University of Venda as an institution situated in the rural area to produce researchers and to publish research work. There is a growing number of students research work from honours to the PhD level. Several student are getting their masters and PhD degree through these initiatives.
Principal Investigator: Dr John Mack
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2019-10-11
Allocation End: 2020-04-08
Used Hours: 8328
Project Name: Rational design of phthalocyanine, porphyrin and BODIPY dyes
Project Shortname: CHEM0796
Discipline Name: Chemistry
The Institute for Nanotechnology Innovation (INI) at Rhodes University under director Prof. Tebello Nyokong carries out research related to the use of molecular dyes in biomedical applications, such as cancer treatment through photodynamic therapy, the use of antimicrobial photodynamic chemotherapy for treating hospital superbugs and as sensors for ions that are harmful to human health. Other applications of interest include wastewater treatment and the development of optical limiters to protect human vision,such as in aviation safety in protecting pilots from the irresponsible use of laser pointers during runway approaches. It is important to understand trends in the electronic and optical properties that make the molecular dyes suitable for these particular applications. The resources of the Centre for High Performance Computing help to facilitate this by making it possible to carry out molecular modelling calculations that can be used to predict how changes to the structures of the molecular dyes will modify their properties. The flexibility that CHPC provides where memory allocations are concerned is often vital. The INI currently has three staff members, nineteen PhD, eight MSc and six Honours students, and three postdoctoral fellows, and usually publishes over forty peer-reviewed publications per year. This rose to a high of sixty-five in 2017 with ten involving the use of CHPC resources.
Principal Investigator: Dr Kiprono Kiptiemoi Korir
Institution Name: Moi University, Eldoret, Kenya
Active Member Count: 6
Allocation Start: 2019-10-14
Allocation End: 2020-05-21
Used Hours: 551030
Project Name: Thermal characterization of MoS2 nanostructures: an ab initio study
Project Shortname: MATS0868
Discipline Name: Material Science
This research group draws its members from Moi University, Computational Material Science Group (CMSG), in addition, we have collaborators: Slimane Haffad of University of Beijaia- Algeria, and Michele Re Fiorentin of Istituto Italiano di Tecnologia (IIT) Italy. Our research activities focus mainly on materials for energy and the ultra-hard industry.
Over the last century, intensive use of carbon-based energy sources has led to increase in atmospheric carbon dioxide gas, which has been attributed to anthropogenic climate change, whose adverse effects on the planet are being felt and projected to worsen, unless drastic CO2 cuts are implemented as proposed in Kyoto protocol. Therefore, the development of alternative energy sources with zero carbon footprint is deemed critical for the survival of the planet.
In this work, graphene, ZnO nanowires, and 2D MoS2 were studied via approaches grounded on principles of quantum and classical mechanics, which have been shown to accurately predict material properties. These predictive approaches require huge computational effort as it entails solving mathematical formulas, such as Schrödinger and Newtonian equations. For this reason, the availability of the state of the art High-Performance Computing facility, such as CHPC is a critical component for the implementation of this work. Solving Schrödinger and Newtonian equations can yield various properties of interest such as structural, mechanical, electronic and optical properties that are essential for the comprehensive characterization of these systems.
For example, in our recent work that is under review, we have shown that the presence of anionic vacancies tends to deplete hardness in both NbC and NbN, this finding may be of great significance in the development of low-cost ultra-hard devices. Other studies on utilization of ZnO nanowires for water splitting have shown that Ti and V dopants of 4% and 2%, respectively, yielded a staggered bandstructure configuration, which is ideal for photoelectrocatalyltic (PEC) water splitting and related applications.
In addition, our results revealed that CO2 is chemisorbed on the CaO surface with a negligible effect on the electronic properties of the absorbent, while CO2 interaction with single-walled carbon nanotube ( SWCNT ) can be categorized as physisorption interaction a process that can be easily reversed using thermal treating at 150 °C. Thus CaO is found to be ideal for long term storage of CO2 while SWCNT reported superior performance in CO2 sensing and capture.
Therefore, these findings may assist in identifying the appropriate dopants and dosages and may contribute to tuning the properties of ZnO nanowires for optimal PEC water splitting activity.
Principal Investigator: Dr Evans Benecha
Institution Name: University of South Africa
Active Member Count: 7
Allocation Start: 2019-10-15
Allocation End: 2020-04-15
Used Hours: 926961
Project Name: Defect engineering in novel 2-D materials
Project Shortname: MATS1025
Discipline Name: Physics
The research programme titled "Defect engineering in novel 2-D materials" focuses on investigation of the properties of defects in single layered materials - usually one atom thick. The group spearheading this research is headed Dr Evans Benecha and it consists of senior researchers, postdocs and graduate students from the University of South Africa. Single atom layered materials possess interesting properties as opposed to many atom thick materials. For example, graphene – which a single layer of carbon atoms –enables electrons to flow much faster than silicon, is the world's strongest material, harder than diamond, yet lightweight and flexible. This unique combination of superior properties makes it a credible material for new technologies in a wide range of fields. Some of the envisaged applications of graphene as well as other single atom layered materials include making of medical implants, solar cells, stronger sports equipment, and batteries; just to name a few. However, the properties of these materials are not well understood for these applications to be realized. Dr Benecha and his group's approach towards understanding these materials involves use of large computational resources, and access to the CHPC computing facility has significantly reduced the time needed to generate and analyze data. The results from this project will not only assist in the current understanding of the role of defects in these materials, but will also help to reveal potential new functionalities.
Principal Investigator: Mr Theo Fischer
Institution Name: eScience
Active Member Count: 4
Allocation Start: 2019-10-15
Allocation End: 2020-04-12
Used Hours: 7282
Project Name: Acid Deposition
Project Shortname: ERTH0851
Discipline Name: Earth Sciences
The 2010 Mpumalanga Highveld region power station sulphur dioxide emissions amount to 2.2 million tons. After full oxygenation and the addition of cations, this represents an increased total dissolved salt deposition load of 4.6 million tons. This is 23 times higher than the natural annual average TDS load in the runoff from the entire 38 600 km2 Vaal Dam catchment. Although only a fraction of this salt load falls on the Vaal Dam catchment, outfall of only 4% of the anthropogenically emitted sulphur could double the long-term equilibrium salt export of the Vaal Dam catchment.
The importance of this investigation arises from the economic and environmental impact of the deposition of anthropogenically emitted salts on water users in the strategic heartland of South Africa on the one hand, and the expensive decisions arising from the location and technology of new power stations and industrial plant on the other. Rational decision making requires evaluation of the high costs associated with both atmospheric deposition impacts and the cost of reducing them.
Principal Investigator: Dr Jeremy Woodward
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2019-10-16
Allocation End: 2020-04-13
Used Hours: 9846
Project Name: Rational Biocatalyst Design
Project Shortname: CHEM1281
Discipline Name: Other
Dr Jeremy Woodward, Dr Arthur Sarron and Dr Andani Mulelu from the University of Cape Town have achieved excellent progress in determining the first structure of a nano-scale protein compartment from Mycobacterium tuberculosis. The team recently determined the first high resolution Cryo-EM structure in Africa through their cutting edge research into nitrilase enzymes. These projects were made possible by collaboration with Diamond Light Source Ltd in the UK through the Global Challenges Research Fund's Synchrotron Techniques for African Research and Technology Programme (GCRF START).
Bacterial nanocompartments are hollow icosahedral shells of ~25 nm diameter. They self assemble, from sixty identical subunits, and enclose enzymes involved in allowing bacteria to survive environments of high oxidative stress. In mycobacteria, they are exported from the cell and they appear to be required for establishing a tuberculosis infection. This makes them attractive targets for anti-tuberculosis treatment.
We have artificially produced nanocompartment protein, which successfully self-assembles to form icosahedral nanocompartments, these we have bound to a 2 nm thick layer of carbon and rapidly cooled to form a thin layer of vitreous water. We sent these samples to the Electron Bio-Imaging Centre (eBIC) at Diamond Light Source for imaging and got back ~4 Tb of data consisting of thousands of 60-frame movies. These represent images of the particles as they move around under the electron beam from multiple different orientations. The sheer size of the dataset and computational complexity of generating a three-dimensional reconstruction at close-to-atomic resolution means that high-performance computing is an absolute necessity. We anticipate that the reconstruction itself will contain sufficient information to identify the location of at least 80% of the 122 000 non-hydrogen atoms with a precision of less than 0.1 nm.
Principal Investigator: Prof Stefan Ferreira
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2019-10-17
Allocation End: 2020-04-14
Used Hours: 192619
Project Name: Astrospheres
Project Shortname: ASTRO1277
Discipline Name: Astrophysics
The aim of this project is to successfully simulate astrospheres via a full three-dimensional magneto-hydrodynamic numerical model in order to compare results with telescope observations to gain a deeper understanding of these. From telescope observations there is very limited certainty on different evolution parameters like mass-loss rate, ambient density, magnetic fields, radiative cooling etc. The combination of such a code with observations will enhance our understanding of these cavities around stars. Also of importance is to calculate the cosmic ray distribution inside these cavities to account for their possible contribution to possible habitable planets close to the stars. For this purpose researchers from the North-West University and Center for High Performance Computing (CHPC) in South Africa has teamed up with two German Universities, namely the Ruhr-Universitat Bochum and the Christian Albrechts University in Kiel to bring together expertise. Central to this project is the successful implementation and execution of the Cronos MHD model at the CHPC. Currently we have successfully tested and obtained first results which will be used in a forthcoming publication.
Principal Investigator: Prof Ed Sturrock
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2019-10-17
Allocation End: 2020-04-14
Used Hours: 60699
Project Name: Structural elucidation of Angiotensin Converting Enzyme using cryo-electron microscopy
Project Shortname: HEAL0931
Discipline Name: Health Sciences
Enzymes play important roles in a variety of biological processes in the human body. Angiotensin converting enzyme (ACE), for example, regulates blood pressure and is also involved in scar tissue development (fibrosis). Conditions such as diabetes and tuberculosis can lead to excessive scar tissue formation, which ultimately stops proper organ function. Currently, there is no specific treatment for fibrosis. Hypertension, on the other hand, is a major risk factor for cardiovascular disease and stroke which accounted for 15.2 million global deaths in 2016. The Zinc Metalloprotease lab, led by Prof Edward Sturrock, is based in the Department of Integrative Biomedical Sciences at the University of Cape Town and has a long-standing interest in ACE.
Although ACE inhibitors reduce fibrosis and are widely used for treating hypertension, certain patients experience the life-threatening side-effect of severe swelling below the skin surface of the throat and tongue. In order to design safer ACE inhibitors, a detailed understanding of the structure of ACE is required. A postdoctoral research fellow in Prof Sturrock's lab, Dr Lizelle Lubbe, is using a technique called cryo-electron microscopy (cryo-EM) to better understand how ACE functions. This involves using an electron microscope to visualize the protein immobilized in various orientations in a thin layer of ice. Dr Lubbe has collected a large cryo-EM dataset at the Diamond Light Source synchrotron (UK) and is using the CHPC's resources to reconstruct the 2-dimensional views of the protein into a 3-dimensional model. Interestingly, she has observed monomeric and dimeric forms of the protein. Solving the 3D structure to high resolution will thus not only allow the design of improved drugs for fibrosis and hypertension but also provide a better understanding of the overall shape of the molecule. This may enable researchers to design diagnostic tests using antibodies for diseases where ACE is dysregulated.
Principal Investigator: Dr Thishana Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2019-10-18
Allocation End: 2020-04-15
Used Hours: 97127
Project Name: Combined kinetics,quantum-chemical investigation of reaction mechanisms involving catalysts
Project Shortname: CHEM0821
Discipline Name: Chemistry
The TS Computational Chemistry Research Group (University of Kwazulu-Natal, School of Chemistry and Physics) carries out quantum chemical modelling of homogenously catalysed organic reactions in the inter-domain field of Physical-Organic Chemistry. Computational Chemistry can be classified as 'Green Chemistry' as it is sustainable and does not generate chemical waste. The focus of this research group is primarily on catalytic asymmetric synthesis that have many applications in the pharmaceutical and fine chemical industry. The optimisation of a catalyst offers a good understanding of the factors that are responsible for the rate and selectivity of a reaction. Theoretical calculations, together with experimental kinetic measurements, often can pin down the mechanism. Using this methodology, it is possible to understand, and more importantly, design effective catalysts for a number of asymmetric, catalytic processes. The CHPC provides the facilities: hardware, in the form of the Lengau cluster and software programs such as Gaussian16, amongst many others. Thus far the current project has yielded two publications since 2019.
Principal Investigator: Prof Juliet Hermes
Institution Name: SAEON
Active Member Count: 4
Allocation Start: 2019-10-21
Allocation End: 2020-04-18
Used Hours: 45437
Project Name: SAEON Coastal and Regional Ocean Modelling Programme
Project Shortname: ERTH1103
Discipline Name: Earth Sciences
The Coastal and Regional Ocean Modelling Programme is a modelling initiative of the South African Environmental Observation Network (SAEON) Egagasini Node based in Cape Town. The aim of this programme is to use ocean models to understand regional and coastal shelf dynamics. The ORCA025 configuration, extending from the Angola gyre, Mozambique channel and including the Southern Ocean is used in this programme. A high resolution grid is used which zooms the coastal region including the St Helena Bay region which is an important nursery ground for fish and also the main generation zone of low oxygen water. The low oxygen generated in the St Helena Bay region result in the formation of greenhouse gases including nitrous oxide which has a global warming potential about 265¬-310 times higher than that of carbon dioxide. With climate change there is also a need to understand implications for primary production and expansion of low oxygen regions in the ocean. The coupled ocean model in this programme is used to understand these processes and the results obtained can be used to fill knowledge gaps and advance coastal modelling. Currently the model is being validated and the next step is to increase resolution to capture fine scale processes.
Principal Investigator: Dr Gerhard Venter
Institution Name: University of Cape Town
Active Member Count: 12
Allocation Start: 2019-10-21
Allocation End: 2020-04-18
Used Hours: 211549
Project Name: Simulation of Ionic Liquids
Project Shortname: CHEM0791
Discipline Name: Chemistry
Dr Venter's research group is part of the Scientific Computing Research Unit at the University of Cape Town and uses computer simulation and machine learning methods to study the properties of a special class of solvents, called "ionic liquids". These simulations provide insight into the fundamental thermodynamic properties and intermolecular interactions in these liquids. A better understanding of ionic liquids can lead to the rational design of new, environmentally friendly solvents systems that have applications in chemical engineering and material science.
High performance computing is required for all research conducted in this group and without the resources and infrastructure provided by the Centre for High Performance Computing (CHPC), the research will not be possible.
Principal Investigator: Dr Zipporah Muthui
Institution Name: Chuka University, Chuka, Kenya
Active Member Count: 4
Allocation Start: 2019-10-21
Allocation End: 2020-04-18
Used Hours: 177013
Project Name: Electronic Structure and Magnetic Properties of Heusler Compounds
Project Shortname: MATS1112
Discipline Name: Physics
Electronic Structure and Magnetic Properties of Heusler Compounds research group is composed of the PI, Dr Zipporah Muthui and students Ms.Jane Mbae, Ms. Eunice Gitonga from Chuka University as well as Mr. Hezbon Opiti, from the university of Nairobi. We are mainly studying transition metal oxides for photocatalytic applications and Heusler compounds for spintronic applications. Heusler compounds have the potential to lead to the fabrication of electronic devices that consume less power, are fast and also have non volatile memory, which means that data is saved and if there is power loss the work is not lost. The transition metal oxides will find application in water treatment applications.
The CHPC is being utilized at the moment, mainly by the post-graduate members of the group. Electronic structure calculations for materials, targeting photocatalytic and spintronic applications have been under study. More research is underway, targeting these main areas of application. Without the CHPC, these computations would not be possible from this group, which we are positive will grow and do lots of research.
Principal Investigator: Dr Shankara Radhakrishnan
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2019-10-22
Allocation End: 2020-04-19
Used Hours: 156099
Project Name: Solar energy and CO2 Reduction
Project Shortname: CHEM0869
Discipline Name: Chemistry
We at the Chemistry Department from the University of Pretoria are the renewable energy group and work
on Conversion of CO2 to useful chemicals such which in future is expected to replace gasoline and other coal burnt fuel production processes. Thus, the aim is to mitigate the CO2 expelled into the atmosphere along with use of renewable energy to meet electrical demand which at this stage comes from fossil fuels in South Africa. This will also serve in providing solution to the global climate change which is one of the most
important national imperative.
Principal Investigator: Prof Enrico B Lombardi
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2019-10-22
Allocation End: 2020-04-29
Used Hours: 905912
Project Name: Defects in wide-bandgap semiconductors and 2D materials
Project Shortname: MATS1160
Discipline Name: Material Science
The research group of Prof Lombardi, at the University of South Africa focuses on defects in wide band gap semiconductors and 2D materials, exploring defects in 2D materials which influence the host material's functionality and efficiency. Point defects are inevitable in solid crystals, and are noticeable in chemically grown 2D materials due to the imperfection of the growth process. Our group have been able to add to the existing knowledge of defect in 2D materials by predicting intrinsic point defects as well as other likely defects that might be observed under frequently occurring conditions. The results of our research provide insight to the physics of defects that are grown via chemical vapour deposition and electron irradiation. These defects are responsible for large variation of electric and optical properties, and also act as good efficient traps for electrons holes and excitons which strongly influence transport and optical properties of semiconductors. This research is performed using the state-of-the-art Density Function Theory. The CHPC has provided substantial computational resources, enabling this project to be carried out effectively.
Principal Investigator: Prof Kevin Naidoo
Institution Name: University of Cape Town
Active Member Count: 7
Allocation Start: 2019-10-22
Allocation End: 2020-04-19
Used Hours: 1248522
Project Name: Reaction Dynamics of Complex Systems
Project Shortname: CHEM0840
Discipline Name: Chemistry
All three laboratories make direct or indirect of CHPC resources to develop diagnostics for Cancer or Therapeutics in Biomedicine. Of national interest is the collaboration between the SCRU laboratories and the CHPC to make advance computation more easily accessible to South African researchers in the fields of Biology and Chemistry through the CHPC's hosting of the Galaxy Biomolecular Reaction Interaction Dynamics Global Environment (BRIDGE). Prof. Naidoo's research groups are mostly interested in the development and applications of methods useful to Life Scientists. He is a domain specialist in code development for Free Energy methods, Molecular Dynamics and unsupervised Machine Learning. Flagship codes developed by Prof Naidoo and his students are the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF), Free Energy Force Induced (FEFI) coarse grained molecular dynamics and the Denoising Autoencoder Self Organising Map (DASOM). The SCRU Cancer Translational Science Laboratory links the computation and informatics technologies with laboratory experiments to provide models for cancer research scientists aiming to achieve Translational Research goals cancer care.
Principal Investigator: Dr Madison Lasich
Institution Name: Mangosuthu University of Technology
Active Member Count: 12
Allocation Start: 2019-10-22
Allocation End: 2020-04-19
Used Hours: 81591
Project Name: Chem Thermo
Project Shortname: CHEM1028
Discipline Name: Chemical Engineering
The Thermodynamics, Materials, and Separations Research Group at Mangosuthu University of Technology (MUT) focuses on industrial separations and the development of novel materials to aid in industrial separation processes. Recently, the group has been studying the use of clays and related minerals to improve renewable and alternative fuel gases, with a view to developing simple systems to unlock more and cleaner energy for rural and peri-urban communities. This work uses computationally intensive molecular calculations requiring the facilities of the CHPC to predict the thermophysical behaviour of materials in novel applications. Recently, two papers were accepted to the SA Chemical Engineering Congress, including work undertaken by a BTech student at MUT.
Principal Investigator: Prof Fernando Albericio
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2019-10-22
Allocation End: 2020-04-19
Used Hours: 5950
Project Name: Peptide chemistry and Organic chemistry
Project Shortname: CHEM1102
Discipline Name: Chemistry
We are Peptide Science Group located at UKZN Westville campus, Durban. The design of the project was proposed to explain the reaction mechanisms happening in the laboratory. The project was brought up with an intend to learn computational chemistry. The project involves synthesis of several organic molecules towards application in oligonucleotide chemistry. With the help of computational tools we aim to predict the reaction mechanism. Since CHPC provides the server which is an added advantage to speed up the calculations in achieving the preliminary results. The project so far had been very appealing in its preliminary stage. We expect to be going ahead with these results for further analysis towards prediction of reaction mechanism involving calculation of activation energy.
Principal Investigator: Prof Moritz Braun
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2019-10-24
Allocation End: 2020-04-21
Used Hours: 1993655
Project Name: Density Functional studies using a variety of different methods and considering materials of current interest
Project Shortname: MATS0924
Discipline Name: Physics
My group is the high performance and computing research group based in University of South Africa. The research focus of our group are on theoretical Physics, computational Physics, inverse Scattering, few-Body Physics and materials science.
The group has actively leveraged on the research facility provided by the CHPC to carry out materials science research and provide validation to some theoretical physics questions. The kind of research carried out within the group would lead to materials design and discovery as well as answer pedagogical scientific queries.
Solving the many-body electron problem is an non-trivial problem for interacting systems which provides appropriate description of most materials. This can be done with the help of computing in a self-consistent manner. Thus, materials science problem such as this, leverages on the CHPC resources to provide meaningful contribution.
Progress has been achieved in the 2D materials for hydrogen storage, bulk materials for luminescence materials (where strong collaboration have been established with experimental group in UNISA) and pedagogical problems we are engaged in.
Principal Investigator: Prof Zenixole Tshentu
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 7
Allocation Start: 2019-10-24
Allocation End: 2020-04-21
Used Hours: 567560
Project Name: Metal-ligand, anion-cation interactions and protein-ligand studies
Project Shortname: CHEM0864
Discipline Name: Chemistry
Our research programme on metal-ligand and cation-anion interaction towards design of selective reagents fro metal ions has been supported by CHPC for the computational chemistry aspect using the Gaussian software and a Shrodinger suite of programs. We are mot grateful for this facility as it allows for smart design of reagents. Studies of protein-ligand interactions have also similarly benefited from the CHPC resources in the design of selective ligands for active site binding.
Principal Investigator: Prof Jacomine Grobler
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2019-10-25
Allocation End: 2020-04-22
Used Hours: 4199
Project Name: Computational intelligence for supply chain optimization
Project Shortname: CSCI1170
Discipline Name: Applied and Computational Mathematics
Due to the rise of e-commerce, consumers can purchase an enormous variety of products and have it delivered to their doorstep anywhere in the world. As a result, last mile deliveries are an important competence for many logistics companies. Unmanned aerial vehicles or delivery drones, is a highly promising technology that can revolutionize the way companies do their last mile deliveries. Drones are a cleaner means of transport, do not require or use road infrastructure, and have positive implications on delivery time and cost. The efficient use of delivery drones, however, require advanced optimization algorithms to allocated deliveries to drones, and schedule these deliveries.
Researchers at the Department of Industrial Engineering at Stellenbosch University are currently working in conjunction with the University of California at Berkeley to develop a drone delivery scheduling algorithm. The development of this algorithm requires significant computational resources and here the collaboration with the Centre for High Performance Computing is critical. Many hours of computer time is required to test different algorithm variations, tune algorithm control parameters and ensure that the algorithm is robust over different data sets and changing input parameters.
Initial results indicate that up to a 30% improvement can be obtained by a delivery drone scheduling system when compared to a traditional road freight delivery service.
Principal Investigator: Dr Emmanuel Sakala
Institution Name: Council for Geoscience
Active Member Count: 17
Allocation Start: 2019-10-28
Allocation End: 2020-04-25
Used Hours: 25413
Project Name: Application of high performance computing at the Council for Geoscience
Project Shortname: ERTH1227
Discipline Name: Earth Sciences
According to the National Government of South Africa (2019), the primary mandate of the Council for Geoscience (CGS) is to develop and publish world-class geoscience knowledge products and to render geoscience-related services to the South African public and industry. In order for the CGS to fulfill this mandate and to advance the geoscience field within South Africa and beyond, this application of high performance computing programme was formulated to expand the current available computing resources at the CGS. The programme involves running high computing packages for geophysical modelling, seismological data processing, geological modelling and any other packages which currently are not optimum for a desktop computing. Research and development of the various geoscience fields (geophysics, geology, geochemistry, hydrogeology) are covered in this programme
Principal Investigator: Prof Giuseppe Pellicane
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2019-10-29
Allocation End: 2020-05-21
Used Hours: 321311
Project Name: Computational Study of Structure-Property Relationships in polymer blends relevant to OPV devices
Project Shortname: MATS0887
Discipline Name: Physics
Organic molecules.such as polymers, are an imprortant component in the field of renewable, sustainable and non-polluting sources of energies. In fact, solar energy is the epithome of green energy sources and polymers allow for a cheap device preparation cost and exhibit relative ease of processability, which paves the way to solar energy as a viable and economic energy source. By the scientific point of view, organic conducting materials are an interesting research niche, that is important to achieve a fundamental understanding of charge transport phenomena at the molecular level. Polymers are also widely used as a potential nano-carrier for drugs in nano-medicine and for pharmaceutical applications. Our research group is lead by Dr G. Pellicane, who is a (honorary) associate professor at UKZN and NRF C1 rated scientist. Members include Mr. S. Mamba (PhD student), Dr F. Gaitho (former PhD student), Prof. Tsige (Full Professor of Polymer Science at the University of Akron, US) and Prof. Workineh (Associate Professor at Bahir Dar University, Ethiopia) and Dr. N. Dlamini (lecturer, UKZN). Our group is operative in the field of theoretical and computational studies of complex fluids. A number of publications in scientific journals are obviously expected as a result of the research efforts in the framework of this project, and we already produced a number of them. We are also presenting the results of our research endeavour in international conferences/workshops, that will allow for sharing and diffusion of vital knowledge with the international scientific community and will be beneficial to the global progress towards a green and sustainable earth planet. Our gratitude always goes to the skilled and resourceful staff members at CHPC, and in particular to Dr Anton Lopis, and to the CHPC itself for the generous allocation of computational resources granted to us by them, which are instrumental to fulfill the goals of this project.
Principal Investigator: Dr Aniekan Ukpong
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2019-10-29
Allocation End: 2020-04-26
Used Hours: 153683
Project Name: Theoretical and Computational Condensed Matter and Materials Physics
Project Shortname: MATS0941
Discipline Name: Physics
I am Dr Aniekan Magnus Ukpong. I work as a Senior Lecturer and the Academic Leader (Physics) at the Pietermaritzburg Campus of the University of KwaZulu-Natal. I hold the National Research Foundation's C3-rating as an Established Researcher. I run the activities of the Theoretical and Computational Condensed Matter and Materials Physics Research Group as Principal Investigator of Research Program: CHPC/MATS0941. My group develops and implements state-of-the-art models for studying complex materials. The CHPC facilitates our access to world-class resources for computational science and pseudo experimentation. With zero samples preparation costs, and no clean-room requirements, the CHPC has offered a valuable, and cost-effective, support to our research.
Current challenges and opportunities in spin-based memory technologies show that on-chip integration of magnetic bits into non-volatile random access memory will require ultrafast-switching at reduced power. Due to poor scalability of conventional methods of electrical spin injection, we pursue alternative ways to generate, transport and detect pure spin currents. We focus on the rational design of quantum materials and the nano-engineering of electronic structure. Of immense research interests are strategies based on material-dependent intrinsic fields, such as spin–orbit coupling (SOC), etc. Strong intrinsic SOC in the heavy metal components of the heterostructure stack drives anomalous Hall effect (AHE), which we explore as the switch of spin currents. Similar to AHE, we investigate spin Hall effect as emergent quantum phases for application in energy-harvesting. Our multilayers are engineered to host nontrivial magnetic skyrmions, when non-centrosymmetric materials are proximitized with topological materials. Such persistent spin textures are used to design racetrack memory cells. We consider the delicate balance between competing internal fields to clarify the formation and dynamic stabilization of spiral skyrmions. Intrinsic Hall conductivities of interface components and heterostructures are employed to study the effects of SOC and low charge conductivities on spin-injection and spin-detection efficiencies.
Principal Investigator: Dr Winfred Mulwa
Institution Name: Egerton University, Egerton, Kenya
Active Member Count: 6
Allocation Start: 2019-10-29
Allocation End: 2020-05-12
Used Hours: 550768
Project Name: Magnetic Refrigeration
Project Shortname: MATS1181
Discipline Name: Physics
Who: MATS1181 under PI Winfred Mulwa from Egerton University Kenya: Magnetic refrigeration. What: Magnetization and demagnetization of magnetic materials known as magnetic refrigeration that rely on magnetocaloric effect (MCE). In cooling technology, magnetic refrigeration which depends on magnetocaloric effect is commonly used in refrigerators to achieve exceptionally low temperatures. Why: . Magnetic refrigeration does not rely on the uses of harmful and ozone-depleting coolant gases. How: This work is done computationally. We use the Quantum Espresso code (Density Functional Theory). This purely depends on CHPC because all the calculations have to be done in CHPC. Thanks to CHPC. How is the project progressing: We have achieved all the objectives. Two manuscripts have been submitted to peer reviewed journals. The project is as planned.
Principal Investigator: Dr Pedro Monteiro
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 12
Allocation Start: 2019-10-30
Allocation End: 2020-05-14
Used Hours: 106619
Project Name: Southern Ocean Carbon - Climate Observatory SOCCO
Project Shortname: ERTH0834
Discipline Name: Earth Sciences
SOCCO is a CSIR-led and DST co-funded programme that uses the comparative geographical advantage that South Africa has in the Southern Hemisphere to contribute to the global research challenge of understanding the role of the Southern Ocean in global and regional climate. The SOCCO research niche is to explore the role played by fine scale ocean dynamics in improving the climate sensitivity of ocean and coupled numerical models with a special focus in understanding the Southern Ocean's role in the CarbonClimate links.
To address the scales of dynamics in the ocean, we primarily use the coupled NEMO-PISCES model in a hierarchy of resolutions from 200 km to 2 km - using the models as experimental platforms. The finer the resolution, the greater the number processes that contribute to ocean-atmosphere carbon exchange. This understanding contributes to reducing model biases in process models and climate projections as well as the development of a South African Earth Systems Model (ESM).
This work advances research in global climate change based on the importance of feedbacks of the Southern Ocean dynamics on the carbon-climate system. Additionally, the ESM will be used to explore how the climate sensitivities of the Southern Ocean evolve over the 21st century as well as being South Africa's first submission to the 6th Assessment Report of the IPCC. ESM will be the basis for the medium to long term climate projections in Africa which will then support societal needs in health, water resource planning, agriculture, biodiversity management and more broadly in economic development in the region.
From regional, forced ocean models to fully-coupled earth system models comprising of interacting ocean, ice, atmosphere, land, ocean biogeochemical models, numerical modelling of earth system components require massively parallel computing resources. The size and complexity of these models are such, that for SOCCO's work, the CHPC is indispensable for the resources and service it provides.
Principal Investigator: Dr Bahareh Honarparvar
Institution Name: University of KwaZulu-Natal
Active Member Count: 12
Allocation Start: 2019-10-30
Allocation End: 2020-04-27
Used Hours: 529874
Project Name: Computer-aided HIV/TB drug design
Project Shortname: CHEM0808
Discipline Name: Health Sciences
My research interest is mainly focused on applying a range of computational chemistry approaches for structure-based design. CHPC is beneficial to my research members to increase their research output and publications and graduation. My research members use commercial software packages such as Materials Studio,Gaussian and Amber. All these commercial software packages are installed in CHPC.
Principal Investigator: Dr Chris Barnett
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2019-10-29
Allocation End: 2020-04-26
Used Hours: 178641
Project Name: Analysis of disease related polymers
Project Shortname: CBBI1063
Discipline Name: Bioinformatics
I investigate the shapes, structures, and properties of molecules by using computational modelling techniques. I'm
particularly interested in complex sugars (glycans), which are interesting to study because they are involved in intricate
molecular recognition processes in cells, for example, playing a role in cell signalling, adhesion, and immunity. Further
understanding of these molecules and the complex systems they are involved in may lead to the generation of
additional diagnostic markers and inhibitors that can be used to combat disease. The CHPC provides a platform for
being able to run large-scale and highly parallel simulations which is a great help in making rapid progress towards
solving research questions. The CHPC is also a test bed when carrying out computation on and developing algorithms
for large datasets.
Principal Investigator: Prof Abu Yaya
Institution Name: University of Ghana
Active Member Count: 6
Allocation Start: 2019-10-30
Allocation End: 2020-05-27
Used Hours: 540342
Project Name: DFT modeling of weak interactions; a case study for Carbon nanosystems
Project Shortname: MATS0990
Discipline Name: Material Science
The project is concerned with using larger number of computers known as a cluster to guide the manufacture of a gas sensor that can detect carbon dioxide (CO2) and carbon monoxide (CO) which are poisonous gases from car exhaust fumes that can lead to diseases such as pneumonia and other respiratory conditions in humans.
Boron Nitride, which is a tube-like material, is used as a suitable candidate for the detection of these gases in the air. In order to be able to do this, the large computer at Center for High Performance Computing (CHPC) called Lengau is used to obtain the models of the gases sensors and to understand the processing and working conditions on these computers before the sensors can be made in the laboratory. Thus, the Lengau computer serves as a means for really understanding the way these gas sensors can be made, so that it can function efficiently before it is made in the laboratory. This therefore will help reduce the cost of these gas sensors when they are finally made in the laboratory and make them more useful for a very long time.
The groups involved in this project are from the University of Ghana, which is mostly made up of final year undergraduate and postgraduate students.
Principal Investigator: Dr Jenny-Lee Panayides
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 5
Allocation Start: 2019-10-31
Allocation End: 2020-04-28
Used Hours: 244071
Project Name: Lead Discovery & Process Development Programme
Project Shortname: CHEM0934
Discipline Name: Chemistry
Alzheimer's disease is the most common form of dementia. To date, there is no cure for the disease and only symptomatic treatments are available. Using in silico and in vitro biological screening techniques, a team from CSIR Biosciences and the University of Pretoria are currently testing thousands of compounds to identify new pharmacophores for development into drugs for the treatment of Alzheimer's disease.
Using the computational resources provided by the CHPC, very large numbers of compounds can be tested with greater accuracy than what is possible with standard computational hardware. Hit compounds identified through this screening effort will be optimised using computer-aided drug design, to improve their effectiveness against a particular target within the human body prior to the expensive and time-consuming synthesis of the compounds for advanced biological screening. During this optimisation process, many aspects will be considered, including the ability of the human body to absorb the compound and possible toxic side-effects. Thus, utilisation of the CHPC resources can potentially accelerate drug development in a significantly more cost-effective manner.
Principal Investigator: Dr Anna Bosman
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2019-10-31
Allocation End: 2020-04-28
Used Hours: 1594
Project Name: Deep Learning and Neural Network Research at CS UP
Project Shortname: CSCI1166
Discipline Name: Computer Science
The research program of the Computer Science Department, University of Pretoria (UP), is headed by Dr Anna Bosman, and forms a part of the Computational Intelligence Research Group (CIRG) at UP. The focus of the program is on the following research topics: fitness landscape analysis of neural networks and real-life applications of deep learning. The following deep learning applications are currently investigated: (1) convolutional neural networks for satellite image analysis; (2) long short-term memory networks for anomaly detection; (3) convolutional neural networks for radio astronomy. Stuyding fitness landscapes of neural networks deepens our general understanding of the fundamental principles of neural network research, and enables progress in fundamental artificial intelligence. Deep learning applications allow us to apply modern artificial intelligence techniques in the South African context. Thus, the usage of CHPC helps us strengther machine learning and artificial intelligence research in South Africa. Sampling and estimation techniques for fitness landscape analysis are used to probe the error surfaces of the deep and shallow neural networks. The research is of empirical nature, and entails heavy sampling of the search space. Such experiments would not be feasible without access to a computer cluster. Deep learning applications benefit significantly from being run on a GPU, therefore, access to the GPUs allows us to upscale the experiments to real-life applications. Recently, a journal article and a conference paper resulted from the experiments run on the CHPC were published. This indicates that the research program is productive, and delivers academic outputs.
Principal Investigator: Prof Sybrand van der Spuy
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2019-10-31
Allocation End: 2020-04-28
Used Hours: 504477
Project Name: CFD simulation of turbomachinery
Project Shortname: MECH1187
Discipline Name: Computational Mechanics
The turbomachinery research group of Stellenbosch University focuses on the simulation and testing of cooling fans and gas turbine components. The ability to simulate these components is of importance to both power and defense industries in South Africa. The physical process inside these machines is not only one associated with a large geometry but also includes highly non-linear physics like turbulent flow, heat transfer and combustion. The CHPC enables us to simulate these really large turbomachinery problems. This is an ability that is not only held in high esteem nationally but also internationally.
Principal Investigator: Prof Graham Jackson
Institution Name: University of Cape Town
Active Member Count: 6
Allocation Start: 2019-11-03
Allocation End: 2020-05-01
Used Hours: 6300
Project Name: Insect neuropeptides
Project Shortname: CHEM1101
Discipline Name: Chemistry
Hormones are involved in the control of energy release during insect flight. These hormones bind to G-protein coupled receptors. Using the CHPC, models of the solution structure of some of these hormones and receptors were constructed. These models will now be used to design species specific insecticides. To date models of the migratory locust, malaria mosquito, honey bee, flesh fly, and fruit fly have been constructed
Principal Investigator: Prof Chris Meyer
Institution Name: Stellenbosch University
Active Member Count: 6
Allocation Start: 2019-11-04
Allocation End: 2020-05-02
Used Hours: 996005
Project Name: Development of CFD models
Project Shortname: MECH1077
Discipline Name: Computational Mechanics
The research activity is led by Prof CJ Meyer from Stellenbosch University and is focused on developing computational models of industrial thermo- and fluid dynamic processes. There is a specific emphasis on the use of free software under the GNU General Public License. The industrial processes under consideration are those relevant to specific segments of industry in South Africa most notably power generation. Current projects include the simulation of large-scale air-cooled condensers as well as detailed simulations concerning the flow through axial flow fans used in the energy sector. The cohort of students are making excellent progress with 3 students having upgraded to PhD-level and the rest to submit their MEng thesis shortly.
Principal Investigator: Prof Matthew Adeleke
Institution Name: University of KwaZulu-Natal
Active Member Count: 11
Allocation Start: 2019-11-04
Allocation End: 2020-05-02
Used Hours: 105409
Project Name: Computational and Evolutionary Genomics
Project Shortname: CBBI1231
Discipline Name: Bioinformatics
Quantitative and Computational Genomics is a research group in the Discipline of Genetics at the University of KwaZulu-Natal, Durban South Africa. We employ Quantitative Genetics, Bioinformatics, metagenomics to detect pathogens (parasites and bacteria), understand their diversity and how it contributes to adaptation, drug resistance and control/prevention. Computational approach is also being used to characterize vaccine candidates against these pathogens.
Metagenomics as well as identification and characterization of the vaccine candidates require working with large sequence data and genomes of these pathogens. Some of the softwares required for manipulating the genomic sequences are available on CHPC in addition to the high computing power required for the analysis which is available again on CHPC.
The doctoral student working on rumen microbiome using metagenomics should be completing her PhD this year. The work on vaccine development using computational approach is still in formative stage and 3 masters student are just starting work on it this year. We hope that this approach will lead to reduction both in price and period relative to traditional vaccine development methods.
Principal Investigator: Dr Ndumiso Mhlongo
Institution Name: University of KwaZulu-Natal
Active Member Count: 11
Allocation Start: 2019-11-05
Allocation End: 2020-05-21
Used Hours: 123382
Project Name: Biomolecular Modelling Research Unit
Project Shortname: HEAL1002
Discipline Name: Health Sciences
Biomolecular Modelling Research Unit is located at the University of KwaZulu-Natal, Howard College Campus and headed by Dr Ndumiso N. Mhlongo. This research group employs CHPC resources to conduct molecular dynamics simulations to analyse the dynamical properties of macro-molecules such as folding and allosteric regulations; ligand-receptor interactions; atom-to-atom interactions; protein-protein interaction;virtual screening and molecular docking of active molecules; QSAR etc, for the design and development of inhibitors against diseases and disorders. Through the use of CHPC resources, we have designed potential inhibitors against M. tuberculosis and cancer treatment. These have made contributions to discovery new inhibitors & new knowledge which could directly translate into real health benefits of the society.
Principal Investigator: Prof Krishna Bisetty
Institution Name: Durban University of Technology
Active Member Count: 4
Allocation Start: 2019-11-07
Allocation End: 2020-05-25
Used Hours: 44714
Project Name: Computational Modelling & Bioanalytical Chemistry
Project Shortname: CHEM0820
Discipline Name: Chemistry
Our main focus is on the design of electrochemical biosensors for the detection of different analytes with application in food industry.
However, the computational tools available on the CHPC platform has led to complimentary studies currently undertaken in our group to validate the experimental results.
Our design of an aptamer for the detection of hotness in chili-based foods, using Molecular docking and MD simulations has let to a provisional patent approved in 2019 (P78572ZA00)
Principal Investigator: Dr Francois van Heerden
Institution Name: Nuclear Energy Cooperation of SA
Active Member Count: 2
Allocation Start: 2019-11-08
Allocation End: 2020-05-06
Used Hours: 26736
Project Name: Research Reactor Fuel Burnup and Material Activation
Project Shortname: INDY0788
Discipline Name: Physics
The Radiation and Reactor Theory (RRT) group at the South African Nuclear Energy Corporation (Necsa) provides calculational support for the SAFARI-1 research reactor, and perform research in the general area of nuclear analysis. We also develop and maintain our own suite of reactor simulation software, called OSCAR. This suite is the primary operational support tool for the SAFARI-1 reactor, and is used at a number of international facilities, which range from small university based research reactors, to larger national facilities.
During the past 5 years, CHPC computing resources were utilised for a project facilitated by the International Atomic Energy Agency (IAEA) through a Collaborative Research Project (CRP) aimed at the collection of experimental data suitable for code benchmarking and validation. We are participating by providing experimental data from our own facility, the SAFARI-1 research reactor, and by calculating a number of experimental benchmarks from other member states. This particular CRP focuses on fuel depletion and material activation, which is important for the economic and safe operation of research reactors. Most of the primary analysis work has been completed, and we are well on target to deliver final reports in the last research meeting scheduled for October 2019. These reports will eventually be incorporated in a formal technical publication by the IAEA, available to all member states.
The latest version of our tool set, OSCAR-5, provides a platform that combines different analysis codes, from fast diffusion solvers suitable for fuel depletion tasks, to high fidelity particle transport solvers, which can be used to do detailed local activation analysis, in a consistent manner. High Performance Computing plays an important role in the data preparation step for the diffusion solver, and in the use of transport solvers to estimate neutron flux distributions in the core.
Benchmarks developed in this CRP forms the backbone of the OSCAR-5 validation case for research reactor support.
Principal Investigator: Prof Ignacy Cukrowski
Institution Name: University of Pretoria
Active Member Count: 8
Allocation Start: 2019-11-08
Allocation End: 2020-05-06
Used Hours: 790227
Project Name: Understanding chemistry from QM study of molecular systems
Project Shortname: CHEM0897
Discipline Name: Chemistry
Activities in chemistry (in science in general) can be seen as made of two distinctive approaches: 1) development of new theories and methodologies that should lead to better understanding of concepts and chemical process (reactions) and 2) practical implementation of known or new methodologies that should lead to routine and highly efficient experimental/computational operations. Our research group in the Department of Chemistry, University of Pretoria (Prof. Ignacy Cukrowski (the leader), Dr. Jurgens de Lange, several PhD, MSc and Honours students as well as a postdoctoral Fellows) is involved in fundamental studies. Our focus is primarily on understanding fundamentals governing inter-atomic and inter-fragment interactions from the electron density distribution throughout a molecule, or molecular system in general. For instance, there are many kinds of chemical bonds but still there is no an ultimate general theory of bonding. Hence, there are various approximate quantum chemical models that are being used to describe and explain just a specific kind of bonding. In our group we prefer to interpret classical chemical bonding, regardless of its kind, as an interaction governed by universal laws of physics. This allows us to extend the concept of interactions from classical 2-atom approach (a chemical bond) to poly-atomic interactions involving fragments of a molecular system. Such approach proved to be very useful in modelling reaction mechanisms to understand (on atomic and molecular fragment level) how and why new compounds are or are not formed as planned by a synthetic (in)organic chemist. Full understanding of successful and failed synthetic processes is of great importance as it must aid the development of, e.g., new drugs needed for treatment of (i) highly contagious diseases, such as tuberculosis, HIV/AIDS, or (ii) Alzheimer, a disease with reported cases growing rapidly throughout the world. It is important to realize that such theoretical work requires, due to the size of molecular systems under investigations, dedicated and expensive computational facilities, such as CHPC, with a dedicated staff to ensure that research groups can access and make use of computational centre 24/7.
Principal Investigator: Dr Mehdi Mehrabi
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2019-11-11
Allocation End: 2020-05-09
Used Hours: 12765
Project Name: Modeling of heat transfer characteristics and pressure drop of nanofluids in micro and mini tubes.
Project Shortname: MECH1086
Discipline Name: Other
This project is conducted in the Clan Energy Research at the University of Pretoria to model heat transfer characteristics and pressure drop of nanofluids in micro and mini tubes. This project is defined to find an innovative solution to the thermal management challenges of today especially in microfluidics. The progress of the project is satisfactory and the initial results of the project are set to an international journal for possible publications.
Principal Investigator: Dr Hezekiel Kumalo
Institution Name: University of KwaZulu-Natal
Active Member Count: 13
Allocation Start: 2019-11-13
Allocation End: 2020-05-11
Used Hours: 376279
Project Name: Molecular modeling and computer aided drug design
Project Shortname: HEAL1009
Discipline Name: Health Sciences
The group covers a wide range of computational and molecular modeling research areas with main focus on biological systems and drug design approaches.
Main interest is related to design and study of biologically and therapeutically oriented targets. This is achieved by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We are involved in projects such Understanding drug resistance mechanisms via different computational tools QM/MM MD simulations Quantitative Structure Activity Relationship (QSAR) Conformational Analysis of biomolecules Bioinformatics tools applications Development Projects Approaches to enhance binding free energy calculations results Developing parameters for biomolecules: on-going projects Software implementations: on-going projects. All the projects that we do in the group contribute to the training of pharmaceutical scientists with specific skills for both the pharmaceutical industry and academia. This has the potential of stimulating the local pharmaceutical industries in South Africa to manufacture pharmaceuticals of quality, excellence and affordability for optimum and cost effective patient health, instead of being dependent on multinational pharmaceutical companies. We are still young group therefore funding is problem, therefore for the resources at HPC allows us to generate hypotheses for subsequent experimental testing in a much quicker manner and higher throughput than using experiment alone to generate hypotheses that you'd like to test. It has h given us an opportunity to be able explain experimental data we could not explain easily such the binding landscapes of different enzymes and the mechanism of action for different inhibitors.
Principal Investigator: Prof Edet Archibong
Institution Name: University of Namibia
Active Member Count: 4
Allocation Start: 2019-11-15
Allocation End: 2020-05-13
Used Hours: 5343
Project Name: (1) Computational Study of Semiconductor Clusters. (2) Computational Study of Bio-active Molecules Extracted from Plants
Project Shortname: CHEM0969
Discipline Name: Chemistry
Drinking water and our atmosphere are very important to our health. The treatment of water for the purpose of being used for drinking require that we scientists understand the chemical compounds and the reactions of the compounds. Ozone is one of the chemicals used in the treatment of water and phenols are found in waste waters that are treated for consumption. The work in our group focus on the reaction of ozone with phenols. This study will allow for a better understanding of processes occurring in waste water treatment and enable scientists to devise efficient and safe procedures for the treatment of water.
Principal Investigator: Dr George Manyali
Institution Name: Masinde Muliro University of Science and Technology, Kakamega, Kenya
Active Member Count: 6
Allocation Start: 2019-11-18
Allocation End: 2020-05-27
Used Hours: 197727
Project Name: Ab Initio study of Thermoelectric Materials
Project Shortname: MATS0712
Discipline Name: Material Science
The Computational and Theoretical Physics (CTheP) Group with branches at Kaimosi friends University College and Masinde Muliro University of Science and Technology, comprise of a team of researchers and students dedicated to the development and application of computational modeling to outstanding problems in materials science. In general, the group seeks a deeper understanding of quantum-mechanical descriptions of interacting electrons and nuclei in order to predict and design properties of materials and devices using density functional theory as a tool for the first-principles simulation. This kind of simulation generates volumes of data that cannot be handled by the common desktop computers. High-performance computing provides the computational environment that includes parallel processing, large memory, and storage of the big data. Therefore, Center for High-Performance Computing facility in Cape Town, South Africa, plays a vital role in providing the resources that aid the discovery of new materials and accelerates its application in the industry, an achievement that would have been in vain with desktop computers. Some specific projects for our group include the characterization of already known thermoelectric materials. The information gained from this project is used as identifiers in search for new thermoelectric materials with the tailored figure-of-merit. Such materials are used to enhance the efficiency of the thermoelectric generator power system for renewable energy. Such outcomes of our projects have an impact on the livelihood of the rural communities in Kenya.
Principal Investigator: Prof George Amolo
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 11
Allocation Start: 2019-11-18
Allocation End: 2020-05-16
Used Hours: 2017621
Project Name: Properties of Materials for Green Energy Harnessing
Project Shortname: MATS862
Discipline Name: Material Science
The MATS862 is mainly a Kenyan group that uses computational modeling in materials science (CMMS) as an important component of decision making to support experimental study and predictive capability that can be crucial to industrial as well as service productivity. CMMS also draws from experimental studies to provide insights that may not have been revealed otherwise. One member, Mr Mangoungou, of my group comes from the Congo Brazzaville and is a PhD student from a collaborating partner in Central Africa. The PI of this group is based at the Department of Physics, The Technical University of Kenya, Nairobi.
My group makes an effort to tackle topical issues of interest at the national level and the developing world at large, especially in the area of materials for green energy conversion, which in a number of cases is coupled with environmental protection. This is done using computational modeling informed by experimental data, where available, or from a predictive approach. With sufficient computational resources the models are made as realistic as possible and recommendations made for conversion into service and device fabrication. We are engaged in this kind of work to create an understanding of the fundamental properties of materials in order to inform applications and eventually generate new services and products.
A typical process would be to identify a research question that has not been answered or has generated controversy then study carefully its current status in terms of attempts to clarify of resolve outstanding issues and propose ways of entry to tackle the problem. The CHPC would be expected to avail resources as well as expertise until there is good and credible data for further analysis.
Following research findings in our team, we have been able to conduct two workshops on the use of Siesta and yambo codes with participation at the national level at the Technical University of Kenya. We are doing well based on the average output of at least two publications every 6 months and attendance of local, regional and international conferences/workshops.
We remain active in this period of staying away from the office due to the threat of the COVID-19 by participation on web conferencing within Kenya and collaborations overseas. The web conferencing is provided by our supporting partner, the Kenya Education Network.
MATS862 members greatly appreciate the provision of these computational resources to our research team and is thankful to the CHPC as well as the government of the Republic of South Africa, for the continued service even during this period of lockdown of normal operations.
Principal Investigator: Prof Michelle Kuttel
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2019-11-18
Allocation End: 2020-05-16
Used Hours: 197047
Project Name: Molecular modelling of microbial polysaccharides and glycoconjugates
Project Shortname: CHEM1242
Discipline Name: Chemistry
The group is the Carbohydrate Vaccine Group at the University of Cape Town, run by Prof. Michelle Kuttel (Computer Science Dept.) and Prof. Neil Ravenscroft (Chemistry Dept.). We are primarily involved with simulations of carbohydrates to inform the development of anti-microbial conjugate vaccines, but also have research into inhibitors with potential therapeutic applications. Such work has clear ultimate benefits to public health. The work uses molecular dynamics and quantum mechanical simulations to investigate the properties and interactions of the molecules under study. The collaboration is successful, with regular publications and significant funding.
Principal Investigator: Dr Stefan du Plessis
Institution Name: Stellenbosch University
Active Member Count: 10
Allocation Start: 2019-11-18
Allocation End: 2020-06-12
Used Hours: 3147
Project Name: Shared Roots
Project Shortname: HEAL0793
Discipline Name: Health Sciences
Shared Roots is a collaborative research project undertaken by researchers from the departments of psychiatry, neurology and genetics at Stellenbosch University and researchers from the South African National Bioinformatics Institute (SANBI). It is a MRC Flagship funded study and the principal investigator on the study is the executive head of the department of psychiatry Professor Soraya Seedat. Dr Stéfan du Plessis is responsible for the neuroimaging component. Our study included participants with posttraumatic stress disorder (PTSD), schizophrenia or Parkinson's disease. It is known that individuals with mental illness as well as other common brain disorders have higher rates of heart disease and stroke than the general population. It is not clear why this is the case. Our study therefore aims to collect information about all the potential factors that can play a role, to better understand the increased risk and enable the development of treatment strategies. To achieve this goal we will combine state-of-the-art research techniques such as genetic evaluations and the latest neuroimaging techniques. This will be combined in analysis with information evaluating the brain disorders, general health and lifestyle factors.
For our neuroimaging component, we scanned over 600 participants using Magnetic Resonance Imaging (MRI). Here we investigate potential brain changes associated with increased metabolic risk. We proceeded to calculate precise measurements of around 70 known brain regions using the MRI scans, which will be compared between cases and healthy controls. Processing takes around 24 hours for each scan. To finish in a timely manner, we used the Centre for High Performance Computing Rosebank, Cape Town, Sun Intel Lengau cluster.
Principal Investigator: Dr Sean February
Institution Name: SKA
Active Member Count: 3
Allocation Start: 2019-11-19
Allocation End: 2020-05-17
Used Hours: 182981
Project Name: MeerKAT Open Time Projects - Feasibility Study
Project Shortname: ASTR1114
Discipline Name: Astrophysics
The South African Radio Astronomy Observatory manages the currently operating 64-dish MeerKAT telescope located in Carnarvon in the Karoo. It is expected that approximately 30% of MeerKAT's observing time will be taken up by smaller research groups who do not necessarily have the computing capacity to carry out the required processing of the data. The aim of this research programme is to conduct ongoing, as needed, feasibility studies for anticipated open-time projects. Our most recent a proof of concept test involved looking at two particular aspects of a radio astronomy imaging task: 1) create a synthetic "dirty" image of the sky (embarrassingly parallel), 2) perform various "clean" operations to produce a scientifically accurate radio astronomy images (less parallel, more memory intensive). All this was done using the Singularity container runtime which we've originally helped get going on Lengau. A formal report on our findings has been circulated to the wider community, and we are confident that it will spark further uptake of Lengau resources by other radio astronomers. Finally, we are hoping to make continued use of Lengau - not just to conduct continued feasibility tests as they arise, but to also provide keen students with exposure to both radio astronomy and HPC.
Principal Investigator: Dr Thabang Ntho
Institution Name: Mintek
Active Member Count: 12
Allocation Start: 2019-11-20
Allocation End: 2020-05-18
Used Hours: 18488
Project Name: Hydrogen Storage Materials and Catalysis
Project Shortname: MATS0799
Discipline Name: Material Science
Advanced Material division, Mintek,
The Advanced Materials Division is a dynamic and multi-disciplinary division that addresses the need for specific research into the end-use of metals in the manufacturing, fabrication and mining industries. The group run several projects such as synthesis of solid state hydrogen storage materials (carbon nanotubes, metal hydrides and metal organic frameworks) to support the national HySA (Hydrogen South Africa) program. Electronic and structural properties of these materials will be modeled at DFT/MP2 level. Macro and fluid dynamic properties of these materials will be computed using finite element method via OpenFoam CFD. Under this program, general properties and reactivity of PGM-based catalysts will also be modeled in line with the research activities of the Catalysis Group at Mintek.
The group also plays in the beneficiation of metals such as Au at a nanoscale level for application in health. A nanotechnology group specializes in the fabrication of point of care test kits for infectious disease which burden ailing economies. The interaction of the nanomaterials with the biological molecules will be simulated using the tools. This will benefit the end user because testing will be possible.
The group which run several projects including the few mentioned in the preceding paragraphs requires HPC. Without HPC the trial and errors in the laboratory will take longer and consume lots of reagents. HPC facilitate the experimental part of the projects by subtracting a lot of trial and errors and speeding up the process. The group is product oriented which can take a while without the help of the modeling tools. The products are for the end users which include diagnostic tools for malaria and tuberculosis.
The process involve modelling calculations to tailor the experimental approaches, the experimental process to come up with prototypes and development of product. Therefore HPC is the backbone of the structure.
Principal Investigator: Prof Catharine Esterhuysen
Institution Name: Stellenbosch University
Active Member Count: 12
Allocation Start: 2019-11-20
Allocation End: 2020-05-27
Used Hours: 133492
Project Name: Computational chemistry analysis of intermolecular interactions
Project Shortname: CHEM0789
Discipline Name: Chemistry
The Computational Supramolecular Chemistry group at Stellenbosch University aims to understand the fundamental role that intermolecular interactions play in directing the properties of solid materials. For instance, sorption, i.e. uptake, of gases and solvents by porous materials occurs as a result of intermolecular interactions, which further directly influence the sorptive properties of the porous material. Calculations performed using the CHPC's computational facility allow us to explain the role that intermolecular interactions play in the unusual sorption properties of various porous compounds, which in turn enables us to establish methodologies for determining the behaviour of a variety of compounds. Our aim is to understand the role of intermolecular interactions in the mechanisms of catalytic and biological processes in order to predict improved catalysts and biologically active compounds.
Principal Investigator: Dr Nana Ama Browne Klutse
Institution Name: Ghana Space Science and Technology Institute
Active Member Count: 2
Allocation Start: 2019-11-25
Allocation End: 2020-05-23
Used Hours: 5197
Project Name: Regional Climate modeling over Africa
Project Shortname: ERTH1087
Discipline Name: Earth Sciences
The CHPC system has provided access to a supervisor from the Department of Physics, the University of Ghana, and students from the West African Science Service Center on Climate Change and Adapted Land Use (WASCAL). We are climate scientists but do not have the system in our countries to run our experiments. We model the climate and the impact on water and land. The CHPC has made our research possible. One PhD student has graduated.
We thank the South African government and all partners involved in CHPC for making this possible. We also thank the hard working scientists, engineers and the general staff of the CHPC for keeping up the good services.
We continue to depend on the South Africa CHPC for our research computation.
Principal Investigator: Prof Bruce Bassett
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 2
Allocation Start: 2019-11-25
Allocation End: 2020-05-23
Used Hours: 139822
Project Name: Machine Learning for Astronomy
Project Shortname: ASTR1157
Discipline Name: Astrophysics
Mr Evander Nyoni (AIMS, UCT) and Prof Bruce Bassett (AIMS, UCT, SAAO, SARAO) are working on training machine translation models for Southern African low-resource languages, in particular for English to Zulu, English to Xhosa, and English to Shona. The preliminary results are promising and the goal is to study techniques for improving the quality of translation through a technique called transfer learning. Transfer learning aims to exploit machine learning on one dataset for application to a related dataset. In this context it should allow the machine translation models to transfer learnings from languages with a lot of available text to languages for which there is little available text.
Principal Investigator: Prof Regina Maphanga
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 6
Allocation Start: 2019-11-29
Allocation End: 2020-06-17
Used Hours: 443197
Project Name: Energy Storage Materials
Project Shortname: MATS0919
Discipline Name: Material Science
The Design and Optimisation group is a group under Operational Intelligence Impact Area in the Next Generation Enterprises and Institutions cluster of CSIR and uses multiscale methods to develop novel energy storage materials with desired properties and enhanced properties for existing materials. The envisaged outcome of this project is to develop energy storage materials models with improved performance and consistency, which will be cheaper and environmentally benign. The ever-increasing global energy needs and depleting fossil-fuel resources demand the pursuit of sustainable energy alternatives, including renewable sources to replace carbon intensive energy sources. Sustainable and renewable energy is considered to be the most effective way to minimize CO2 emissions. Hence, finding sustainable energy storage technologies is vital for optimally harnessing the renewable energy.
Computational methodologies are very effective in predicting material-structure-property correlations. In this project simulation methods and models based on parallel computing are developed to probe energy materials properties. Centre for High Performance Computing (CHPC) resources are used to develop these parallel computing methods and algorithms for large and complex material models. Thus, CHPC resources provide a platform to simulate the evolution of material properties at a wide range of external conditions that are not accessible experimentally and fast track acquisition of results. The major of aim of this project is to create a predictive, reliable and robust set of models of materials for energy storage across the materials modelling length scale, leading to integrated multi-scale capability.
Principal Investigator: Dr Roelf Du Toit Strauss
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2019-11-28
Allocation End: 2020-05-26
Used Hours: 320737
Project Name: Computational Space Weather
Project Shortname: PHYS0918
Discipline Name: Physics
One of the biggest hurdles faced by manned exploration of space is the high levels of natural radiation present in the solar system. This is not only an important consideration faced by future astronauts on board spacecraft, but also by future colonizers of Mars, and inhabitants of future moon bases and space stations. This important risk is acknowledged by both SpaceX and NASA, and planned bases and spacecraft try to accommodate so-called "space storm shelters", where space dwellers can hide from dangerous radiation levels. At the Centre for Space Research of the North-West University, South Africa, we are doing our part to mitigate these possible harmful effects by developing state-of-the-art numerical models that can simulate and predict the levels of harmful natural radiation. To simulate the intensity of these so-called "cosmic ray" particles, complicated and large-scale numerical models are run on large scale computer clusters, such as the Lengau cluster of the Centre for High Performance Computing (CHPC) in Cape Town, South Africa.
Principal Investigator: Prof Eno Ebenso
Institution Name: North-West University
Active Member Count: 5
Allocation Start: 2019-12-03
Allocation End: 2020-05-31
Used Hours: 253847
Project Name: Theoretical Investigations of Corrosion Inhibition Activities of Organic Compounds
Project Shortname: CHEM1176
Discipline Name: Chemistry
Our research group, Materials Science Innovations and Modelling Research Focus Area is domiciled at the Mafikeng Campus of North-West University.
About 75% of our work is on the design of new corrosion inhibitor solutions to mitigate the rate at which metal (alloys) corrode in various environments. Other works in the group include of electrochemical sensors development and thermodynamics of solutions. Our research works involve quite a volume of computational studies, especially quantum chemical calculations using the Gaussian software and Molecular dynamics simulations using the Materials Studio software. The computational studies are often used to corroborate experimental results in our continuously robust and comprehensive investigations. For instance, the potentials of an organic compound to inhibit corrosion of metal is often dependent on its ability to adsorb on metal surface, which in turns depends on its molecular reactivity. Determining corrosion inhibition mechanism is central in such research, and computational study is an important aspect of the research. For a timely output, conventional personal computer (PC) is not an option in the kind of research we do. Continuous access to software license is also not negotiable. Hence, enrollment of our research group on CHPC resources is very important.
For a quantum chemical calculation that takes an average of 15 days per molecule to complete on a PC (if it does not end up crashing due to insufficient memory, as it's often the case), and an investigation involving at least 4 organic molecules (often, more compounds are considered), an investigator will be highly frustrated without a resource like CHPC.
Since our enrollment on CHPC resources, our project has been progressing satisfactorily and the time spent on a particular project has been reduced due to speedy computations. Hence, we have the opportunity of designing more elaborate projects executable within reasonable space of time.
Principal Investigator: Prof Richard Tia
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 26
Allocation Start: 2019-12-03
Allocation End: 2020-05-31
Used Hours: 3042504
Project Name: Computational Chemistry and Materials Science
Project Shortname: CHEM1044
Discipline Name: Chemistry
We have not yet issued a press release but with the progress made in the our work, especially the work pertaining to the conversion and utilization of carbon dioxide, it should be possible to make a press release in the near future. With increasing interest of the scientific community and government agencies on the mitigation of rising carbon dioxide levels and the attractiveness of using carbon dioxide as a feed-stock for industrial processes, this work might be very suitable for a press release as and when we get interesting results.
Very recently, we have also started to use modeling to help address some questions pertaining to the coronavirus/COVID-19 pandemic. We are hopeful that we will make good progress and we do it will certainly be a press issue and CHPC will be duly acknowledged.
Our research activities fall under two broad areas, namely;
1. Molecular modeling - Exploring the mechanisms of organic, inorganic and organometallic reactions.
These studies afford important molecular-level mechanistic details of industrially-relevant chemical reactions that are difficult, if not impossible, to obtain experimentally. Molecular level understanding enable chemical reactions to be guided quickly and efficiently along desirable pathways, with the effect of producing the right product with minimal energy consumption and minimal environmental impact. A key aspect of this work is the development of homogeneous transition metal catalysts for the depolymerization of lignin, an abundant natural resource, for fuel.
2. Materials modeling
The atomic- and molecular-level mechanistic insight gained from these studies are useful for the design of novel catalysts for the conversion of CO2 and other green-house gases as well as stranded gases from the petroleum refining into useful fuels. This addresses the problem of global warming as well as providing an environmentally friendly alternative sources of fuel.
The research objectives described here are very computationally-demanding and using the CHPC resources is highly beneficial. Without that, we would not be able to carry out some of these calculations.
Principal Investigator: Dr Md Ataul Islam
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2019-12-11
Allocation End: 2020-05-21
Used Hours: 198819
Project Name: DR. MA Islam
Project Shortname: CBBI1198
Discipline Name: Bioinformatics
Dr. MA Islam's research interest is determining the effectiveness of pharmaceutical compounds by developing new computational methodologies, protein-ligand/ protein-protein docking analysis, employing molecular dynamics simulations or DFT-based quantum mechanical calculations etc., to better understand the underlying mechanisms of biological functions for several disease models. CHPC facilities are being used by this group since February 2019. This research group has successfully completed several computer-aided drug-design projects in Alzheimer's disease, dengue, HIV-AIDS infections, tuberculosis, cancer, diabetes, Chagas disease etc. This research group is extensively utilizing Schrodinger, Amber, Gromacs tools for the completion of their research objectives. Majorly, their research work is highly rigorous and extremely is in need to access of CHPC server to fulfill the objectives of the present ongoing projects. On behalf of the research group, Dr. MA Islam want to thank the entire CHPC team members for their constant determination for supporting us.
Principal Investigator: Dr Uljana Hesse
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2019-12-11
Allocation End: 2020-06-08
Used Hours: 5525
Project Name: Medicinal Plant Genomics
Project Shortname: CBBI1133
Discipline Name: Bioinformatics
Knowledge on the genomic background of rooibos, an endemic South African medicinal plant, can help to identify biosynthetic pathways involved in the production of medicinal compounds; and genes associated with biotic and abiotic stress resistance of the plant. The rooibos genome has been sequenced by the research team of Dr Uljana Hesse, Department of Biotechnology, University of the Western Cape. The genome assembly is conducted at CHPC, which provides the extensive computational resources essential for plant genome assembly. One MSc study on bench-marking biocomputational procedures for genome assembly and evaluation of genome characteristics towards establishing a computational pipeline for high-throughput plant genome assembly and annotation has been completed.
Principal Investigator: Prof Nicola Mulder
Institution Name: University of Cape Town
Active Member Count: 14
Allocation Start: 2019-12-13
Allocation End: 2020-06-10
Used Hours: 2723
Project Name: H3ABioNet
Project Shortname: CBBI0825
Discipline Name: Bioinformatics
The H3ABioNet project has used CHPC for various studies, including imputation of genotyping data to increase coverage of SNPs and assess different imputation tools and reference panels. The resource has also been used to study pneumococcal genomes isolated in Malawi to study the factors that cause some serotypes to be more invasive and cause disease.
Principal Investigator: Dr Geoff Nitschke
Institution Name: University of Cape Town
Active Member Count: 9
Allocation Start: 2019-12-13
Allocation End: 2020-06-10
Used Hours: 366460
Project Name: Evolving Complexity
Project Shortname: CSCI1142
Discipline Name: Computer Science
This research is an evolutionary robotics study, which investigates the use of simulated robots in virtual worlds to study the impact of different sensor types and motor-configurations (bodies) on the robots capabilities to collectively accomplish tasks (such as collective transport and construction). Real-world examples of these tasks include toxic-waste disposal and automated construction of buildings.
Principal Investigator: Prof Ponnadurai Ramasami
Institution Name: University of Mauritius
Active Member Count: 5
Allocation Start: 2019-12-19
Allocation End: 2020-06-16
Used Hours: 118987
Project Name: Computational Chemistry Methods to Study Structural and Spectroscopic Parameters
Project Shortname: CHEM1290
Discipline Name: Chemistry
I am the group leader of the Computational Chemistry Group in the Department of Chemistry of the University of Mauritius. The research interest of the group ranges from fundamental to applied chemistry. One of the research interests is to predict structural and spectroscopic parameters of novel compounds. In this context, we are currently predicting the structures of two-dimensional nanomaterials prior to their synthesis. We are also studying the electronic structure of metal oxide nanoparticles. These projects involve the use of Quantum Espresso.
We are also collaborating with experimentalists, mainly organic and inorganic chemists from African countries. From the organic chemistry perspective, we are studying cycloaddition reactions to provide insights into the reaction mechanism so as to explain the formation of the observed products. From the inorganic chemistry aspects, we are studying inorganic complexes using computational method so as to complement the experimental research in terms of structural and spectroscopic parameters. However, in some cases, where experimental data are not available, the computed parameters are useful to the experimentalists for the interpretation of results. For these projects, we are using Gaussian software.
Without the use of the CHPC facility, it would not have been possible to carry out high level computations for the projects that we have planned. This facility is allowing us to aim at carrying out high level research and to eventually have good publications in high impact factor journals.
We have recently started using the CHPC facility and we are currently still running calculations and interpreting data. We have also started drafting manuscripts for publications.
Principal Investigator: Dr Nikhil Agrawal
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2020-01-08
Allocation End: 2020-07-06
Used Hours: 70519
Project Name: Molecular Modeling of proteins using different computational tools
Project Shortname: HEAL1189
Discipline Name: Health Sciences
Detergent play important role in chemistry of proteins and also effect biological processes such as folding. So identification of its binding sites on proteins and effects of binding on protein structures in important. In our project we employed MD simulations technique to reveal the binding sites of detergents on proteins and its structure.
Principal Investigator: Prof Orde Munro
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2020-01-08
Allocation End: 2020-07-06
Used Hours: 5033
Project Name: Bioinorganic Chemistry
Project Shortname: CHEM1065
Discipline Name: Chemistry
BIOINORGANIC RESEARCH GROUP – WITS UNIVERSITY
The Bioinorganic Research Group at WITS University is led by Prof. Orde Munro, who is currently the SARChI Chair of Bioinorganic Chemistry. At present, the WITS group comprises two post-doctoral research fellows (Drs. Catherine Slabber and Angelique Blanckenberg as well as, formerly, Dr Zeynab Fakhar), four PhD students, and 2 MSc students.
NATURE OF OUR WORK
The work involves the design, synthesis, and testing of novel metallodrug candidates for chemotherapy. The compounds incorporate ligands that can facilitate and control the interaction of the metal ion with biomolecules such as DNA and/or proteins. Molecular simulations are used not only to design compounds with desirable biological behaviour, but also to gain fundamental insights on their mechanisms of action and electronic structures. We are particularly interested in exploiting and controlling the reactivity of both endogenous and non-natural metal ions to kill drug-resistant pathogenic bacteria such as TB (Mycobacteria) and cancer cells.
WHY WE USE SIMULATIONS
Modern drug discovery uses in silico methods for a number of reasons, including screening large libraries of compounds for binding efficacy to enzyme targets. The enzyme targets are crucial proteins for the survival and replication of cancer cells, bacteria and viruses. Screening many thousands of compounds using computer programs is an efficient way to select a handful of compounds that can ostensibly bind to the enzyme target of interest because they have the correct shape and functional groups. The small library so generated may then be synthesized in the laboratory and tested against the pathogen of interest and the putative enzyme target. In this way, computational methods shorten the time required to find promising new compounds for further testing and development as the medicines of tomorrow. Finally, computer simulations offer important three dimensional details about how drug-like compounds inhibit their enzyme targets, thereby guiding optimization of the compound's structure for enhanced target affinity and, in principle, improved in vivo efficacy.
Principal Investigator: Dr Brigitte Glanzmann
Institution Name: Stellenbosch University
Active Member Count: 15
Allocation Start: 2020-01-08
Allocation End: 2020-07-06
Used Hours: 77703
Project Name: SAMRC Precision Medicine African Genomics Centre
Project Shortname: CBBI1195
Discipline Name: Bioinformatics
The advent and evolution of next generation sequencing (NGS) has considerably impacted genomic research, including precision medicine. High-throughput technology currently allows for the generation of billions of short DNA or RNA sequence reads within a matter of hours. This becomes extremely important in the case of genetic disorders where rapid and inexpensive access to a patient's individual genomic sequence is imperative and enables target variant identification. NGS technologies do, however lead to the generation of large data sets which require extensive bioinformatic and computational resources. Computational life sciences therefore relies on the implementation of well-structured data analysis pipelines as well as high-performance computing (HPC) for large-scale applications. To date, more than 150 whole genome sequences have been sequenced and the data analysed in collaboration with the Centre for High Performance Computing (CHPC). This equates to more than 5TB of human data generated on the African continent, some of the largest data sets to date for this type of sequencing. Efficient parallel and distributed implementations of common time-consuming NGS algorithms on modern computational infrastructures are imperative. The latter becomes pivotal as NGS will continue to transcend from research labs to clinical applications in the near future. Fast and efficient processing of data means that this can be directly translated back to the patient, directly impacting patient treatment and management.
Principal Investigator: Prof Richard Betz
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 15
Allocation Start: 2020-01-08
Allocation End: 2020-07-14
Used Hours: 82731
Project Name: Artificial Photosynthesis
Project Shortname: CHEM0872
Discipline Name: Chemistry
How do plants "do it"? Producing oxygen we breathe and food we consume by having nothing more than water, carbon dioxide, sun light and its leaves at their disposal?
Stay tuned for the answer...
Principal Investigator: Mr Ndumiso Mthembu
Institution Name: Epsilon Engineering
Active Member Count: 1
Allocation Start: 2020-01-10
Allocation End: 2022-12-08
Used Hours: 215146
Project Name: Epsilon Aerospace Computational Mechanics
Project Shortname: INDY1292
Discipline Name: Computational Mechanics
The Aerospace Epsilon Computational Mechanics is a research program that is offered by Epsilon Engineering Services. The program focuses on the use of Computational Fluid Dynamics (CFD) and Structural (FEA) analysis with Aeronautical applications (Manned and unmanned aerial vehicles) in defence. The analysis aids the development and or optimization of new or existing aircraft concepts.
CFD software currently in use is Star CCM+, Ansys Fluent and OpenFoam. FEA software in current use is Ansys Mechanical and Solidworks.
Epsilon is involved in a weapon systems integration project to develop a pylon for external store carriage. This particular project has made substantial use of the CHPC facility for high speed aerodynamic simulations that aided the development of the pylon. The simulations made use of the OpenFoam CFD code with the HISA solver add-in and Python for data postprocess. The appropriate computational resources provided by CHPC made the CFD analysis a practical part of the development process. Mandated by the design standard, a large Aerodynamic loads data set was necessary which included loads data at critical flight envelope points and corresponding aircraft maneuvers. The pylon development is still in progress and we are pleased to say that Epsilon Engineering is now in the second phase of the Aero-Mechanical design of a pylon and will be making use of the CHPC facility.
Principal Investigator: Prof Peter Nyasulu
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2020-01-13
Allocation End: 2020-07-11
Used Hours: 15480
Project Name: SimpactSimulation
Project Shortname: CBBI1184
Discipline Name: Applied and Computational Mathematics
SimpactSimulation as identified at CHPC, is a group from the University of Stellenbosch working on a project that simulate heterosexual transmission of HIV and prevention in complex sexual networks. The simulations in this project are implemented through individual based models (IBMs) which allow individuals in the model to behave autonomous for an individual goal; one such is starting or ending a sexual relationship. The great gains in the nature of our work is that our model can be used as experiments in certain cases where it is unethical to perform in the real world.
In our current work, we seek to evaluate the impact of early access to antiretroviral drugs among adults on HIV incidence in young woman. For the model to be realistic we need to mimic the target population summary statistics by carefully calibrate the model. This is a very computational intensive process due to the complexity and computational burden associated with large number of model parameters and a large number of target statistics.
However, through the availability of CHPC and parallesation capabilities we are able to run model simulation with big enough population that allow huge amount of data storage for surrogates statistics to be computed from and matched to the real world summary statistics.
To-date, we have successfully developed a new calibration procedure which ihas been submitted at PlosOne for publication (Still waiting for feedback). The application paper were we have customized the Simpact model motivated by the eSwatini stepped wedge community randomized trial termed "MaxART". Therein, the study setting makes it difficult to make inferences about the effect of the study intervention on young people, 15-24 year-old. We anticipate our modelling study findings will inform the Treatment-as-Prevention strategy to reduce new HIV infections among young women taking into account age-disparate relationships, HIV viral load, treatment retention on the infected individual among other variables.
Principal Investigator: Dr Bubacarr Bah
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 9
Allocation Start: 2020-01-13
Allocation End: 2020-07-11
Used Hours: 71464
Project Name: Large Scale Computations in Data Science
Project Shortname: CSCI0972
Discipline Name: Applied and Computational Mathematics
The AIMS Data Science Research Group conducts research on data science, a significant component of which applies data science algorithms to solve real-world problems. For example, the leading user on this CHPC account, Samuel Mensah (a PhD student in the group), is working on the prediction of diseases from images of the retina. The images a huge and hence take a lot of space in memory and the deep learning algorithms do a lot of cycles (epochs) through the data. These simulations (training) would have been extremely slow if it was done on the student's personal computer. The CHPC facility has therefore helped the student make tremendous progress in his work. We are happy with the results he is getting and are in the process of preparing a manuscript from this work.
Principal Investigator: Dr Ruben Cloete
Institution Name: University of Western Cape
Active Member Count: 4
Allocation Start: 2020-01-14
Allocation End: 2020-07-12
Used Hours: 743830
Project Name: HIV-1C integrase drug resistance
Project Shortname: CBBI1154
Discipline Name: Bioinformatics
The research group of Dr Ruben Cloete is based at the South African National Bioinformatics Institute, University of the Western Cape. The work in my group is primarily focussed on molecular modelling and drug design. Here we focus on protein structure prediction, molecular docking and simulation studies of protein-drug, protein-protein systems. Our research efforts is in understanding HIV-1 drug resistance, identifying novel drugs to treat drug resistant Tuberculosis and the prioritization of novel genes associated with Parkinson's disease in South African families. This work has led to the identification of new drugs to treat Tuberculosis. Furthermore, ongoing work might also contribute to the understanding of the development of Parkinson's disease and the better treatment of HIV-1 infected individuals within South Africa. For this to become a reality requires the use of structural computational methods to understand the binding of drugs to the molecular machines called proteins. Therefore, large scale computing resources are required to run large protein systems. Currently we are running simulations for several protein-DNA-drug complexes on the CHPC cluster We may even require more resources.
Principal Investigator: Dr Katherine de Villiers
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2020-01-14
Allocation End: 2020-07-12
Used Hours: 60464
Project Name: Investigations of drugable targets relevant to antimalarial action
Project Shortname: CHEM0801
Discipline Name: Chemistry
The Bioinorganic research group (Haem Team) at Stellenbosch University (Dept. Chemistry and Polymer Science) is led by Dr Katherine de Villiers. Our primary research focus is towards understanding mechanism(s) of action of clinical antimalarials so that we are better informed when designing altogether new treatments. The latter is important because of resistance by the malaria parasite. The disease burden caused by malaria is a particular challenge in Africa, and this motivates our research efforts further. We have made use of the CHPC facilities to enable us to investigate drug-target interactions that would otherwise not be possible via experiment. In particular, we have used Materials Studio to investigate the interaction of antimalarials to the surface of crystals of synthetic malaria pigment, and Schrodinger to investigate drug-enzyme interactions.
Principal Investigator: Mr kirodh Boodhraj
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 2
Allocation Start: 2020-01-15
Allocation End: 2020-07-13
Used Hours: 49737
Project Name: Geospatial modelling regarding satellite imagery, oceans and coastal areas using machine learning, ODC and STAC
Project Shortname: CSIR1266
Discipline Name: Earth Sciences
Projects:
1) Creating forecasts for the ocean.
We are creating a set of machine learning models to use atmospheric data (rain, air temperature, solar radiation, humidity, wind) and create al least a 2 day forecast. These forecasts will be used in an ocean model (NEMO) to create an ocean forecast. This process involves the creation of custom machine learning models for each atmospheric variable. The models will need to be run on the CHPC due to the shear volume of data and the time it will take to run the models. The ocean model will be tuned and developed for the South African region encompassing the Agulhas and Benguela current in specific. Having an ocean forecast will be useful for boundary conditions for coastal models, navigation of ships at sea and also tracking possible weather anomalies among other uses.
2) Flow and Wave modelling using Delft 3d.
Delft 3d is used to model the complex behavior of the ocean interfacing the land, i.e. the coastal zone. Model development will help to answer many of the ports questions of ship safety, port crew safety and possible dangerous waves or current pattern shifts. Furthermore, the ocean forecasts (when operational) can provide boundary conditions to the coastal model and thereby provide forecasts.
Principal Investigator: Prof Tony Ford
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2020-01-15
Allocation End: 2020-07-13
Used Hours: 102146
Project Name: Computational studies of the properties of molecular complexes
Project Shortname: CHEM1134
Discipline Name: Chemistry
The press release currently on file is still valid. One collaborator, Dr Nkululeko Damoyi (Mangosutho University of Technology) is still active on the cycloaddition project. My other local collaborator, Professor Catharine Esterhuysen (Stellenbosch University) and I do not have a current project on which we are engaged, but the collaboration is open-ended.
The work seeks to establish the properties of a variety of molecular complexes of diverse natures, with the aim of establishing the common features of the various kinds of non-covalent bonding encountered among small molecules.
The computational procedure involves optimizing the structures of the various complexes by searching for energy minima on the particular potential energy surfaces, and computing the vibrational spectroscopic properties, using the standard computational software Gaussian-16. The computations, when carried out at a high level, require large amounts of resources, beyond the capacity of the average standard home laptop computer. Without the availability of the resources of CHPC this work would not be possible.
The project is open-ended, and novel systems are investigated as new ideas come to mind.
Being open-ended, the lifetime of the project is indeterminate; currently progress is favourable, within the time limitations referred to above.
Principal Investigator: Dr Gaston Mazandu Kuzamunu
Institution Name: University of Cape Town
Active Member Count: 13
Allocation Start: 2020-01-16
Allocation End: 2020-07-14
Used Hours: 18879
Project Name: Sickle Africa Data Coordinating Center (SADaCC)
Project Shortname: CBBI1243
Discipline Name: Health Sciences
Sickle Cell Disease is the most common monogenic diseases mainly caused by a single-point mutation in the beta-subunit of haemoglobin, the principal oxygen transporter in red blood cells. Because of the protective effect of the sickle cell mutation against malaria, sickle cell disease has the highest incidence and prevalence in tropical regions, particularly in Sub-Saharan African countries, where more than 70% of patients live, affecting approximately 300 000 newborn babies every year and more than 20 million people globally. Thus, the Sickle Africa Coordinating Center project at University of Cape Town, Faculty of Health Sciences under the Division of Human Genetics has been set to coordinate different type of sickle cell datasets across Africa: collection and analyses, and tackle issues related to this condition, including phenotype pattern prediction, diagnostics and treatments. Genetics being a key components for this condtions and considering more than 11000 patients that have been identified across Africa (Tanzania, Ghana and Nigeria), genomic datasets are now being carried out predicting and prioritizing in silico mutations leading to optimal therapeutics. This is important, especially with the current trend of gene therapy that is being suggested. With this sample size, which is expected to increase as the project is planning to expand to more African countries, High Performance Computing, such as CHPC is really needed to design scalable pipeline to effectively process these datasets to contribute to overcoming this disease.
Principal Investigator: Dr Rhiyaad Mohamed
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2020-01-17
Allocation End: 2020-07-22
Used Hours: 50836
Project Name: Advanced materials for oxygen evolution reaction
Project Shortname: MATS1123
Discipline Name: Chemical Engineering
Hydrogen is seen as an integral part of the sustainable energy future. Through fuel cell and electrolyser technologies, energy storage and conversion will be possible. This will resolve some of the more critical challenges faced by most renewable energy sources. Co-hosted by the University of Cape Town and operating under the Catalysis Institute, HySA Catalysis (Hydrogen South Africa Catalysis), part of a flagship programme funded by the Department of Science and Technology, aims to find efficient and market ready catalyst technologies for both hydrogen fuel cells and water electrolysers. The former has been an age-old activity with a strong internal knowledge base. On the other hand, water electrolyser research is a new venture with many unresolved and unknown challenges. The Electrolyser Research Group is a new, young and dedicated group in the area of water electrolysis within HySA Catalysis.
We aim to take advantage of both experimental techniques and fundamental principles to predict and design new and better catalysts. Our research is broken down into two main categories, catalyst design and electrode membrane assembly development for commercialisation. Computational resources provided by CHPC's Lengau supercomputer enables us to perform quantum-chemical calculations to understand material properties. Whilst traditionally, unsupported iridium oxide has been used as an electrolyser catalyst, the scarcity and cost of iridium is a good justification to pursue research in supported iridium catalysts—these catalysts will of course require durable and conductive supports. Since some of these materials have never been synthesised before it is critical to methodically predict stable and electrically conductive material for use in water electrolysers. Based on chemical intuition we have identified a class of materials, doped oxides, which may possess excellent electrochemical properties. We have identified doped tin oxide and titanium dioxide as potential catalysts supports—our computational studies have now given us electronic properties of doped tin oxide.
In summary our current results suggests that better control of the doped-oxide stoichiometry hold great potential for the design of conductive support materials for electrolyser catalysts.
Principal Investigator: Dr Steven Hussey
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-01-20
Allocation End: 2020-07-18
Used Hours: 68370
Project Name: Forestry Molecular Genetics - transcriptional and epigenetic regulation of wood formation
Project Shortname: CBBI1010
Discipline Name: Bioinformatics
The Forest Molecular Genetics Programme is a joint venture of the University of Pretoria and South African forestry industry partners aimed at developing biotechnology applications for tree improvement. It focuses on the genetic basis of tree growth, wood formation and defence against pests and pathogens. The SA forestry industry produces over 20 million tons of wood per year for a wide array of renewable products such as timber, pulp, paper, packaging, cellulose, textiles, pharmaceuticals and food additives. Increasingly, there is interest in using trees as biorefineries, i.e. energy-efficient production platforms for high-value biopolymers and biochemicals. Timber from genetically improved plantations can also be processed into advanced building materials for sustainable housing and construction. In part, the Programme aims to understand the biology of wood formation and how it is regulated at various levels. For example, the metabolism and incorporation of carbon-rich compounds formed from photosynthesis into cellular structures such as wood, and the role of networks of genes coordinating the activation of genes at the correct stages of growth and wood formation. An important part in understanding these process is the use of DNA sequencing technologies that produce data requiring high-performance computation to analyze it. These tools were central to decoding the genome or DNA sequence of Eucalyptus grandis, an important fast-growing tree. Our Programme has most recently relied on the Centre for High Performance Computing to understand how cellular organelles participate in wood formation by analysing gene expression patterns associated with the poorly understood plastid organelles found in wood, and implementing novel transfer machine learning approaches to infer gene regulatory networks underlying wood formation in Eucalyptus based on machine learning models built on thousands of gene expression and gene-gene interaction datasets from the model plant Arabidopsis.
Principal Investigator: Prof Gerrit Basson
Institution Name: Stellenbosch University
Active Member Count: 6
Allocation Start: 2020-01-20
Allocation End: 2020-07-18
Used Hours: 323341
Project Name: CFD modelling of Hydraulic Structures in Rivers
Project Shortname: MECH0985
Discipline Name: Computational Mechanics
The Institute for Water & Environmental Engineering Stellenbosch University has 3 Doctoral students and 3 Post-Doctoral student who are investigating CFD modelling of hydraulic structures with complex vortices and sedimentation. Key aspects of the research are related to the improved prediction of bridge pier scour, to investigate the addition of flares on spillways, to reduce rock bed scour in plunge pools at spillways, to optimize the design of vortex settling basins, sand traps and settlers for sedimentt removal at hydropower and water abstraction plants. The simulations are too computationally intensive for standard computers and the CHPC assists in the research by allowing the students to more extensively explore the hydraulic behaviour of these structures.
Principal Investigator: Dr Leigh Johnson
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2020-01-20
Allocation End: 2020-07-18
Used Hours: 793279
Project Name: MicroCOSM: Microsimulation for the Control of South African Morbidity and Mortality
Project Shortname: HEAL1049
Discipline Name: Health Sciences
The MicroCOSM project, based at the Centre for Infectious Disease Epidemiology and Research at the University of Cape Town, is a project to simulate the spread of infectious diseases, as well as the incidence of non-infectious diseases, in the South African population. By simulating the social and biological factors that contribute to disease transmission, we can better understand which sub-populations need to be targeted for special interventions. We can also evaluate the impact that various prevention and treatment programmes have had in South Africa to date, and evaluate the potential impact of new programmes. This simulation involves generating nationally representative samples of 20,000-40,000 South Africans and tracking them over their life course. Because this involves many individual-level calculations, the model requires substantial computing power, and the CHPC is therefore critical to the conduct of these simulations. We have recently used the model to inform WHO guidelines on screening for cervical cancer.
Principal Investigator: Prof Lyudmila Moskaleva
Institution Name: University of the Free State
Active Member Count: 0
Allocation Start: 2020-01-21
Allocation End: 2020-07-27
Used Hours: 172150
Project Name: Understanding surface reactivity of solids using DFT simulations
Project Shortname: CHEM1294
Discipline Name: Chemistry
We investigate surface reactivity of solids at the atomic level using first-principles quantum-chemical methods, molecular dynamics, statistical theory, microkinetic modelling and thermodynamics. Quantum chemical methods, in particular, those based on density functional theory (DFT), are becoming increasingly popular and powerful. They can be used successfully to achieve a mechanistic understanding at the microscopic level, which is needed to optimize functional materials (such as catalysts, electrocatalysts, semiconductors, optoelectronic materials) with respect to their target properties.
We would like to mention two of our recent successful projects. One of them is a computational study on the properties of a hybrid 2D system which comprises in-plane graphene and hexagonal boron nitride (h-BN) components. We have investigated the influence of graphene or h-BN domain size on the atomic geometries, electronic properties and thermodynamic properties of prototypical graphene/h-BN hybrid systems by first-principles calculations. We have demonstrated that the band gap and the thermodynamic properties can be tuned by varying the graphene or h-BN domain size. The results of this study are currently submitted to FlatChem.
Another successful project relates to the chemistry of nanoporous gold (np-Au), a versatile material possessing interesting mechanical, optical, and catalytic properties. Our study is focused on the remarkable low-temperature catalytic activity of np-Au and its high selectivity toward partial oxidation reactions. Oxidation of methanol has been studied as a model that could be extended to higher alcohols. Our theoretical studiy provides a detailed mechanistic picture of a complex reaction energy network on the stepped Au(321) surface from methanol co-adsorbed with O2 all the way to methyl formate partial oxidation product. The mechanism includes over 20 elementary steps. Each elementary step has been characterized by a transition state structure and two minima of the reactants and products. Furthermore, we have studied the effect of Ag and Cu impurities (commonly present in np-Au) on the reaction energies and barrier heights. A manuscript describing this work is currently in preparation.
Principal Investigator: Dr Adeola Joseph Oyenubi
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2020-01-21
Allocation End: 2020-07-19
Used Hours: 52748
Project Name: Optimizing balance in for Impact Evaluation
Project Shortname: ECON1213
Discipline Name: Economics and Finance
This research is conducted by Dr Oyenubi, a lecturer at the University of the Witwatersrand.
Usually policy interventions (like the child support grant programme) require assessment in terms of the impact of the policy on beneficiaries. To do this a researcher must compare the response units under the policy with units that are not under the policy. For this comparison to be valid the two groups should have identical characteristics or covariates. This is achieved by comparing the distribution of covariates using various balance statistics e.g. mean and standardized difference in means.
This work assesses if the performance of different balance statistics vary in terms of their ability to compare the distribution of covariates. The premise is that differences in the performance of balance measures will lead to variation in the estimate of policy impact. With no guidance on the performance of various balance measures it will be difficult to identify the correct impact estimate.
This work will provide guidance to researchers on how to use the various balance measures that are available when estimating the impact of a policy. However doing this require extensive Monte Carlo experiments. This experiments are computationally expensive and without the CHPC the work will be virtually impossible.
The process involves setting up a data generating process that mimics various condition that is encountered in real life impact assessment. In this fictitious world we know what the correct impact estimate is. We then use various method to try and estimate this (known) impact estimate. The idea is that some methods will perform well while others will fail. This knowledge (about what method performs better and under what conditions) can then be used on real life data where we do not know the correct impact estimate.
The first part of this project is completed, and the second part is just starting.
Principal Investigator: Prof Mahmoud soliman
Institution Name: University of KwaZulu-Natal
Active Member Count: 33
Allocation Start: 2020-01-21
Allocation End: 2020-07-19
Used Hours: 1367001
Project Name: Drug Design, development and modelling
Project Shortname: HEAL0790
Discipline Name: Health Sciences
The research scope of the Molecular Bio-Computation and Drug Design Research Lab covers a wide range of computational and molecular modeling research areas with main focus on biological systems and drug design approaches. Main interest is related to design and study of biologically and therapeutically oriented targets by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We show keen interest in diseases of global burden and evident prevalence within the south African populace such as HIV/AIDS, Tuberculosis and Cancer. The computational resources provided by CHPC is employed in performing the molecular dynamic calculations and the corresponding post molecular dynamic simulation analysis.
Principal Investigator: Dr Gwynneth Matcher
Institution Name: Rhodes University
Active Member Count: 6
Allocation Start: 2020-01-21
Allocation End: 2020-07-19
Used Hours: 13092
Project Name: Microbial Ecology in Antarctic and aquatic ecosystems
Project Shortname: CBBI0952
Discipline Name: Environmental Sciences
Our research group, at Rhodes University, focuses on Antarctic microbial ecology. Antarctica experiences extreme physical conditions (e.g. low temperatures, high UV radiation, etc.) all of which impose enormous survival pressures on the fauna and flora. What is not commonly known is that the vast majority of the biomass in Antarctica is represented by microbes which, for most regions, have not been investigated. In order to provide accurate and holistic distribution patterns of the biota in Antarctica, these knowledge gaps need to be filled in. The relative simplicity of the trophic systems found in Antarctica make these ecosystems particularly vulnerable to the effects of global climate change. In order to assess the effect of global climate change on biodiversity, the current biodiversity of microbial species and their contribution to ecosystem functioning (e.g. decomposition, nutrient cycling, etc.) needs to be established. Our research assesses microbial populations using sequence analysis of target genes and metagneomic analyses. The data generated is analysed on the CHPC servers and allows us to identify which microbial species are present and their role in the functioning of these ecosystems.
Principal Investigator: Dr Melanie Rademeyer
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-01-21
Allocation End: 2020-07-19
Used Hours: 21919
Project Name: Properties of organic-inorganic hybrids
Project Shortname: MATS0823
Discipline Name: Material Science
The Material Science Research Group at the University of Pretoria, lead by Prof Melanie Rademeyer, focuses, among others, on the computation of the magnetic properties of organic-inorganic hybrid materials. Magnetic materials are important materials due to their potential technological applications, and organic-inorganic hybrid materials offer a unique opportunity in terms of the material design approach followed.
The successful calculation of the magnetic properties of these materials will allow for the identification of hybrid materials with promising magnetic properties. The materials identified via the computational method will then be synthesised in the laboratory and their magnetic properties measured experimentally via SQUID magnetometry.
The computational method involves the use of the single crystal structure of the material, as well as quantum mechanical and statistical thermodynamic calculations.
Significant progress has been made, with the magnetic properties of a number of organic-inorganic hybrid compounds having been calculated successfully employing the resources offered by the CHPC.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2020-01-21
Allocation End: 2020-07-19
Used Hours: 19560
Project Name: CFD modelling of jet impingement with phase change
Project Shortname: MECH1296
Discipline Name: Computational Mechanics
Jet impingement heat transfer with boiling is a promising new heat transfer method for use in power electronics cooling. Jet impingement flow is difficult to simulate because of its transient nature and multiple flow regimes involved (from laminar to turbulent). Previous research by Prof Ken Craig's group has developed techniques based on Large Eddy Simulation to evaluate the effect of round jets with and without swirl on solar receiver heat transfer surfaces. This program extends that work to having phase change as well in the form of boiling. The latent heat absorbed by boiling works in addition to the enhance convection provided by the jet. Various case studies are being developed for application in the electronics cooling industry.
Principal Investigator: Prof Tahir Pillay
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2020-01-24
Allocation End: 2020-07-22
Used Hours: 86001
Project Name: Molecular Modelling of ligands and receptors
Project Shortname: HEAL0876
Discipline Name: Health Sciences
Prof Tahir Pillay's research group in the Department of Chemical Pathology, University of Pretoria is actively working on the field of pharmcoinformatics applications in the genetic and acquired diseases. We have been using the facility of CHPC since 2014. The research group uses several pharmacoinformatics tools to design computational models followed by screening of small molecular databases and simulations for therapeutic application in several diseases including HIV/AIDS, Tuberculosis, Alzheimer's, Malaria, etc. For this purpose we are extensively using Schrodinger, Amber, Gromacs etc. Therefore, the research work is entirely dependent on pharmacoinformatics tools available in the CHPC server. The department does not have sufficient infrastructure to carry out the research in the current project. Hence, our research group requires access to the CHPC server to fulfil the objectives of the current project. We are quite happy with the services available in the CHPC server and would like to thank entire team for their efforts and support.
Principal Investigator: Prof Nelishia Pillay
Institution Name: University of Pretoria
Active Member Count: 8
Allocation Start: 2020-01-24
Allocation End: 2020-07-31
Used Hours: 922303
Project Name: Nature Inspired Computing Optimization
Project Shortname: CSCI0806
Discipline Name: Computer Science
The NICOG (Nature Inspired Computing Optimization Group), based at the University of Pretoria, employs machine learning techniques, taking an analogy from nature, to solve real world problems to attain the sustainable development goals defined by the United Nations. This research is solving problems in the health sector, e.g. disease prediction, agriculture, e.g. disease and pest prediction and industry, e.g. logistics, scheduling and classification problems. As we move into the fourth industrial revolution, machine learning is playing a major role in solving these problems. The algorithms used to solve these problems are computationally expensive and hence high performance computing is needed for the implementation of the algorithms. We are at point where we need to make these approaches easily accessible to non-experts. Hence, one of the current foci of NICOG is the automated design of machine learning techniques to produce off-the-shelf tools for non-experts. Such automated design, which is essentially an optimization problem, is also computationally expensive and thus also requires high performance computing.
Principal Investigator: Dr Calford Otieno
Institution Name: Kisii University, Kisii, Kenya
Active Member Count: 3
Allocation Start: 2020-01-27
Allocation End: 2020-09-03
Used Hours: 43390
Project Name: FIRST PRINCIPLE ELECTRONIC STRUCTURE CALCULATIONS OF EMERGING MATERIALS FOR SOLAR CELL APPLICATIONS.
Project Shortname: MATS1083
Discipline Name: Physics
Our Computational Condensed matter Group is a computational material modelling group with research areas in; Emerging materials for solar cell applications and energy harvesting, superconducting materials for various industrial and novel oxides for various industrial applications. There is need for clean and renewable energy sources and such research groups as ours seek to study new/emerging materials for energy harvesting and how that energy will be transported with minimal loss. Our research basically employs Opensource software to carry out first principle calculations and due to high cost in computing we employ the capability of the CHPC. The research is progressing well and students in Masters of Science and Doctor of Philosophy are due READY to gradute soon as the PANDEMIC IS CONTAINED
Principal Investigator: Prof Charalampos (Haris) Skokos
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2020-01-27
Allocation End: 2020-07-25
Used Hours: 1576959
Project Name: Chaotic behavior of Hamiltonian systems
Project Shortname: CSCI1007
Discipline Name: Applied and Computational Mathematics
Using modern numerical techniques of Nonlinear Dynamics and Chaos Theory we investigate in a unified mathematical way the behavior of models describing the energy transport in disordered and granular media, as well as the properties of new elastic materials like graphene and molecules like the DNA. This research is performed by members of the 'Nonlinear Dynamics and Chaos Group' in the Department of Mathematics and Applied Mathematics at the University of Cape Town. The performed investigations constitute an innovative combination of Applied Mathematics, Chaos Theory, Hamiltonian Dynamics and Nonlinear Lattice Dynamics. Their outcomes will provide answers to some fundamental questions about the effect of chaos on the energy transport in disordered and granular media, and on the behavior of graphene and DNA. Some of the questions we try to address are: Does the presence of impurities and nonlinearities enhance or suppress the propagation of energy (e.g. heat) in solids, of light in crystals, and of vibrations in granular material? How does the ratio of the different base pairs in DNA chains affect their structural stability and the temperature at which the double-stranded DNA breaks to single-stranded DNA?
Principal Investigator: Dr Mohammad Moghimi Ardekani
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-01-28
Allocation End: 2020-07-26
Used Hours: 190534
Project Name: R&D in Solar Energy in particular Concentrating Solar Power Research
Project Shortname: MECH1137
Discipline Name: Computational Mechanics
Dr Moghimi Ardekani and his research team from University of Pretoria working on delivering Clean Energy Technologies especially Solar Energy.
Solar Energy is one of the abundant sources of energy which significantly can solve energy crisis in Africa in particular south Africa. This abundant source of energy can secure the future energy reliability of South Africa.
In our research group we are working on series of computational simulations which highly rely on these resources to run all those simulations.
This continuous project is running well and so far 1 master student got graduated and two more are getting graduate by April 2021.
Principal Investigator: Prof Gerhard Venter
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2020-01-28
Allocation End: 2020-07-26
Used Hours: 3879
Project Name: Finite Element Analysis and Numerical Design Optimization
Project Shortname: MECH0883
Discipline Name: Computational Mechanics
Again - nothing much to report yet. We are just getting started again. However the project is in collaboration with a local truck manufacturer and hopefully press worthy results will be generated.
Principal Investigator: Prof Eric van Steen
Institution Name: University of Cape Town
Active Member Count: 9
Allocation Start: 2020-01-28
Allocation End: 2020-07-26
Used Hours: 1080384
Project Name: Lateral interactions on surfaces
Project Shortname: CHEM0780
Discipline Name: Chemistry
Catalysis plays an important role in the production of all kind of materials required in our life (and over 75% of all materials has seen a catalyst during its manufacture). Catalysis is a surface phenomenon and our understanding of the processes taking place has grown dramatically with the advent of modern DFT-tools (requiring CHPC resources). For instance, DFT has given greater insight on how molecules interact with each other on the surface. Furthermore, it has given us insight into why some reactions may or may not proceed over a certain catalyst.
The development of improved catalysts is essential in order to design energetically more efficient processes and safer processes. This program gives us directions to find these catalysts with better characteristics.
Principal Investigator: Prof Josua Meyer
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2020-01-28
Allocation End: 2020-07-26
Used Hours: 1384741
Project Name: Fundamentals of forced and mixed convection in heat exchangers
Project Shortname: MECH1094
Discipline Name: Computational Mechanics
In-tube condensation is widely seen in many industries such as desalination, power plants and air conditioning. Thoroughly understanding of the condensation phenomenon would lead to better design of the systems which consequently causes the improvement of system efficiency. Although in majority of applications the circular tubes are used, there are some particular cases, like in air-cooled steam condensers, in which non-circular tubes such as rectangular tubes and flattened tubes are utilized. It has been proved that the thermal efficiency of such tubes are better as compared to the conventional circular tubes under specific operating conditions.
This work is being done by the Clean Energy Research Group (CERG) at the University of Pretoria. This group is involved in experimental and numerical heat transfer research focused on clean energy applications. CERG, falling under the Department of Mechanical and Aeronautical Engineering at the University of Pretoria, has a number of world class experimental facilities focused on heat transfer, balanced by a Computational Fluid Dynamics (CFD) division. The Group members have developed, designed and built five unique, state of-the-art experimental set-ups, which are being used for leading-edge heat transfer research.
Due to lack of water resources in South Africa, the research works on the optimizing and performance enhancement of systems working with water as the working fluid should be greatly developed. Such activities will definitely lead to lower energy and water consumption within the country in the future.
It is the purpose of this research work to numerically investigate the effect of inclination on condensation of steam inside a long flattened channel. Thoroughly understanding of this problem via numerical simulations would assist in proper design of ACCs with low cost and time compared to experimentation.
At the moment, most of the work has been done, and a research paper is going to be prepared.
Principal Investigator: Dr Mervlyn Moodley
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2020-01-29
Allocation End: 2020-07-27
Used Hours: 16093
Project Name: Computational studies of corrosion in transformers
Project Shortname: MATS1120
Discipline Name: Physics
The Computational Studies group based at University of Kwazulu-Natal is set to understand the corrosion mechanisms involved in the failure of transformers. The failures of transformers have been linked to the interaction of copper sulphide and copper windings and due to the interaction of silver sulphide on silver surfaces. The copper sulphide is a product of copper particles that react with the corrosive sulphur within the transformer oil. This copper sulphide thereafter deposits on the vacant sites of the copper windings. Density functional theory (DFT) techniques are used in various fields of study and have proved most effective in handling interactions between molecules and surfaces. In this research the DFT techniques are used to understand the interaction of copper sulphide on copper surfaces to obtain energetic, electronic and thermodynamic properties of the system. The interactions of sulphur containing molecules on silver surfaces were also investigated. The understanding of the failures on a computational level would help in creating a model to prevent further failures and to track current failures caused by corrosion. The failures of transformers have also been found to affect both financial and economic sectors due to the high cost in repairing or replacing these failed transformers. This research relies heavily on CHPC resources due to the extensive computational methods needed to understand this complex system. The CHPC provides the Materials Studio Software and a connection to the Lengau Cluster which increases the accuracy of the results and reduces computational time. This project has so far obtained results of the copper sulphide interaction with the copper surface. Upon investigation it was found that more research is required to fully understand the method of corrosion and the interaction of additives in the transformer oil. The CHPC resources are also needed to compute a remedial process to prevent further transformer failures.
Principal Investigator: Dr Kevin Lobb
Institution Name: Rhodes University
Active Member Count: 7
Allocation Start: 2020-01-30
Allocation End: 2020-07-28
Used Hours: 158757
Project Name: Computational Mechanistic Chemistry and Drug Discovery
Project Shortname: CHEM0802
Discipline Name: Chemistry
In the current cycle use has been made of the CHPC particularly in one facet of our research programme - and that is with mechanistic chemistry or determining how reactions occur.
However we also have made progress on studies exploring more medicinal chemical routes with two completed studies identifying how a series of synthesized chemical analogues interact with malarial proteins; and a third different study looking at DHPS.
Current new work that is starting is with two MSc students exploring possible active compounds against SARS-CoV-2 main protease.
Principal Investigator: Mr Reshendren Naidoo
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2020-01-30
Allocation End: 2020-07-28
Used Hours: 84276
Project Name: Influence of Gas Phase Kinetics on a Pulverised Coal Flame
Project Shortname: MECH1298
Discipline Name: Computational Mechanics
The combustion of coal particles is a complex process and there are several physical processes at play. These processes are in turn highly dependent on the quality of coal being combusted and hence there must be direct link between the numerical methods employed and the true heterogeneous nature of coal. One of these facet is the way combustible material is released from coal particles. The chemical mechanisms that are used to predict the flame characteristics are important to understand the ignition/stability and emissions profile of a given combustion regime. Hence it is important to study these chemical mechanisms.
Principal Investigator: Dr Malebogo Ngoepe
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2020-01-30
Allocation End: 2020-07-28
Used Hours: 39055
Project Name: PROTEA
Project Shortname: MECH1194
Discipline Name: Computational Mechanics
Our group focuses on studying problems related to biomechanics or the overlap of biomechanics and biochemistry. These are currently applied to the study of thrombosis, hair, myocardial infarction and congenital heart disease. Our use of HPC largely relates to the use of computational fluid dynamics codes to develop interventional planning tools, both for thrombosis and congenital heart disease. Thrombosis is the main underlying condition in a large number of cardiovascular diseases and understanding its progression will be beneficial for management of chronic diseases, which are on the rise. Similarly, understanding congenital heart disease will contribute to long term management of conditions which continue to affect individuals over a lifetime.
Principal Investigator: Prof KHALED ABOU-EL-HOSSEIN
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 0
Allocation Start: 2020-02-05
Allocation End: 2022-06-02
Used Hours: 7515
Project Name: Ultra-High Precision Machining of Optical Materials
Project Shortname: MATS0971
Discipline Name: Material Science
We at the Nelson Mandela University are absolutely thankful to the Centre of High Performance Computing for facilitating the use of their computing facilities. This have allowed us to conduct high performance simulations at the molecular level of some optical materials used in the aerospace and optical industries. The simulation results have been useful to understand the behaviour of optical materials when they are shaped into optical components without the the need to run extremely expensive laboratory experiments.
A number of PhD students who have been helped by CHPC have already graduated from the Machatronics of Nelson Mandela University
Principal Investigator: Prof Juliet Pulliam
Institution Name: Stellenbosch University
Active Member Count: 21
Allocation Start: 2020-02-05
Allocation End: 2020-08-03
Used Hours: 48429
Project Name: South African Centre for Epidemiological Modelling and Analysis
Project Shortname: CBBI1106
Discipline Name: Other
SACEMA is a DSI-NRF Centre of Excellence focused on Epidemiological Modelling and Analysis, hosted at Stellenbosch University. We use computational approaches to address questions of public health relevance to South Africa and the African continent. We use the CHPC primarily to run stochastic simulations and for simulation-based validation of novel inference methods.
Principal Investigator: Dr David Pearton
Institution Name: Oceanographic Research Institute (ORI)
Active Member Count: 6
Allocation Start: 2020-02-05
Allocation End: 2020-08-03
Used Hours: 1326
Project Name: Responses of South African Coral Reefs to Climate Change
Project Shortname: CBBI1072
Discipline Name: Environmental Sciences
The reef team of the Oceanographic Research Institute, part of the South African Association for Marine Biological Research, is dedicated to preserving and understanding the incredibly rich and important reef ecosystems of the amazing South African coasts. These critical ecosystems provide food and livelihoods to millions of people across the globes but are under threat from a wide variety of sources, including climate change, ocean acidification, pollution and overfishing. The ORI reef team is using a combination of traditional and cutting edge techniques to better understand the rich biodiversity and ecosystem processes in order to enhance their resilience and safeguard them for future generations. The resources and facilities provided by the CHPC are critical for us to analyse the vast amount of data generated by new techniques including metabarcoding, transcriptomics and RADSeq that allow us to understand both how both ecosystems and individual organism interact with each other and the environment and to environmental change.
Principal Investigator: Dr Mary-Jane Bopape
Institution Name: South African Weather Service
Active Member Count: 19
Allocation Start: 2020-02-06
Allocation End: 2020-08-04
Used Hours: 28586
Project Name: Very Short Range Forecasting
Project Shortname: ERTH1022
Discipline Name: Earth Sciences
Weather and climate extremes can have adverse effects on the society. The CHPC cluster is making it possible for scientists within the Southern African Development Community (SADC) region to study the sensitivity of simulating high impact weather events on different physics processes and resolution. These studies will help meteorological services who have a mandate to provide weather and climate services for the safety of lives and property decide on the best model configurations to use for weatehr forecasting.
Principal Investigator: Prof Penny Govender
Institution Name: University of Johannesburg
Active Member Count: 11
Allocation Start: 2020-02-10
Allocation End: 2020-08-08
Used Hours: 916887
Project Name: Design of MOFs-based sorbent materials for capturing carbon dioxide
Project Shortname: CHEM0797
Discipline Name: Material Science
Environmental and energy problems are important topics globally due to the fast development of urbanization, huge population increases and industrialization. Recently, water pollution is a major issue in developing countries, particularly in regions where people rely on groundwater for domestic and drinking purposes. Almost 40 % of the world's population is facing water shortage. Most countries depend on the low-efficient power generation from the burning fossil fuels as their source of energy. The burning of fossil fuels normally generates a huge amount of CO2, which induces environmental concerns, such as greenhouse effect. As non-renewable natural resources, fossil fuels cannot be sustainable and depleted shortly in the next century owing to their environmental issues and high consumption rate. This has led to the investigation of photocatalysis as a possible solution to the problem. Despite significant concern and substantial efforts, the design of semiconductor photocatalyst materials that is both efficient and robust enough for water/wastewater treatment and energy production is still lacking. Due to the complexity of the experimental process, it is difficult to know the mechanism and origin of the enhanced photocatalytic performance. The first-principles approach is highly desirable in the area of materials science, particularly for understanding both the photocatalysis of nanomaterials, as well as the subsequent physical and chemical properties. Density functional theory (DFT) calculations was used as the method of clarification as it has already proven its superiority in studying the structural stabilities, electronic properties, work functions, charge transfer, and carrier effective mass of several semiconductor photocatalyst materials due to its reduced computational cost in calculating the electron density rather than the wave function.
Principal Investigator: Prof Daniel Joubert
Institution Name: University of the Witwatersrand
Active Member Count: 16
Allocation Start: 2020-02-10
Allocation End: 2020-08-08
Used Hours: 2004566
Project Name: Energy Materials: Numerical explorations
Project Shortname: MATS0800
Discipline Name: Physics
Imagine designing a material atom by atom. Imagine analysing the properties of tomorrow's novel materials before they exist. Computational materials science plays an important role at every of level of the design and engineering of new materials. The rapid advances in computer processing power and memory has given virtual, fundamental, materials design a boost. The first problem faced in designing a virtual material, a material that has not yet been made, is to find the stable configurations in which the atoms in the mix will settle into. The designer must find the configuration of electrons and nuclei, the building blocks of atoms, which result from the interactions among a number of particles that, even for a small piece of material, exceeds the number of particles of sand on all the beaches in the world. This daunting task has a simple solution. Instead of finding the configuration of the real material, the problem is solved for a fictitious material where the constituent particles do not interact. All that is necessary is to find the particle density distribution of the fictitious material, which by design, is the same as that of the real material. A Noble prize was awarded for this idea to the chemists Walter Kohn and John Pople in 1998.
A group of postgraduate students at the University of the Witwatersrand use the computer power at the national Centre for High Performance Computing to conduct virtual experiments on existing and novel materials to examine their potential as energy harvesters. They examine the potential of a selection of materials that can be used as cheap components in solar cells, materials that can generate electricity from waste heat and materials that can be used to split water molecules to extract hydrogen for energy production.
Principal Investigator: Prof Mwadham Kabanda
Institution Name: University of Venda
Active Member Count: 2
Allocation Start: 2020-02-10
Allocation End: 2020-08-08
Used Hours: 257518
Project Name: Reaction mechanism for atmospheric relevant molecules
Project Shortname: CHEM1161
Discipline Name: Chemistry
The study of reaction mechanisms related to atmospheric environment is still a challenge from both experimental and theoretical approaches. The biggest challenges to quantum chemical approaches is the selection of computationally affordable methods that allows for the estimation of the reaction enthalpies and kinetics with high accuracy to species with unpaired electrons. In our research group, headed by Prof MM Kabanda (University of Venda – Department of Chemistry) and his PhD student KP Otukile (University of Venda – Department of Chemistry), the study of the reaction of NO3 radical species in the atmosphere is being investigated. This specieas has proved challenging to model, especially using density functional theory. It is there necessary that a large set of functionals be tested to determined their ability for utilisation in the estimation of the properties of NO3 radical before the study of the reactions involving this radical can be performed.
So far, the research has produced preliminary results and we look forward to publish the results in the near future. Meanwhile we are continuing with identify other functionals that could be deemed useful for utilisation in the study of NO3 radical properties.
Principal Investigator: Prof Robin Emsley
Institution Name: Stellenbosch University
Active Member Count: 6
Allocation Start: 2020-02-10
Allocation End: 2020-08-08
Used Hours: 1625
Project Name: EONCKS
Project Shortname: CBBI1064
Discipline Name: Health Sciences
The Schizophrenia Research Unit is nested within the Department of Psychiatry at Stellenbosch University. The Unit has been involved in research for decades and continues to produce Master's and PhD students of the highest calibre. The team's focus is on improving outcome in first-episode schizophrenia patients and their work contributes knowledge that can help improve the quality of patient-care in the South African health-care system. The Schizophrenia Research Unit is committed to delivering the highest level of care to the patients that come through our door as well as providing the best quality training to the students and researchers under our tutelage.
Our continued collaboration with the CHPC has been integral to our efforts to better understand schizophrenia through the use of their Lengau cluster to process MRI brain scans included in our research project. This has allowed us to investigate the effect of antipsychotic medication on the brain. Using the Lengau cluster allows our unit to remain on the cutting edge of new neuroimaging techniques by speeding up our processing timelines and ensuring that we can publish our results and make meaningful contributions in far shorter times than it would otherwise be possible.
Principal Investigator: Mr Muaaz Bhamjee
Institution Name: University of Johannesburg
Active Member Count: 5
Allocation Start: 2020-02-11
Allocation End: 2020-08-09
Used Hours: 74598
Project Name: Modelling of Multiphase Flow in Process Equipment
Project Shortname: MECH0837
Discipline Name: Computational Mechanics
The research group is from the Department of Mechanical Engineering Science at the University of Johannesburg. The primary area of interest in the research is the use of coupled computational fluid dynamics and computational granular dynamics models to investigate the complex multiphase interaction in process equipment.
The models are based on multiple continuum and meso-scopic based approaches which are couple with models such as the Discrete Element Method, Immersed Boundary Method and Eulerian Dense Discrete Phase Models. Both commercial and open-source software has been used in the research. Primarily the research has been focused on
hydrocyclones. However, the research is moving onto fluidised beds, spiral concentrators, highly concentrated slurry flows and gas cyclones. The models are benchmarked accuracy) against experimental measurements as well as for computational efficiency. Accurate and computationally efficient modelling of such phenomena is vital to the design of hydrocyclones which is crucial to the mining industry. The research group has also begun to use this platform to model fluid dynamics in biomedical applications. The research group has produced numerous publications and has supported the research of four post-graduate students. Research into the computational efficiency of the models is continuing with the aid of the Centre for High Performance Computing (CHPC) facilities. Due to the complex physics and fidelity required in the problems tackled by the research group large computational resources are required. The CHPC provides a computational platform that is vital to the ongoing work and success of the research group.
Principal Investigator: Mr Jean Pitot
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2020-02-11
Allocation End: 2020-08-09
Used Hours: 161584
Project Name: SAFFIRE Programme
Project Shortname: MECH1121
Discipline Name: Computational Mechanics
The University of KwaZulu-Natal's Aerospace Systems Research Group (ASReG) is at the forefront of rocket propulsion research in academia, both in South Africa and Africa as a whole. Located at the University's Discipline of Mechanical Engineering, ASReG primarily conducts research in the areas of liquid and hybrid rocket propulsion, as well sounding rocket development. The SAFFIRE Programme aims to develop South Africa's first fully-integrated liquid rocket engine, which is being designed for use in a small satellite launch vehicle. The long-term intention of the programme is for the engine to enable the indigenous development of a South African space launch capability. To meet its developmental goals, the programme requires the simulation of complex computational models to predict the fluid dynamic, thermochemical and structural performance of various engine components. These simulations are typically very computationally-expensive, and require extensive computational resources to run within a reasonable time frame. The CHPC offers the only realistic means of obtaining access to such resources. The programme is progressing well, and 2020 has seen the intake of numerous new postgraduate and undergraduate students. In total, 15 postgraduate students and 23 honours-level undergraduate students are currently involved in ASReG's cutting-edge projects.
Principal Investigator: Dr Zibo Keolopile
Institution Name: University of Botswana
Active Member Count: 2
Allocation Start: 2020-02-12
Allocation End: 2020-08-10
Used Hours: 113267
Project Name: Physics
Project Shortname: MATS1303
Discipline Name: Physics
MATS1303: Our research group is based in the Department of Physics, University of Botswana. It is focused on electronic structure calculations of molecular systems. Here we study gas phase molecular systems comprised a cluster of 1 to 10 molecules depending on the availability of research and computer manpower. Most calculations cannot be performed on normal workstation, but a supercomputer, therefore, a need for a more robust High Performance Computer. We have, so far, studied molecular trimers of neutral oxalic acid and the journal paper is underway. We will then focus our attention on anionic trimers of oxalic acid clusters.
Principal Investigator: Dr Ian Heywood
Institution Name: Rhodes University
Active Member Count: 0
Allocation Start: 2020-02-12
Allocation End: 2020-08-10
Used Hours: 37433
Project Name: Black holes near and far
Project Shortname: ASTR1301
Discipline Name: Astrophysics
The South African MeerKAT radio telescope is presently the most powerful of its kind in the world, and has undertaken a campaign to image the centre of our Milky Way galaxy as a test of its scientific readiness. The view of this region that is provided by imaging using radio waves reveals features that are invisible when observing by other means. This gives astrophysicists insight into some of the unique physical processes that allow the central supermassive black hole (weighing the same as 4 million suns) to influence the evolution of our entire galaxy. The CHPC is being used to re-process the MeerKAT observations to provide us with the best ever view of the Galactic Centre, work led by Ian Heywood (Univerisity of Oxford and Rhodes University) and PhD student Isabella Rammala (Rhodes University and SARAO). The process involves making sure the raw telescope measurements (some 60 TB of them) are properly calibrated, and then turning these into an image of the sky using a process called aperture synthesis. It is computationally intensive, so the CHPC has been a vital resource for this work. The MeerKAT data archive is also in the same building as the Lengau cluster, which has allowed rapid retrieval of the raw data products. We expect the final radio images to be ready for publication and use by the South African and global scientific community by the end of the year.
Principal Investigator: Prof Jeanet Conradie
Institution Name: University of the Free State
Active Member Count: 4
Allocation Start: 2020-02-12
Allocation End: 2020-08-10
Used Hours: 3773926
Project Name: Computational chemistry of transition metal complexes
Project Shortname: CHEM0947
Discipline Name: Chemistry
This project is concerned with the computational chemistry of transition metal complexes, with special focus on the application of computational chemistry in determining the structure and energy of transition metal complexes, transition states and reaction-intermediates. This is reflected in the outputs of my research group during the period of report. The outputs gave a better understanding of experimental observation and of the factors influencing the reactivity of metal complexes, in order to streamline them for use in different applications, for example in catalysis or energy sources (batteries and solar cells).
Principal Investigator: Prof Thulani Makhalanyane
Institution Name: Stellenbosch University
Active Member Count: 7
Allocation Start: 2020-02-13
Allocation End: 2020-08-11
Used Hours: 12425
Project Name: Metagenomics of extreme environments
Project Shortname: CBBI1023
Discipline Name: Bioinformatics
Over the past year, the team from the Microbiome group at the University of Pretoria have coauthored several studies on the microbial ecology of human and natural environments. The studies on human microbiomes have included gut microbiome studies of South African individuals from urban and rural locations. These studies have provided the first insights on the fungal microbiome of these individuals.
The studies on environmental microbiology have assessed the effects of climate change on extreme environments. For instance, a mesocosm experiment revealed the effects of temperature on soil microbiota. Another study revealed the innate immune systems linked to bacteria from these environments.
Microbial communities are numerically abundant, and vary markedly in terms of phylogeny and function. Access to CHPC computational resources has facilitated the analysis of 'big' microbial datasets. Such data place a computational burden on local servers and we would not have been able to produce our outputs without access to the CHPC.
Principal Investigator: Prof Mario Santos
Institution Name: University of Western Cape
Active Member Count: 18
Allocation Start: 2020-02-13
Allocation End: 2020-08-11
Used Hours: 877114
Project Name: Cosmology with Radio Telescopes
Project Shortname: ASTR0945
Discipline Name: Astrophysics
The Centre for Radio Cosmology (CRC) at UWC aims to fully explore the use of the next generation of radio telescopes for measurements in cosmology, in particular with MeerKAT and SKA. CRC staff is closely involved in the South African and international SKA projects. About 10 postdoctoral researchers and 10 PhD/MSc students are doing their research within the CRC. Our work at the CHPC is mostly focused on running simulations of signals we expect to observe with MeerKAT/SKA and test how well radio telescopes can constrain certain cosmological models. This is a crucial component in the process to use these telescopes for cosmology since we need to understand the signals we are observing. The project include simulations of the hydrogen emission from the early universe, simulations of the contaminants, simulations of the telescope itself and analysis of the constraining power of such telescopes on cosmological models.
Principal Investigator: Dr Krishna Govender
Institution Name: University of Johannesburg
Active Member Count: 6
Allocation Start: 2020-02-13
Allocation End: 2020-08-11
Used Hours: 379465
Project Name: Computational approaches to design novel anticancer agents
Project Shortname: CHEM0792
Discipline Name: Chemistry
This programme is mainly for benchmarking and testing of various codes on the cluster.
A small amount of time is devoted to research that is currently being established as a collaboration between myself and individuals from Sri Lanka.
Principal Investigator: Prof Thuto Mosuang
Institution Name: University of Limpopo
Active Member Count: 8
Allocation Start: 2020-02-13
Allocation End: 2020-08-11
Used Hours: 1309
Project Name: Computational studies of various ultra-hard materials
Project Shortname: MATS0875
Discipline Name: Material Science
This is a sensors and energy materials group at the Department of Physics, University of Limpopo. The group has two Doctoral and two Masters students. Computationally the research projects investigate nanomaterials like copper selenide, gallium nitride, graphene oxide, and boron nitride. Specifically electronic, structural, thermodynamic properties are investigated to enhance semiconductivity. These properties are then mapped with experimental properties for possible gas sensing and energy materials. DL_POLY software through the CHPC is being utilised in the structural, dynamical, and thermodynamic properties. The exciting code also through the CHPC is being utilised in the electronic and excited properties of the materials.
Principal Investigator: Prof Jean Greyling
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 2
Allocation Start: 2020-02-13
Allocation End: 2020-08-11
Used Hours: 79592
Project Name: A Generalized Bootstrapped Neuro-Simulator
Project Shortname: CSCI1305
Discipline Name: Computer Science
A Generalized Bootstrapped Neuro-Simulator is a research project belonging to the niche research group that was formed by Professor Greyling and Professor Calitz within the Computing Sciences Department at Nelson Mandela University. The research project is concerned with the development of an Evolutionary Algorithm that can be used to evolve successful software agents for complex environments whilst leveraging discovered information using modern Machine Learning techniques. The resultant algorithm has been shown to be more sample efficient than its counterparts. The research provides a theoretical justification for a powerful tool that has practical implications. The research project requires the use of CHPC resources as it dramatically increases the rate at which experiments can be performed and significantly improves the quality and quantity of research that can be produced. The project is on schedule and should be complete by the end of 2020.
South Africa's National Development Plan 2030 has placed a priority on and coupled Research and Development and Higher Education goals. CHPC has allowed for higher calibre research for our research project and has improved the research capacity of the students working within the group, thus aligning the project with the National Development Plan 2030 and preparing knowledge workers for the 4th Industrial Revolution.
Principal Investigator: Prof Rebecca Garland
Institution Name: University of Pretoria
Active Member Count: 13
Allocation Start: 2020-02-13
Allocation End: 2020-08-11
Used Hours: 3092658
Project Name: Development of the first African-based earth system model VRESM and its projections of future climate change over Africa
Project Shortname: ERTH0859
Discipline Name: Earth Sciences
The first African-based Earth System Model (ESM) is under development at the Council for Scientific and Industrial Research (CSIR) in South Africa, through collaboration with the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Australia and South Africa's Centre for High Performance Computing (CHPC). The new ESM is unique in the sense that it is being developed in Africa and through the lens of African and Southern Hemisphere climate processes. That is, the reliable simulation of climate issues critical to Africa, such as the occurrence of drought in in response to El Niño events, wide-spread flooding over Mozambique due to landfalling tropical cyclones and increased occurrences of heat-waves under global warming are key issues in the development of the new model. The model development process is also focussed on the Southern Ocean's role in regulating southern African climate, as well as the global climate through the absorption of carbon dioxide in the ocean. The application of an Earth System Model is a computationally extensive endeavour, and was impossible to undertake in South Africa before the Lengau cluster of the CHPC became available in 2018. The CSIR-CHPC has led to the most detailed set of projections of future climate change over southern Africa obtained to date. These simulations have provided new insight into the plausible impacts of climate change in South Africa, including how the frequencies of droughts, heat-waves and landfalling tropical cyclones may change over the next few decades. These projections were key in informing South Africa's Third National Communication on Climate Change, which was published in 2018 under the science leadership of the CSIR. Moreover, the research papers based on the projections have directly informed the Special Report on Global Warming of 1.5 ºC of the Intergovernmental Panel on Climate Change (IPCC).
Principal Investigator: Dr Henry Otunga
Institution Name: Maseno University, Kisumu, Kenya
Active Member Count: 2
Allocation Start: 2020-02-14
Allocation End: 2020-09-17
Used Hours: 22395
Project Name: Computational Study of Hematite Clusters
Project Shortname: MATS0888
Discipline Name: Material Science
Sunlight is the most abundant renewable energy resource and considered to be the ultimate solution to address the global energy problem: The Tetrawatt Challenge. However, the vision of solar energy providing a substantial fraction of global energy infrastructure is still far from being realized. The major challenge is to develop an efficient and cost-effective approach for storing solar energy that can be used on demand on a global scale. Splitting water photoelectrochemically is a promising way in which solar energy can be harvested and stored through photocurrent-driven chemical bond rearrangement leading to the formation of molecular hydrogen (2H2O→2H2+O2, E0=1.23 eV, Standard Hydrogen Electrode, SHE), which can be used directly as fuel or as an intermediate in the production of other fuels. Hematite (alpha-Fe2O3) has emerged as a candidate photoanode material due to several favorable features: a band gap of about 2.0 eV (which allows for a large fraction of solar spectrum to be absorbed), excellent stability under aqueous environments, and abundance in nature. Converting energy from the Sun to electricity efficiently via photoelectrochemical splitting of water is based on photo-induced charge separation at an interface (semiconductor/water interface) and the mobility of photogenerated carriers (electron-hole pairs). However, in bulk hematite, the separated charges recombine very fast (very short lifetimes of electron-hole pairs) and have very low mobility, hindering the conversion efficieny. These limitations can be dealt with by nanostructuring hematite, by growing ultrathin films of hematite, and by introducing impurity atoms i hematite. In this work, the structure and energetics of various size clusters of Fe2O3 have been investigated using the plane-wave pseudopotential approach to Density Functional Theory (DFT) and ab initio Molecular Dynamics (MD). These calculations require a significant amount of compute resources in terms of memory and cpu scaling. In this respect, I am grateful to the CHPC for granting me access to their supercomputing facilities and I hope for more collaboration in future.
Principal Investigator: Prof Malik Maaza
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2020-02-14
Allocation End: 2020-08-28
Used Hours: 337716
Project Name: Modelling of Functional Materials at the Nanoscale
Project Shortname: MATS1306
Discipline Name: Physics
•The rapid emergence of aggressive, multidrug-resistant Mycobacteria strain & the sudden
appearance of SARS-COV-2 represents the main cause of the current major global health
problem. This project involving partners from South Africa, Africa & the South is aiming to
engineer a hybrid nano-bio therapeutics for SARS-COV-2 inhibition. This later is based on Hydroxychloroquine or Artemesia Afra bio-conjugated Silver nanoparticles in a form of colloidal
suspension. The initial computational & experimental results which are promising so far require
deeper biostudies as well as in-vitro & in-vivo precise investigations.
This pivotal if not the cornerstone Computational research uses complex models in a variety of ways, all of which advance materials science and engineering. These computational models can help researchers understand the outcome of an experiment, identify the most promising avenues for future experiments, and give us insight into processes that can't be easily explored in the lab. The U2ACN2 center thanks CHPC as an outstanding High-Performance Computing center, which assists our researchers by providing access to computational resources necessary to construct, analyze, and interpret their complex data in the field of nano and materials science.
Principal Investigator: Dr Ndanduleni Lethole
Institution Name: University of Fort Hare
Active Member Count: 1
Allocation Start: 2020-02-17
Allocation End: 2020-08-15
Used Hours: 5799
Project Name: Computational Studies of MxPt1-x (M; Mn, Fe, Co and Ni) alloys for magnetic data storage and biomedical applications.
Project Shortname: MATS1309
Discipline Name: Material Science
The research group is located under the department of Physics, University of Fort Hare. The group started in February 2020 and is composed of the Principal Investigator and one student. Currently, the group entirely depends on the Centre of High Performance Computing (CHPC) facility as it uses Material Studio modeling and simulation environment accessed via the CHPC as its only simulation package. The group aims to grow to at least three students in the year 2021 and also acquire a license for the Vienna ab initio simulation package.
The group is currently undertaking computer simulation studies on the M-Pt (M: Mn, Fe, Co and Ni) alloys for potential application as advanced performance permanent magnets, new storage of ultra-high-density magnetic data and in biomedical applications. The current study is significant since there has been a remarkable increase in data storage density of magnetic disk drives in the past few decades which is projected to be restricted by the "super-paramagnetic limit" (loss of data due to activated fluctuations of magnetization) in the near future. Super-paramagnetic limit can be overcome by designing new magnetic storage materials which are energetical, electronical, magnetical, mechanical and dynamical stable. Thanks to modern simulation packages and sufficient computing resources available at the CHPC, augmentation of various properties of the crystal structure is possible by theoretically calculating the forces acting on the nuclei. Simulations are set up on the local desktop computer using the BIOVIA Materials Studio modeling and simulation environment and submitted to the CHPC computing resources using the CASTEP code. On the negative note, the progress of the project has been disadvantaged by the ongoing lockdown in South Africa. However, few results have been attained. These include; heats of formation, elastic constants, density of states and band structure on the MnPt alloy.
Principal Investigator: Dr Holliness Nose
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 1
Allocation Start: 2020-02-15
Allocation End: 2020-08-13
Used Hours: 55286
Project Name: Inorganic Computational Chemistry
Project Shortname: CHEM1003
Discipline Name: Chemistry
My research project involves preparation of photosensitizers for water purification. Water treatment strategies commonly adopted include chlorination, distillation, UV-radiation, boiling and reverse osmosis. While these methods have proved to be effective in water decontamination, they have not been completely efficient in treatment of microbe polluted water. This is attributed to emergence of anti-microbial resistant (AMR) microorganisms such as Methicillin-resistant Staphylococcus aureus and Amphotericin-resistant Candida albican. AMR pathogens find their way into drinking water, causing waterborne diseases. Photodynamic antimicrobial therapy (PACT) provides an alternative and viable method of water disinfections, especially in addressing the anti-microbial resistant bacteria. PACT makes use of a photosensitizer, which when localized in microorganisms can be activated by irradiating it with light of appropriate wavelength to generate a reactive oxygen species (ROS). This ROS is able to destroy or affect biological structures such as cell wall material, nucleic acids, peptides and lipids therefore leading to cytotoxicity. Therefore, this method allows the photosensitizer to bind to the bacterial or fungal cell wall, inhibiting cell growth, with no possibility of recovery or development of resistance against it. My group is working towards designing and developing the photosensitizers computationally, followed by synthesis of the metal complexes and finally carrying-out biological assays to examine their cytotoxicity. This project therefore relies on CHPC heavily as we need to design the photosensitizers theoretically before we go to the laboratory to synthesize them and test for their biological activities. This project began on June 1st 2019 and is currently ongoing. But without the CHPC facilities, we are unable to do this type of research. The project is proceeding on well despite the Covid 19 pandemic, thanks to CHPC, South Africa for their continued support.
Principal Investigator: Prof Phuti Ngoepe
Institution Name: University of Limpopo
Active Member Count: 26
Allocation Start: 2020-02-17
Allocation End: 2020-08-28
Used Hours: 9665533
Project Name: Computational Modelling of Materials: Energy Storage
Project Shortname: MATS0856
Discipline Name: Material Science
Materials Modelling Centre (MMC), at the University of Limpopo (UL), employs High Performance Computing (HPC) methods to design and predict properties of valuable materials. Firstly, the demand of lithium ion batteries is increasing significantly owing to rapidly expanding automotive and energy storage markets. MMC simulates fabrication of lithium ion battery cathode particles made of nickel, manganese and cobalt, which are similar to those grown in production plant reactors. This is intended to reduce deterioration and breakage of such cathodes during charging and discharging in order to extend distances to be covered by electric vehicles in one charge. The work is conducted to support the production of cathode precursors at a pilot plant hosted by UL and supported by the Department of Science and Technology. Batteries beyond lithium ion, with higher capacity are also being investigated. Secondly, high recoveries of precious group metals from mines with the less understood platreef, particularly in Limpopo province, are not easily achieved. MMC, in collaboration with various research groups, use HPC to simulate the design of near green reagents for better recovery. A proof of concept on how simulations reproduce experimental approaches in such designs has been conducted on known sulphide minerals. The concept is being extended to explore ores with precious metal minerals containing less sulphur, with intention of enhancing their recoveries. Lastly, titanium powder metallurgy facilitates convenient manufacturing of alloys. MMC employs simulations to predict properties of high temperature titanium platinum based shape memory alloys. Furthermore, growth of titanium nanoclusters is modeled and provides valuable insights on titanium growth in a pilot plant at the Council for the Scientific and Industrial Research. Simulations across these three themes, are highly computer intensive and are achievable by use of HPC where UL postgraduate students are main beneficiaries.
Principal Investigator: Prof Martin van Eldik
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2020-02-18
Allocation End: 2020-08-16
Used Hours: 29519
Project Name: Thermal-Fluid modelling
Project Shortname: MECH1247
Discipline Name: Computational Mechanics
The Thermal-Fluid Modelling research group, is situated in the Faculty of Engineering at the North-West University. Students using the CHPC currently consists of 2 Masters students and 1 PhD. All students are using Star-CCM+ for their studies which is computationally intensive.
The one masters student is investigating the thermal fluid modelling of a titanium helically coiled fluted tube. The other Masters is conducting an aeroacoustic analysis of a glider plane component and how to identify the source and replicate it.
The PhD student is investigating the CFD modelling of a sinter mixing drum to improve the production throughput.
The part of the research group focusing on CFD studies is still relatively new and hope to make progress in this year. One of the masters studies will be concluded this year and the PhD is in its first year. The
The CHPC makes it possible for the students to be able to complete their work on time, which otherwise would not have been able to.
Principal Investigator: Prof Prof Abidemi Paul Kappo
Institution Name: University of Johannesburg
Active Member Count: 1
Allocation Start: 2020-02-19
Allocation End: 2020-08-17
Used Hours: 57868
Project Name: Structural bioinformatics of druggable proteins in diseases
Project Shortname: HEAL1252
Discipline Name: Health Sciences
The study of druggable proteins from one of the 18 neglected tropical diseases is of paramount interest to my research group. This is due to the fact that the disease of interest, Schistosomiasis is mostly prevalent in sub-Saharan African and have been shown to be a predisposing infection to many cancer morbidities and the incidence has been on the increase. More so, the first line treatment drug of choice, Praziquantel has been shown in many studies to have less effective on the schistosome worms and hence, the need to discover, design and develop new drugs in form of small molecules or/and inhibitors in order to combat this infection. Bioinformatics tools have been applied to hasten the the process of drug discovery.
Principal Investigator: Prof Evans Adei
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 13
Allocation Start: 2020-02-19
Allocation End: 2020-09-03
Used Hours: 1024471
Project Name: Materials For Energy and Fine Chemicals
Project Shortname: CHEM1046
Discipline Name: Chemistry
Our work at KNUST Kumasi Ghana with the support of resources from CHPC is geared towards the development of environmentally friendly catalysts for industrial applications, the mechanisms of reactions for applications in the pharmaceutical industry, and the development of functional materials that address issues of renewable energy and climate change. These are pressing real-world problems and our contributions would not have been possible without the support of CHPC.
CHPC has become an extremely important ally in our research activities. For students who are compelled to work with realistic molecular/material systems, the increase in their productivity when they start working on the CHPC platform becomes quite apparent.
The lack of funding for graduate students made the opening of modeling research experience door to undergraduate students who show interest in the work we do an obvious and pragmatic move to sustain our research activities.
Recent Research Output within the reporting period are as follows:
(i) Pipim, G. B., et. al., doi.org/10.1016/j.jmgm.2020.107672
(ii) Amoah, A., et al. doi.org/10.1016/j.tet.2020.131422
(iii) Akuamoah, D.A., et al. (2020) doi.org/10.1007/s00214-020-02653-5
(iv) Samba K. W., et al., (2020) J. Phy Org Chem. – in press. Manuscript ID POC-20-0142.R2
(v) Umar, A. R., et al., (2020) doi.org/10.1007/s00894-020-4299-6
(vi) Arhin, G., Pipim, G. B., Adams, A. H., et al. (2020) doi.org/10.1007/s00214-019-2529-8
The highlighted co-authors are all undergraduate students. The potential for future research work of some of our 2nd (Lower) students could not have been demonstrated through publication (doi.org/10.1016/j.tet.2020.131422); had it not been the considerable generosity of CHPC CPU resource to enable us to accommodate them.
We are aware that CHPC is catalyzing Ghana to establish its HPC center in Accra. However, with our present limited HPC resource here at KNUST Kumasi we hope that CHPC will continue to support us with HPC resources in the short and medium terms.
Principal Investigator: Dr Samuel Iwarere
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2020-02-19
Allocation End: 2020-08-17
Used Hours: 102834
Project Name: Understanding Plasma-Liquid Interaction
Project Shortname: MECH1107
Discipline Name: Chemical Engineering
The research is being carried out under the guidance of the Thermodynamics Research Unit based in the School of Chemical Engineering at the University of KwaZulu-Natal. The understanding of plasma-liquid interactions is of prime importance in the context of environmental remediation and wastewater treatment applications. Plasma treatment of wastewater involves complex chemical and physical phenomena, which makes the comprehensive modelling of phenomena such as gas phase reaction, turbulence and heat transfer a difficult task. In order to gain insight into the complex processes associated with the use of plasma wastewater treatment, Computational Fluid Dynamics (CFD) will be used to study the relevant chemistry and fluid dynamic effects at the plasma-liquid interface. The Centre for High Performance Computing (CHPC) allows for calculation within realistic time frames, allowing the researchers to determine the accuracy of the simulations encountered in plasma physics. Simulation of the plasma arc is progressing well with the researchers working in conjunction with other scientists in the plasma field.
Principal Investigator: Prof Peter Teske
Institution Name: University of Johannesburg
Active Member Count: 3
Allocation Start: 2020-02-19
Allocation End: 2020-08-17
Used Hours: 188059
Project Name: Coevolution of mangroves and mangrove-associated crabs
Project Shortname: CBBI0979
Discipline Name: Bioinformatics
Who?
Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg
What?
Analysis of DNA and RNA data from a large portion of animal genomes.
Why?
To improve the management of commercially exploited species, optimise conservation efforts aimed at saving endangered species from extinction, and understand evolutionary relationships in nature.
How?
Genomic data sets generated using massive parallel sequencing technology results can only be assembled by means of supercomputers. Using CHPC, we are able to assemble a huge number of short reads into a meaningful sequence that reflects their order in the animal genome.
Progress?
CHPC and the valuable expertise it has gathered in one place has allowed our small lab to punch well above its weight, and we are now on our way of becoming an international player in the field of genomics who are being noticed by much larger (and much better funded) international research groups. 2020 is already a very productive year (14 publications published or under review) and over the next 6 months we expect to complete work on several high impact papers.
Principal Investigator: Prof Gert Kruger
Institution Name: University of KwaZulu-Natal
Active Member Count: 12
Allocation Start: 2020-02-20
Allocation End: 2020-08-18
Used Hours: 352231
Project Name: CPRU molecular modeling
Project Shortname: HEAL0839
Discipline Name: Health Sciences
(Who) The Catalysis and Peptide Research Unit at UKZN (http://cpru.ukzn.ac.za/Homepage.aspx) is currently working on the mechanism of action on the HIV PR with respect to the natural substrates. (What) We use an quantum chemical/molecular mechanics hybrid (Oniom) approach that gives us high level results on the thermodnamics and kinetics of the reaction. Our model enables us to study application of both electronics and sterics to change the bond strenght and binding energies of new potential inhibitors. The same approach is followed for transpeptidases, essential enzymes for the inhibition of TB. (Why) HIV is a major health threat in SA and new drugs is required due to the constant development of drug resistance. Similarly, TB and TB co-infection with HIV is a mojor health issue. (How) Our theoretical studies will allow us to test a computational model that correctly describes the interactions between the respective enzymes and existing drugs. We are improving our computational model to the extent where are now in a position to make and test new potential drug leads for synthesis. This can only be done with large computational resources provided by the CHPC.
Principal Investigator: Dr Fabio Mathias Correa
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2020-02-27
Allocation End: 2020-08-25
Used Hours: 54908
Project Name: Evaluation of South African students' in math tests
Project Shortname: CBBI1312
Discipline Name: Other
The research project aims to identify mutation points in the cacao genome and determine the responsible genes that can assist in plant propagation using clones. Without the assistance of CHPC and the Helpdesk, it would not be possible to carry out the analyzes. It would not be possible to analyze 480 GB of genome on a conventional computer. I hope to be able to extend the CHPC usage time for the project.
Principal Investigator: Prof Liliana Mammino
Institution Name: University of Venda
Active Member Count: 4
Allocation Start: 2020-02-27
Allocation End: 2020-09-11
Used Hours: 28281
Project Name: computational study of biologically active molecules of natural origin
Project Shortname: CHEM0959
Discipline Name: Chemistry
WHO?
A professor emeritus (Liliana Mammino), a PhD student (Neani Tshilande) and an M.Sc. student (Thembani Vukeya), at the University of Venda.
WHAT?
We study biologically active molecules.
L. Mammino is working on antioxidant acylphloroglucinols, and also investigating other aspects of this class of compounds, always in view of their potentialities for drug development. N.Tshilande is studying acylphloroglucinols with antimalarial and anticancer activities. T.S. Vukeya is studying a number of sulfonylureas molecules with antidiabetic potentialities.
If a recently submitted proposal involving three BRICS countries (Brazil, South Africa and India) is approved, L. Mammino will also work on the study of molecules for the treatment of COVID.
WHY?
The computational study of biologically active molecules provides information relevant to understand their biological activities, which, in turn, is relevant for the design of improved drugs for the treatment of diseases.
We are studying molecules for the treatment of diseases that are responsible for a high number of deaths worldwide (malaria, cancer, diabetes). Antioxidants are important for the prevention of neurodegenerative diseases Alzheimer disease, Parkinson disease, and the like).
HOW?
The computational studies of molecules use the methods developed within theoretical chemistry to obtain information about the properties of molecules. Once obtained, these properties can be related to the activities (e.g., antimalarial, anticancer or antidiabetic activity). Knowing these relationships will be useful for the design of enhanced pharmaceuticals.
HOW is the project progressing?
The project had been progressing quite well until the disruption caused by the COVID pandemic. All of us (participants) have been in lockdown in places with limited or no internet access. We are now resuming the computational work and we plan to do our best to make up for the time lost because of the pandemic.
Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 5
Allocation Start: 2020-02-28
Allocation End: 2020-08-26
Used Hours: 5078
Project Name: African Multi-Omics Data Science
Project Shortname: CBBI1039
Discipline Name: Bioinformatics
CBBI1039: UCT Applied Genomics (AGe) is a training programme, running from the University of Cape Town, South Africa. This research programme is fundamentally aiming 1) to provide postgraduate students with the knowledge skills and bioinformatics tools they need to understand the models of medical population genetics and of computational molecular biology; 2) to enable graduate students at the University of Cape Town, across the country and African continent to be able to relate the models and data of statistical genetics to the constraints of inheritance and the molecular mechanisms of genetic data, including DNA sequence data, next generation sequences and to develop the skills to work with these massive data sets. 3) to ask the assistance of CHPC, South Africa, Cape Town in training the trainers along this proposed programme to efficiently use the resources and master the portable bash servers (PBS) and the implementation of large-scale genomic project under CHPC's resources. The accumulation of experimental DNA data in Biology and new high throughput experiments are growing rapidly and give a huge number of data difficult to manage, to store and to analyse this existing and future dispersed information. Therefore, high-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring the field of bioinformatics to use high-performance computing resources and carry out data management and analysis tasks on large scale. Today, the use of HPC has increased our training portfolio to meet the international standard with respect to large scale genomic era in training and increasing data analysis skills of our students and other trainees across the continent. This programme has developed several genomic-based, Bioinformatics, programming courses that address the African training needs around large-scale genomic data in order to meet the international standard required in this field. Lockdown did not affected this programme from operating and training remotely.
Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 19
Allocation Start: 2020-02-28
Allocation End: 2020-08-26
Used Hours: 591039
Project Name: Computational and statistical methodologies for human and environmental health prediction
Project Shortname: CBBI0818
Discipline Name: Bioinformatics
Computational and statistical methodologies for human and environmental health prediction research programme (CBBI0818) is running from the University of Cape Town, South Africa. This research programme is fundamentally aiming 1) to determinate the environment and genetic variation that cause human species to look different, having difference in allergy, drug responses and treatment. 2) to identify and quantify the pattern of inheritance of the observed trait, drug response and treatment variation among human. These are addressed through the design of machine intelligence and artificial intelligent methodologies and statistical approaches to analysis large-scale DNA data of thousands affected/unaffected subjects. In doing so, and the use of CHPC in this programme is contributing to human health by increasing understanding of the genetic and environmental underpinnings of complex traits, drug/treatment responses and drug/dosage responses.
The accumulation of experimental DNA data in Biology and new high throughput experiments are growing rapidly and give a huge number of data difficult to manage, to store and to analyse this existing and future dispersed information. As really DNA data become more and more available and big, better the health prediction is, therefore there is a critical need for national life and long -term storage and robust fast accessible memories. Up to today and during lockdown, the use of parallel High-Performance Computing at CHPC has critically increased our researcher portfolio to meet the international standard with respect to large scale genomic era. This program has already developed of genomic-based software tools that address African genetic variation challenges and provided advanced training around parallel programming with respect to large-scale genomic data to African postgraduate students/researchers.
Principal Investigator: Prof Paulette Bloomer
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2020-02-28
Allocation End: 2020-08-26
Used Hours: 158649
Project Name: Molecular Ecology and Evolution Programme
Project Shortname: CBBI1030
Discipline Name: Bioinformatics
The Molecular Ecology and Evolution Programme (MEEP) is a research group in the Division of Genetics, Department of Biochemistry, Genetics and Microbiology at the University of Pretoria. We investigate the evolutionary history and current genetic diversity of many vertebrate species (marine and terrestrial), using genetics and genomics tools, and try to link the patterns we see with ecological and human-mediated events. We currently have two projects (Cape buffalo and bowhead whales) that make use of the CHPC resources, with additional projects on the Asian Houbara bustard and wildebeest in the pipeline.
Cape buffalo have recently been up listed on the IUCN Red List of Endangered Species, from Least Concern to Near Threatened, owing to a declining population across Africa mainly due to human expansion and subsequent habitat loss. In South Africa, natural buffalo populations are highly fragmented due to past disease outbreaks, colonial hunting and the eventual fencing-in of protected areas. We use genetics and genomics techniques to determine the effects of these events, and others in the more distant past, on the genomic and population diversity of these buffalo populations, such as loss of diversity and inbreeding. By understanding and quantifying the effects of the past, we can help the species to be more resilient to changes in the future.
The genetic work on the bowhead whale uses empirical and simulation data to investigate the effects that different Nearctic human cultures exploiting the whale had on the abundance of the population. This means that genetic data may have more resolution than previously thought and is sufficient to detect subtle changes in population size in relation to exploitation and climate change. This is of great importance as there are many applications. We believe that the work will have sufficient impact to be of interest to the general public in South Africa and internationally.
The development of a new molecular clock calibration method for tropical reef species makes use of simulations for validation. This calibration enables genetic time to be related to chronological time. This method may then be applied to empirical data to identify driving factors for increases in population size of reef dependent species in the tropics.
Principal Investigator: Prof Warren du Plessis
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2020-02-27
Allocation End: 2020-08-25
Used Hours: 603096
Project Name: Electronic Warfare (EW) Technologies
Project Shortname: MECH0989
Discipline Name: Electrical Engineering
Prof. Warren du Plessis of the University of Pretoria has been using the CHPC to determine the optimal configurations of thinned linear antenna arrays. Thinned arrays reduce the cost of antenna arrays by reducing the number of antenna elements required, thereby addressing one of the major barriers to the wider adoption of antenna arrays. This is a problem that has been studied since at least the 1960s, and while good algorithms exist, the optimal solutions are currently unknown. The work is nearing its completion, with the major result being that even the best algorithms do not come close to finding optimal configurations. This work would simply not be possible without the CHPC.
One of Prof. du Plessis' postgraduate students, Llewellyn Strydom, is investigating the use of artificial intelligence (AI) techniques in separating radio signals. This is an important problem in many applications, including cognitive radio. The results to date have been encouraging with signals in even challenging cases being correctly identified. This work would be far more difficult without the resources provided by the CHPC.
Principal Investigator: Prof Gerard Tromp
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2020-03-02
Allocation End: 2020-08-29
Used Hours: 1063
Project Name: South African Tuberculosis Bioinformatics Initiative
Project Shortname: CBBI0999
Discipline Name: Bioinformatics
The South African Tuberculosis Bioinformatics Initiative (SATBBI) performs an important role in tuberculosis research by supporting numerous research projects with data analysis and modeling. The CHPC is a vital resource for these activities.
Principal Investigator: Prof Ozlem Tastan Bishop
Institution Name: Rhodes University
Active Member Count: 21
Allocation Start: 2020-03-02
Allocation End: 2020-08-29
Used Hours: 6285825
Project Name: Structural Bioinformatics for Drug Discovery
Project Shortname: CBBI0867
Discipline Name: Bioinformatics
In our recent article "Sheik Amamuddy O, Verkhivker GM, Tastan Bishop Ö. Impact of early pandemic stage mutations on molecular dynamics of SARS-CoV-2 Mpro [published online ahead of print, 2020 Aug 27]. J Chem Inf Model. 2020;10.1021/acs.jcim.0c00634. doi:10.1021/acs.jcim.0c00634" we identified the structural and functional effects of mutations on the COVID-19 drug target Mpro, and also identified novel allosteric drug targeting site. This work will help to design inhibitors against evolving viral protein.
Principal Investigator: Dr Rian Pierneef
Institution Name: University of Pretoria
Active Member Count: 8
Allocation Start: 2020-03-02
Allocation End: 2020-08-29
Used Hours: 53628
Project Name: Bioinformatic and Computational Biology analyses of organisms
Project Shortname: CBBI1124
Discipline Name: Bioinformatics
The CHPC is an integral part of research in South Africa and provides the opportunity for researchers to analyze a wealth of information in a single location. The current trend in research is big data. The CHPC allows all researchers to investigate their big data and rapidly analyze large data sets. As the fourth industrial revolution has started, the CHPC is a critical component in the current research and science landscape. The CHPC further aids in the development of human capital by providing an easy to use platform to students and early career researchers.
Principal Investigator: Prof Francois Engelbrecht
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2020-03-03
Allocation End: 2020-08-30
Used Hours: 51239
Project Name: WITS Climate Modelling
Project Shortname: ERTH1200
Discipline Name: Earth Sciences
Release 1
One of the world's first climate-sensitive Covid-19 models was developed at the Global Change Institute of the University of the Witwatersrand during the period March-August 2020. This included the development of a Climate Correction Factor (CCF) that modfies the Covid-19 infection rate in epidemiological models. This methodology was applied in the spatial epidemiological model of the National Institute for Communicable Diseases (NICD), which in turn contributed to South Africa's official Covid-19 projections. Two research papers were also prepared on this work, which the research team hope will be published in the last quarter of 2020 (pending peer-review). Building the spatially-sensitive CCF into the epidemiological models relied heavily on climate downscalings previously performed on the Lengau cluster of the CHPC.
Release 2
A new climate modelling research group has been established at the Global Change Institute (GCI) of the Universit of the Witwatersrand. This includes 9 new post-graduate students, 7 of these PhD students, of which 5 have completed their proposals by August 2020 and are now moving into the research phase of their work. The research group and the related Earth System Science Research Programme of the NRF depends entirely for their research on the Lengau cluster of the CHPC.
Principal Investigator: Prof Scott Hazelhurst
Institution Name: University of the Witwatersrand
Active Member Count: 4
Allocation Start: 2020-03-03
Allocation End: 2020-08-30
Used Hours: 101700
Project Name: Bioinformatics and Experimental Algorithms (BEAT)
Project Shortname: CBBI0930
Discipline Name: Bioinformatics
The Wits Bioinformatics group is collaborating on an Africa-wide project investigating the ADME genes -- a group of genes responsible for drug metabolism. Using a novel data set of African genomes we are characterised common variations found in African population with potential impact on drug efficacy and safety. A subset of these variations that have the highest potential impact are being modelled at the CHPC. The body uses genes to produce proteins which are responsible for many cell behaviours -- variations in genes change the biochemical properties and shapes of the proteins which in turn has impact on cell functioning. We are focussing on drug metabolism -- variations could cause a drug to be more or less potent. Using the graphical processing units (GPUs) at the CHPC we can accuratlely model the shape and molecular dynamics of proteins of interests -- we can compare the behaviour of the proteins produced by genes with and without varation and provide evidence of the impact of these variations.
Principal Investigator: Prof Tien-Chien Jen
Institution Name: University of Johannesburg
Active Member Count: 21
Allocation Start: 2020-03-05
Allocation End: 2020-09-01
Used Hours: 1819336
Project Name: Developing an Innovative Metal Matrix Composite Membrane for Hydrogen Purification
Project Shortname: MATS0991
Discipline Name: Material Science
Hydrogen is an excellent energy carrier because of its high enthalpy of combustion with less environmental impact. Hydrogen fuel can be directly used in cars, ships, aircraft, and other transportation equipment. Although there are many problems to be resolved for implementation of hydrogen technology, it is generally believed that hydrogen will become a key energy carrier in this century. Until sufficient quantities of hydrogen can be derived from renewable energy sources, it will have to come from hydrogen separation using existing fuels (e.g., diesel, natural gas) as the feedstock. Hydrogen separation units can generate highly purified hydrogen from the feedstock gas mixtures, however, a certain amount of CO and other chemicals will make it into the hydrogen stream and cause catalyst failure on the fuel cell electrode. This significantly deteriorates the activity of the catalyst layer, particularly for Proton exchange membrane (PEM) fuel cells. This deterioration greatly reduces the efficiency of power generation and the life cycle of the fuel cell. Overcoming this obstacle is necessary for the wider use of highly efficient fuel cells. The objective of this proposal is to develop a new composite metal membrane (CMM) that can achieve extremely high flux and selectivity of the hydrogen separation and achieve the lifetime goal set by the U.S. department of energy (DOE). To accomplish these goals, a research team formed by the University of Johannesburg (UJ), Council for Scientific and Industrial Research (CSIR) and Hydrogen South Africa (HySA) will combine two major technologies: Electrostatic-Force-Assisted Cold Gas Dynamic Spraying (ECGDS) and Laser-Assisted Manufacturing (LAM) to develop this new type of membrane. The proposed new membrane will eliminate the hydrogen embrittlement, catalyst failure, and avoid the difficulty of forming a defect-free, ultrathin Pd film on the substrate surface. The proposed CMM will exhibit superior reliability and can be produced with a relatively low-cost and scalable process. Along with the development process, numerous numerical methods are utilized to simulate the material properties and behaviour as well as the optimization fabrication procedure. To accomplish these task HPC services from CHPC plays a crucial role in understanding the numerous unknown phenomena's. This service enables the research to be simulated from feature scale to reactor scale .Note that this project is currently supported by the NRF for 2017-2021
Principal Investigator: Dr Jaco Badenhorst
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 3
Allocation Start: 2020-03-05
Allocation End: 2020-09-01
Used Hours: 7409
Project Name: Automatic transcription of broadcast data
Project Shortname: CSIR0978
Discipline Name: Other
The Digital Audio Visual Technology (DAVT) Research Group at the CSIR Nextgen Enterprises and Institutions (NGEI) cluster develop speech and language-related technologies for the South African context to enhance access to information and communication. Given the multilingual nature of South Africa, human language technologies (HLTs) can make information and services accessible to a larger proportion of the South African population in a sustainable way, by reaching people in remote locations, people who are not necessarily trained in using technology, or people who are not fluent in English. HLTs can also provide access to information to people with disabilities. HLT can support language diversity and providing of information in multiple languages in an affordable and equitable fashion. The development of all 11 official languages is a national priority, which requires significant attention to HLT in all of these languages. HLT can be of significant economic importance – both by empowering citizens of the country to work more productively, and by forming the core of an exportable set of technologies (since such technologies are currently not available to most of the developing world).
The HLT Research Group operates in a vibrant environment consisting of researchers, developers, project managers and students from backgrounds as diverse as engineering, linguistics and sociology. We conduct basic and applied research into projects related to the following areas of research: automatic speech recognition, text-to-speech synthesis, natural language processing, machine translation, human language analytics, text and speech resource development, speech and language technology system design and implementation, and usability and user experience evaluation of speech and language technology.
Principal Investigator: Dr Gurthwin Bosman
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2020-03-05
Allocation End: 2020-09-17
Used Hours: 139610
Project Name: Quantum computations for photoinduced reactions
Project Shortname: CHEM1126
Discipline Name: Physics
The research group is one of the arms of the Laser Research Institute in the Department of Physics of Stellenbosch University. Laser Research Institute of the Stellenbosch University, boasts of ongoing formidable research projects in the fields of ultrafast science, spectroscopy and laser diagnostics, laser development, trapped ion quantum control and bio-photonics and imaging, with a number of laboratories housing ultra-modern equipment. Our research group is focussed on ultrafast transient absorption spectroscopy on chemical compounds ranging from simple molecules to polymers. Experimental set ups for ultrafast transient absorption spectroscopy have been thoroughly developed over the years by different masters, doctoral and postdoctoral students. The research projects conducted in the ultrafast laboratory had produced masters' and doctoral theses, as well as peer reviewed publications.
Scientific observation being made by experiments in our research group need to be properly understood and interpreted for proper communication to the general community. Therefore, a level of theoretical simulation which will allow deeper insights is needed. Part of these theoretical simulation is the density functional calculation, a theory well accepted to interpret molecular and/or structural dynamics we observe experimentally. The calculations can take forever if run on a single computer. This is where the Centre for High Performance Computing (CHPC) comes in.
Centre for High Performance Computing (CHPC) offers a wide range theoretical coding and simulation with the advantage of supercomputing on parallel computers. This enables users' jobs submission to run on a faster scale. Our research group is privileged to have access to these supercomputing capabilities and the provision of simulation software for our calculations.
We are running series of density functional calculation ranging from simple molecules to polymers using Gaussian 09, ORCA and Maestro that is provided by CHPC.
Principal Investigator: Mr Adebayo Azeez Adeniyi
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2020-03-06
Allocation End: 2020-09-02
Used Hours: 313285
Project Name: Drug Discovery Research Using Quantum and Molecular Dynamic Simulation
Project Shortname: CHEM0958
Discipline Name: Chemistry
Recently we have expanded our research focus in addition to Drug Discovery, we have included vaccine development, photochemistry and polymer chemistry. We make used of several packages for Bioinformatics, Quantum and Molecular Dynamic Simulation. The reason for expanding our research focus is based on the pressing need of the society and global challenges, that lead us into epitopes based vaccine development from the genomes of the pathogens, polymer chemistry, photochemistry of small molecules for application photoactive compounds and molecular electrochemistry. Our research use theoretical modelling to give rational insight into identified problems which can help in the experimental designs for possible solutions. CHPC is an important facility to our research group, we make use of the facilities and the softwares like Gaussian, Orca, Games and Newchem; also used molecular dynamic packages like Gromacs, Amber and Lammps. We have applied quantum packages to study the chemical and spectroscopic properties of small molecules of which we have been able to reproduced some of the experimental results.
It is obvious that our research progress and achievement revolve around the service of CHPC and many of our research output would not have been possible in without the support from CHPC.
Principal Investigator: Dr Annerine Roos
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2019-09-03
Allocation End: 2020-03-26
Used Hours: 14358
Project Name: DCHS and MRI studies
Project Shortname: HEAL1267
Discipline Name: Health Sciences
The Drakenstein Child Health Study is affiliated with the Universities of Cape Town and Stellenbosch, and supported principally by the Bill and Melinda Gates Foundation. The study investigates risk and protective factors of child health. The communities participating in the study are those who access the main public clinics in the Drakenstein region, and are of low socio-economic status. There is a high prevalence of poverty, violence and substance abuse in these communities. The study follows >1000 mother-child dyads from pregnancy to 6 year of age. The Psychosocial component of this study investigates neurodevelopmental correlates after prenatal exposure to substances, depression or HIV in a subset of children. Prenatal exposure to substances including alcohol and methamphetamine remain alarmingly high in these communities, even when woman are aware of the potential adverse effects on their health and child development. Not much is known about early neurodevelopmental effects of prenatal substance exposure that may have lifelong outcomes. We rely on CHPC to analyse multimodal brain imaging data that require intensive analysis capacity. Because the analysis of brain data is intense it also requires multiple computer facilities in order to have output in a relatively short period. It takes a conventional computer months to compute what can be computed in a week by CHPC. It is important to disseminate findings timely to have relevance to health care and have factual information available to communities to change harmful behaviours to child development. The Psychosocial/Brain imaging component is currently following up children with prenatal exposures at age 6 years. We have imaged these children shortly after birth and at age 2 years and will have longitudinal data available that may assist in identifying critical windows during development for intervention. Children who receive early interventions after developmental insults have better outcomes.
Principal Investigator: Prof Fourie Joubert
Institution Name: University of Pretoria
Active Member Count: 39
Allocation Start: 2020-03-10
Allocation End: 2020-09-06
Used Hours: 23770
Project Name: NGS Bioinformatics
Project Shortname: CBBI0905
Discipline Name: Bioinformatics
Students and post-doctoral fellows from the University of Pretoria make use of the the internal cluster at UP for bioinformatics analysis, but also of the CHPC for large analyses. The CHPC resources are primarily used for two projects: the 62 E. coli genomes from aquatic environments, where a manuscript is currently being written, and the ATAC-Seq and RNA-Seq data from lymph node-residing T-lymphocytes in HIV patients. The HIV research is particularly important in the context of SDG 3 on health.
Principal Investigator: Mrs Chantel Niebuhr
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-03-11
Allocation End: 2020-09-07
Used Hours: 641000
Project Name: Hydrokinetic turbine analysis
Project Shortname: MECH1174
Discipline Name: Other
The Water division at the University of Pretoria has had a large focus on hydropower development within water infrastructure in South Africa in recent years. Due to the large network on conveyance canals/channels and rivers, hydrokinetic (in-stream) turbines have been considered. To ensure success of these installations the hydrodynamic results (wake length/damming etc) needs to be well understood. CFD models allow simpler more in depth analysis of these characteristics, however due to the complexity, requires large computational resources. Through the use of the HPC development of an accurate model, capturing the wake complexities has been developed and validated with experimental results. The results have been submitted for publication and will provide further guidelines for any future models to ensure accuracy specifically in the design cases where model validation is not done.
Principal Investigator: Dr Adam Skelton
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2020-03-10
Allocation End: 2020-09-06
Used Hours: 44094
Project Name: Molecular modelling of biomolecules and materials
Project Shortname: CHEM0798
Discipline Name: Chemistry
I am Dr. Adam Skelton and I work at the College of Health Science university of KwaZulu-Natal. I work on understanding the behaviour of biological and material systems on the molecular level. A particlar interest is in using molecular simulation to direct the rationale design of functionalized nanoparticles for a range of applications such as drug delivery, water treatment and catalysis. In particular, drug delivery is the use of nanoparticles to carry antiviral or antibacterial drugs into parts of the body that are difficult for conventional drugs to reach. Drug-delivery is, therefore, of huge importance in South Africa, especially in the battle against HIV and Tubercolosis. The research requires running a series of computar simulations, which may take hours at a time. CHPC has had a great impact since it provides me with the facilities to perform such simulations. Since the project started, my group has published more than 15 papers in international journals and has provided deep insight into biological and material systems on the molecular level.
Principal Investigator: Dr Vuyani Moses
Institution Name: Rhodes University
Active Member Count: 24
Allocation Start: 2020-03-11
Allocation End: 2020-09-07
Used Hours: 2252476
Project Name: Bioinformatics and Computational Chemistry Applications
Project Shortname: CBBI1122
Discipline Name: Bioinformatics
Our research group is based in Grahamstown which is asssociated with the Rhodes University Research Unit in Bioinformatics (RUBi). Our interests are using computational techniques to solve biological problems such as drug discovery and biofuel production. The work is of outmost importance as it allows for the understating of these biological programs providing solutions such is the design of new drugs for a wide variety of diseases. We are also interested in using the cluster for understanding enzymatic reactions that are crucial for biofuel production. Access to the CHPC allows us to be able to perform these calculations as it would be difficult to perform these calculations without access to the resources provided at the CHPC. Data generated at the CHPC is crucial for the production publications and thesis which allows us to graduate numerous MSc and PhD students. The research is currently growing each year and this is largely due to the access we have to the CHPC.
Principal Investigator: Mr Anban Pillay
Institution Name: University of KwaZulu-Natal
Active Member Count: 11
Allocation Start: 2020-03-12
Allocation End: 2020-09-08
Used Hours: 25050
Project Name: Deep Learning Approaches
Project Shortname: CSCI1078
Discipline Name: Computer Science
The Deep Learning research group belongs to the Centre for Artificial Intelligence Research Node at the University of KwaZulu-Natal. The Centre for Artificial Intelligence Research (CAIR) (CAIR.za.net) is a South African distributed Research Network that conducts foundational, directed and applied research into various aspects of Artificial Intelligence. The research group conducts foundational research in machine learning in general and deep learning in particular. Deep learning projects require substantial computing resources and the CHPC is vital to its success. The projects involve various area of deep learning that include deep reinforcement learning, convolutional and recurrent neural networks. Application areas include image processing, natural language processing and speech recognition. Several students are busy with projects at present.
Principal Investigator: Dr Michael Owen
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2020-03-12
Allocation End: 2020-09-08
Used Hours: 59700
Project Name: Industrial heat exchanger simulation and analysis
Project Shortname: MECH1210
Discipline Name: Computational Mechanics
The Thermofluids Division at Stellenbosch University's Department of Mechanical and Mechatronic Engineering has a long history of research in industrial heat exchangers and has conducted pioneering work in the field of dry cooling for large thermal power plants in particular.
Research in this field continues with a focus on understanding and improving the performance of these water conserving cooling systems under a variety of ambient conditions (including strong winds). Work of this nature benefits greatly from the CHPC which allows us to investigate an unprecedented number of scenarios in a short amount of time using computational fluid dynamics (CFD) and parallel computing.
Dry cooling is a key technology for South Africa's energy sector since thermal energy production (coal, nuclear, combined cycle gas and solar thermal) is typically a water intensive process which South Africa can ill afford considering the arid nature of our country. Ensuring robust operation of dry cooling systems can contribute significantly to the sustainability of South Africa's energy production.
Principal Investigator: Prof Jaco Dirker
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2020-03-12
Allocation End: 2020-09-23
Used Hours: 103227
Project Name: Heat Transfer Enhancement in Thermal Systems
Project Shortname: MECH1029
Discipline Name: Computational Mechanics
Our current energy supply dilemma requires complementing solutions, including the use of thermodynamic cycles where a fluid is used as an energy carrier. In concentrated solar power systems, renewable solar energy is absorbed into the fluid (such as water) during a boiling process, whereafter a portion of this energy is transferred to a turbine to produce elecricity while the remaining portion is passed to the atmosphere via condensation. The support from the CHPC allowed the investigation of the phase change processes of water and other fluids to better utilise and understand the transient nature of solar thermal energy. The result of the research will help improve the design, operation and live span of solar thermal installations.
Principal Investigator: Dr Annerine Roos
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2020-03-11
Allocation End: 2020-09-07
Used Hours: 4175
Project Name: DCHS and MRI studies
Project Shortname: HEAL1267
Discipline Name: Health Sciences
The aim of the Drakenstein Child Health Study is to investigate determinants of early child development in a cohort of >1000 mother-child dyads of the Drakenstein district in the Western Cape of South Africa. The communities participating in the study represent a low-middle income country setting that is characterised by high substance abuse, poverty and violence. The Brain imaging subgroup include international collaborators of the Universities of Cape Town, Stellenbosch and Los Angeles, California. We aim to assess longitudinally cognitive, behavioural and neural outcomes in children from birth to 6 years of age, to identify vulnerable groups and key periods for intervention that may optimise development. Evidence show the earlier the interventions, the better the outcomes.
CHPC resources are used by this programme to analyse brain imaging data including structural data, of children with prenatal exposure to substances. Substance exposure is potentially harmful to brain development, but is understudied in young children. These include alcohol, tobacco and methamphetamine that is commonly used in the specific study community. We also aim to elucidate the neural effects of prenatal exposure to maternal depression as this has been shown to affect mother-child bonding and emotional regulation.
Our results are providing clues to brain regions that may be affected by prenatal substance exposure and depression. Numerous papers are currently being drafted for publication using results from CHPC analyses.
Principal Investigator: Dr Adeniyi ogunlaja
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 4
Allocation Start: 2020-03-12
Allocation End: 2020-09-08
Used Hours: 41806
Project Name: Chemistry and Material Science
Project Shortname: MATS1070
Discipline Name: Chemistry
Dr Adeniyi Ogunlaja (Research group -Analytical/Inorganic) at Nelson Mandela University.
Refractory polyaromatic hydrocarbons found in fuels such as dibenzothiophene, quinoline and its alkylated derivatives emits nitrous oxides and sulfur oxides to the environment when combusted, thereby reducing air quality. Desulfurization by means of oxidative desulfurization and adsorptive denitrogenation has been proposed to complement the hydrodesulfurization (HDS) and hydrodenitrogenation (HDN) processes, currently employed to remove sulfur and nitrogen compounds in fuels. At Nelson Mandela University analytical chemistry research group, we design materials that can selectively remove these sulfur and nitrogen compounds. Molecular modelling based upon the density functional theory (DFT) was employed to understand the mode of adsorption (interaction) between synthesised materials and the various compounds to be removed from fuels. Computational study assists with the understanding of the electronic and thermodynamic properties of synthesised materials prior to application. It also gives an insight as to the specific properties to be targeted when designing adsorbents for environmental clean-up. So far, progress has been made around the design and adsorption of some toxic molecules in fuels. HPC assist our group to build models that could be employed in explaining complex phenomena. It has also enabled us to ask big questions around activity of our materials and to test for possible answers computationally. CHPC has created the platform for where researchers like me could assess the HPC and has also assisted me and my students with solving problems some computation problems.
Principal Investigator: Dr Babatunde J. Abiodun
Institution Name: University of Cape Town
Active Member Count: 28
Allocation Start: 2020-03-16
Allocation End: 2020-09-12
Used Hours: 2069707
Project Name: CSAG-Atmospheric Modelling
Project Shortname: ERTH0904
Discipline Name: Earth Sciences
The highlights of our research during the reporting period include:
• Climate model simulations projects a future increase in the intensity and frequency of extreme rainfall events over some African four cities (i.e. Harare, Johannesburg, Lusaka and Nacala)
• Projections from climate models indicates that the ongoing global warming may lead to an increase in photovoltaic power potential but an increase in concentrated solar power output and wind power over the continent.
Principal Investigator: Dr Rose Modiba
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 5
Allocation Start: 2020-03-13
Allocation End: 2020-09-09
Used Hours: 121518
Project Name: Computational modelling of light metals
Project Shortname: MATS1097
Discipline Name: Material Science
We are the Advanced Materials and Engineering group within manufacturing cluster at CSIR. Our group is mainly focused on the Ti and Platinum group metals beneficiation using both experimental and first principle approach. The stability predictions of alloys are done using Materials Studio at CHPC and the results validated using experimental procedures. The modeling approach using CHPC resources helps in minimizing cost and time spend in the lab. Some materials can also be harmful to use in the labs hence modeling comes with such benefits. The work is progressing well wherein students are at the last stage of writing their thesis and some using their results to perform some of the experiments for validation.
Principal Investigator: Dr Sunita Kruger
Institution Name: University of Johannesburg
Active Member Count: 1
Allocation Start: 2020-03-16
Allocation End: 2020-09-12
Used Hours: 541049
Project Name: Environmental Heat Transfer
Project Shortname: MECH0995
Discipline Name: Computational Mechanics
This research group in the Mechanical Engineering Science Department of the University of Johannesburg is currently focusing on environmental heat transfer. Specifically heat transfer in naturally ventilated greenhouses. Greenhouses are used to protect plants from adverse weather conditions and insects. Ventilation of greenhouses are of vital importance to ensure quality crop production. If temperatures in a greenhouse is too high, poor plant growth may result, and an increased need for frequent watering. A mechanical ventilation system might be required to cool the inside of the greenhouse. Natural ventilation is an alternative option used to ventilate greenhouses. Natural ventilation uses temperature and wind to control the indoor climate of greenhouses. Unfortunately greenhouses are extremely energy intensive. Energy costs are the third highest cost related to greenhouse crop cultivation. Reducing the operating costs of energy associated with greenhouse cultivation may result in a price reduction of greenhouse cultivated crops. Conducting experimental work on ventilation of greenhouses can be costly and cumbersome. Using computational methods such as CFD (Computational Fluid Dynamics) to obtain qualitative and quantitative assessment of greenhouses can reduce costs and time involved. The computer cluster at the Centre for High Performance Computing has been used to conduct the numerical investigation using CFD. Currently research is being conducted on a large commercial greenhouse. Smaller greenhouses containing a single span have also been investigated. Currently, three dimensional models of greenhouses subject to buoyancy driven flow are being investigated.
Principal Investigator: Dr Samson Khene
Institution Name: Rhodes University
Active Member Count: 7
Allocation Start: 2020-03-16
Allocation End: 2020-09-12
Used Hours: 2916
Project Name: Synthesis, Spectroscopy and Nonlinear Optical Properties of Phthalocyanines
Project Shortname: CHEM0975
Discipline Name: Chemistry
Many of today's optical sensors are based on optical materials in which non-linear optics may play a role. Defects in the cable can have an effect of reducing the light (which carries information) in an optical fiber or cable. This phenomenon is also present in a variety of non-linear active materials or molecules. This nonlinear reduction of light phenomenon can be used as a sensing method for detection and correction of signals that are sent in cables. The aim of our research (at Rhodes University in the Chemistry department) is to make and study molecules which will help improve signal transmission using a nonlinear process. This work will not be possible if it was not supported by CHPC facilities.
Principal Investigator: Dr ADEDAPO ADEYINKA
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2020-03-16
Allocation End: 2020-09-12
Used Hours: 201360
Project Name: Computational Design of Molecules
Project Shortname: CHEM1221
Discipline Name: Chemistry
The Computational Design of Molecules research group is based at the University of Johannesburg. We aim to
design new and improved molecules and materials for applications in Catalysis and renewable energy. Since
the availability of energy is one of the main challenges of the African continent, being able to achieve our aims
as a group will provide clean energy solutions for the continent. We use computational chemistry software to
explore the properties of molecules which is responsible for their activity and then use the knowledge gained to
design more efficient and improved materials.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2020-03-17
Allocation End: 2020-09-13
Used Hours: 83396
Project Name: SANAP CFD
Project Shortname: MECH1196
Discipline Name: Earth Sciences
The sub-Antarctic is one of the windiest regions in the world, with the biotic and abiotic conditions of the sub-Antarctic islands thought to be strongly affected by wind patterns. However, for these isolated terrestrial ecosystems we have a very poor understanding of within-island variation in wind speed and direction, and of how variation in wind patterns impact biotic communities. As a result, despite clear recent changes in broad-scale wind patterns in the sub-Antarctic, we have little quantitative basis for predicting the impacts that climate change-related shifts in wind speed and direction have on the biota of these islands. Computational Fluid Dynamic (CFD) models provide a robust methodology for estimating wind patterns, and have previously proved successful in understanding fine-scale air flow patterns in this system. However, the application of CFD to island-scale wind simulation is still an under-utilized approach despite recent relevant advances. Therefore, in this project we develop, and then apply, an island-scale CFD model to simulate wind flow patterns across an entire island, testing the potential for this approach to provide accurate insight into spatial variation of wind patterns across the island. The resources at the CHPC help in running large CFD models of the wind patterns on the island for all the predominant wind directions as obtained from the ongoing experimental wind mast study. The CFD results are of interest to botanists and those studying bird behaviour. Another spin-off is to investigate the use of wind power on parts of the island not inhabited by birds in order to replace the current diesel power generation.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2020-03-17
Allocation End: 2020-09-13
Used Hours: 982276
Project Name: CFD Modelling of Concentrated Solar Power Applications
Project Shortname: MECH0873
Discipline Name: Computational Mechanics
Central tower solar power plants are the most promising concentrated solar with research into new receivers and heat transfer fluids and collectors (heliostats) being ongoing world-wide. Researchers at the University of Pretoria's Clean Energy Research group under the leadership of Prof Ken Craig are using the resources at the CHPC to speed up calculations of both heliostat analysis (involving wind loads and fluid-structure interaction) as well as those required for a new point-focus central receiver design being developed. For heliostats, knowledge has been gained in predicting the peak loads that these reflectors will experience during all orientations and wind conditions. Ongoing work is focused on further reducing the cost of these Computational Fluid Dynamics (CFD) hybrid Large Eddy Simulation (LES):Reynolds-Averaged Navier-Stokes models to make them feasible on smaller-scale computers. This project has been ongoing since 2013 with the involvement of CHPC resources since 2016. The project has already delivered two masters students (Dawie Marais and Joshua Wolmarans) with Jesse Quick and Derwalt Erasmus nearing completion. PhD student Pierre Poulain is also nearing the end of this investigation into LES modelling of the atmospheric boundary layer. For central receivers, work is ongoing to enhance heat transfer. Of specific interest here is the use of jet impingement, especially in the transient mode through either passive or active excitation. This phenomenon of heat transfer enhancement, although conceptually simple, it very hard to model accurately, and here the resources of the CHPC are invaluable, especially as LES is required to model the transient and 3D nature of swirling jet, the focus of the work of Jesse Quick. CHPC resources is also being used to investigate the thermal performance solar dish receivers by accurate simulation of heat losses due to dish orientation and wind speed.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-03-17
Allocation End: 2020-09-13
Used Hours: 226758
Project Name: CFD modelling of jet impingement with phase change
Project Shortname: MECH1296
Discipline Name: Computational Mechanics
Jet impingement heat transfer with boiling is a promising new heat transfer method for use in power electronics cooling. Jet impingement flow is difficult to simulate because of its transient nature and multiple flow regimes involved (from laminar to turbulent). Previous research by Prof Ken Craig's group has developed techniques based on Large Eddy Simulation to evaluate the effect of round jets with and without swirl on solar receiver heat transfer surfaces. This program extends that work to having phase change as well in the form of boiling. The latent heat absorbed by boiling works in addition to the enhance convection provided by the jet. Various case studies are being developed for application in the electronics cooling industry.
Principal Investigator: Mr Darren Martin
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2020-03-19
Allocation End: 2020-09-15
Used Hours: 14528
Project Name: New Method for Measuring Telomeres at High Resolution
Project Shortname: CBBI1262
Discipline Name: Bioinformatics
We have been developing a new method for sequencing and understanding the protective caps on the end of chromosomes known as telomeres. Telomeres shorten as we age and are a well-known marker for longevity. The current methods used to measure telomeres only yield a mean length for a group of cells, thus hiding a lot of important information. For this reason, we decided to try measure individual telomeres to better understand the spread of lengths in a group of cells, and uncover some of the mysteries of how telomere length is linked to longevity.
Principal Investigator: Prof Andries Engelbrecht
Institution Name: Stellenbosch University
Active Member Count: 15
Allocation Start: 2020-03-19
Allocation End: 2020-09-15
Used Hours: 801393
Project Name: Computational Intelligence for Optimization
Project Shortname: CSCI0886
Discipline Name: Computer Science
Novel nature-inspired optimization algorithms have been developed to solve optimization problems. These algorithms are all based on very simple models of bird flocking behaviors, and applied to solve complex problems such as portfolio optimization, and developing more efficient machine learning algorithms.
Principal Investigator: Dr Ernest Odhiambo
Institution Name: University of Nairobi
Active Member Count: 1
Allocation Start: 2020-03-20
Allocation End: 2020-09-16
Used Hours: 19537
Project Name: Computational Modeling of Heat Containment Systems
Project Shortname: MECH1178
Discipline Name: Computational Mechanics
Since the last press release issued, the MECH1178 Computational Simulation group that is housed at the department of mechanical and manufacturing engineering has welcomed a new member to the group. Mr John Kisilu, a masters student is focusing on determining accurate smoke layer height for a building on fire. He is mainly concerned with smoke movement in high rise buildings found in the hospitality industry.
The problems the MECH1178 group considers are based on fluid dynamics, thermodynamics and heat transfer. Computational simulation tools are used to model practical instances of fluid and structural interaction while at the same time resolving the thermodynamics and heat transfer characteristics of such flow situations. A typical example is the resolution of the behaviour of smoke for a building on fire.
Apart from the focus on fire safety, the ME1178 group is also carrying out work in the energy sector where the focus is on the computationally modelling of a wind turbine premised on the Magnus lift force. The aim is to enhance the capture of wind energy so as to make more efficient the generation of electricity.
The African economy is mainly driven by agricultural activities. Thus we have in the group a team whose objective is to improve the survivability of crops for better harvest by computationally modelling the optimal greenhouse environment.
A group of students from the MECH1178 are currently working on the modelling of the causes and remedies of respiratory diseases. This has become even more significant given the outbreak of the novel Corona (Covid-19) virus.
The above highlighted research activities have been made possible through the use of the CHPC Lengau cluster, without which our progress would really be hampered. At least two researchers in the MECH1178 group are in the process of publishing some data obtained from their results.
Principal Investigator: Prof Veikko Uahengo
Institution Name: University of Namibia
Active Member Count: 6
Allocation Start: 2020-03-20
Allocation End: 2020-09-30
Used Hours: 764899
Project Name: Solar Materials
Project Shortname: MATS1043
Discipline Name: Material Science
The research group from the University of Namibia, is a Material Chemistry based group working on metal oxides of copper and zinc. The group is focusing in harnessing the properties of these materials for a variety of applications, ranging from catalysts, photocatalyst, solar materials (thin films) and biological activities. This is done through different synthetic or fabrication methods such as sol gel, molecular precursor methods, through introduction of different dopants. In the end, this will not only harness the applications of these abundant and easy-to-make materials, but it will also add values to these locally available materials, which are normally exported in their raw forms.
Our research employs quantum-mechanical simulations based on density functional theory (DFT) to help identify new solar harvesting materials. Currently, our focus lies on ZnO and ZnP2, two compounds that have promising electronic and optic properties. Modelling them from a theoretical point of view gives complementary insight into processes that govern photon absorption, electron-hole creation, and transportation of charges across the bulk. We have shown how basic DFT is inadequate to model our two zinc compounds and have identified Hubbard corrections (or hybrid functionals) as the next step forward. Once the modelling of the basic properties has been done, we shall move to performing doping, creating surfaces and possibly create band-aligned structures, to improve the photovoltaic properties of ZnO and ZnP2.
Furthermore, some students are looking into improving the light absorption efficiency of inorganic complex dyes by tuning the optical properties of these complexes to absorb in the visible region. In addition to ZnO and ZnP2, the group has also looked into the TiO2 doped with sliver-nanoparticles to improve its photo voltaic properties, with the results so far outstanding. This work is sandwiched between Cardiff University and UNAM, for which ideas are shared among the two teams, as well as other member within the scope of our collaborative consortium.
The CHPC (has) and is still a major contributing factor to our work, because before we start with experimental work, we have to simulate the designs of our materials and see which ones are most suitable, in terms of energetics and dynamics, then select thereafter, thus by using the HPC facilities we are managing to select the favorable cases, leaving us with straight forward choices. This is not only saving us time, but it is also saving us money, which we use to buy chemicals for experiments. Instead of trying out all possible cases experimentally, simulation/computation can do it easily and leave you with the most possible cases (experimentally).
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 12
Allocation Start: 2020-03-20
Allocation End: 2020-09-16
Used Hours: 4202609
Project Name: Structural, electronic, magnetic properties and anisotropy energy in some metallic and non-metallic heterostructures
Project Shortname: MATS0988
Discipline Name: Material Science
The research work is a collaboration between the Dr. Raji ( Physics Department, UNISA, South Africa) and the group of Dr. Brice Rodrigue Malonda (Marien Ngouabi University, Republic of Congo). The focus of the research is numerical studies of electronic, optical, transport and magnetic properties of selected two-dimensional (2D) and three-dimensional (3D) solid materials for potential applications in high-capacity data storage, catalysis and renewable energy. The study employs density-functional theory (DFT) as the numerical method, to probe atomic-level properties of these materials. Our approach is mainly atomic and defect engineering of these solids which involve modifying the properties of the solids through the introduction of external atoms into their otherwise pristine structure. The last two decades have witnessed the discovery of several 2D materials, and have opened new possibilities to further miniaturization of existing electronic and magnetic devices. Therefore, fundamental understanding of properties of these materials systems is necessary to support experimental research and to aid technological applications. One of the aims of our research therefore, is to discover novel materials that can be synthesized in the laboratory for potential technological applications.
The numerical implementation of DFT is computational intensive, requiring several computational hours, large data storage and memory requirements, beyond the capacity of ordinary table-top computers. Therefore, high-capacity computer clusters such as the one provided by the Center for High Performance Computing (CHPC) is sine -qua-non for the research. There are about twelve postgraduate students working in various aspects of the project. At the moment, four Masters students have completed their studies and two of them are continuing to doctorate. This research, as well as the CHPC, has enabled collaboration between South Africa based academic researcher and colleagues in Congo, Mexico and Italy. There have been research outputs in form of publications, and the scope of the project will guarantee regular postgraduate students training who are able to undertake cutting-edge research and contribute to scientific development.
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 2
Allocation Start: 2020-03-23
Allocation End: 2020-09-19
Used Hours: 430144
Project Name: Magnetocaloric effect in selected metallic nanoclusters on two-dimensional (2D) substrates, and in selected rare-earths.
Project Shortname: MATS1156
Discipline Name: Material Science
The research study is based at the Department of Physics of the University of South Africa (UNISA). The study concerns fundamental study and potential applications of two-dimensional (2D) nanomaterials in ultrathin refrigeration, air-conditioning system, and in cooling of nanoelectronic devices or any system where nanoscale cooling is needed. Specifically, the research aims to study the phenomenon of magnetocaloric effect (MCE) in metallic nanostructures deposited on various two-dimensional substrates, such as graphene, silicene, and similar 2D materials. Magnetocaloric effect is a property of magnetic materials which could be exploited for refrigeration purposes. While the conventional refrigerator system is based on compression and evaporation of often environmentally unfriendly gases, magnetic refrigeration systems is based on magnetizing and demagnetizing a magnetic material. In the last few years, the focus in magnetocaloric research seems to have shifted toward ultrathin materials. Because of plethora of candidate materials that may be investigated as possible candidates for MCE, performing experimental investigations may be time and resources consuming, and thus, computational studies could provide the lead and narrow the range of materials that could be considered for further experimental investigations. Performing ab-initio density-functional theory (DFT) study to determine the properties of candidate material systems is a viable and state-of-the-art approach which can complement experimental efforts. DFT calculations require specialized softwares as well as high-capacity data storage and memory requirements which are often beyond the capability of desktop computers. Thus, the availability of high-performance computing (HPC) facility is absolutely necessary.
Principal Investigator: Dr John Mack
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2020-03-23
Allocation End: 2020-09-19
Used Hours: 3303
Project Name: Rational design of phthalocyanine, porphyrin and BODIPY dyes
Project Shortname: CHEM0796
Discipline Name: Chemistry
The Institute for Nanotechnology Innovation (INI) at Rhodes University under director Prof. Tebello Nyokong carries out research related to the use of molecular dyes in biomedical applications, such as cancer treatment through photodynamic therapy, the use of antimicrobial photodynamic chemotherapy for treating hospital superbugs and as sensors for ions that are harmful to human health.
Other applications of interest include wastewater treatment and the development of optical limiters to protect human vision,such as in aviation safety in protecting pilots from the irresponsible use of laser pointers during runway approaches. It is important to understand trends in the electronic and optical properties that make the molecular dyes suitable for these particular applications. The resources of the Centre for High Performance computing help to facilitate this by making it possible to carry out molecular modelling calculations that can be used to predict how changes to the structures of the molecular dyes will modify their properties. The flexibility that CHPC provides where memory allocations are concerned is often vital.
The INI currently has three staff members, fifteen PhD, four MSc and six Honours students, and three postdoctoral fellows, and usually publishes over forty peer-reviewed publications per year. This rose to a high of sixty-five in 2017 with ten involving the use of CHPC resources.
Principal Investigator: Prof Jan Jacobs
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2020-03-24
Allocation End: 2020-09-23
Used Hours: 67948
Project Name: Machine-learning-based modeling of electromagnetic and sound devices and applications
Project Shortname: MECH1317
Discipline Name: Other
The research group of Professor Pieter Jacobs in the Department of Electrical, Electronic and Computer Engineering at the University of Pretoria is concerned with the machine-learning-based modeling of electromagnetic and sound (specifically music) related phenomena.
In the past year, CHPC allocated resources have been devoted to antenna (i.e. electromagnetic) deep learning modeling. While various regression methods (neural networks, Gaussian processes, support vector machines) have previously been used for the modelling of antenna characteristics, deep learning methods have remained relatively unexplored. Fast models of antenna responses are essential for the efficient optimization of antenna structures, and could significantly reduce the time required to design antennas by reducing the time spent on computationally expensive electromagnetic simulations. Deep learning can potentially provide more accurate models than the current state-of-the-art methods.
Use of the CHPC made it possible to train and analyse thousands of different deep learning neural network models as part of the process of carrying out comprehensive hyperparameter sweeps aimed at discovering optimal neural network architectures. The CHPC enabled these models to be trained and analyzed in parallel, which greatly decreased the time required to compare different models. In a further step, deep neural network learning, as an antenna modeling tool, could for the first time be compared to other, similarly computationally expensive, deep learning strategies such as deep (stacked) Gaussian processes, and deep kernel learning (a hybrid between neural networks and Gaussian processes).
The above work on the CHPC was carried out by a master's degree student who made significant progress with his research; it is anticipated that he will hand in his dissertation by the end of 2020, and a paper based on this work will be submitted to an international peer-reviewed journal.
Principal Investigator: Dr Quinn Reynolds
Institution Name: Mintek
Active Member Count: 4
Allocation Start: 2020-03-24
Allocation End: 2020-10-01
Used Hours: 55662
Project Name: Computational Modelling of Furnace Phenomena
Project Shortname: MINTEK776
Discipline Name: Applied and Computational Mathematics
Pyrometallurgical smelting is one of the world's oldest industrialised technologies, with its origins in archaeological production of copper, iron, and steel. Despite being studied and used for thousands of years, its sheer complexity in terms of the overwhelming number of physical and chemical effects involved have meant that much of the fundamental behaviour of high-temperature processing has remained a mystery.
Until now.
For the first time in human history, our ability to perform numerical and computational solutions of the complex mathematics of fluid flow, heat transfer, electromagnetics, and other phenomena at extreme scales is allowing us to open the black box of pyrometallurgical furnaces and look inside. By combining computational models inside frameworks for virtual prototyping, systems modelling and automation, and numerical experimentation, deep insight and knowledge can be rapidly gained and transferred to industry for grand-challenge problems such as furnace tapping and plasma arc smelting.
With the aid of powerful computers such as those available at CHPC, Mintek is performing research into new process and equipment technologies that will allow us to digitally unlock the mineral wealth of South Africa and the world in economically- and environmentally-responsible ways.
Principal Investigator: Dr Zaid Kimmie
Institution Name: NICD
Active Member Count: 0
Allocation Start: 2020-03-26
Allocation End: 2020-09-22
Used Hours: 59074
Project Name: Covid-19 Decision Support
Project Shortname: CBBI1319
Discipline Name: Data Science
The research was conducted by a multi-disciplinary team from the MRC, CSIR, University of Pretoria, UKZN and Wits University.
The aim of our work was to implement a spatial model for predicting the spread of Covid-19, and to assess the importance of ecological and social factors in the spread of the epidemic. We believe that spatial aspects are a significant component of epidemic modelling and will allow for more accurate forecasts.
The spatial model is implemented over 4000 wards and requires significant processing power to implement. Using the CHPC allowed the team to complete a simulation run in near-real time.
We are currently preparing a number of papers investigating the spatial aspects of the Covid-19 epidemic.
Principal Investigator: Dr Gavin Gouws
Institution Name: SAIAB
Active Member Count: 10
Allocation Start: 2020-03-26
Allocation End: 2020-09-22
Used Hours: 3060
Project Name: RADseq studies of aquatic biodiversity
Project Shortname: CBBI1274
Discipline Name: Other
The Marine Fish Research Team in the Aquatic Genomics Research Platform at the National Research Foundation - South African Institute for Aquatic Biodiversity employs a variety of genetic tools to understand the evolution and ecology of marine fishes (and marine invertebrates). We are interested in the relationships between species, populations and individuals, and in the movement and migration of individuals, with a view to informing conservation and management. Over the last year, we have conducted studies examining whether the genetic diversity of commercially-exploited marine fishes have changed over time, as a result of harvesting, and whether an endangered line-fish exists as and should be managed as a single population along the South African coast. For the former, SNP genotype data were generated and analysed using applications on the CHPC, while the latter used the CHPC and it's applications to model patterns of migration, dispersal and changes in population size using mitochondrial and nuclear genetic data. Some of this research is currently in press, with additional manuscripts currently being prepared.
Principal Investigator: Prof Bettine van Vuuren
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2020-03-26
Allocation End: 2020-09-22
Used Hours: 19484
Project Name: Biocomplexity on sub-Antarctic islands
Project Shortname: CBBI1153
Discipline Name: Bioinformatics
- We are a research group at the Centre of Ecological Genomics and Wildlife Conservation based at the University of Johannesburg, South Africa.
- We are conservation geneticists and are interested in studying spatial and temporal genetic patterns in multiple organisms (plants and invertebrates) on sub-Antarctic islands, with a special focus on Marion Island. We aim to investigate genetic patterns and structure in the context of environmental changes (for example, climate change). We intend on using our study species as proxies for monitoring global change and its impact on biodiversity as a whole.
- We are well aware of the concept of environmental change (such as climate change, which is more pronounced in the sub-Antarctic region). As conservation geneticists, we will investigate the impact that change has on biodiversity. Understanding genetic patterns is crucial, and our results will bring about far-reaching implications for the development of conservation management programs for Marion Island and on a global scale too.
- To do this, we have generated next-generation sequencing (NGS) data using various sequencing chemistries. We will use the CHPC cluster to analyse our NGS data to answer transcriptomic questions, and phylogenomic and population genomic related analyses. The above mentioned data is exceptionally large, and therefore we will not be able to conduct our research without the CHPC resources since no other platforms can handle these large datasets.
- We are in the process of completing three research articles to be submitted for publication soon. In the near future, and based on the work from Daniela and Shilpa, we hope to publish several articles next year.
We are happy with the progress we have made thus far and thank the CHPC for this (the CHPC has been acknowledged in the publications).
Principal Investigator: Mr Randall Paton
Institution Name: University of the Witwatersrand
Active Member Count: 12
Allocation Start: 2020-03-26
Allocation End: 2020-09-22
Used Hours: 1590456
Project Name: Compressible Gas Dynamics
Project Shortname: MECH0847
Discipline Name: Other
The compressible gas dynamics research group uses computational tools to reinforce and extend experimental work pertaining principally to the flows associated with supersonic air craft. This includes modelling the flow around highly-manoeuvrable aircraft with greater accuracy than before. We are also looking at applying our understanding to low-speed flows in the wake of the COVID-19 pandemic to start developing models to improve public health decision making for shared spaces such as public transport, offices, and shopping malls.
Principal Investigator: Dr Madison Lasich
Institution Name: Mangosuthu University of Technology
Active Member Count: 15
Allocation Start: 2020-03-30
Allocation End: 2020-09-26
Used Hours: 49117
Project Name: Chem Thermo
Project Shortname: CHEM1028
Discipline Name: Chemical Engineering
The Thermodynamics, Materials and Separations Research Group at the Mangosuthu University of Technology employed multi-scale modelling and simulation to investigate industrially relevant systems. By considering intermolecular interactions as well as fluid flow dynamics, the group has studied surface fluorination processes in conjunction with researchers at UKZN and NECSA, with a view to improving domestic fuel tank production. In addition, by coupling microscopic interactions with macroscopic phase behaviour, the group has developed guidelines for systems to purify and improve fuel gases, such as those produced from biomass.
Principal Investigator: Dr Lucy Kiruri
Institution Name: Kenyatta University, Nairobi, Kenya
Active Member Count: 6
Allocation Start: 2020-03-31
Allocation End: 2020-09-27
Used Hours: 150277
Project Name: KU Computational Chemistry Research Group
Project Shortname: CHEM1032
Discipline Name: Chemistry
CHEM1032: Kenyatta University Computational Chemistry Research Group
The members of the group are in 3 different areas of Molecular modeling, namely quantum mechanics, Molecular Mechanics and Molecular Dynamics. Katana Chengo has completed his Ph.D. and is awaiting graduation.. His work entailed DFT study of Cationic iron half-sandwich complexes of mixed donor ligands for treatment of tuberculosis.
Daniel M. Shadrack graduated on 29/08/2020 with a PhD in Biophysics in NM-AIST Tengeru campus, Arusha. Some of his work was done using the CHPC.
Wycliffe is a third year PhD student working on Molecular Dynamics applied to study conformational transitions (structural changes) in some biomolecules that are important in how malaria is transmitted.
Dr. Lucy is the principal investigator and working on a number of projects. One is with her Tanzanian collaborators on Covid-19 whereby by they are repurposing drugs as well as using East Africa natural compounds to perform MD calculations against SARS-CoV-2. For this work, we are using GROMACS 2018.6 and Plumed plug in. Other calculations include the DFT/TDDFT for various superconductors using Gaussian 16.
Our aim is to publish manuscript from all the above-mentioned work. We are therefore grateful to the CHPC in fast-tracking our work since we were using core i5 desktop before where calculations would take much longer. Since the start of using the CHPC, we have made much progress on our research work.
Principal Investigator: Dr Sean February
Institution Name: SKA
Active Member Count: 3
Allocation Start: 2020-03-31
Allocation End: 2020-09-27
Used Hours: 243290
Project Name: MeerKAT Open Time Projects - Feasibility Study
Project Shortname: ASTR1114
Discipline Name: Astrophysics
The South African Radio Astronomy Observatory manages the currently operating 64-dish MeerKAT telescope located in Carnarvon in the Karoo. It is expected that approximately 30% of MeerKAT's observing time will be taken up by smaller research groups who do not necessarily have the computing capacity to carry out the required processing of the data. The aim of this research programme is to conduct ongoing, as needed, feasibility studies for anticipated open-time projects. Our most recent job submissions focussed on a specific science-case: the accurate calculations of the MeerKAT primary beams. The latter is important for imaging/calibration purposes. With the help of a vacation student, we managed to calculate primary beams for 4096 MeerKAT frequency channels -- arguably the best semi-empirical estimates we thus far. While the latter is broadly applicable to many science-cases, to first order, we feel there are further benefits to allow for user-defined parameters.
Principal Investigator: Prof Fernando Albericio
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2020-04-01
Allocation End: 2020-09-28
Used Hours: 77863
Project Name: Peptide chemistry and Organic chemistry
Project Shortname: CHEM1102
Discipline Name: Chemistry
Being from experimental background, our lab uses computational to explain the feasibility of reactions. We are in process of completing some manuscripts for publication.
Principal Investigator: Dr Njabulo Gumede
Institution Name: Walter Sisulu University
Active Member Count: 1
Allocation Start: 2020-04-01
Allocation End: 2020-09-28
Used Hours: 14687
Project Name: Computer-Aided drug design for cancer therapy
Project Shortname: CHEM1058
Discipline Name: Chemistry
I am using computer aided drug design approaches in conjunction with AI/ML methods such as PathFinder enumeration and DeepQSAR (active learning) approaches to design new chemical entities for prostate, breast cancers and COVID-19. I am based at Mangosuthu University of Technology. Having partnerships with researchers from here in RSA, India, Brazil, Italy and Spain.
Principal Investigator: Prof Thomas Niesler
Institution Name: Stellenbosch University
Active Member Count: 11
Allocation Start: 2020-04-03
Allocation End: 2020-09-30
Used Hours: 286930
Project Name: Automatic Speech Recognition for Under-resourced Languages
Project Shortname: CSCI1059
Discipline Name: Electrical Engineering
The era of big data and deep learning has resulted in huge advances in many fields, including automatic speech recognition. However, many of the techniques that are considered to be "state of the art" rely on vast volumes of data and extensive computing power. South Africa's 11 official languages - and many other languages in the world - are under-resourced. This means that, for these languages, resources like corpora of annotated speech and text data are either small or do not exist at all. One of the challenges that the Digital Signal Processing Group at Stellenbosch University's Department of Electrical and Electronic Engineering is therefore addressing is how to develop automatic speech recognition and keyword spotting systems for languages in which very little or no annotated speech data is available.
A related challenge in multilingual countries is to correctly process utterances in which speakers switch between languages. This phenomenon is called code-switching and speech recognition systems do not make provision for this type of speech but are designed for monolingual input. Being a multilingual country, South Africa is one of the places where people often use more than one language in a conversation or even a sentence. The group is developing automatic speech recognition systems to process South African code-switched speech.
All the pattern recognition techniques used by the group to process speech currently rely heavily on deep and recurrent neural networks. Training these networks within reasonable time frames and running multiple experiments to optimise system configurations require access to substantial computational resources. Having access to CHPC has enabled the group to train more complex systems and to run more experiments which, in turn, enabled them to study different aspects of the issues they are investigating in more detail. The work on CHPC has accelerated progress on investigations aimed at detecting speech in audio streams as well as expanding existing data sets by using semi-supervised labelling techniques.
Principal Investigator: Dr Joseph Mutemi
Institution Name: University of Nairobi
Active Member Count: 3
Allocation Start: 2020-04-05
Allocation End: 2020-10-02
Used Hours: 2601
Project Name: Numerical weather and climate modeling, prediction, forecasting and change projections for Africa and sub regions
Project Shortname: ERTH1131
Discipline Name: Earth Sciences
The ERTH1131 research group is using CHPC resources in studying important processes in climate models in order to improve early warning information, in regards to severe weather and inform policy. Given the severe rainfall season in March-May 2018, the team identified that models could give useful early warning at good lead times. Study on land-atmosphere interactions also using the sixth generation of Coupled Model Intercomparsion Project (CMIP6) models identified that land-atmosphere interactions are generally under-represented over East Africa. This implies weaknesses in model representation of the lower atmosphere energy and water balance, possibly due to the parameterizations adopted. In addition, CMIP6 models were unable to accurately resolve the topography induced Turkana jet. This weakness hinders proper utilization of the models for wind power resource assessment as part of harnessing renewable energy sources.
Principal Investigator: Prof Hasani Chauke
Institution Name: University of Limpopo
Active Member Count: 9
Allocation Start: 2020-04-06
Allocation End: 2020-10-03
Used Hours: 38160
Project Name: Computational Modelling of Minerals, Metals and Alloys
Project Shortname: MATS1047
Discipline Name: Material Science
The minerals, metal and alloy development programme (MATS1047), led by Professor Hasani Chauke (primary investigator, PI) is amongst others one of the major strategic research niche at the Materials Modelling Centre (MMC), University of Limpopo. The work employ first-principles quantum mechanical approaches and molecular dynamics based methods, which employs various academic and commercial software's with different types of interfaces. These computers based software's are linked to local servers (MMC) and the Centre for High Performance Computing (CHPC). The programme continue to receive enormous support from the CHPC, particular to run large scale calculations at a more reasonable time.
Principal Investigator: Prof Werner Van Zyl
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2020-04-06
Allocation End: 2020-10-25
Used Hours: 34683
Project Name: Theoretical studies on molecular species in bulk and at interface
Project Shortname: CHEM1244
Discipline Name: Material Science
We are a 10 member research group situated within the School of Chemistry and Physics at UKZN, Westville Campus. Our research focuses on sustainable water, energy, and biomass (SUSWEB). We have made the most progress in the area of energy and biomass conversion. We also study large hydride clusters of copper and silver where CHPC resources come in handy. We have published 10 papers in these areas of research for the past 1 year. We also currently have 2 postdoctoral fellows that help with the research. The project is commencing very well and our annual goals have been met, despite lockdown. With postgraduate students slowly allowed to continue their research the pace will pick up.
Principal Investigator: Prof Rosemary Dorrington
Institution Name: Rhodes University
Active Member Count: 10
Allocation Start: 2020-04-06
Allocation End: 2020-10-03
Used Hours: 27631
Project Name: Marine Natural Products Research
Project Shortname: CBBI0963
Discipline Name: Bioinformatics
Marine Natural Products Research Group, Department of Biochemistry and Microbiology, Rhodes University
The Marine Natural Products (MNPs) Research Platform covers the broad field of marine biodiscovery, focusing on the potential of bioactive secondary metabolites produced by marine organisms endemic to the Agulhas Bioregion as lead compounds for drug discovery. More than half of new pharmaceutical drugs on the market or in clinical trials are natural products and their derivatives and the majority of these are now coming from marine macrofauna and their associated microbiomes.
The MNPs research programme is active across the broad field of marine biodiscovery, focusing on exploring the potential of marine invertebrates and their associated microorganisms as sources of novel bioactive small molecules. Research projects include: (1) Biodiversity mapping of benthic habitats in the Agulhas bioregion, focusing on invertebrates, ascidians, soft corals and their associated microbiota; (2) Isolation and characterization of bioactive secondary metabolites of marine organisms; (3) screening marine natural product libraries for anti-viral, anti-cancer and antibacterial activity and (4) elucidating the metabolic pathways that result in the production of lead compounds to pave the way for engineering recombinant systems for their production for the pharmaceutical industry. Associated projects focus on the application of high throughput metagenomic and analytical chemistry technologies to map patterns and processes in marine ecosystems. These "omics" approaches e.g. next generation DNA and RNA sequencing and high resolution tandem mass-spectrometry generate very large and complex datasets, the analysis of which requires the high performance computing capacity provided by the CHPC.
Principal Investigator: Prof Cornie van Sittert
Institution Name: North-West University
Active Member Count: 20
Allocation Start: 2020-04-06
Allocation End: 2020-10-09
Used Hours: 1537224
Project Name: Computational Chemistry within LAMM at NWU (Potchefstroom)
Project Shortname: CHEM0778
Discipline Name: Chemistry
Since the 1880 the main source of energy for South Africa was coal and at present coal provides 77% of South Africa's primary energy needs. However, the electricity comes at a very high cost, namely air pollution and the influence of the air pollution to human health. In 2004 the South African government reformed the legislation with regard to air pollution. In an effort to contribute to the management of air quality new energy sources must be investigated. These new energy sources must be affordable, clean and renewable. Some of these alternative energy sources are fuel cells and batteries. Electricity from fuel cells and batteries are obtainable through the use of electrochemistry, where free energy of spontaneous reactions is transformed into electricity. A potential replacement form of energy is the hybrid sulphur (HyS) cycle. The HyS cycle is a two-step water-splitting process, which could be used for the production of hydrogen. In the HyS cycle, the anode material used is platinum. However, because platinum is a rare and expensive metal, it is not an economical viable option for long term and large scale production of hydrogen. Hence, various attempts to reduce or eliminate the platinum content, while not compromising the process performance has been made. In the order to understand the electrochemistry on the anode and make informed decisions on the type and amount of metal to be used in various platinum alloys, investigations on a fundamental level is needed. These type of investigations could be classified as computational chemistry. The resources needed for these type of investigations, namely various types of hardware and software is of cardinal importance. Although resources are available at NWU, it is not nearly enough to fully support the research covered in the Laboratory of Applied Molecular Modelling (LAMM). So if we as researchers within the LAMM did not have access to the CHPC resources the progress of our research will be much slower.
Principal Investigator: Dr Steve Peterson
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2020-04-06
Allocation End: 2020-10-03
Used Hours: 16684
Project Name: Development of a Prompt Gamma Imaging Device
Project Shortname: PHYS0830
Discipline Name: Physics
The UCT Prompt Gamma Imaging (PGI) Group is a part of the Measure Research Unit based in the Department of Physics at the University of Cape Town. PGI is a new form of imaging that will be used in conjunction with proton radiation therapy cancer treatments. The protons that are used to attack the cancer cells produce gamma-rays that we are detecting and using to produce images of the dose deposited in the patient. PGI is still a technology in development and relies heavily on computing resources for both detector design and image reconstruction.
Principal Investigator: Prof Rebecca Garland
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2020-04-06
Allocation End: 2020-10-03
Used Hours: 46329
Project Name: Simulating atmospheric composition
Project Shortname: ERTH0846
Discipline Name: Earth Sciences
Air pollution can have large negative impacts on human health, agriculture, ecosystems, visibility and climate. In South Africa, although ambient air quality is regulated, many areas are out of compliance with the National Ambient Air Quality Standards. In order to protect human health and mitigate impacts, it is critical to improve air quality. The Constitution provides that everyone has a right to have an environment that is not harmful to their health. The Atmospheric Composition Focus Area (ACFA) in the CSIR Climate and Air Quality Modelling research group aims to provide the evidence base to quantify the impacts of air quality and to improve air quality.
The group uses the CHPC to run an air quality model to simulate urban and regional air quality at high resolution. This chemical transport model simulates the physics and chemistry of the atmosphere. The processes represented within the model are complex, and thus computationally intensive, which makes use of the CHPC facility a necessity. The CSIR ACFA is the only group in South Africa routinely running a chemical transport model to simulate air quality for management purposes.
Using the CHPC resources, the team has been able to simulate the impact of policy interventions on air quality in cities. Additionally, the team has simulated the health risk from air pollution regionally in South Africa. In the past, this has been done using monitoring station data only, which then limits the analysis to only those living directly around the station. The team has also simulated the impact of climate change on air pollution. These simulations use the climate projections from the CSIR's CCAM-CABLE, which is also run at CHPC, to provide meteorology input into the air quality model.
These outputs directly provide the evidence base needed for decision makers to draft and implement policies and interventions to effectively improve air quality as well as understand its impacts, now and into the future.
Principal Investigator: Dr Stewart Bernard
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 2
Allocation Start: 2020-04-06
Allocation End: 2020-10-03
Used Hours: 6277
Project Name: Marine EO Cubes
Project Shortname: ERTH1271
Discipline Name: Environmental Sciences
The Earth observation research group (EO RG) within the Ecosystem Services Impact area of the CSIR focusses on the development and validation of regionally appropriate satellite-derived chlorophyll-a (Chl-a) concentrations (as a proxy for phytoplankton) and Sea surface temperature (SST). Both these products serve as convenient proxies for the derivation of phenologies relevant to understanding intra- and inter-annual changes in coastal ecosystem functioning. Since primary production is the driver of marine food chains, observed changes in upwelling and primary production phenologies have implications for the management of downstream resource exploitation by fisheries industries, small-scale fishers and marine aquaculture concerns. The EO RG will use a 20 year time series of daily products to facilitating both the characterisation of the current state and historical variability of the BCLME as well as future work on predictive AI development. These capabilities will significantly enhance the value of the Oceans and Coastal Information Management System (OCIMS) Fisheries and Aquaculture Support Tool with respect to rapid ecosystem state/change analysis, thereby contributing to greater efficiencies within operational and resource management. Analysis has only started in 2020 and will continue throughout the OCIMS2 project up to 2025.
Principal Investigator: Dr Aijaz Ahmad
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2020-04-07
Allocation End: 2020-10-04
Used Hours: 28749
Project Name: Molecular modelling and drug design
Project Shortname: HEAL1257
Discipline Name: Health Sciences
We are based at WITS university. We are currently involved in multi drug resistant mechanism of candida albicans. I am understanding the protein drug interaction using molecular docking and molecular dynamic simulations using AMBER18 software licensed with CHPC server.
Principal Investigator: Prof Yin-Zhe Ma
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2020-04-07
Allocation End: 2020-10-04
Used Hours: 4790
Project Name: Machine learning in 21-cm cosmology
Project Shortname: ASTR1323
Discipline Name: Astrophysics
We are from the Astrophysics Research Centre (ARC) which is part of the College of Agriculture, Engineering and Science at the University of KwaZulu-Natal (UKZN). Working with the supervision of Prof. Yin-zhe Ma, our group is working in cosmology and problems pertaining to Cosmological Microwave Backgroud (CMB), 21-cm cosmology. We plan to use the GPU facilities in CHPC to work on pattern recognition of the cosmic microwave background radiation map, and the future data of 21-cm signal from HERA (Hydrogen Epoch Reionization Array) and SKA. The pattern recognition is done through the machine learning technique, where we feed thousands of simulated map to train the neural network to learn the underlying features pertaining to the map and come up with feature extraction which technically can give us the weightage of each feature giving raise to the cmb map. Once the network is trained with the test data, we feed the training data to network to measure its performance. If the performance is satisfactory then we feed in the data from the observation to do feature extraction without having to do the traditional statistics to extract the data.
Principal Investigator: Prof Stefan Ferreira
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2020-04-07
Allocation End: 2020-10-04
Used Hours: 3687037
Project Name: Astrospheres
Project Shortname: ASTRO1277
Discipline Name: Astrophysics
With upcoming missions such as the James Webb Space Telescope, the European Extremely Large Telescope, and the Atmospheric Remote-sensing Infrared Exoplanet Large-survey, we soon will be on the verge of detecting and characterizing Earth-like exoplanetary atmospheres for the first time. These planets are most likely to be found around smaller and cooler K- and M-type stars. However, recent observations showed that their radiation environment might be much harsher than that of the Sun. Thus, the exoplanets are most likely exposed to an enhanced stellar radiation environment, which could affect their habitability, for example, in the form of a hazardous flux of energetic particles. Knowing the stellar radiation field, and being able to model the radiation exposure on the surface of a planet, is crucial to assess its habitability. In this study, we present 3D magnetohydrodynamic-based model efforts investigating M-stars, focusing on V374 Peg, Proxima Centauri, and LHS 1140, chosen because of their diverse astrospheric quantities. We show that V374 Peg has a much larger astrosphere (ASP) than our Sun, while Proxima Centauri and LHS 1140 most likely have ASPs comparable to or even much smaller than the heliosphere, respectively. Based on a 1D transport model, for the first time, we provide numerical estimates of the modulation of Galactic cosmic rays (GCRs) within the three ASPs. We show that the impact of GCRs on the Earth-like exoplanets Proxima Centauri b and LHS 1140 b cannot be neglected in the context of exoplanetary habitability.
Principal Investigator: Dr Fabio Cinti
Institution Name: NITHEP
Active Member Count: 4
Allocation Start: 2020-04-07
Allocation End: 2020-10-15
Used Hours: 603983
Project Name: Quantum Monte Carlo for ultra-cold atoms
Project Shortname: PHYS0892
Discipline Name: Physics
The emergence of self-organised structures from an initially disordered phase
still remains a key subject of investigation in several branches of physics.
In particular, different physical processes, both in and out of equilibrium,
may display pattern formations usually describable by peculiar symmetries
owing to the scrutinised systems.
On the hard condensed matter side, over the past few years a huge effort has been devoted to investigate and simulate novel phases of matter that could be observed in tenable synthetic systems at different energy and length scales. Along this line, it is becoming of chief importance the theoretical understanding of phases genuinely ruled by quantum mechanisms such as supersolid droplets, stripes, hexatic or smectic liquid crystals. For example, quantum quasicrystals structures have been proposed in optical lattices and cavity; whereas the realisation of droplets and supersolids are proposed in magnetic systems.
Finally, advances in computational material science are particularly useful in understanding pattern formation, especially when experiments are not easily realisable. For example astro-materials typically are present under extreme conditions, such as very high pressure, making them inaccessible to laboratory experiments. Coulomb crystals in the interior of cold white dwarfs and in neutron star crusts are examples of hard/soft astro-materials.
Principal Investigator: Dr Aniekan Ukpong
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2020-04-08
Allocation End: 2020-10-05
Used Hours: 359623
Project Name: Theoretical and Computational Condensed Matter and Materials Physics
Project Shortname: MATS0941
Discipline Name: Physics
I am Dr Aniekan Magnus Ukpong and I obtained my PhD in Physics from the University of Cape Town, in 2008. I am a Senior Lecturer and the current Academic Leader and Head of Department of Physics at the Pietermaritzburg Campus of the University of KwaZulu-Natal. I also hold the National Research Foundation's C3-rating, as an Established Researcher. I run the activities of the Theoretical and Computational Condensed Matter and Materials Physics Research Group as Principal Investigator of Research Program: CHPC/MATS0941. My research group develops and implements state-of-the-art models for studying complex materials. The CHPC has facilitated our access to world-class computing resources for scientific research and pseudo experimentation. With a zero net cost due to absence of sample preparation requirements, the CHPC has offered a cost-effective, and valuable support to our research.
Data from our recent computations have enabled us to conclusively demonstrate a significant catalytic activity in the non-oxidative dehydrogenation of propane to propene using functionalized graphene substrates. By exploiting the interrelationship between the intrinsic capacity for hydrogen abstraction, thermodynamic stability and catalytic activity in the non-oxidative dehydrogenation of propane to propene, we have shown that graphene can catalyse the conversion of propane to propene – a major feedstock in the industrial production of plastic. Based on the insights derived from this study, we demonstrated that it is actually the formation of narrow graphene strips instead of the formation of large area graphene sheets that should constitute the major strategy in the rational design of the graphene catalysts. This is an important insight because the finding is experimentally testable, since graphene synthesis is now commonplace. Secondly, the view of our research is that since South Africa is rich in coal - a primary feedstock for graphene synthesis - a clear pathway for the beneficiation of graphene towards the production propylene from propane has emerged. This could represent a major front for creating new economic opportunities for South Africa based on insights from Computational Materials Sciences.
Principal Investigator: Mr Theo Fischer
Institution Name: eScience
Active Member Count: 4
Allocation Start: 2020-04-09
Allocation End: 2020-10-06
Used Hours: 20588
Project Name: Acid Deposition
Project Shortname: ERTH0851
Discipline Name: Earth Sciences
The 2010 Mpumalanga Highveld region power station sulphur dioxide emissions amount to 2.2 million tons. After full oxygenation and the addition of cations, this represents an increased total dissolved salt deposition load of 4.6 million tons. This is 23 times higher than the natural annual average TDS load in the runoff from the entire 38 600 km2 Vaal Dam catchment. Although only a fraction of this salt load falls on the Vaal Dam catchment, outfall of only 4% of the anthropogenically emitted sulphur could double the long-term equilibrium salt export of the Vaal Dam catchment. The importance of this investigation arises from the economic and environmental impact of the deposition of anthropogenically emitted salts on water users in the strategic heartland of South Africa on the one hand, and the expensive decisions arising from the location and technology of new power stations and industrial plant on the other. Rational decision making requires evaluation of the high costs associated with both atmospheric deposition impacts and the cost of reducing them.
Principal Investigator: Dr Phillip Nyawere
Institution Name: Kabarak University, Nakuru, Kenya
Active Member Count: 5
Allocation Start: 2020-04-09
Allocation End: 2020-10-22
Used Hours: 39686
Project Name: Barium Floride and Perovskites
Project Shortname: MATS0996
Discipline Name: Physics
Our group is BARIUM FLORIDE AND PEROVSKITE based in Kabarak University, Kenya. It is comprised of researchers who are students from over four university in Kenya which are Kabarak University, Catholic University of East Africa, Kisii University and Masinde Muliro University.
Barium Fluoride is a simple crystal but very useful for understanding properties of related crystal. One of its uses is in lithography and has also been found to be useful as an electrolyte in battery. When this material is doped with other elements its usage is enhanced and can be a good electrolyte at elevated temperatures. It is in this interest that our group BARIUM FLORIDE AND PEROVSKITE has been formed to study many properties of this material and other related compounds.
We have also looked at Gadolinium perovskite which has superconducting properties. Superconductors are able to conduct electricity with zero resistance but it has been a challenge to get the compound that is superconducting at room temperature.
Using computational techniques we can predict temperatures suitable for superconducting temperature of a compound. This is done using Quantum Espresso code installed on CHPC machine.
We have a group of five students in partnership with other researchers from other university.
Principal Investigator: Dr Bahareh Honarparvar
Institution Name: University of KwaZulu-Natal
Active Member Count: 12
Allocation Start: 2020-04-12
Allocation End: 2020-10-09
Used Hours: 852243
Project Name: Computer-aided HIV/TB drug design
Project Shortname: CHEM0808
Discipline Name: Health Sciences
The progress of group members is significant. around 10 publications, 4 manuscripts are under review and few under submission.
Principal Investigator: Prof Graham Jackson
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2020-04-11
Allocation End: 2020-10-08
Used Hours: 37977
Project Name: Insect neuropeptides
Project Shortname: CHEM1101
Discipline Name: Chemistry
Most pharmaceutical drugs target G-protein coupled receptors. We have used the same targets to develop species specific insecticides. Together with the US Department of Agriculture we have investigated the adipokinetic hormone from the honey bee in order to differentiate it from insect pest. This would allow us to develop insecticides that do not affect the beneficial honey bee.
Principal Investigator: Prof Ed Sturrock
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2020-04-11
Allocation End: 2020-10-08
Used Hours: 145498
Project Name: Structural elucidation of Angiotensin Converting Enzyme using cryo-electron microscopy
Project Shortname: HEAL0931
Discipline Name: Health Sciences
Enzymes play important roles in a variety of biological processes in the human body. Angiotensin converting enzyme (ACE), for example, regulates blood pressure and is also involved in scar tissue development (fibrosis). Conditions such as diabetes and tuberculosis can lead to excessive scar tissue formation, which ultimately stops proper organ function. Currently, there is no specific treatment for fibrosis. Hypertension, on the other hand, is a major risk factor for cardiovascular disease and stroke which accounted for 15.2 million global deaths in 2016. The Zinc Metalloprotease lab, led by Prof Edward Sturrock, is based in the Department of Integrative Biomedical Sciences at the University of Cape Town and has a long-standing interest in ACE.
Although ACE inhibitors reduce fibrosis and are widely used for treating hypertension, certain patients experience the life-threatening side-effect of severe swelling below the skin surface of the throat and tongue. In order to design safer ACE inhibitors, a detailed understanding of the structure of ACE is required. A postdoctoral research fellow in Prof Sturrock's lab, Dr Lizelle Lubbe, is using a technique called cryo-electron microscopy (cryo-EM) to better understand how ACE functions. This involves using an electron microscope to visualize the protein immobilized in various orientations in a thin layer of ice. Dr Lubbe has collected a large cryo-EM dataset at the Diamond Light Source synchrotron (UK) and is using the CHPC's resources to reconstruct the 2-dimensional views of the protein into a 3-dimensional model. Interestingly, she has observed monomeric and dimeric forms of the protein. Solving the 3D structure to high resolution will thus not only allow the design of improved drugs for fibrosis and hypertension but also provide a better understanding of the overall shape of the molecule. This may enable researchers to design diagnostic tests using antibodies for diseases where ACE is dysregulated.
Principal Investigator: Dr Brigitte Glanzmann
Institution Name: Stellenbosch University
Active Member Count: 21
Allocation Start: 2020-04-14
Allocation End: 2020-10-11
Used Hours: 356076
Project Name: SAMRC Precision Medicine African Genomics Centre
Project Shortname: CBBI1195
Discipline Name: Bioinformatics
The advent and evolution of next generation sequencing (NGS) has considerably impacted genomics research, including precision medicine. High-throughput technology currently allows for the generation of billions of short DNA or RNA sequence reads within a matter of hours. This becomes extremely important in the case of genetic disorders where rapid and inexpensive access to a patient's individual genomic sequence is imperative and enables target variant identification. NGS technologies however lead to the generation of large data sets which require extensive bioinformatic and computational resources. Computational life sciences therefore relies on the implementation of well-structured data analysis pipelines as well as high-performance computing (HPC) for large-scale applications. Here, we report the sequencing of the first six whole human genomes in South Africa and the processing of the data in collaboration with the Centre for High Performance Computing (CHPC). Efficient parallel and distributed implementations of common time-consuming NGS algorithms on modern computational infrastructures are imperative. The latter becomes pivotal as NGS will continue to transcend from research labs to clinical applications in the near future.
Principal Investigator: Prof Arnaud Malan
Institution Name: University of Cape Town
Active Member Count: 6
Allocation Start: 2020-03-05
Allocation End: 2020-09-01
Used Hours: 203949
Project Name: UCT CFD
Project Shortname: MECH1314
Discipline Name: Computational Mechanics
The InCFD Research Group at the University of Cape Town used the CHPC resources for the purpose of research conducted on the development of multi-phase liquid-gas flows. This being one of the key research areas today, the work has resulted in 2 journal articles in top rated international journals. Thank you for the support Team CHPC!
Principal Investigator: Prof Mohsen Sharifpur
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-04-14
Allocation End: 2020-10-11
Used Hours: 395549
Project Name: Computational Heat transfer
Project Shortname: MECH1073
Discipline Name: Computational Mechanics
Our research group is from the Department of Mechanical and Aeronautical engineering at the University of Pretoria. The main research field of our research group is related to improve heat transfer systems and investigation on a new generation of heat transfer fluids. Because nowadays energy plays a key role in human's life, and daily the energy demand is increasing. But to investigating energy using high-performance computing is mandatory because of its complex equations.
Principal Investigator: Dr Zipporah Muthui
Institution Name: Chuka University, Chuka, Kenya
Active Member Count: 4
Allocation Start: 2020-04-14
Allocation End: 2020-10-11
Used Hours: 21331
Project Name: Electronic Structure and Magnetic Properties of Heusler Compounds
Project Shortname: MATS1112
Discipline Name: Physics
Electronic Structure and Magnetic Properties of Heusler Compounds research group is composed of the PI, Dr Zipporah Muthui and students from Chuka University as well the University of Nairobi. We are carrying out electronic structure calculations of photocatalytic materials and Heusler systems. Photocatalytic materials are of great interest and relevance in applications such as water treatment. The work is being carried out by an Msc student, to obtain an Msc degree.
I am working on Heusler systems, that I have experience in and I'm aiming to publish the results together with collaborators working experimentally. The CHPC has provided us the facility needed for these large systems that we are working on. Most of the calculations for the photocalysts are complete, unless some clarification will be required when writing. Most of those for the Nickel based Heusler are complete, only some checking still needs to be done for some systems where crystal structure distortions were carried out.
Principal Investigator: Dr Gerhard Venter
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2020-04-15
Allocation End: 2020-10-12
Used Hours: 94631
Project Name: Simulation of Ionic Liquids
Project Shortname: CHEM0791
Discipline Name: Chemistry
Dr Venter's research group is part of the Scientific Computing Research Unit at the University of Cape Town and uses computer simulation to study the chemical and physical properties of organic molecules and biopolymers in a special class of solvents, called "ionic liquids". These simulations provide insight into the intermolecular interactions and chemical behaviour that control the dissolution and subsequent reactivity of these naturally occuring polymers. A better understanding of these processes can lead to the rational design of new, environmentally friendly solvents systems that can dissolve biomass and enhance its reactivity. The dissolution of biomass is the first step in converting naturally occuring polymers to biofuels and other platform chemicals.
High performance computing is required for all research conducted in this group and without the resources and infrastructure provided by the Centre for High Performance Computing (CHPC), the research will not be possible.
Principal Investigator: Dr Ryno Laubscher
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2020-04-15
Allocation End: 2020-10-12
Used Hours: 60936
Project Name: University of Cape Town Applied Thermal-Fluid Research Unit
Project Shortname: MECH1279
Discipline Name: Computational Mechanics
The Applied Thermofluid Process Modelling Research Unit at the University of Cape Town is busy with research in the field of surrogate modelling which combines the fields of physics simulation and artificial intelligence to better visualize, monitor, optimize and predict the performance of utility-scale energy systems. Currently, the work focusses on coal-fired plants and development of tools which enable near real-time estimation of combustion chamber performance. The end goal is to offer a prediction system which not only will act as virtual sensors but also help optimize the performance of the combustion system. The way this is achieved is by developing an efficient fluid dynamics model of the combustion chamber which captures effects such as heat transfer and reactions. The model is then used to generate 100s-1000s of simulation results which in turn is used to train an artificial intelligence prediction system. The prediction system is then able to in near real-time make predictions of what is happening inside the combustion chamber such as pollutant formation, metal temperatures and gas temperatures. To date, an efficient CFD model has been developed which eliminates the need for multiphase modelling. This enables the simulation of utility-scale combustion chambers in a reasonable time, which is required to generate a large simulation database. The artificial intelligence prediction system concept has also been verified by using the results of 50 simulations.
Principal Investigator: Prof Juliet Hermes
Institution Name: SAEON
Active Member Count: 4
Allocation Start: 2020-04-15
Allocation End: 2020-10-12
Used Hours: 108528
Project Name: SAEON Coastal and Regional Ocean Modelling Programme
Project Shortname: ERTH1103
Discipline Name: Earth Sciences
The Coastal and Regional Ocean Modelling Programme is a modelling initiative of the South African Environmental Observation Network (SAEON) Egagasini Node based in Cape Town. The aim of this programme is to use ocean models to understand regional and coastal shelf dynamics. The ORCA025 configuration, extending from the Angola gyre, Mozambique channel and including the Southern Ocean is used in this programme. A high resolution grid is used which zooms the coastal region including the St Helena Bay region which is an important nursery ground for fish and also the main generation zone of low oxygen water. The low oxygen generated in the St Helena Bay region result in the formation of greenhouse gases including nitrous oxide which has a global warming potential about 265-310 times higher than that of carbon dioxide. With climate change there is also a need to understand implications for primary production and expansion of low oxygen regions in the ocean. The coupled ocean model in this programme is used to understand these processes and the results obtained can be used to fill knowledge gaps and advance coastal modelling. Currently the model is being validated and the next step is to increase resolution to capture fine scale processes.
Principal Investigator: Prof Richard Tia
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 25
Allocation Start: 2020-04-16
Allocation End: 2020-10-13
Used Hours: 2596311
Project Name: Computational Chemistry and Materials Science
Project Shortname: CHEM1044
Discipline Name: Chemistry
The work being conducted in this research programme involves the development of active and selective catalysts for conversion of greenhouse gases like carbon dioxide into useful fuels and fine chemicals, the depolymerization of lignin, an abundant resource in plant biomass, into value-added chemicals and fuels and studies on the computer-aided synthesis of organic molecules of applications in medicine.
With increasing interest of the scientific community and government agencies on the mitigation of rising carbon dioxide levels and the attractiveness of using carbon dioxide as a feed-stock for industrial processes, this work has direct benefit for humanity.
Our research activities fall under two broad areas, namely;
1. Molecular modeling - Exploring the mechanisms of organic, inorganic and organometallic reactions.
These studies afford important molecular-level mechanistic details of industrially-relevant chemical reactions that are difficult, if not impossible, to obtain experimentally. Molecular level understanding enable chemical reactions to be guided quickly and efficiently along desirable pathways, with the effect of producing the right product with minimal energy consumption and minimal environmental impact. A key aspect of this work is the development of homogeneous transition metal catalysts for the depolymerization of lignin, an abundant natural resource, for fuel.
2. Materials modeling
The atomic- and molecular-level mechanistic insight gained from these studies are useful for the design of novel catalysts for the conversion of CO2 and other green-house gases as well as stranded gases from the petroleum refining into useful fuels. This addresses the problem of global warming as well as providing an environmentally friendly alternative sources of fuel.
The research objectives described here are very computationally-demanding and using the CHPC resources is highly beneficial. Without that, we would not be able to carry out some of these calculations.
Principal Investigator: Prof Matthew Adeleke
Institution Name: University of KwaZulu-Natal
Active Member Count: 13
Allocation Start: 2020-04-16
Allocation End: 2020-10-13
Used Hours: 10845
Project Name: Computational and Evolutionary Genomics
Project Shortname: CBBI1231
Discipline Name: Bioinformatics
Quantitative and Computational Genomics is sitting in Genetics, School of Life Sciences at University of KwaZulu-Natal. The group seeks to understand the genetics of parasites of veterinary and medical importance as well as host-pathogen interaction that will help in the control of animal diseases and also provide baseline information using immunoinformatics to facilitate vaccine prediction. The wet lab phase uses molecular biology technology to understand how different species are related evolutionarily and screen for antigens and then know how diverse the antigens are since this is crucial to the effectiveness of current vaccine or possible to develop new vaccine so as to match the current parasite challenge on the field. The second phase of our work is computational and therefore relies on the use of CHPC. At this phase, we use bioinformatics to understand how natural forces has left some some selection signatures for parasite adaptation, survival and pathogenicity. At this phase as well, immunoinformatics approach is used to screen for epitopes that will elicit immune response, cover wider human population and without allergic reactions. This will give some level of confidence on the potential safety of the vaccine being predicted. If we are successful, we will hand it over collaboratively to those that will do the actual synthesis, animal model studies and clinical trial eventually.
Principal Investigator: Dr Thishana Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2020-04-17
Allocation End: 2020-10-14
Used Hours: 45424
Project Name: Combined kinetics,quantum-chemical investigation of reaction mechanisms involving catalysts
Project Shortname: CHEM0821
Discipline Name: Chemistry
The TS Computational Chemistry Research Group (University of Kwazulu-Natal, School of Chemistry and Physics) carries out quantum chemical modelling of homogenously catalysed organic reactions in the inter-domain field of Physical-Organic Chemistry. Computational Chemistry can be classified as 'Green Chemistry' as it is sustainable and does not generate chemical waste. The focus of this research group is primarily on catalytic asymmetric synthesis that have many applications in the pharmaceutical and fine chemical industry. The optimisation of a catalyst offers a good understanding of the factors that are responsible for the rate and selectivity of a reaction. Theoretical calculations, together with experimental kinetic measurements, often can pin down the mechanism. Using this methodology, it is possible to understand, and more importantly, design effective catalysts for a number of asymmetric, catalytic processes. The CHPC provides the facilities: hardware, in the form of the Lengau cluster and software programs such as Gaussian16, amongst many others. This year our projects have yielded three publications.
Principal Investigator: Prof Sybrand van der Spuy
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2020-04-17
Allocation End: 2020-10-14
Used Hours: 172701
Project Name: CFD simulation of turbomachinery
Project Shortname: MECH1187
Discipline Name: Computational Mechanics
The turbomachinery research group at Stellenbosch University has been making use of the CHPC for their CFD simulation work during the past two years. The use of the CHPC enables the accurate and detailed modelling of aspects like gas turbine combustion and fan noise. The results achieved to date have been world class.
Principal Investigator: Prof Kevin Naidoo
Institution Name: University of Cape Town
Active Member Count: 10
Allocation Start: 2020-04-19
Allocation End: 2020-10-16
Used Hours: 1373097
Project Name: Reaction Dynamics of Complex Systems
Project Shortname: CHEM0840
Discipline Name: Chemistry
The Scientific Computing Research Unit under the direction of Prof. Kevin J. Naidoo has recently released an Open Source Open data platform that enables chemists, biologists and chemical biologists to undertake drug discovery research. The platform shares not only computers methods but research practices requireing complex High performance computational modelling. This key enabling technology will benefit all research in South Africa requiring the development of drugs and vaccines to advance to make possible a healthier nation. By invitation of the editor of prestigious Bio-Protocol journal that partners with amongsts others the journal Science (https://www.eurekalert.org/pub_releases/2019-08/aaft-alc081219.php?from=timeline&isappinstalled=0) Professor Naidoo published practical details to further assist inexperienced as well as seasoned researchers wanting to incorporate computational modelling into their drug discovery programmes.
Principal Investigator: Prof Chris Meyer
Institution Name: Stellenbosch University
Active Member Count: 6
Allocation Start: 2020-04-19
Allocation End: 2020-10-16
Used Hours: 1202669
Project Name: Development of CFD models
Project Shortname: MECH1077
Discipline Name: Computational Mechanics
The research activity is led by Prof CJ Meyer from Stellenbosch University and is focused on developing computational models of industrial thermo- and fluid dynamic processes. There is a specific emphasis on the use of free software under the GNU General Public License. The industrial processes under consideration are those relevant to specific segments of industry in South Africa most notably power generation. Current projects include the simulation of large-scale air-cooled condensers as well as detailed simulations concerning the flow through axial flow fans used in the energy sector. The cohort of students are making excellent progress with 3 students having upgraded to PhD-level and the rest to submit their MEng thesis shortly.
Principal Investigator: Prof Ponnadurai Ramasami
Institution Name: University of Mauritius
Active Member Count: 5
Allocation Start: 2020-04-21
Allocation End: 2020-10-18
Used Hours: 276291
Project Name: Computational Chemistry Methods to Study Structural and Spectroscopic Parameters
Project Shortname: CHEM1290
Discipline Name: Chemistry
Ponnadurai Ramasami is the group leader of the Computational Chemistry Group in the Department of Chemistry of the University of Mauritius. The research interest of the group ranges from fundamental to applied chemistry. One of the research interests is to predict structural and spectroscopic parameters of novel compounds. In this context, we are currently predicting the structures of two-dimensional nanomaterials prior to their synthesis. We are also studying the electronic structure of metal oxide nanoparticles. These projects involve the use of Quantum Espresso.
We are also collaborating with experimentalists, mainly organic and inorganic chemists from African countries. From the organic chemistry perspective, we are studying cycloaddition reactions to provide insights into the reaction mechanism so as to explain the formation of the observed products. From the inorganic chemistry aspects, we are studying inorganic complexes using computational method so as to complement the experimental research in terms of structural and spectroscopic parameters. However, in some cases, where experimental data are not available, the computed parameters are useful to the experimentalists for the interpretation of results. For these projects, we are using Gaussian software.
Without the use of the CHPC facility, it would not have been possible to carry out high level computations for the projects that we have planned. This facility is allowing us to aim at carrying out high level research and to eventually have good publications in high impact factor journals.
We have been using the CHPC facility for the past 6 months and we have already submitted two manuscripts for publications.
Principal Investigator: Dr Shankara Radhakrishnan
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-04-21
Allocation End: 2020-10-18
Used Hours: 93733
Project Name: Solar energy and CO2 Reduction
Project Shortname: CHEM0869
Discipline Name: Chemistry
The research group aims at the catalytic activity of variety of macrocycles / metal-complexes on electrochemical reduction of CO2
Principal Investigator: Prof Philip Machanick
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2020-04-22
Allocation End: 2020-10-19
Used Hours: 503481
Project Name: Motif quality assessment
Project Shortname: CBBI0922
Discipline Name: Bioinformatics
Machanick Group at Rhodes University, in collaboration with Caleb Kibet, a former PhD student, currently based at the International Center of Insect Physiology and Ecology are upgrading the MARS (http://bioinf.ict.ru.ac.za/), a server that evaluates binding models. MARS is useful in human research but has the potential in assessing models generated from other organisms, including insects. Presently research involving insect has become relevant; insects are key to food security and sustainability for the future. Despite their importance, insects are also the vectors of many harmful pathogens to human health. The new release will be considerable expansion and update of the previous version, with benchmark data analysis facilitated by the CHPC.
Principal Investigator: Prof Zenixole Tshentu
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 9
Allocation Start: 2020-04-22
Allocation End: 2020-10-19
Used Hours: 377185
Project Name: Metal-ligand, anion-cation interactions and protein-ligand studies
Project Shortname: CHEM0864
Discipline Name: Chemistry
The group at NMU Chemistry Department under the leadership of Prof Tshentu is engaged in developing selective chemistry for beneficiation of earth and secondary resources. The work on developing reagents that are selective for precious metals has made gains and continues to produce reliable materials that could have industrial applications. The work on desulfurization and denitrogenation of fuel has contributed to the search for selective methods for removal of contaminants from fuel (N and S) and is therefore contributing to upgrading of fuel to a zero-sulfur level. Theoretical studies contribute to the smart design of selective reagents and functional materials. We are grateful to CHPC for the computational chemistry facilities.
Principal Investigator: Prof Jacomine Grobler
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2020-04-23
Allocation End: 2020-10-20
Used Hours: 6913
Project Name: Computational intelligence for supply chain optimization
Project Shortname: CSCI1170
Discipline Name: Applied and Computational Mathematics
Due to the rise of e-commerce, consumers can purchase an enormous variety of products and have it delivered to their doorstep anywhere in the world. As a result, last mile deliveries are an important competence for many logistics companies. Unmanned aerial vehicles or delivery drones, is a highly promising technology that can revolutionize the way companies do their last mile deliveries. Drones are a cleaner means of transport, do not require or use road infrastructure, and have positive implications on delivery time and cost. The efficient use of delivery drones, however, require advanced optimization algorithms to allocated deliveries to drones, and schedule these deliveries.
Researchers at the Department of Industrial Engineering at Stellenbosch University are currently working in conjunction with the University of California at Berkeley to develop a drone delivery scheduling algorithm. The development of this algorithm requires significant computational resources and here the collaboration with the Centre for High Performance Computing is critical. Many hours of computer time is required to test different algorithm variations, tune algorithm control parameters and ensure that the algorithm is robust over different data sets and changing input parameters.
Initial results indicate that up to a 30% improvement can be obtained by a delivery drone scheduling system when compared to a traditional road freight delivery service. Testing is currently underway to determine the impact of a multiple vehicle system.
Principal Investigator: Dr Eric Maluta
Institution Name: University of Venda
Active Member Count: 12
Allocation Start: 2020-04-23
Allocation End: 2020-10-20
Used Hours: 275393
Project Name: Energy Material Modeling in the Application of different Photovoltaic Technologies
Project Shortname: MATS0827
Discipline Name: Physics
The Department of Physics at the University of Venda is working on the understanding of the properties of different materials for application in renewable energy technologies through the density functional theory simulations as performed under the CHPC cluster. The main aim is to reduce the cost of the material used in renewable energy technologies for the future use and mitigate climate change through energy supply. We are also building capacity of the rural students on the postgraduate studies and skill development. The CHPC is a gateway for the department of Physics of the University of Venda as an institution situated in the rural area to produce researchers and to publish research work. There is a growing number of students research work from honours to the PhD level. Several student are getting their masters and PhD degree through these initiatives.
Principal Investigator: Dr Gebremedhn Gebreyesus Hagoss
Institution Name: University of Ghana
Active Member Count: 5
Allocation Start: 2020-04-23
Allocation End: 2020-10-20
Used Hours: 1012581
Project Name: Atomistic simulations and condensed matter
Project Shortname: MATS1031
Discipline Name: Physics
The condensed matter research group at the Physics Department at the University of Ghana is focused on the study of the structural, electronic, magnetic, and optical properties of 2D and bulk materials. Computational simulations of the properties of these materials are carried out using density functional theory with the inclusion of onsite and inter-site Hubbard corrections, GW approximation of many-body perturbation theory (MBPT), and the Bethe-Salpeter equation (BSE).
Our computational work would not be possible without the enhanced computing resources available at the CHPC in South Africa. Typically, we prepare our input files on our laptops and run our calculations in the CHPC. The job is monitored at least once a day and the results downloaded when completed.
Our main areas of research:
1. Electronic, magnetic, structural, and optical properties of transition-metal oxides.
First principle calculations carried out to study the structural, electronic, optical, and magnetic properties of transition metal oxides. The results are compared to our experimental results.
2.Perovskite Materials for energy applications
The accurate description of the structural. Electronic, and optical properties of low-temperature phase perovskite are not yet well established. In this project, we focus on the investigation of structural, electronic, dielectric, and vibrational properties of low-temperature phase perovskite materials using density functional theory with the inclusion of the onsite and inter-site Hubbard correction.
3. Two-dimensional Materials Research
The 2D transition metal dichalcogenides are compounds that we are interested to study in this project, have a chemical formula MX2 (where M = Ti, Mo, Nb, W, Hf, Re, etc. and X = S, Se, and Te). In particular, we focus on controlling the excitonic properties of 2D HfS2 monolayer via lanthanide substitutional doping using GW and BSE.
4. Ruddlesden-Popper perovskite ruthenates
The Ruddlesden-Popper perovskite ruthenates have a chemical formula (Sr, Ca)n+1RunO3n+1. The magnetic and electronic properties of these materials depend on the layer number and on the structural distortions. In this project, we focus on investigating the structural, electronic, and magnetic properties of Sr4Ru3O10 using DFT with the inclusion of the onsite Hubbard correction and spin-orbit coupling.
Principal Investigator: Dr Anna Bosman
Institution Name: University of Pretoria
Active Member Count: 8
Allocation Start: 2020-04-24
Allocation End: 2020-10-21
Used Hours: 282058
Project Name: Deep Learning and Neural Network Research at CS UP
Project Shortname: CSCI1166
Discipline Name: Computer Science
The research program of the Computer Science Department, University of Pretoria (UP), is headed by Dr Anna Bosman, and forms a part of the Computational Intelligence Research Group (CIRG) at UP. The focus of the program is on the following research topics: fitness landscape analysis of neural networks and real-life applications of deep learning. The following deep learning applications are currently investigated: (1) convolutional neural networks for satellite image analysis; (2) long short-term memory networks for anomaly detection; (3) convolutional neural networks for radio astronomy. Stuyding fitness landscapes of neural networks deepens our general understanding of the fundamental principles of neural network research, and enables progress in fundamental artificial intelligence. Deep learning applications allow us to apply modern artificial intelligence techniques in the South African context. Thus, the usage of CHPC helps us strengthen machine learning and artificial intelligence research in South Africa. Sampling and estimation techniques for fitness landscape analysis are used to probe the error surfaces of the deep and shallow neural networks. The research is of empirical nature, and entails heavy sampling of the search space. Such experiments would not be feasible without access to a computer cluster. Deep learning applications benefit significantly from being run on a GPU, therefore, access to the GPUs allows us to upscale the experiments to real-life applications. Recently, a journal article and a conference paper resulted from the experiments run on the CHPC were published. This indicates that the research program is productive, and delivers academic outputs.
Principal Investigator: Dr Mehdi Mehrabi
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2020-04-27
Allocation End: 2020-10-24
Used Hours: 69027
Project Name: Modeling of heat transfer characteristics and pressure drop of nanofluids in micro and mini tubes.
Project Shortname: MECH1086
Discipline Name: Other
Centre for high performance computing in Cape Town is playing an important role in the computational research capability of South Africa. This center by providing service to researchers, enables them to produce high quality research out puts can compete with other researchers around the world. Funding for this center is essential for the future of STEM fields of research and needs to be given a very high priority.
Principal Investigator: Prof Eno Ebenso
Institution Name: North-West University
Active Member Count: 5
Allocation Start: 2020-04-27
Allocation End: 2020-10-24
Used Hours: 152150
Project Name: Theoretical Investigations of Corrosion Inhibition Activities of Organic Compounds
Project Shortname: CHEM1176
Discipline Name: Chemistry
Our research group, Materials Science Innovations and Modelling Research Focus Area is domiciled at the Mafikeng Campus of North-West University.
About 75% of our work is on the design of new corrosion inhibitor solutions to mitigate the rate at which metal (alloys) corrode in various environments. Other works in the group include of electrochemical sensors development and thermodynamics of solutions. Our research works involve quite a volume of computational studies, especially quantum chemical calculations using the Gaussian software and Molecular dynamics simulations using the Materials Studio software. The computational studies are often used to corroborate experimental results in our continuously robust and comprehensive investigations. For instance, the potentials of an organic compound to inhibit corrosion of metal is often dependent on its ability to adsorb on metal surface, which in turns depends on its molecular reactivity. Determining corrosion inhibition mechanism is central in such research, and computational study is an important aspect of the research. For a timely output, conventional personal computer (PC) is not an option in the kind of research we do. Continuous access to software license is also not negotiable. Hence, enrollment of our research group on CHPC resources is very important.
For a quantum chemical calculation that takes an average of 15 days per molecule to complete on a PC (if it does not end up crashing due to insufficient memory, as it's often the case), and an investigation involving at least 4 organic molecules (often, more compounds are considered), an investigator will be highly frustrated without a resource like CHPC.
Since our enrollment on CHPC resources, our project has been progressing satisfactorily and the time spent on a particular project has been reduced due to speedy computations. Hence, we have the opportunity of designing more elaborate projects executable within reasonable space of time.
Principal Investigator: Dr Chris Barnett
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2020-04-28
Allocation End: 2020-10-25
Used Hours: 209236
Project Name: Analysis of disease related polymers
Project Shortname: CBBI1063
Discipline Name: Bioinformatics
I investigate the shapes, structures, and properties of molecules by using computational modelling techniques. I'm particularly interested in complex sugars (glycans), which are interesting to study because they are involved in intricate molecular recognition processes in cells, for example, playing a role in cell signalling, adhesion, and immunity. Further understanding of these molecules and the complex systems they are involved in may lead to the generation of additional diagnostic markers and inhibitors that can be used to combat disease. The CHPC provides a platform for being able to run large-scale and highly parallel simulations which is a great help in making rapid progress towards solving research questions. The CHPC is also a test bed when carrying out computation on and developing algorithms for large datasets.
Principal Investigator: Dr Luna Pellegri
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2020-04-29
Allocation End: 2020-10-26
Used Hours: 4417
Project Name: Developing of new techniques for real-time verification in proton-therapy
Project Shortname: PHYS1327
Discipline Name: Physics
One of the most critical issues in proton-therapy is the real-time verification of the dose delivered during the treatment. An approach for monitoring the treatment planning system accuracy during the irradiation is investigated in this project. The methodology is based on enhancing the production of high-energy (E>5 MeV) prompt-gammas in the tumour. The work is performed by Dr L. Pellegri and Ms S. Hart from the University of the Witwatersrand and iThemba LABS in collaboration with the group of Prof. C La Tessa from the University of Trento (Italy). The first part of the project consisted in the verification via GEANT4 simulations of the feasibility of the project. Due to the heavy computing power that these simulations require, the use of the CHPC Lengau Cluster was crucial. The preliminary results show that the gamma ray response is very sensitive to the doping nucleus investigated and to the experimental data available in the nuclear database implemented in the simulations. The simulations performed will be compared with experimental data collected at iThemba LABS facility.
Principal Investigator: Dr MC du Plessis
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 3
Allocation Start: 2020-04-30
Allocation End: 2020-10-27
Used Hours: 112514
Project Name: ACO Routing for OBS Networks
Project Shortname: CSCI1211
Discipline Name: Computer Science
Optical Burst Switching (OBS) is a next-generation paradigm which holds the promise of improved capacity on fibre optic networks. However, there is a gap for effective, efficient and responsive network resource management algorithms, to ensure that OBS can fulfill it's promise. Research is being done at the Nelson Mandela University, Center for Broadband Communications by postgrad computer science students, Joshua Oladipo and Francois du Plessis, under the supervision of Dr MC du Plessis from the department of computer science and Prof Tim Gibbon from the department of physics to apply the machine learning algorithm known as Ant Colony Optimisation to this problem. The CHPC has been crucial to the research by providing computational resources for long running network simulations which are used to study the performance of the algorithms.
Principal Investigator: Dr Pedro Monteiro
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 13
Allocation Start: 2020-04-29
Allocation End: 2020-10-26
Used Hours: 4545422
Project Name: Southern Ocean Carbon - Climate Observatory SOCCO
Project Shortname: ERTH0834
Discipline Name: Earth Sciences
SOCCO is a CSIR-led and DSI co-funded programme that uses the comparative geographical advantage that South Africa has in the Southern Hemisphere to contribute to the global research challenge of understanding the role of the Southern Ocean in global and regional climate. The SOCCO research niche is to explore the role played by fine scale ocean dynamics in improving the climate sensitivity of ocean and coupled numerical models with a special focus in understanding the Southern Ocean's role in the CarbonClimate links.
To address the scales of dynamics in the ocean, we primarily use the coupled NEMO-PISCES model in a hierarchy of resolutions from 200 km to 2 km - using the models as experimental platforms. The finer the resolution, the greater the number processes that contribute to ocean-atmosphere carbon exchange. This understanding contributes to reducing model biases in process models and climate projections as well as the development of a South African Earth Systems Model (ESM).
This work advances research in global climate change based on the importance of feedbacks of the Southern Ocean dynamics on the carbon-climate system. Additionally, the ESM will be used to explore how the climate sensitivities of the Southern Ocean evolve over the 21st century as well as being South Africa's first submission to the 6th Assessment Report of the IPCC. ESM will be the basis for the medium to long term climate projections in Africa which will then support societal needs in health, water resource planning, agriculture, biodiversity management and more broadly in economic development in the region.
From regional, forced ocean models to fully-coupled earth system models comprising of interacting ocean, ice, atmosphere, land, ocean biogeochemical models, numerical modelling of earth system components require massively parallel computing resources. The size and complexity of these models are such, that for SOCCO's work, the CHPC is indispensable for the resources and service it provides.
Principal Investigator: Prof Michelle Kuttel
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2020-05-04
Allocation End: 2020-10-31
Used Hours: 377372
Project Name: Molecular modelling of microbial polysaccharides and glycoconjugates
Project Shortname: CHEM1242
Discipline Name: Chemistry
This drug discover modelling project is driven by post-doc student Dr Badichi-Akher of Michelle Kuttel's research group at UCT. The latest publication focusses on the use of molecular modelling for the design of inhibitors for anti-lung cancer therapy. We use multiple modelling methods to explore the binding of fluorinated drugs to the epidermal growth factor receptor (EGFR), mutations of which have been linked to nonsmall-cell lung cancer. Our work provides an explanation for why a difluorinated inhibitor, 25g, has 4 times greater potency against the mutated receptor than an unfluorinated inhibitor, 25a. This work should be useful for the future rational structure-based design of novel inhibitors with improved potency and selectivity.
Principal Investigator: Dr Winfred Mulwa
Institution Name: Egerton University, Egerton, Kenya
Active Member Count: 7
Allocation Start: 2020-05-04
Allocation End: 2020-10-31
Used Hours: 986299
Project Name: Magnetic Refrigeration
Project Shortname: MATS1181
Discipline Name: Physics
Who: MATS1181 under PI Winfred Mulwa from Egerton University Kenya: Magnetic refrigeration. What: Magnetization and demagnetization of magnetic materials known as magnetic refrigeration that rely on magnetocaloric effect (MCE). In cooling technology, magnetic refrigeration which depends on magnetocaloric effect is commonly used in refrigerators to achieve exceptionally low temperatures. Why: . Magnetic refrigeration does not rely on the uses of harmful and ozone-depleting coolant gases. How: This work is done computationally. We use the Quantum Espresso code (Density Functional Theory). This purely depends on CHPC because all the calculations have to be done in CHPC. Thanks to CHPC. How is the project progressing: We have achieved all the objectives. The project is as planned. Two of my MSc students are graduating this year.
Principal Investigator: Prof Ignacy Cukrowski
Institution Name: University of Pretoria
Active Member Count: 11
Allocation Start: 2020-05-05
Allocation End: 2020-11-01
Used Hours: 926496
Project Name: Understanding chemistry from QM study of molecular systems
Project Shortname: CHEM0897
Discipline Name: Chemistry
Activities in chemistry (in science in general) can be seen as made of two distinctive approaches: 1) development of new theories and methodologies that should lead to better understanding of concepts and chemical process (reactions) and 2) practical implementation of known or new methodologies that should lead to routine and highly efficient experimental/computational operations. Our research group in the Department of Chemistry, University of Pretoria (Prof. Ignacy Cukrowski (the leader), Dr. Jurgens de Lange, several PhD, MSc and Honours students as well as a postdoctoral Fellows) is involved in fundamental studies. Our focus is primarily on understanding fundamentals governing inter-atomic and inter-fragment interactions from the electron density distribution throughout a molecule, or molecular system in general. For instance, there are many kinds of chemical bonds but still there is no an ultimate general theory of bonding. Hence, there are various approximate quantum chemical models that are being used to describe and explain just a specific kind of bonding. In our group we prefer to interpret classical chemical bonding, regardless of its kind, as an interaction governed by universal laws of physics. This allows us to expend the concept of interactions from classical 2-atom approach (a chemical bond) to poly-atomic interactions involving fragments of a molecular system. Such approach proved to be very useful in modelling reaction mechanisms to understand (on atomic and molecular fragment level) how and why new compounds are or are not formed as planned by a synthetic (in)organic chemist. Full understanding of successful and failed synthetic processes is of great importance as it must aid the development of, e.g., new drugs needed for treatment of (i) highly contagious diseases, such as tuberculosis, HIV/AIDS, or (ii) Alzheimer, a disease with reported cases growing rapidly throughout the world. It is important to realize that such theoretical work requires, due to the size of molecular systems under investigations, dedicated and expensive computational facilities, such as CHPC, with a dedicated staff to ensure that research groups can access and make use of computational centre 24/7.
Principal Investigator: Prof Enrico B Lombardi
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2020-05-05
Allocation End: 2020-11-25
Used Hours: 835956
Project Name: Defects in wide-bandgap semiconductors and 2D materials
Project Shortname: MATS1160
Discipline Name: Material Science
• The materials research group of Prof Lombardi at the University of South Africa (UNISA) focuses on defects in wide band gap semiconductors and 2 dimensional (2D) materials. This research group is exploring a range of defects 2D materials which affect their functionality and efficiency, for applications ranging from next generation spintronics devices, to nano-electronic an opto-electronic devices. As in all solid state materials systems, point defects are inevitable, and is particularly important in new chemically grown 2D materials due to the imperfection of the growth process, including, amongst others, 2D transition metal chalcogenides. Our group has contributed to the understanding of fundamental defects and defect processes in these 2D materials, predicting the properties of intrinsic point defects and other likely defects, and the conditions under which they are likely to occur. These results provide insight to the physics of defects that are grown via chemical vapour deposition, as well as in electron irradiated materials. These defects are responsible for large variation of electric and optical properties, while they may also act as efficient electron or hole traps, which strongly influence transport and optical properties of semiconductors, in turn strongly impacting their applicability to next generation devices. This research is performed using the state-of-the-art density functional theory, and has made extensive use of CHPC compute resources.
Principal Investigator: Prof Bruce Bassett
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 2
Allocation Start: 2020-05-06
Allocation End: 2020-11-02
Used Hours: 69893
Project Name: Machine Learning for Astronomy
Project Shortname: ASTR1157
Discipline Name: Astrophysics
We are not ready yet but should be at the end of the next phase.
Principal Investigator: Prof Edet Archibong
Institution Name: University of Namibia
Active Member Count: 4
Allocation Start: 2020-05-07
Allocation End: 2020-11-03
Used Hours: 7842
Project Name: (1) Computational Study of Semiconductor Clusters. (2) Computational Study of Bio-active Molecules Extracted from Plants
Project Shortname: CHEM0969
Discipline Name: Chemistry
Understanding the reaction of ozone with phenolic compounds is important in basic and environmental chemistry. Several phenolic compounds are toxic and are found in waste waters which are treated for consumption purposes. Ozone is one of the disinfectants used in the treatment of wastewater that are subsequently consumed. It is imperative to know how ozone reacts with these phenolic compounds in order to improve the water treatment processes. Also, ozone is found in the atmosphere where it can react with phenols that are pumped into the lower atmosphere by the industries. Again, understanding the chemistry of the atmosphere is important for the survival of living things that occupy planet Earth.
Principal Investigator: Dr Evans Benecha
Institution Name: University of South Africa
Active Member Count: 10
Allocation Start: 2020-05-06
Allocation End: 2020-11-02
Used Hours: 671495
Project Name: Defect engineering in novel 2-D materials
Project Shortname: MATS1025
Discipline Name: Physics
The research programme titled "Defect engineering in novel 2-D materials" focuses on investigation of the properties of defects in single layered materials - usually one atom thick. The group spearheading this research is headed Dr Evans Benecha and it consists of senior researchers, postdocs and graduate students from the University of South Africa. Single atom layered materials possess interesting properties as opposed to many atom thick materials. For example, graphene – which a single layer of carbon atoms –enables electrons to flow much faster than silicon, is the world's strongest material, harder than diamond, yet lightweight and flexible. This unique combination of superior properties makes it a credible material for new technologies in a wide range of fields. Some of the envisaged applications of graphene as well as other single atom layered materials include making of medical implants, solar cells, stronger sports equipment, and batteries; just to name a few. However, the properties of these materials are not well understood for these applications to be realized. Dr Benecha and his group's approach towards understanding these materials involves use of large computational resources, and access to the CHPC computing facility has significantly reduced the time needed to generate and analyze data. The results from this project will not only assist in the current understanding of the role of defects in these materials, but will also help to reveal potential new functionalities.
Principal Investigator: Dr Kiprono Kiptiemoi Korir
Institution Name: Moi University, Eldoret, Kenya
Active Member Count: 6
Allocation Start: 2020-05-12
Allocation End: 2020-11-12
Used Hours: 949900
Project Name: Thermal characterization of MoS2 nanostructures: an ab initio study
Project Shortname: MATS0868
Discipline Name: Material Science
This research group draws its members from Moi University, Computational Material Science Group (CMSG), in addition, we have collaborators: Slimane Haffad of University of Beijaia- Algeria, and Michele Re Fiorentin of Istituto Italiano di Tecnologia (IIT) Italy. Our research activities focus mainly on materials for energy, optoelectronics, and ultra-hard industry.
Single-photon emitters in hexagonal boron nitride have attracted great attention over the last few years due to their excellent optoelectronic properties. Despite the vast range of results reported in the literature, studies on substitutional impurities belonging to the 13th and 15th groups have not been reported yet. Here, through theoretical modeling, we provide direct evidence that hexagonal boron nitride can be opportunely modified by introducing impurity atoms such as aluminum or phosphorus that may work as color centers for single-photon emission. These results may open up new possibilities for employing innovative quantum emitters based on hexagonal boron nitride for emerging applications in nano-photonics and nanoscale sensing devices
While in ultra-hard industry, increased demand for hard materials whose performance are comparable or better than that of the diamond but with low cost has necessitated the search for material with superior hardness and related properties where 3d, 4d or 5d transition metals incorporated with light elements such as carbon and nitrogen has been identified as a potential candidate. However, the process of developing such devices poses a major technological challenge and an in-depth understanding of these materials is needed, which may lead to the development of new principles, characterization techniques, and methods essential for addressing some of the bottle-necks associated with these materials.
In this work, graphene, NbC, NbN, ZnO nanowires, monolayer h-BN and 2D MoS2 were studied via approaches grounded on principles of quantum and classical mechanics, which have been shown to accurately predict material properties. These predictive approaches require huge computational effort as it entails solving mathematical formulas, such as Schrödinger and Newtonian equations. For this reason, the availability of the state-of-the-art High-Performance Computing facility, such as CHPC is a critical component for the implementation of this work. Solving Schrödinger and Newtonian equations can yield various properties of interest such as structural, mechanical, electronic, and optical properties that are essential for the comprehensive characterization of these systems. For example, in our recent work, we have analyzed the energetic and electronic properties of point defects in h-BN obtained through the substitution of a boron or a nitrogen atom with a heteroatom belonging to their respective group. It is noted that B-substitutions generate neutral defect levels that can be exploited for single-photon emission.
Principal Investigator: Prof Krishna Bisetty
Institution Name: Durban University of Technology
Active Member Count: 4
Allocation Start: 2020-05-12
Allocation End: 2020-11-08
Used Hours: 38051
Project Name: Computational Modelling & Bioanalytical Chemistry
Project Shortname: CHEM0820
Discipline Name: Chemistry
In our pursuit to undertake interdisciplinary studies in the development of biosensors. We now wish to strengthen our focus and strategic direction with regards to characterisation and detection of engineered nanoparticles in aqueous and biological samples. The impact of this work, especially the molecular modelling and simulation studies would directly contribute to the development of human skills in SA. Young Black postgraduate students will have hands-on experience with the state-of-the-art simulation protocols.
Principal Investigator: Prof George Amolo
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 11
Allocation Start: 2020-05-12
Allocation End: 2020-11-25
Used Hours: 2892714
Project Name: Properties of Materials for Green Energy Harnessing
Project Shortname: MATS862
Discipline Name: Material Science
The MATS862 is a Kenyan materials modeling group consisting of mainly young faculty and graduate students based at the School of Physics and Earth Sciences, The Technical University of Kenya, Nairobi. Some students and team members are based outside Nairobi. One PhD student is based in the Democratic Republic of Congo.
We use scientific codes written to simulate the properties of materials based on fundamental principles of chemistry, physics, mathematics and computer science. The work is focused on materials that have potential socio-economic values to the community with regard to new or more efficient materials and hence better devices for energy conversion.
The work is being done to create capacity in skills and knowledge to handle new and emerging societal needs in the energy sector by complementing experimental research groups as well as providing useful information to guide product development.
Known information about elements is placed in an input file and submitted to the supercomputer to enable reproduction of independent information obtain by other techniques. Once this is done successfully, combinations of similar or new elements are tested to check if additional or new value can be obtained. The CHPC comes in to provide computational resources that allow calculations to be done in a short time.
We are doing very well based by the number of numbers of publications, graduation rate, attendance of conferences as well as invited talks.
Principal Investigator: Dr Ndumiso Mhlongo
Institution Name: University of KwaZulu-Natal
Active Member Count: 11
Allocation Start: 2020-05-12
Allocation End: 2020-11-08
Used Hours: 137267
Project Name: Biomolecular Modelling Research Unit
Project Shortname: HEAL1002
Discipline Name: Health Sciences
Biomolecular Modelling Research Unit is located at the University of KwaZulu-Natal, Howard College Campus and headed by Dr Ndumiso N. Mhlongo. This research group employs CHPC resources to conduct molecular dynamics simulations to analyse the dynamical properties of macro-molecules such as folding and allosteric regulations; ligand-receptor interactions; atom-to-atom interactions; protein-protein interaction;virtual screening and molecular docking of active molecules; QSAR etc, for the design and development of inhibitors against diseases and disorders. Through the use of CHPC resources, we have designed potential inhibitors against M. tuberculosis and cancer treatment. These have made contributions to discovery new inhibitors & new knowledge which could directly translate into real health benefits of the society.
Principal Investigator: Prof Giuseppe Pellicane
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2020-05-14
Allocation End: 2020-11-10
Used Hours: 373265
Project Name: Computational Study of Structure-Property Relationships in polymer blends relevant to OPV devices
Project Shortname: MATS0887
Discipline Name: Physics
Polymers are an important material, which is present in energy devices based on renewable and non-polluting sources, because they can be used as the active photovoltaic component of solar cells. By the scientific point of view, polymers are also widely used as a potential nano-carrier for drugs in nano-medicine and for pharmaceutical applications. The group leader is Dr G. Pellicane, who is a (honorary) associate professor at UKZN and NRF C1 rated scientist. Members include Mr. S. Mamba (PhD student), Prof. Tsige (Full Professor of Polymer Science at the University of Akron, US) and Prof. Workineh (Associate Professor at Bahir Dar University, Ethiopia. Our research focus is on theoretical and computational studies of complex fluids, and within this project we mainly use density functional theory calculations and molecular dynamics simulations. We already published several publications in scientific journals within the framework of this project, and more are to come in the near future. We are also presenting our results in international conferences/workshops, that will allow for sharing and diffusion of vital knowledge with the international scientific community. We are deeply grateful to the skilled and resourceful staff members at CHPC (Dr Anton Lopis), and for the generous allocation of computational resources granted to us by them, which are instrumental to fulfill the goals of this project.
Principal Investigator: Dr Nikiwe Mhlanga
Institution Name: Mintek
Active Member Count: 12
Allocation Start: 2020-05-15
Allocation End: 2020-11-11
Used Hours: 316134
Project Name: Hydrogen Storage Materials and Catalysis
Project Shortname: MATS0799
Discipline Name: Material Science
The aim of this Research Program is to synthesize, screen and model various materials which are of interest in the Advanced Materials Division (AMD). AMD is a dynamic and multi-disciplinary division that addresses the need for specific research into the end-use of metals in the manufacturing, fabrication and mining industries. It houses four research groups; catalysis, nanotechnology, Biomed and physical metallurgy. The catalysis group focuses on solid-state hydrogen storage materials (carbon nanotubes, metal hydrides and metal-organic frameworks) to support the national HySA (Hydrogen South Africa) program. Electronic and structural properties of these materials will be modelled at DFT/MP2 level. Macro and fluid dynamic properties of these materials will be computed using the finite element method via OpenFoam CFD. Under this program, general properties and reactivity of PGM-based catalysts will also be modelled in line with the research activities of the Catalysis Group at Mintek. The nanotechnology group fabricates diagnostic techniques based on nanoparticles. Its uses the HPC to access chemistry codes such as Gaussian. The codes are used to study the properties of the nanomaterials, to improve their applications. The physical metallurgy group uses Castep to study the properties of different alloys. The ADM projects are envisioned for production of commercial products which will be used by the masses, e.g., malaria diagnostics. The HPC enables the modelling of most of the AMD systems and hence facilitate the laboratory processes and help to save of laboratory trial and error times. Progress has been achieved on the malaria diagnostics with the registered prototype.
Principal Investigator: Dr Parvesh Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 6
Allocation Start: 2020-05-14
Allocation End: 2020-11-25
Used Hours: 102695
Project Name: Molecular dynamics and docking studies of organic compounds
Project Shortname: CHEM0795
Discipline Name: Chemistry
My research group at UKZN is working on designing and synthesis of heterocyclic scaffolds that have potential against bacterial, cancer and diabetes. We are employing different computer-based technologies such as molecular docking, QSAR, QSPR and pharmacophore modelling to predict novel chemical assemblies from the online databases. The identified lead molecules are synthesized in our organic laboratory and tested in vitro. All the computer simulations are performed on the CHPC cluster. This computing facility has been very useful to find very useful information that was not possible to solve had we not this facility available. Running these jobs on normal computers would have taken months of time to finish or would die in middle. With this supercomputing facility in our hand, we not only managed to run complex calculations but obtained constructive scientific explanations for our experimental results. Consequently, we managed to this compiled data in reputed chemistry journals. Moreover, my post graduate students has learnt different computational tools that are being used in drug design and drug discovery field.
Principal Investigator: Dr Rendani Mbuvha
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2020-05-15
Allocation End: 2020-11-11
Used Hours: 41678
Project Name: Bayesian Methods for Neural Networks
Project Shortname: CSCI1332
Discipline Name: Data Science
We are part of a research group that is lead by Prof Tshilidzi Marwala at the Universities of Johannesburg and Witwatersrand. The group focuses on bayesian methods in machine learning. Bayesian methods allow for a principled understanding of the uncertainty around the parameters of complex methods like neural networks. Bayesian inference frequently requires the use of computationally intensive methods such as markov chain monte Carlo - that require CHPC resources to accelerate experimental time through extensive parellization. The work has results in two publications as well as numerous works in progress.
Principal Investigator: Dr Hezekiel Kumalo
Institution Name: University of KwaZulu-Natal
Active Member Count: 15
Allocation Start: 2020-05-19
Allocation End: 2020-11-15
Used Hours: 502289
Project Name: Molecular modeling and computer aided drug design
Project Shortname: HEAL1009
Discipline Name: Health Sciences
The group covers a wide range of computational and molecular modeling research areas with main focus on biological systems and drug design approaches.
Main interest is related to design and study of biologically and therapeutically oriented targets. This is achieved by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We are involved in projects such Understanding drug resistance mechanisms via different computational tools QM/MM MD simulations Quantitative Structure Activity Relationship (QSAR) Conformational Analysis of biomolecules Bioinformatics tools applications Development Projects Approaches to enhance binding free energy calculations results Developing parameters for biomolecules: on-going projects Software implementations: on-going projects. All the projects that we do in the group contribute to the training of pharmaceutical scientists with specific skills for both the pharmaceutical industry and academia. This has the potential of stimulating the local pharmaceutical industries in South Africa to manufacture pharmaceuticals of quality, excellence and affordability for optimum and cost effective patient health, instead of being dependent on multinational pharmaceutical companies. We are still young group therefore funding is problem, therefore for the resources at HPC allows us to generate hypotheses for subsequent experimental testing in a much quicker manner and higher throughput than using experiment alone to generate hypotheses that you'd like to test. It has given us an opportunity to be able explain experimental data we could not explain easily such the binding landscapes of different enzymes and the mechanism of action for different inhibitors.
Principal Investigator: Mr Sakhile Masoka
Institution Name: SKA
Active Member Count: 6
Allocation Start: 2020-05-21
Allocation End: 2020-12-02
Used Hours: 7343
Project Name: MeerKAT software development
Project Shortname: ASTR1333
Discipline Name: Astrophysics
The Radio Astronomy Research Group (RARG) of SARAO is engaged in development of radio astronomy calibration and imaging techniques. Over the past decades, second-generation calibration (2GC) algorithms, as software and methods blossomed, have benefitted the science community on a large scale. But now, as we have seen a surge in the development of new radio telescopes, such as the SKA pathfinders, of which MeerKAT is a prime example, the capabilities of these instruments would be compromised by the old 2GC methods. With the SKA around the corner, it has become increasingly clear that new methods need to be developed. This has fuelled demand for third-generation (3GC) techniqueus, and has provoked a very rapid development of the field. DIRISA's CHPC and SANEREN have played vital roles by proving computing resources for the processing of observation data and fast bandwidth for data transfers
Principal Investigator: Dr George Manyali
Institution Name: Masinde Muliro University of Science and Technology, Kakamega, Kenya
Active Member Count: 10
Allocation Start: 2020-05-20
Allocation End: 2020-11-25
Used Hours: 211543
Project Name: Ab Initio study of Thermoelectric Materials
Project Shortname: MATS0712
Discipline Name: Material Science
The Computational and Theoretical Physics (CTheP) Group with branches at Kaimosi friends University College and Masinde Muliro University of Science and Technology, comprise of a team of researchers and students dedicated to the development and application of computational modeling to outstanding problems in materials science. In general, the group seeks a deeper understanding of quantum-mechanical descriptions of interacting electrons and nuclei in order to predict and design properties of materials and devices using density functional theory as a tool for the first-principles simulation. This kind of simulation generates volumes of data that cannot be handled by the common desktop computers. High-performance computing provides the computational environment that includes parallel processing, large memory, and storage of the big data. Therefore, Center for High-Performance Computing facility in Cape Town, South Africa, plays a vital role in providing the resources that aid the discovery of new materials and accelerates its application in the industry, an achievement that would have been in vain with desktop computers. Some specific projects for our group include the characterization of already known thermoelectric materials. The information gained from this project is used as identifiers in search for new thermoelectric materials with the tailored figure-of-merit. Such materials are used to enhance the efficiency of the thermoelectric generator power system for renewable energy. Such outcomes of our projects have an impact on the livelihood of the rural communities in Kenya.
Principal Investigator: Dr Roelf Du Toit Strauss
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2020-05-22
Allocation End: 2020-11-18
Used Hours: 5624778
Project Name: Computational Space Weather
Project Shortname: PHYS0918
Discipline Name: Physics
One of the biggest hurdles faced by manned exploration of space is the high levels of natural radiation present in the solar system. This is not only an important consideration faced by future astronauts on board spacecraft, but also by future colonizers of Mars, and inhabitants of future moon bases and space stations. This important risk is acknowledged by both SpaceX and NASA, and planned bases and spacecraft try to accommodate so-called "space storm shelters", where space dwellers can hide from dangerous radiation levels. At the Centre for Space Research of the North-West University, South Africa, we are doing our part to mitigate these possible harmful effects by developing state-of-the-art numerical models that can simulate and predict the levels of harmful natural radiation. To simulate the intensity of these so-called "cosmic ray" particles, complicated and large-scale numerical models are run on large scale computer clusters, such as the Lengau cluster of the Centre for High Performance Computing (CHPC) in Cape Town, South Africa
Principal Investigator: Prof Ashwil Klein
Institution Name: University of Western Cape
Active Member Count: 1
Allocation Start: 2020-05-22
Allocation End: 2020-11-18
Used Hours: 7216
Project Name: Molecular dynamic simulation
Project Shortname: CHEM1241
Discipline Name: Bioinformatics
For the various studies we used in silico and molecular approaches including docking and MD simulation study to achieve project objectives. The tools used from the Schrodinger suit are not freely available and formed an integral part of our data analysis, therefore access to CHPC cluster was of paramount importance. Significant progress was made with this project and the data generated from these studies resulted in the publication of 5 manuscripts in reputable science journals with an significant impact. All work published was done in collaboration with colleagues who share similar research interest.
Principal Investigator: Prof Catharine Esterhuysen
Institution Name: Stellenbosch University
Active Member Count: 10
Allocation Start: 2020-05-25
Allocation End: 2020-11-21
Used Hours: 172599
Project Name: Computational chemistry analysis of intermolecular interactions
Project Shortname: CHEM0789
Discipline Name: Chemistry
The Computational Supramolecular Chemistry group at Stellenbosch University studies the intermolecular interactions involved in a range of compounds in order to determine the relationship between the structures and properties of the materials. For instance, the sorptive properties of a porous material are determined by the intermolecular interactions between its porous framework and the compound being adsorbed, such as gases like CO2 or solvents like water. Calculations performed using the CHPC's computational facility allow ed us to understand the role of intermolecular interactions in the mechanisms of sorption, catalytic and biological processes in order to predict improved catalysts and biologically active compounds as well materials for the sorption and sequestration of greenhouse gases.
Principal Investigator: Prof Abu Yaya
Institution Name: University of Ghana
Active Member Count: 8
Allocation Start: 2020-05-25
Allocation End: 2020-11-21
Used Hours: 451312
Project Name: DFT modeling of weak interactions; a case study for Carbon nanosystems
Project Shortname: MATS0990
Discipline Name: Material Science
With the advent of poisonous materials ending up in the hands of terrorist and other suspicious characters in our societies, it has become imperative to design systems that can detect these poisonous chemicals and warfare agents. With the help of larger computers in South Africa, we have been able to make a prototype design to detect gases that are poisonous to humans when inhaled to some extent such as carbon dioxide, phosgene gases. These were modelled using materials that are very small which are termed nanomaterials (examples are carbon nanotube, boron nitride nanotube and graphene).
Principal Investigator: Dr Geoff Nitschke
Institution Name: University of Cape Town
Active Member Count: 10
Allocation Start: 2020-05-25
Allocation End: 2020-11-21
Used Hours: 1009958
Project Name: Evolving Complexity
Project Shortname: CSCI1142
Discipline Name: Computer Science
This was research done by the evolutionary machine learning group at the University of Cape Town. The research falls under the umbrella of deep-learning applied to real-world applications. The motivation for the research is that recent deep-learning methods have achieved remarkable success in finding hidden structure in high-dimensional data and yielding high classification accuracy in various tasks including: image and speech recognition, drug discovery and genomics. However, for such tasks, key ingredients to the success of deep-learning is finding convolutional neural
network architectures that pair suitably with the training dataset.
Significant work has been done on evolving convolutional
neural network architectures, but little attention has been paid
to evolving the data augmentation that often accompanies such
architectures. For many data-sets, data augmentation is critical as
it bolsters otherwise incomplete, noisy or under-sized data into
complete training data-sets, thus enabling neural architectures
to be effectively trained for the given classification task. This
paper considers a timely addition to deep-learning literature,
via co-evolving both the neural network architecture and data-augmentations
to achieve a classification accuracy that would not otherwise be possible on a popular computer-vision data-set. The use of very large data-sets and deep-neural network models requires the use of CHPC so as to practically reduce computational run-time from weeks to hours. The research work remains in progress through preliminary results have been accepted for publication in the proceedings of the 2020 Symposium Series for Computational Intelligence.
Principal Investigator: Prof Walter Schmitz
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2020-05-26
Allocation End: 2020-11-22
Used Hours: 9035
Project Name: Particle segregation
Project Shortname: MECH1258
Discipline Name: Computational Mechanics
The Pulverized Coal (PC) used in a coal-fired boiler consists of fine powder crushed and grinded from raw coal chunks of about 50 mm in diameter down to particles of about 100 microns and smaller. The presence of foreign material other than carbon particles contributes to a multitude of problems including wear of mill internals, boiler tube leaks, poor combustion and production of harmful emissions. The removal of unwanted non-carbon particles from PC (also called coal beneficiation) is therefore much needed in the quest for clean coal combustion.
The segregation of solid particles in an air Fluidized Bed (FB) as described in this paper finds application in the coal beneficiation industry. Two application stages are considered; Firstly raw crushed coal with particle size range between 1 and 15 mm ready to enter the mill and secondly inside the mill where particles with a size range between 0.1 and 1 mm is targeted. Particle segregation in a FB is based on a sink / float principle. Particles ending up at the bottom is called Jetsam and those at the top Flotsam. Particles segregate due to combinations of density and size differences. With particles of similar density the large size particles will tend to sink while small size particles will rise. With similar size particles the denser particles will sink and lighter particle will rise. Complication may arise however with particles mixtures consisting of small dense particles and larger less dense particles.
In order to optimally employ differences in particle density and size for the purpose of segregation a thorough understanding is needed of the segregation mechanisms involved. Towards this end numerical analysis is used to replicate some previous experiments and then to apply it to the application of coal beneficiation above. The multi-phase Computational Fluid Dynamics (CFD) code Neptune_CFD is used. The numerical simulations are carried out on the supercomputer at the Centre for High Performance Computing (CHPC) in Cape Town.
Principal Investigator: Dr Francois van Heerden
Institution Name: Nuclear Energy Cooperation of SA
Active Member Count: 5
Allocation Start: 2020-05-28
Allocation End: 2020-11-24
Used Hours: 12863
Project Name: Research Reactor Fuel Burnup and Material Activation
Project Shortname: INDY0788
Discipline Name: Physics
The Radiation and Reactor Theory (RRT) group at the South African Nuclear Energy Corporation (Necsa) provides calculational support for the SAFARI-1 research reactor, and perform research in the general area of nuclear analysis. We also develop and maintain our own suite of reactor simulation software, called OSCAR. This suite is the primary operational support tool for the SAFARI-1 reactor, and is used at a number of international facilities, which range from small university based research reactors, to larger national facilities. During the past 5 years, CHPC computing resources were utilised for a project facilitated by the International Atomic Energy Agency (IAEA) through a Collaborative Research Project (CRP) aimed at the collection of experimental data suitable for code benchmarking and validation. We are participating by providing experimental data from our own facility, the SAFARI-1 research reactor, and by calculating a number of experimental benchmarks from other member states. This particular CRP focuses on fuel depletion and material activation, which is important for the economic and safe operation of research reactors. Most of the primary analysis work has been completed, and we are well on target to deliver final reports in the last research meeting scheduled for October 2019. These reports will eventually be incorporated in a formal technical publication by the IAEA, available to all member states. The latest version of our tool set, OSCAR-5, provides a platform that combines different analysis codes, from fast diffusion solvers suitable for fuel depletion tasks, to high fidelity particle transport solvers, which can be used to do detailed local activation analysis, in a consistent manner. High Performance Computing plays an important role in the data preparation step for the diffusion solver, and in the use of transport solvers to estimate neutron flux distributions in the core. Benchmarks developed in this CRP forms the backbone of the OSCAR-5 validation case for research reactor support.
Principal Investigator: Prof Serestina Viriri
Institution Name: University of KwaZulu-Natal
Active Member Count: 15
Allocation Start: 2020-06-01
Allocation End: 2020-11-28
Used Hours: 16175
Project Name: Deep Learning in Medical Image Analysis
Project Shortname: CSCI1229
Discipline Name: Computer Science
The Computer Vision and Image Processing Research Group based at UKZN intends to continue using this platform for the Deep Learning in Medical Image Analysis related research work. This proved to be the fastest and reliable platform for any Deep learning related processing. The research work requires parallel computing as it deals with huge data in the form of images. These images are medical images like chest X-rays, lung datasets, knee X-ray images, face datasets, as well as remote sensing images.
The research is mainly done in collaboration with public entities like hospitals, especially for medical imaging. The results achieved are publicly available to be implemented in real-world problem-solving. The proposed solutions are published and made available for public usage, and some of the projects conducted like "Tuberculosis Detection using Chest X-rays; Quantification of Osteoarthritis Severity from knee X-ray Images using Convolutional Neural Networks" culminates in a real-world solution.
The CHPC is providing services such as stable and reliable high-performance computing systems, and general design of high-performance systems optimized for big data processing.
Principal Investigator: Dr Nana Ama Browne Klutse
Institution Name: Ghana Space Science and Technology Institute
Active Member Count: 2
Allocation Start: 2020-05-30
Allocation End: 2020-11-26
Used Hours: 1619
Project Name: Regional Climate modeling over Africa
Project Shortname: ERTH1087
Discipline Name: Earth Sciences
The CHPC of South Africa has been supportive of our research and other research activities in Africa. Our research focuses on atmospheric dynamics and climate variability and change in different regions in Africa using two regional climate models WRF and RegCM. Research is done at Masters, Ph.D., and postdoctoral levels.
Principal Investigator: Dr Sharon Moeno
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2020-06-02
Allocation End: 2020-11-29
Used Hours: 2528
Project Name: Drug Design, Delivery and Bioactivity of Small Phenolic Compounds
Project Shortname: CHEM1287
Discipline Name: Chemistry
Members of the Materials unit fall within the Department of Oral Biological Sciences (part of the School of Oral Health Sciences) in the Faculty of Health Sciences at Wits University. Our group engages in the design of small compounds derived from phenolic compounds. The design of compounds involves the use of computational analysis and in silico screening as a means of determining whether compounds possess adequate drug-likeness. As part of our research activity in the unit, promising compounds are synthesized, characterized, and elucidated. Finally, the bioactivity of prepared compounds is ascertained by way of conducting antimicrobial and cytotoxicity studies. This research work is conducted in an effort to identify lead compounds for possible use as antimicrobial, anticancer, and wound healing agents. The use of the CHPC clusters facilitates the in silico and computational analyses conducted by our group on a regular basis. Docking and modeling studies facilitated by the use of the Lengau cluster of the CHPC enables our group to understand the interaction of the designed and prepared compounds with the identified target proteins. The current project is progressing to its mid-level stage. We are hopeful that this study will yield favorable findings, publishable in accredited journals.
Principal Investigator: Dr Marissa Balmith
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2020-06-03
Allocation End: 2020-11-30
Used Hours: 66188
Project Name: Pharmacology
Project Shortname: HEAL1336
Discipline Name: Health Sciences
As the PI of the Cancer research group at the University of Pretoria, our research is aimed at identifying molecular mediators of cancer metastasis using in silico and in vitro approaches. According to the WHO, approximately 2.3 million new cases were diagnosed in 2020. The metastatic behavior of breast cancer has accentuated the need for specific therapeutic targets, as metastasis is responsible for over 90% of cancer-related deaths. CHPC's portfolio of hardware and software applications have helped streamline many of the in silico aspects of our study which include molecular docking, virtual screening and molecular dynamics. Using the available tools, we have been able to screen for novel inhibitors against cancer metastasis, perform docking studies to better understand the molecular interactions between our target and inhibitor. In addition, MD simulations will be performed to gain a better understanding of the binding landscape of our targets of interest. Through the resources provided by the CHPC, we were able to advance and disseminate knowledge relating to cancer metastasis focusing on the poor and most vulnerable in South Africa as well as train the next generation of cancer researchers in computational design. We have made significant progress with the study and are now ready to run computational simulations which will be shortly followed by the in vitro experiments. A very big thank you to CHPC and Dr Krishna Govender for his continuous technical support and advice. In silico studies are paving the way in the drug design and development sector and this would not be possible with the infrastructure and resources provided to our research institutions by the CHPC!
Principal Investigator: Dr Samuel Iwarere
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2020-06-05
Allocation End: 2020-12-02
Used Hours: 394316
Project Name: Understanding Plasma-Liquid Interaction
Project Shortname: MECH1107
Discipline Name: Chemical Engineering
The research is being carried out under the guidance of the Thermodynamics Research Unit based in the Discipline of Chemical Engineering in the School of Engineering at the University of KwaZulu-Natal. The understanding of plasma-liquid interactions is of prime importance in the context of environmental remediation and wastewater treatment applications. Plasma treatment of wastewater involves complex chemical and physical phenomena, which makes the comprehensive modelling of phenomena such as gas phase reaction, turbulence and heat transfer a difficult task. In order to gain insight into the complex processes associated with the use of plasma wastewater treatment, Computational Fluid Dynamics (CFD) will be used to study the relevant chemistry and fluid dynamic effects at the plasma-liquid interface. The Centre for High Performance Computing (CHPC) allows for calculation within realistic time frames, allowing the researchers to determine the accuracy of the simulations encountered in plasma physics. Simulation of the plasma arc is progressing well with the researchers working in conjunction with other scientists in the plasma field.
Principal Investigator: Dr Jan Buys
Institution Name: University of Cape Town
Active Member Count: 9
Allocation Start: 2020-06-08
Allocation End: 2020-12-05
Used Hours: 35612
Project Name: Deep Learning for Low-resource Natural Language Processing
Project Shortname: CSCI1335
Discipline Name: Computer Science
The University of Cape Town Natural Language Processing group is a research group under the UCT Department of Computer Science that performs research on various topics related to the automated processing of language. The research group is led by Dr. Jan Buys, and currently consists of 4 Masters students and 6 honours students.
The main focus is on developing methods for text generation in low-resource settings. Recent advances in Artificial Intelligence has been driven by the development of large neural networks that can "learn" how to perform various tasks by processing very large datasets - this is referred to as deep learning. For text generation, for example, deep learning systems have been developed that can automatically write realistic-looking news articles or other short pieces of text. However, deep learning techniques perform less well in settings where only small amounts of data are available. While text generation systems can perform well in English, similar systems for other South African languages (such as Nguni languages) are much less accurate or don't exist at all. In this research project, we are performing foundational research to determine how we can adapt deep learning models to perform well in low-resource settings where only small amounts of data are available. Deep learning models are computationally intensive, even on small datasets, so they are trained on Graphical Processing Units to speed up the computations. We have developed language models, which are the models underlying deep learning text generation systems, for multiple South African languages, investigating which type of neural network is most appropriate. Our approach can automatically subdivide words into smaller units in order to enable modelling words that did not appear in the training data. We have shown that training a model on multiple related languages, can improve performance - for example, using both isiZulu and Sepedi data improves the performance of an isiZulu language model.
Principal Investigator: Dr Andre Stander
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2020-06-14
Allocation End: 2020-12-11
Used Hours: 71594
Project Name: In silico estimation of ligand binding energies against cancer- and malaria-associated proteins
Project Shortname: CHEM1055
Discipline Name: Health Sciences
Machine learning artificial intelligence methods and big data was used to develop an algorithm to increase the accuracy of ligand binding efficacy. This in turn will improve drug design programs by designing better compounds for cancer, COVID, malaria etc.
Principal Investigator: Dr Stefan du Plessis
Institution Name: Stellenbosch University
Active Member Count: 11
Allocation Start: 2020-06-15
Allocation End: 2021-01-27
Used Hours: 62265
Project Name: Shared Roots
Project Shortname: HEAL0793
Discipline Name: Health Sciences
Understanding the SHARED ROOTS of Neuropsychiatric Disorders and Modifiable Risk Factors for Cardiovascular Disease.
Shared Roots is a collaborative research project undertaken by researchers from the departments of psychiatry, neurology and genetics at Stellenbosch University and researchers from the South African National Bioinformatics Institute (SANBI). It is a MRC Flagship funded study and the principal investigator on the study is the executive head of the department of psychiatry Professor Soraya Seedat. Dr Stéfan du Plessis is responsible for the neuroimaging component. Our study included participants with posttraumatic stress disorder (PTSD), schizophrenia or Parkinson's disease. It is known that individuals with mental illness as well as other common brain disorders have higher rates of heart disease and stroke than the general population. It is not clear why this is the case. Our study therefore aims to collect information about all the potential factors that can play a role, to better understand the increased risk and enable the development of treatment strategies. To achieve this goal we will combine state-of-the-art research techniques such as genetic evaluations and the latest neuroimaging techniques. This will be combined in analysis with information evaluating the brain disorders, general health and lifestyle factors.
For our neuroimaging component, we scanned over 600 participants using Magnetic Resonance Imaging (MRI). Here we investigate potential brain changes associated with increased metabolic risk. We proceeded to calculate precise measurements of around 70 known brain regions using the MRI scans, which will be compared between cases and healthy controls. Processing takes around 24 hours for each scan. To finish in a timely manner, we used the Centre for High Performance Computing Rosebank, Cape Town, Sun Intel Lengau cluster.
Currently we have closed recruitment end 2017. The processing of the MRI scans was completed early in 2018. We are now the data analysis phase.
Principal Investigator: Dr Richard Klein
Institution Name: University of the Witwatersrand
Active Member Count: 8
Allocation Start: 2020-06-15
Allocation End: 2021-01-27
Used Hours: 124722
Project Name: PRIME
Project Shortname: CSCI1340
Discipline Name: Computer Science
PRIME is a research lab in the School of Computer Science and Applied Mathematics at Wits University. We focus on Machine Learning and Artificial Intelligence techniques for Perception and Representation Learning. The AI models that we train are very large and require weeks of computing to learn. The primary goal of this research is to be able to learn good representations of data that is unlabelled. This means that in the future, AI can learn from large unlabelled datasets which are cheaper to create, and then fine-tune their understanding of the world on smaller, more expensive, labelled dataset.
Principal Investigator: Prof Marco Le Roux
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2020-06-17
Allocation End: 2021-03-04
Used Hours: 81967
Project Name: Coal beneficiation through fluidization
Project Shortname: MECH1254
Discipline Name: Chemical Engineering
This research programme is about the numerical modelling of particle segregation in air fluidized beds. It's application in industry is the cleaning of crushed coal (also called coal beneficiation) whereby impurities such as sand, quarts and pyritic Sulphur need to be removed so that only high quality coal gets to be feed into boilers of a coal-fired power plant. This application is of great importance world-wide but especially so in South Africa where Eskom struggles to meet regulated Sulphur emissions levels and is under risk of having to close some of its power stations due to non-compliance.
North-West University (NWU) has been active in experimental coal beneficiation research over several years but only from late 2019 has numerical simulation been applied in support of experimental work. In this regard support is received from the Institute for Fluid Mechanics of Toulouse (IMFT) in France. A formal collaboration agreement between IMFT and NWU was created to enable support on this complex two-phase research subject. This agreement allowed for the Neptune_CFD research code of IMFT to be installed at CHPC for use.
As far as we know, it is the first time that numerical simulation is applied to particle segregation in a South African study. During November of 2020 substantial progress was made with initial investigations and new insight was obtained into the mechanisms and rate of coal segregation. We were able to present a summary of our work at the December 2020 CHPC conference. The study is expected to continue and completed by December 2021.
Principal Investigator: Prof Thirumala Govender
Institution Name: University of KwaZulu-Natal
Active Member Count: 7
Allocation Start: 2020-06-17
Allocation End: 2021-01-27
Used Hours: 162236
Project Name: IN SILICO EVALUATION OF NANO DRUG DELIVERY SYSTEMS
Project Shortname: MATS0816
Discipline Name: Material Science
The Novel Drug Delivery Unit (NDDU) at University of KwaZulu-Natal is led by Professor Thirumala Govender, a Professor of Pharmaceutics, Head of the UKZN NanoHealth Pillar and Evaluator on the Medicine Control Council of South Africa. The NDDU currently focuses on developing advanced medicine formulations to overcome antibiotic resistance. Antibiotic resistance, considered a global crisis currently, affects the development of human society and has high cost implications to government in terms of finances and resources. Our group has designed various types of novel pharmaceutical materials as well as advanced and new generation "smart" nano drug delivery systems such as nanomicelles, nanoplexes, polymersomes etc. with superior architectural designs which have been prepared by our team and have shown superior activity against sensitive and resistant bacteria. The group philosophy is to use a multidisciplinary integrated approach that will minimize the cost of research and maximize therapeutic outcomes. Hence the facilities provided by CHPC allows our group to integrate molecular modeling with our research that involves extensive in vitro and in vivo animal evaluation of our novel medicines, and is being recognized locally and internationally for excellence.
Principal Investigator: Prof Eric K. K. Abavare
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 5
Allocation Start: 2020-06-17
Allocation End: 2021-02-04
Used Hours: 226602
Project Name: Atomic and Electronic structures of semiconductor interface systems
Project Shortname: MATS1159
Discipline Name: Physics
The research group for Electronic Structure Calculations in the Department of Physics, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana is the Frontier Science Group (FSG). We investigate atomistic and electronic properties of light materials using quantum mechanical approaches based on first principles calculations in the framework of density functional theory and other condense matter approaches, green functions and many body approximations.
Our researchers basically focus on the study of interface materials. All electronic devices and related components in atomic level are interfaced. We study these interfacial morphologies and how they affect the overall performance of device applications.
Experimentally, several important semiconductor materials are growth based, as a consequence complete understanding of how these epitaxial growth are achieved are certainly important for device design and application.
The project work seeks to make new contribution to the semiconductor research in understanding the electronic and atomistic properties of silicon carbide interfacing with silicon that results in layer-by-layer growth.
There have been a lot of reports on the experimental front, the epilayer growth of these two materials in spite of their large lattice mismatch of approximately 20%. However, with special alignment between them, the mismatch can reduce drastically to about 1.5% due the two materials similar inherent symmetry relationship. However, there is no sound theoretical understanding clarifying the interface morphology and the electronic structure, and as a consequence this project seeks to unravel the mystery.
The possibility of solving these scientific interfaces problems hinges very much on the application of high performance computers, which makes the CHPC resources increasingly invaluable to our research. It is on the basis of this our group completely acknowledges the kind help for the use of their CHPC in South Africa.
Principal Investigator: Dr Nkululeko Emmanuel Damoyi
Institution Name: Mangosuthu University of Technology
Active Member Count: 3
Allocation Start: 2020-06-18
Allocation End: 2021-01-27
Used Hours: 71524
Project Name: Surface Reaction Mechanisms
Project Shortname: CHEM1105
Discipline Name: Chemistry
My name is Dr Nkululeko Damoyi and I teach Inorganic Chemistry in the department of Chemistry at Mangosuthu University of Technology (MUT). My present research is in Computational Chemistry (CC) and the modelling calculations are done through the Centre for High Performance Computing (CHPC) in Cape Town. Research is registered at CHPC under the name: Surface Reaction Mechanisms. Presently I am the only member of the group and some students will be included at the beginning of 2019. I supervise some MUT Btech students in small CC research projects although they use their laptops for calculations. Current research output is in a form of two publications in peer-reviewed journals.
A large production of alkanes, for example LPG gas, from imported crude oil and mined natural gas and coal exists in South Africa through a variety of industrial processes. The alkanes are used as starting materials for many other industrial organic compounds, such as plastics. However, the production of some of these industrial organic compounds is too costly and there is a high commercial demand for catalytic methods and new catalysts that would bring down the costs of production. Computer technological advances make it possible to do research in CC in order to model chemical reactions and predict chemical reaction properties which are difficult or impossible to determine from normal laboratory experiments. Most of our present research involves utilising CC to predict the likely chemical reaction mechanisms that produce valuable organic compounds from alkanes with use of catalysts and also without catalysts. Through CHPC we are able to use internet to connect to their cluster computers in order to run the calculations and from the results be able to model the energetics of chemical reactions and predict reaction mechanisms.
Principal Investigator: Prof Regina Maphanga
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 6
Allocation Start: 2020-06-19
Allocation End: 2021-02-04
Used Hours: 274947
Project Name: Energy Storage Materials
Project Shortname: MATS0919
Discipline Name: Material Science
The Design and Optimisation group is a group under Operational Intelligence Impact Area in the Next Generation Enterprises and Institutions cluster of CSIR and uses multiscale methods to develop novel energy storage materials with desired properties and enhanced properties for existing materials. The envisaged outcome of this project is to develop energy storage materials models with improved performance and consistency, which will be cheaper and environmentally benign. The ever-increasing global energy needs and depleting fossil-fuel resources demand the pursuit of sustainable energy alternatives, including renewable sources to replace carbon intensive energy sources. Sustainable and renewable energy is considered to be the most effective way to minimize CO2 emissions. Hence, finding sustainable energy storage technologies is vital for optimally harnessing the renewable energy.
Computational methodologies are very effective in predicting material-structure-property correlations. In this project simulation methods and models based on parallel computing are developed to probe energy materials properties. Centre for High Performance Computing (CHPC) resources are used to develop these parallel computing methods and algorithms for large and complex material models. Thus, CHPC resources provide a platform to simulate the evolution of material properties at a wide range of external conditions that are not accessible experimentally and fast track acquisition of results. The major of aim of this project is to create a predictive, reliable and robust set of models of materials for energy storage across the materials modelling length scale, leading to integrated multi-scale capability.
Principal Investigator: Mr kirodh Boodhraj
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 2
Allocation Start: 2020-06-22
Allocation End: 2021-01-27
Used Hours: 135892
Project Name: Geospatial modelling regarding satellite imagery, oceans and coastal areas using machine learning, ODC and STAC
Project Shortname: CSIR1266
Discipline Name: Earth Sciences
The blue economy is an expanding topic regarding the oceans and we are contributing to it by ocean modelling development and building capacity in this area. The project focuses on using machine learning to create ocean forecasts using a unique methodology. We use the ERA5 product as a test case and will later include other data products into the study.
An ocean forecast is useful for the shipping, fishing, ports and other industries.
Furthermore, coastal models are being developed and calibrated which will be used for testing the coupling between ocean and coastal models. This means that an efficient workflow can be setup to model both the oceans and coastal areas in focus. It may also produce more accurate results when the coastal model boundaries use ocean output data.
Principal Investigator: Dr Georgia Schafer
Institution Name: University of Cape Town
Active Member Count: 0
Allocation Start: 2020-06-24
Allocation End: 2020-12-21
Used Hours: 1648
Project Name: Characterisation of EPHA2 variants associated with KS oncogenesis
Project Shortname: HEAL1345
Discipline Name: Health Sciences
The Emerging Viruses research group has been newly established within the ICGEB and is affiliated with the IDM in the Faculty of Health Sciences at UCT. Our focus is on oncogenic viruses, particularly KSHV which causes Kaposi's Sarcoma (KS). We employ multidisciplinary methods, from clinical studies to laboratory experiments to computational analysis, to better understand susceptibility to KSHV infection and development of KS. This is particularly important in South Africa, as there is a high burden of KS here due to the prevalence of HIV which in conjunction with KSHV drives the oncogenic process. We make use of the CHPC facilities to computationally model the receptor used by KSHV and simulate the effects of mutations in this receptor described in a South African cohort. This project is ongoing and we are confident that it will soon yield novel and exciting results.
Principal Investigator: Dr Lelanie Smith
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2020-06-23
Allocation End: 2021-01-27
Used Hours: 46524
Project Name: Aeronautical Research
Project Shortname: MECH1118
Discipline Name: Other
The Aeronautical Group at the University of Pretoria is considering airframe propulsion integration configurations. In this context various projects related to alternative mathematical models to determine energy efficiency are considered. New fuselage shapes are envisioned with CFD and optimisation codes. Integrated propulsion systems lead to a fuel saving potential that needs new modelling strategies to quantify. Because of the optimisation component the CHPC is essential to model the design spectrum
Principal Investigator: Dr Ruben Cloete
Institution Name: University of Western Cape
Active Member Count: 6
Allocation Start: 2020-06-24
Allocation End: 2021-01-27
Used Hours: 625749
Project Name: HIV-1C integrase drug resistance
Project Shortname: CBBI1154
Discipline Name: Bioinformatics
Our group is based at the University of the Western Cape in the South African National Bioinformatics Institute. The work in my group is primarily focused on molecular modeling and drug design. Here we focus on protein structure prediction, molecular docking and simulation studies of protein-drug, protein-protein systems. Our research efforts is in understanding HIV-1 integrase drug resistance, Tuberculosis drug resistance and identification of novel genes associated with Parkinson's disease. The results of our work may result in the identification of new drugs to treat Tuberculosis and Parkinson's disease and better management of HIV-1 infected individuals within South Africa. The process involves the use of molecular dynamic simulation methods to tease out important movements observed within the protein structure. For this large computing resources are required to simulate large macromolecular systems. Although the project has just started we have completed several objectives by preparing protein structure complexes. We are in the process of uploading our run input files to the CHPC to start with multiple simulation runs. We may even require more resources.
Principal Investigator: Prof Mahmoud soliman
Institution Name: University of KwaZulu-Natal
Active Member Count: 30
Allocation Start: 2020-06-24
Allocation End: 2021-01-27
Used Hours: 1557283
Project Name: Drug Design, development and modelling
Project Shortname: HEAL0790
Discipline Name: Health Sciences
The research scope of the Molecular Bio-Computation and Drug Design Research Lab covers a wide range of computational and molecular modeling research areas with main focus on biological systems and drug design approaches. Main interest is related to design and study of biologically and therapeutically oriented targets by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We show keen interest in diseases of global burden and of high prevalence within the south African populace such as HIV/AIDS, Tuberculosis and Cancer. The computational resources provided by CHPC is employed in performing molecular dynamic calculations and the accompanying post molecular dynamic simulation analysis
Principal Investigator: Dr Matshawandile Tukulula
Institution Name: University of KwaZulu-Natal
Active Member Count: 1
Allocation Start: 2020-06-26
Allocation End: 2021-01-27
Used Hours: 10123
Project Name: Medicinal Chemistry and Computer-Aided Drug
Project Shortname: HEAL1346
Discipline Name: Chemistry
My Medicinal Research Group at the University of KwaZulu Natal has been interested in designing new and selective inhibitors for an enzyme that currently has no 3D crystal structure. To achieve this we need to undertake homology modelling followed by molecular dynamics and docking studies in order to fully understand interactions between ligands and the enzyme on the in silico level. This work is progressing quire well and as mentioned above we recently submitted a peer-reviewed manuscript for publication.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-06-29
Allocation End: 2021-01-27
Used Hours: 442272
Project Name: CFD modelling of jet impingement with phase change
Project Shortname: MECH1296
Discipline Name: Computational Mechanics
Jet impingement heat transfer with boiling is a promising new heat transfer method for use in power electronics cooling. Most of the current research on this topic in literature is experimental, leaving a gap for computational studies to further investigate the relevant influencing parameters. Jet impingement flow is difficult to simulate because of its transient nature and multiple flow regimes involved (from laminar to turbulent). Previous research by Prof Ken Craig's group has developed techniques based on Large Eddy Simulation to evaluate the effect of round jets with and without swirl on solar receiver heat transfer surfaces. This program extends that work to having phase change as well in the form of boiling. The latent heat absorbed by boiling works in addition to the enhance convection provided by the jet. Various case studies are being developed for application in the electronics cooling industry and the approach has been validated using test cases from literature.
Principal Investigator: Prof MESFIN ABAYNEH KEBEDE
Institution Name: University of South Africa
Active Member Count: 3
Allocation Start: 2020-06-26
Allocation End: 2023-10-31
Used Hours: 2687
Project Name: Electrode materials for energy storage systems
Project Shortname: MATS0855
Discipline Name: Material Science
Electrode materials for energy storage systems research program is currently led by Prof Mesfin Kebede a full professor of nanotechnology at University of South Africa (UNISA). Electrode materials for energy storage systems is focusing on studying the structural and electrochemical properties of electrode materials for lithium ion and sodium ion batteries. The computational work on electrode materials is very useful to complement the experimental work. The intention is to get strong understanding on the electrode materials using computational calculations. Before going to laboratory and carryout experiments, it is very useful to do computational research. The computational research work reduces the expenses for chemicals and also save the time to be spend in the experiment. Sometimes, we can get very important information from the computational work than the experimental work. Therefore, the computational research work is very useful. So far, the progress on the research program is satisfactory and more computational work is still necessary to design materials with enhanced properties and performance.
The computational studies are undertaken within the institute for nanotechnology and water sustainability at college of science, engineering and technology of the UNISA.
The works involves the search and identification of suitable materials composition of potential cathode material to be used in Li-ion, Na-ion rechargeable batteries that will yield enhanced properties and high performance.
The computational studies serve as a key guideline towards setting up well informed experimental work aimed at synthesizing electrode material that possess improved electrochemical properties such as stability, capacity and cycleability.
The current work relies heavily on the Materials Studio software license only accessible through CHPC. The access to computational tools and technical support have proved to be quiet useful in our research endeavours.
So far, despite previous challenges faced due to some students struggled with bad internet connectivity, we have now involving new postgraduate students interested to join the group and refocused our research efforts as demonstrated by current collaborations with some of the experts in the computational modelling field. We are convinced with the preliminary work that more exciting predictions will lead us to niche research areas that have potential to be registered as intellectual property.
Principal Investigator: Prof Peter Nyasulu
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2020-06-29
Allocation End: 2021-01-27
Used Hours: 2058
Project Name: SimpactSimulation
Project Shortname: CBBI1184
Discipline Name: Applied and Computational Mathematics
SimpactSimulation as identified at CHPC, is a group from the University of Stellenbosch working on a project that simulate heterosexual transmission of HIV and prevention in complex sexual networks. The simulations in this project are implemented through individual based models (IBMs) which allow individuals in the model to behave autonomous for an individual goal; one such is starting or ending a sexual relationship. The great gains in the nature of our work is that our model can be used as experiments in certain cases where it is unethical to perform in the real world.
In our current work, we seek to evaluate the impact of early access to antiretroviral drugs among adults on HIV incidence in young woman. For the model to be realistic we need to mimic the target population summary statistics by carefully calibrate the model. This is very computational intensive process due to the complexity and computational burden associated with large number of model parameters and a large number of target statistics.
However, the availability of CHPC and parallesation capabilities we are able to run model simulation with big enough population that allow huge amounts of data storage for surrogates statistics to be computed from and matched to the real world summary statistics.
Principal Investigator: Prof Tony Ford
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2020-06-26
Allocation End: 2021-01-27
Used Hours: 160143
Project Name: Computational studies of the properties of molecular complexes
Project Shortname: CHEM1134
Discipline Name: Chemistry
The Computational Chemistry research group at the University of KwaZulu-Natal carries out calculations of the properties of molecules.
Small molecules have a tendency to interact with one another to form complexes to a greater or lesser extent, governed by the properties of the individual partners. These properties are determined largely by the electronic natures of the molecules, and the strength of interaction, measured by the interaction energy, can vary over a wide range, depending on the acidity of basicity, among other features, of the interacting molecules. These interaction energies, and the structures of the resulting complexes, can be predicted using computational methods, and the success of the project is measured by the degree of agreement between the computed properties and those determined by experimental methods such as vibrational or rotational spectroscopy, where such data exist.
The calculations are carried out using a commercially-available computer program which enjoys wide usage throughout the world. The program, by its nature, requires large allocations of memory and time to complete the calculations, and these resources are typically beyond the capacity of single-processor desktop computers. Hence there is a real need in South Africa for a centrally-managed high-performance computing facility, such as the CHPC, which fulfils this requirement.
This project is an ongoing process, and its success depends on the continuation of the availability and regular upgrading of the CHPC facility.
Principal Investigator: Dr Adeola Joseph Oyenubi
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2020-07-01
Allocation End: 2021-01-28
Used Hours: 17559
Project Name: Optimizing balance in for Impact Evaluation
Project Shortname: ECON1213
Discipline Name: Economics and Finance
This research is conducted by Dr Oyenubi, a lecturer at the University of the Witwatersrand.
Usually policy interventions (like the child support grant programme) require assessment in terms of the impact of the policy on beneficiaries. To do this a researcher must compare the response units under the policy with units that are not under the policy. For this comparison to be valid the two groups should have identical characteristics or covariates. This is achieved by comparing the distribution of covariates using various balance statistics e.g. mean and standardized difference in means.
This work assesses if the performance of different balance statistics vary in terms of their ability to compare the distribution of covariates. The premise is that differences in the performance of balance measures will lead to variation in the estimate of policy impact. With no guidance on the performance of various balance measures it will be difficult to identify the correct impact estimate.
This work will provide guidance to researchers on how to use the various balance measures that are available when estimating the impact of a policy. However doing this require extensive Monte Carlo experiments. This experiments are computationally expensive and without the CHPC the work will be virtually impossible.
The process involves setting up a data generating process that mimics various condition that is encountered in real life impact assessment. In this fictitious world we know what the correct impact estimate is. We then use various method to try and estimate this (known) impact estimate. The idea is that some methods will perform well while others will fail. This knowledge (about what method performs better and under what conditions) can then be used on real life data where we do not know the correct impact estimate.
The first part of this project is completed, and the second part is just starting.
Principal Investigator: Dr Gwynneth Matcher
Institution Name: Rhodes University
Active Member Count: 4
Allocation Start: 2020-07-03
Allocation End: 2021-01-28
Used Hours: 1233
Project Name: Microbial Ecology in Antarctic and aquatic ecosystems
Project Shortname: CBBI0952
Discipline Name: Environmental Sciences
My research group, based at Rhodes University (Makhanda), focuses on microbial ecology in Antarctic ecosystems. Antarctic ecosystems are characterised by extreme conditions which impose significant pressures on the ability of fauna and flora to survive. In the majority of these ecosystems, the dominating life form is microbial. These ecosystems are particularly vulnerable to climate change which alter the biodiversity and functional richness of microbial soil populations resulting in significant impacts on ecosystem functioning as a whole. Metagenomics, which is utilised to assess the microbial populations in this project, involves sequencing and analysis of the total genetic material in a given environment. This allows for identification of species present as well as providing information of the impact of environmental drivers. The computational analyses are conducted on the CHPC cluster. To date, this project has investigated the effect of invasive Sagina plants on soil microbiota on Marion Island as well as proving detailed microbial profiles from several previously uncharacterised nunataks in Dronning Maudland.
With respect to estuarine ecology, our research focuses on the Swartkop estuary which is impacted by urban and industrial activities and the Sundays Estuary is influenced by agricultural activities. The health of the river is of fundamental importance to sustainable biodiversity. To date, most monitoring has focused on fish assemblages and targeted analysis of algal blooms. This is time-consuming, labor-intensive and requires a comprehensive and extensive knowledge of the relevant species. Also, this approach completely excludes the fauna and flora not evident to the naked eye. This research project focuses more on rapid molecular characterization techniques which will also increase the frequency at which these estuaries can be monitored.
Principal Investigator: Dr Leigh Johnson
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2020-07-03
Allocation End: 2021-01-28
Used Hours: 1411782
Project Name: MicroCOSM: Microsimulation for the Control of South African Morbidity and Mortality
Project Shortname: HEAL1049
Discipline Name: Health Sciences
The MicroCOSM project, based at the Centre for Infectious Disease Epidemiology and Research at the University of Cape Town, is a project to simulate the spread of infectious diseases, as well as the incidence of non-infectious diseases, in the South African population. By simulating the social and biological factors that contribute to disease transmission, we can better understand which sub-populations need to be targeted for special interventions. We can also evaluate the impact that various prevention and treatment programmes have had in South Africa to date, and evaluate the potential impact of new programmes. This simulation involves generating nationally representative samples of 20,000-40,000 South Africans and tracking them over their life course. Because this involves many individual-level calculations, the model requires substantial computing power, and the CHPC is therefore critical to the conduct of these simulations. We have recently used the model to assess strategies to reduce the future incidence of cervical cancer in South Africa, and to assess the utility of antenatal surveys in evaluating trends in HIV incidence.
Principal Investigator: Dr Nikhil Agrawal
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2020-07-03
Allocation End: 2021-01-28
Used Hours: 77717
Project Name: Molecular Modeling of proteins using different computational tools
Project Shortname: HEAL1189
Discipline Name: Health Sciences
Proteins perform different functions in our body. Functions of proteins directly relate to its dynamics. In our study, we try to understand these how dynamics of proteins affects its overall functions and try to find important proteins residues which help them to bind with membranes and drug molecules. Using CHPC resources we tried to elucidate peptides-interactions membranes and proteins interactions with surfactants.
Principal Investigator: Prof Gerrit Basson
Institution Name: Stellenbosch University
Active Member Count: 6
Allocation Start: 2020-07-03
Allocation End: 2021-01-28
Used Hours: 278958
Project Name: CFD modelling of Hydraulic Structures in Rivers
Project Shortname: MECH0985
Discipline Name: Computational Mechanics
The Institute for Water & Environmental Engineering Stellenbosch University has 3 Doctoral students and 3 Post-Doctoral student who are investigating CFD modelling of hydraulic structures with complex vortices and sedimentation. Key aspects of the research are related to the improved prediction of bridge pier scour, to investigate the addition of flares on spillways, to reduce rock bed scour in plunge pools at spillways, to optimize the design of vortex settling basins, sand traps and settlers for sedimentt removal at hydropower and water abstraction plants. The simulations are too computationally intensive for standard computers and the CHPC assists in the research by allowing the students to more extensively explore the hydraulic behaviour of these structures.
Principal Investigator: Prof Thomas Niesler
Institution Name: Stellenbosch University
Active Member Count: 11
Allocation Start: 2020-07-06
Allocation End: 2021-01-28
Used Hours: 542800
Project Name: Automatic Speech Recognition for Under-resourced Languages
Project Shortname: CSCI1059
Discipline Name: Electrical Engineering
Most languages spoken in Sub-Saharan Africa are not technologically developed. They do not have, for example, the carefully prepared collections of speech and text that are required for the development of automatic speech recognition and associated technologies. The Digital Signal Processing Laboratory, wihch is part of the Department of Electrical and Electronic Engineering at Stellenbosch University, are focussing their research efforts on developing methods that allow the development of automatic speech recognisers from much smaller datasets - small enough to make their compilation feasible for the languages concerned. The developed techniques are equally applicable to South African languages, which also remain largely under resourced. For example, the group has develop the world's first pentalingual speech recognition system that is able to switch back and fourth between five South African languages (isiXhosa, isiZulu, Sesotho, Setswana and English). Such code-switching, where a speaker alternates between languages in the same utterance, is common in spontaneous South African Speech and in other multilingual situations. The development if these speech recognition systems requires the extensive training an optimisation of existing and new neural network architectures. A resource like the CHPC is essential for such computationally demanding work. The programme is progressing steadily, and has gained international attention.
Principal Investigator: Prof Orde Munro
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2020-07-06
Allocation End: 2021-01-28
Used Hours: 33159
Project Name: Bioinorganic Chemistry
Project Shortname: CHEM1065
Discipline Name: Chemistry
BIOINORGANIC RESEARCH GROUP – WITS UNIVERSITY
The Bioinorganic Research Group at WITS University is led by Prof. Orde Munro, who is currently the SARChI Chair of Bioinorganic Chemistry. At present, the WITS group comprises two post-doctoral research fellows (Drs. Catherine Slabber and Zeynab Fakhar), two PhD students, and four MSc students.
NATURE OF OUR WORK
The work involves the design, synthesis, and testing of novel metallodrug candidates for chemotherapy. The compounds incorporate ligands that can facilitate and control the interaction of the metal ion with biomolecules such as DNA and/or proteins. Molecular simulations are used not only to design compounds with desirable biological behaviour, but also to gain fundamental insights on their mechanisms of action and electronic structures. We are particularly interested in exploiting and controlling the reactivity of both endogenous and non-natural metal ions to kill drug-resistant pathogenic bacteria such as TB (Mycobacteria) and cancer cells.
WHY WE USE SIMULATIONS
Modern drug discovery uses in silico methods for a number of reasons, including screening large libraries of compounds for binding efficacy to enzyme targets. The enzyme targets are crucial proteins for the survival and replication of cancer cells, bacteria and viruses. Screening many thousands of compounds using computer programs is an efficient way to select a handful of compounds that can ostensibly bind to the enzyme target of interest because they have the correct shape and functional groups. The small library so generated may then be synthesized in the laboratory and tested against the pathogen of interest and the putative enzyme target. In this way, computational methods shorten the time required to find promising new compounds for further testing and development as the medicines of tomorrow. Finally, computer simulations offer important three dimensional details about how drug-like compounds inhibit their enzyme targets, thereby guiding optimization of the compound's structure for enhanced target affinity and, in principle, improved in vivo efficacy.
Principal Investigator: Dr Kevin Lobb
Institution Name: Rhodes University
Active Member Count: 12
Allocation Start: 2020-07-07
Allocation End: 2021-01-28
Used Hours: 1060057
Project Name: Computational Mechanistic Chemistry and Drug Discovery
Project Shortname: CHEM0802
Discipline Name: Chemistry
This group explores drug discovery across a range of diseases including Malaria and COVID-19. Our latest work has identified four potent antimalarial agents that are already FDA approved, and may therefore be repurposed for malarial treatment.
Principal Investigator: Mr Marco van Dijk
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-07-08
Allocation End: 2021-01-28
Used Hours: 104618
Project Name: Hydropower development and air valve optimization
Project Shortname: MECH1349
Discipline Name: Other
The researchers (Prof SJ van Vuuren, Mr M van Dijk and Dr GL Coetzee) from the University of Pretoria was able to register a new patent as a result of the output from the Computational Fluid Dynamic (CFD) analyses undertaken at the CHPC. Patent no. 2020/04798 was registered on 3 August 2020. The patent entails the optimisation of airflow through the air valve. This improves the functionality of the air valve and improves the operation of hydraulic pipe flow conditions within a water distribution system.
The normal airflow through air valves on pipe distribution networks and pipelines is limited by the ratio of the inlet vs. the outlet orifice diameter. The research undertaken by the University of Pretoria has found that an optimum ratio can be achieved within a specific set of parameters. Without the use of the CHPC this would have not been possible.
Various numerical (CFD) models had to be solved, making use of some 192 cores at a time. Solving of one model, even with all these cores, took 48 hours per model and more than 15 models were already solved.
The study forms part of a three-part research study for air valves. Further research on parts 2 and 3 will continue this year with an extension to hydropower optimisation.
Principal Investigator: Prof Beatriz Garcia de la Torre
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2020-07-07
Allocation End: 2021-01-03
Used Hours: 152780
Project Name: Peptide Chemistry
Project Shortname: CHEM1090
Discipline Name: Chemistry
Our research involves the study of new peptides, their structure, interactions, properties, electronic requirements, and dynamics using ab initio calculations and MD calculations and their applications in drug delivery and study physical properties like magnetism, etc. We pursue Green peptide synthesis reactions using Materials Studio.
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 12
Allocation Start: 2020-07-08
Allocation End: 2021-01-28
Used Hours: 4981274
Project Name: Structural, electronic, magnetic properties and anisotropy energy in some metallic and non-metallic heterostructures
Project Shortname: MATS0988
Discipline Name: Material Science
The research work is a collaboration between the Dr. Raji ( Physics Department, UNISA, South Africa) and the group of Dr. Brice Rodrigue Malonda (Marien Ngouabi University, Republic of Congo). The focus of the research is numerical studies of electronic, optical, transport and magnetic properties of selected two-dimensional (2D) and three-dimensional (3D) solid materials for potential applications in high-capacity data storage, catalysis, spintronics, and renewable energy. The study employs density-functional theory (DFT) as the numerical method, to probe atomic-level properties of these materials. Our approach is mainly atomic and defect engineering of these solids which involve modifying the properties of the solids through the introduction of external atoms into their otherwise pristine structure. The last two decades have witnessed the discovery of several 2D materials, and have opened new possibilities to further miniaturization of existing electronic and magnetic devices. Therefore, fundamental understanding of properties of these materials systems is necessary to support experimental research and to aid technological applications. One of the aims of our research therefore, is to discover novel materials that can be synthesized in the laboratory for potential technological applications.
The numerical implementation of DFT is computational intensive, requiring several computational hours, large data storage and memory requirements, beyond the capacity of ordinary table-top computers. Therefore, high-capacity computer clusters such as the one provided by the Center for High Performance Computing (CHPC) is sine -qua-non for the research. There are about twelve postgraduate students working in various aspects of the project. At the moment, four Masters students have completed their studies and two of them are continuing to doctorate. This research, as well as the CHPC, has enabled collaboration between South Africa based academic researcher and colleagues in Congo, Mexico and Italy. There have been research outputs in form of publications, and the scope of the project will guarantee regular postgraduate students training who are able to undertake cutting-edge research and contribute to scientific development.
Principal Investigator: Prof Warren du Plessis
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-07-09
Allocation End: 2021-01-28
Used Hours: 309733
Project Name: Electronic Warfare (EW) Technologies
Project Shortname: MECH0989
Discipline Name: Electrical Engineering
Prof. Warren du Plessis of the University of Pretoria has been using the CHPC to determine the optimal configurations of thinned linear antenna arrays. Thinned arrays reduce the cost of antenna arrays by reducing the number of antenna elements required, thereby addressing one of the major barriers to the wider adoption of antenna arrays. This is a problem that has been studied since at least the 1960s, and while good algorithms exist, the optimal solutions are currently unknown. The work is nearing its completion, with the major result being that even the best algorithms do not come close to finding optimal configurations. This work would simply not be possible without the CHPC.
One of Prof. du Plessis' postgraduate students, Llewellyn Strydom, is investigating the use of artificial intelligence (AI) techniques in separating radio signals. This is an important problem in many applications, including cognitive radio. The results to date have been encouraging with signals in even challenging cases being correctly identified. This work would be far more difficult without the resources provided by the CHPC.
Principal Investigator: Dr Samuel Atarah
Institution Name: University of Ghana
Active Member Count: 1
Allocation Start: 2020-07-09
Allocation End: 2021-02-11
Used Hours: 62655
Project Name: Ab initio studies of electronic and magnetic properties of selected elements
Project Shortname: MATS1162
Discipline Name: Physics
At the Condensed Matter Physics research group of the Department of Physics in the University of Ghana, DFT and use of similar tool for studying material properties is one of area areas of study. New material remain uncharacterized leaving a lot of unanswered scientific questions. Such studies require computational resource. The CHPC has been an invaluable resource that has enabled our work. Students have been graduated through use of the resource and some student continue to benefit whilst indicating progress in the group's effort.
Principal Investigator: Dr Bubacarr Bah
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 11
Allocation Start: 2020-07-10
Allocation End: 2021-01-28
Used Hours: 53535
Project Name: Large Scale Computations in Data Science
Project Shortname: CSCI0972
Discipline Name: Applied and Computational Mathematics
This is the programme of the AIMS Data Science Research Group. Most of the research the group does that require the use HPC is on the application of deep learning methods to real life problem from health and agriculture. During the period under review four projects made use of the CHPC.
1) Localisation of Lesions in Diabetic Retinopathy, where the task is to predict diabetes from retina images. We have a paper accepted to conference on this work.
2) Post-processing of segmentation of images to detect fruits from images of orchards. We need a few more simulations to write a paper.
3) Pool testing algorithm design for COVID-19 to develop more rapid testing procedures. We are preparing the publication for this.
4) Implementation of Graphs Convolutional Neural Network (CNN) algorithms, which are a special CNN that can handle unstructured data different from images. This one is just starting.
Principal Investigator: Dr Steven Hussey
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-07-13
Allocation End: 2021-01-28
Used Hours: 243071
Project Name: Forestry Molecular Genetics - transcriptional and epigenetic regulation of wood formation
Project Shortname: CBBI1010
Discipline Name: Bioinformatics
The Forest Molecular Genetics Programme is a joint venture of the University of Pretoria and South African forestry industry partners aimed at developing biotechnology applications for tree improvement. It focuses on the genetic basis of tree growth, wood formation and defence against pests and pathogens. The SA forestry industry produces over 20 million tons of wood per year for a wide array of renewable products such as timber, pulp, paper, packaging, cellulose, textiles, pharmaceuticals and food additives. Increasingly, there is interest in using trees as biorefineries, i.e. energy-efficient production platforms for high-value biopolymers and biochemicals. Timber from genetically improved plantations can also be processed into advanced building materials for sustainable housing and construction. In part, the Programme aims to understand the biology of wood formation and how it is regulated at various levels. For example, the metabolism and incorporation of carbon-rich compounds formed from photosynthesis into cellular structures such as wood, and the role of networks of genes coordinating the activation of genes at the correct stages of growth and wood formation. An important part in understanding these process is the use of DNA sequencing technologies that produce data requiring high-performance computation to analyze it. These tools were central to decoding the genome or DNA sequence of Eucalyptus grandis, an important fast-growing tree. Our Programme has most recently relied on the Centre for High Performance Computing to understand how cellular organelles participate in wood formation by analysing gene expression patterns associated with the poorly understood plastid organelles found in wood, and implementing novel transfer machine learning approaches to infer gene regulatory networks underlying wood formation in Eucalyptus based on machine learning models built on thousands of gene expression and gene-gene interaction datasets from the model plant Arabidopsis.
Principal Investigator: Dr Gaston Mazandu Kuzamunu
Institution Name: University of Cape Town
Active Member Count: 13
Allocation Start: 2020-07-14
Allocation End: 2021-01-28
Used Hours: 49075
Project Name: Sickle Africa Data Coordinating Center (SADaCC)
Project Shortname: CBBI1243
Discipline Name: Health Sciences
Sickle Cell Disease is the most common monogenic diseases mainly caused by a single-point mutation in the beta-subunit of haemoglobin, the principal oxygen transporter in red blood cells. Because of the protective effect of the sickle cell mutation against malaria, sickle cell disease has the highest incidence and prevalence in tropical regions, particularly in Sub-Saharan African countries, where more than 70% of patients live, affecting approximately 300 000 newborn babies every year and more than 20 million people globally. Thus, the Sickle Africa Coordinating Center project at University of Cape Town, Faculty of Health Sciences under the Division of Human Genetics has been set to coordinate different type of sickle cell datasets across Africa: collection and analyses, and tackle issues related to this condition, including phenotype pattern prediction, diagnostics and treatments. Genetics being a key components for this condtions and considering more than 11000 patients that have been identified across Africa (Tanzania, Ghana and Nigeria), genomic datasets are now being carried out predicting and prioritizing in silico mutations leading to optimal therapeutics. This is important, especially with the current trend of gene therapy that is being suggested. With this sample size, which is expected to increase as the project is planning to expand to more African countries, High Performance Computing, such as CHPC is really needed to design scalable pipeline to effectively process these datasets to contribute to overcoming this disease.
Principal Investigator: Prof Fernando Albericio
Institution Name: University of KwaZulu-Natal
Active Member Count: 6
Allocation Start: 2020-07-13
Allocation End: 2021-01-28
Used Hours: 61982
Project Name: Peptide chemistry and Organic chemistry
Project Shortname: CHEM1102
Discipline Name: Chemistry
We are Peptide Science Group at UKZN Westville campus. The project was brought up with an intend to learn computational chemistry. The project involves synthesis of several organic molecules towards application in oligonucleotide chemistry. With the help of computational tools we aim to predict the reaction mechanism. Since CHPC provides the server which speeds up the calculations and helps in achieving the preliminary results. The project so far had been very promising in predicting the mechanism. We expect to be going ahead with these results for further analysis towards prediction of reaction mechanism.
Principal Investigator: Dr Rhiyaad Mohamed
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2020-07-15
Allocation End: 2021-01-28
Used Hours: 388811
Project Name: Advanced materials for oxygen evolution reaction
Project Shortname: MATS1123
Discipline Name: Chemical Engineering
Hydrogen is seen as an integral part of the sustainable energy future. Through fuel cell and electrolyser technologies, energy storage and conversion will be possible. This will resolve some of the more critical challenges faced by most renewable energy sources. Co-hosted by the University of Cape Town and operating under the Catalysis Institute, HySA Catalysis (Hydrogen South Africa Catalysis), part of a flagship programme funded by the Department of Science and Technology, aims to find efficient and market ready catalyst technologies for both hydrogen fuel cells and water electrolysers. The former has been an age-old activity with a strong internal knowledge base. On the other hand, water electrolyser research is a new venture with many unresolved and unknown challenges. The Electrolyser Research Group is a new, young and dedicated group in the area of water electrolysis within HySA Catalysis.
We aim to take advantage of both experimental techniques and fundamental principles to predict and design new and better catalysts. Our research is broken down into two main categories, catalyst design and electrode membrane assembly development for commercialisation. Computational resources provided by CHPC's Lengau supercomputer enables us to perform quantum-chemical calculations to understand material properties. Whilst traditionally, unsupported iridium oxide has been used as an electrolyser catalyst, the scarcity and cost of iridium is a good justification to pursue research in supported iridium catalysts—these catalysts will of course require durable and conductive supports. Since some of these materials have never been synthesised before it is critical to methodically predict stable and electrically conductive material for use in water electrolysers. Based on chemical intuition we have identified a class of materials, doped oxides, which may possess excellent electrochemical properties. We have identified doped tin oxide and titanium dioxide as potential catalysts supports—our computational studies have now given us electronic properties of doped tin oxide.
We have now identified two systems we would like to investigate further. These materials presents some interesting electronic properties. Our current efforts are now aimed at studying their stability under operating conditions.
Principal Investigator: Prof Tien-Chien Jen
Institution Name: University of Johannesburg
Active Member Count: 21
Allocation Start: 2020-07-16
Allocation End: 2021-02-09
Used Hours: 1609091
Project Name: Developing an Innovative Metal Matrix Composite Membrane for Hydrogen Purification
Project Shortname: MATS0991
Discipline Name: Material Science
Hydrogen is an excellent energy carrier because of its high enthalpy of combustion with less environmental impact. Hydrogen fuel can be directly used in cars, ships, aircraft, and other transportation equipment. Although there are many problems to be resolved for implementation of hydrogen technology, it is generally believed that hydrogen will become a key energy carrier in this century. Until sufficient quantities of hydrogen can be derived from renewable energy sources, it will have to come from hydrogen separation using existing fuels (e.g., diesel, natural gas) as the feedstock. Hydrogen separation units can generate highly purified hydrogen from the feedstock gas mixtures, however, a certain amount of CO and other chemicals will make it into the hydrogen stream and cause catalyst failure on the fuel cell electrode. This significantly deteriorates the activity of the catalyst layer, particularly for Proton-Exchange Membrane (PEM) fuel cells. This deterioration greatly reduces the efficiency of power generation and the life cycle of the fuel cell. Overcoming this obstacle is necessary for the wider use of highly efficient fuel cells. The objective of this mproposal is to develop a new composite metal membrane (CMM) that can achieve extremely high flux and selectivity of the hydrogen separation and achieve the lifetime goal set by the U.S. Department of Energy (DOE). To accomplish these goals, a research team formed by the University of Johannesburg (UJ), Council for Scientific and Industrial Research (CSIR) and Hydrogen South Africa (HySA) will combine two major technologies: Electrostatic-Force-Assisted Cold Gas Dynamic Spraying (ECGDS) and Laser-Assisted Manufacturing (LAM) to develop this new type of membrane. The proposed new membrane will eliminate the hydrogen embrittlement, catalyst failure, and avoid the difficulty of forming a defect-free, ultrathin Pd film on the substrate surface. The proposed CMM will exhibit superior reliability and can be produced with a relatively low-cost and scalable process. Along with the development process, numerous numerical methods are utilized to simulate the material properties and behaviour as well as the optimization fabrication procedure. To accomplish these task HPC services from CHPC plays a crucial role in understanding the numerous unknown phenomena's. This service enables the research to be simulated from feature scale to reactor scale .Note that this project is currently supported by the NRF for 2017-2021
Principal Investigator: Mr Reshendren Naidoo
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2020-07-16
Allocation End: 2021-01-28
Used Hours: 91003
Project Name: Influence of Gas Phase Kinetics on a Pulverised Coal Flame
Project Shortname: MECH1298
Discipline Name: Computational Mechanics
The combustion of coal particles is a complex process and there are several physical processes at play. These processes are in turn highly dependent on the quality of coal being combusted and hence there must be direct link between the numerical methods employed and the true heterogeneous nature of coal. One of these facet is the way combustible material is released from coal particles. The chemical mechanisms that are used to predict the flame characteristics are important to understand the ignition/stability and emissions profile of a given combustion regime. Hence it is important to study these chemical mechanisms.
Principal Investigator: Prof Charalampos (Haris) Skokos
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2020-07-17
Allocation End: 2021-01-28
Used Hours: 1329666
Project Name: Chaotic behavior of Hamiltonian systems
Project Shortname: CSCI1007
Discipline Name: Applied and Computational Mathematics
Using modern numerical techniques of Nonlinear Dynamics and Chaos Theory we investigate in a unified mathematical way the behavior of models describing the energy transport in disordered and granular media, as well as the properties of new elastic materials like graphene and molecules like the DNA. This research is performed by members of the 'Nonlinear Dynamics and Chaos Group' in the Department of Mathematics and Applied Mathematics at the University of Cape Town. The performed investigations constitute an innovative combination of Applied Mathematics, Chaos Theory, Hamiltonian Dynamics and Nonlinear Lattice Dynamics. Their outcomes will provide answers to some fundamental questions about the effect of chaos on the energy transport in disordered and granular media, and on the behavior of graphene and DNA. Some of the questions we try to address are: Does the presence of impurities and nonlinearities enhance or suppress the propagation of energy (e.g. heat) in solids, of light in crystals, and of vibrations in granular material? How does the ratio of the different base pairs in DNA chains affect their structural stability and the temperature at which the double-stranded DNA breaks to single-stranded DNA?
Principal Investigator: Prof Josua Meyer
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2020-07-17
Allocation End: 2021-01-28
Used Hours: 931313
Project Name: Fundamentals of forced and mixed convection in heat exchangers
Project Shortname: MECH1094
Discipline Name: Computational Mechanics
In-tube condensation is widely seen in many industries such as desalination, power plants and air conditioning. Thoroughly understanding of the condensation phenomenon would lead to better design of the systems which consequently causes the improvement of system efficiency. Although in majority of applications the circular tubes are used, there are some particular cases, like in air-cooled steam condensers, in which non-circular tubes such as rectangular tubes and flattened tubes are utilized. It has been proved that the thermal efficiency of such tubes are better as compared to the conventional circular tubes under specific operating conditions.
This work is being done by the Clean Energy Research Group (CERG) at the University of Pretoria. This group is involved in experimental and numerical heat transfer research focused on clean energy applications. CERG, falling under the Department of Mechanical and Aeronautical Engineering at the University of Pretoria, has a number of world class experimental facilities focused on heat transfer, balanced by a Computational Fluid Dynamics (CFD) division. The Group members have developed, designed and built five unique, state of-the-art experimental set-ups, which are being used for leading-edge heat transfer research.
Due to lack of water resources in South Africa, the research works on the optimizing and performance enhancement of systems working with water as the working fluid should be greatly developed. Such activities will definitely lead to lower energy and water consumption within the country in the future.
It is the purpose of this research work to numerically investigate the effect of inclination on condensation of steam inside a long flattened channel. Thoroughly understanding of this problem via numerical simulations would assist in proper design of ACCs with low cost and time compared to experimentation.
At the moment, most of the work has been done, and a research paper is going to be prepared.
Principal Investigator: Dr Collins Obuah
Institution Name: University of Ghana
Active Member Count: 0
Allocation Start: 2020-07-20
Allocation End: 2021-01-28
Used Hours: 31713
Project Name: Bioinorganic Chemistry
Project Shortname: CHEM1351
Discipline Name: Chemistry
The Bioinorganic research group is at the Department of Chemistry, University of Ghana, where we look at DNA mismatch. When DNA replicate there are times the replication in not perfect. This problem leads to some physiological issue. My research group want to find a simple and more effect way of identifying these mismatch. We are use computational modeling where compounds containing metals could be use to identify DNA mismatch.
We using the CHPC recourses, we have the tool and facility we need to compute various reaction path ways to achieve our goal.
We have just started this project about 6 months ago and we are look forward to interesting results soon.
Principal Investigator: Dr Katherine de Villiers
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2020-07-20
Allocation End: 2021-01-28
Used Hours: 382260
Project Name: Investigations of drugable targets relevant to antimalarial action
Project Shortname: CHEM0801
Discipline Name: Chemistry
The Bioinorganic research group (Haem Team) at Stellenbosch University (Dept. Chemistry and Polymer Science) is led by Dr Katherine de Villiers. Our primary research focus is towards understanding mechanism(s) of action of clinical antimalarials so that we are better informed when designing altogether new treatments. The latter is important because of resistance by the malaria parasite. The disease burden caused by malaria is a particular challenge in Africa, and this motivates our research efforts further. We have made use of the CHPC facilities to enable us to investigate drug-target interactions that would otherwise not be possible via experiment. In particular, we have used Materials Studio to investigate the interaction of antimalarials to the surface of crystals of synthetic malaria pigment, and Schrodinger to investigate drug-enzyme interactions.
Principal Investigator: Prof Juliet Pulliam
Institution Name: Stellenbosch University
Active Member Count: 19
Allocation Start: 2020-07-20
Allocation End: 2021-01-28
Used Hours: 67104
Project Name: South African Centre for Epidemiological Modelling and Analysis
Project Shortname: CBBI1106
Discipline Name: Other
SACEMA is a DSI-NRF Centre of Excellence focused on Epidemiological Modelling and Analysis, hosted at Stellenbosch University. We use computational approaches to address questions of public health relevance to South Africa and the African continent. We use the CHPC primarily to run stochastic simulations and for simulation-based validation of novel inference methods.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2020-07-20
Allocation End: 2021-01-28
Used Hours: 1101831
Project Name: CFD Modelling of Concentrated Solar Power Applications
Project Shortname: MECH0873
Discipline Name: Computational Mechanics
Central tower solar power plants are the most promising concentrated solar with research into new receivers and heat transfer fluids and collectors (heliostats) being ongoing world-wide. Researchers at the University of Pretoria's Clean Energy Research group under the leadership of Prof Ken Craig are using the resources at the CHPC to speed up calculations of both heliostat analysis (involving wind loads and fluid-structure interaction) as well as those required for a new point-focus central receiver design being developed. For heliostats, knowledge has been gained in predicting the peak loads that these reflectors will experience during all orientations and wind conditions. Ongoing work is focused on further reducing the cost of these Computational Fluid Dynamics (CFD) hybrid Large Eddy Simulation (LES):Reynolds-Averaged Navier-Stokes models to make them feasible on smaller-scale computers. This project has been ongoing since 2013 with the involvement of CHPC resources since 2016. The project has already delivered three masters students (Dawie Marais, Joshua Wolmarans and Derwalt Erasmus) with Jesse Quick nearing completion. PhD student Pierre Poulain is also nearing the end of this investigation into LES modelling of the atmospheric boundary layer and determining peak loads on solar collectors. For central receivers, work is ongoing to enhance heat transfer. Of specific interest here is the use of jet impingement, especially in the transient mode through either passive or active excitation. This phenomenon of heat transfer enhancement, although conceptually simple, it very hard to model accurately, and here the resources of the CHPC are invaluable, especially as LES is required to model the transient and 3D nature of swirling jet, the focus of the work of Jesse Quick. CHPC resources was also used to investigate the thermal performance solar dish receivers by accurate simulation of heat losses due to dish orientation and wind speed.
Principal Investigator: Prof Nithaya Chetty
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2020-07-20
Allocation End: 2021-02-10
Used Hours: 789744
Project Name: Advanced Computational Resources for members of ASESMA
Project Shortname: MATS1050
Discipline Name: Material Science
Work on two dimensional (2D) materials is now firmly established as an area of excellence at the theoretical and computational solid state physics group of the University of Pretoria. The focus in the past years was mainly on the study of the popular 2D materials such as molybdenum disulphide, graphene and boronitrene. The 2D hexagonal-like transition metal oxides (TMO) materials such as molybdenum dioxide (MoO2) monolayer is also predicted to be thermodynamically stable, however, a detailed study on the structural, electronic and dynamical properties of these new oxide materials is still missing. Therefore, research about these properties is important and could bring them from the laboratory to commercial products. Recently (over the past two years) a 2D bilayer of zeolite has been experimentally synthesized by scientists in the USA. This is an area of promising new research for computational studies, and worth to be explored. We are mainly interested in the use of these 2D materials for catalysis such as CO catalytic oxidation. To achieve these goals, creating complex systems such as introducing defects or adatoms will enhance the properties of the MoO2 and the 2D zeolite model. To ensure that the introduced defects are isolated, the study should be done on a large supercell which is computationally expensive, and could not be done on a local computer. Powerful computers with large and faster CPUs such as CHPC cluster are necessary. Our results provide detailed understanding and important information to the 2D materials experimental and computational community.
Principal Investigator: Dr David Pearton
Institution Name: Oceanographic Research Institute (ORI)
Active Member Count: 4
Allocation Start: 2020-07-20
Allocation End: 2021-01-28
Used Hours: 9337
Project Name: Responses of South African Coral Reefs to Climate Change
Project Shortname: CBBI1072
Discipline Name: Environmental Sciences
Coral reefs are critical ecosystems that provide food, coastal protection and other vital ecosystem services to millions of people in some of the world's most vulnerable nations.
They are also extremely threatened by anthropogenic climate change, under current climate change trajectories we are projected to lose > 90% of corals by 2050.
Marine Protected Areas are a critical tool in protecting these vulnerable ecosystems, but, in order to be effective, they need to protect a high proportion of vulnerable ecosystems and species. The optimal way to ensure this is for various MPAs to form an interconnected network. In order to determine whether the existing and newly promulgated MPAs along the east coast of SA form a resilient network we looked at the genetic population connectivity of two coral species between MPAs along the KZN coast. To do this we used a new technique called RADseq that generates orders of magnitude more data at lower cost than previous methods. The CHPC was used to analyse this huge amount of data and showed that (1) there are cryptic species in the two corals and (2) the pattern of connectivity is driven largely by ecological factors rather than distance and currents. Both of these findings are directly relevant to the management and design of MPAs and conservation strategies.
Principal Investigator: Prof Penny Govender
Institution Name: University of Johannesburg
Active Member Count: 11
Allocation Start: 2020-07-18
Allocation End: 2021-01-28
Used Hours: 1529424
Project Name: Design of MOFs-based sorbent materials for capturing carbon dioxide
Project Shortname: CHEM0797
Discipline Name: Material Science
Environmental and energy problems are important topics globally due to the fast development of urbanization, huge population increases and industrialization. Recently, water pollution is a major issue in developing countries, particularly in regions where people rely on groundwater for domestic and drinking purposes. Almost 40 % of the world's population is facing water shortage. Most countries depend on the low-efficient power generation from the burning fossil fuels as their source of energy. The burning of fossil fuels normally generates a huge amount of CO2, which induces environmental concerns, such as greenhouse effect. As non-renewable natural resources, fossil fuels cannot be sustainable and depleted shortly in the next century owing to their environmental issues and high consumption rate. This has led to the investigation of photocatalysis as a possible solution to the problem. Despite significant concern and substantial efforts, the design of semiconductor photocatalyst materials that is both efficient and robust enough for water/wastewater treatment and energy production is still lacking. Due to the complexity of the experimental process, it is difficult to know the mechanism and origin of the enhanced photocatalytic performance. The first-principles approach is highly desirable in the area of materials science, particularly for understanding both the photocatalysis of nanomaterials, as well as the subsequent physical and chemical properties. Density functional theory (DFT) calculations was used as the method of clarification as it has already proven its superiority in studying the structural stabilities, electronic properties, work functions, charge transfer, and carrier effective mass of several semiconductor photocatalyst materials due to its reduced computational cost in calculating the electron density rather than the wave function.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2020-07-23
Allocation End: 2021-01-28
Used Hours: 14982
Project Name: SANAP CFD
Project Shortname: MECH1196
Discipline Name: Earth Sciences
The sub-Antarctic is one of the windiest regions in the world, with the biotic and abiotic conditions of the sub-Antarctic islands thought to be strongly affected by wind patterns. However, for these isolated terrestrial ecosystems we have a very poor understanding of within-island variation in wind speed and direction, and of how variation in wind patterns impact biotic communities. As a result, despite clear recent changes in broad-scale wind patterns in the sub-Antarctic, we have little quantitative basis for predicting the impacts that climate change-related shifts in wind speed and direction have on the biota of these islands. Computational Fluid Dynamic (CFD) models provide a robust methodology for estimating wind patterns, and have previously proved successful in understanding fine-scale air flow patterns in this system. However, the application of CFD to island-scale wind simulation is still an under-utilized approach despite recent relevant advances. Therefore, in this project we developed, and then applied, an island-scale CFD model to simulate wind flow patterns across an entire island, testing the potential for this approach to provide accurate insight into spatial variation of wind patterns across the island. The resources at the CHPC helped in running large CFD models of the wind patterns on the island for all the predominant wind directions as obtained from the ongoing experimental wind mast study. The CFD results are of interest to botanists and those studying bird behaviour and for other ecological studies. Another spin-off is to investigate the use of wind power on parts of the island not inhabited by birds in order to replace the current diesel power generation.
Principal Investigator: Prof Eric van Steen
Institution Name: University of Cape Town
Active Member Count: 7
Allocation Start: 2020-07-23
Allocation End: 2021-01-28
Used Hours: 1043849
Project Name: Lateral interactions on surfaces
Project Shortname: CHEM0780
Discipline Name: Chemistry
The modelling group in the Catalysis Institute at UCT headed by the SARChI in Reaction Engineering, Prof. E. van Steen, studies catalytic reactions of interest to the South African chemical industry using molecular modelling. The understanding of catalytic reactions is key to improve these processes making them environmentally more benign. Some reactions are currently out of reach and the modelling studies we perform gives us insight under which conditions these reactions may become feasible. For instance, the hydrogenation of CO2 is a sought-after reaction to reduce CO2 emission to the atmosphere. Many researchers focus on using catalysts for CO hydrogenation for this type of research. Insight into these reactions can be obtained from molecular modelling using the CHPC facility; we have shown that CO2 hydrogenation is fundamentally different from CO hydrogenation and different type of catalyst is required for this reaction.
Furthermore, we create unique models, based on experimental data, to model industrial catalysts. These modes are within reach of computational tools as supplied by CHPC nowadays. For instance, we model metals on a support, by putting a support-like structure on a metal. The importance here is the understanding of different components in the catalyst and how they affect the reactivity of catalysts. We have found through calculation that oxygen removal is the important step in CO hydrogenation over cobalt-based catalysts and noble metals, but also promoters such as manganese assist in the removal for oxygen from the catalytically active surface.
Principal Investigator: Dr Benjamin Lamptey
Institution Name: University of Ghana
Active Member Count: 11
Allocation Start: 2020-07-23
Allocation End: 2021-01-28
Used Hours: 41011
Project Name: Weather, Climate and Water
Project Shortname: ERTH0955
Discipline Name: Earth Sciences
The group consists of scientists from universities, operational centres like Ghana Meteorological Agency and a Regional Climate Centres like AGRHYMET and the Pan African Regional Climate Centre, African Centre of Meteorological Applications for Development (ACMAD). The CHPC system is being used for weather, climate, ocean modeling in parallel with sensitivity tests to obtain optimal model configurations as well as appropriate specifications for the relevant infrastructure.
There are plans to conduct more experiments especially in high resolution modelling (e. g. testing the suitability of model characteristics for a given purpose), coupled atmosphere-ocean modeling and many more. More work on the marine environment is also envisaged. This work will involve plastics as well as impact of climate change on coastal regions. Catastrophic Risk Modeling is another area that may be explored
Principal Investigator: Dr Phumlani Mdluli
Institution Name: Mintek
Active Member Count: 2
Allocation Start: 2020-07-27
Allocation End: 2021-02-10
Used Hours: 2433
Project Name: Gold SERS nanoprobes as sensors for detection of trace levels of acidic pharmaceuticals in water
Project Shortname: MATS0891
Discipline Name: Material Science
Our research group falls under the environmental chemistry research focuss area at the department of chemistry, Durban University of Technology
Our research is mainly focusing on developing nanoprobes for detecting water pollutants in waste water. Firstly, we have to synthesize nanomaterial that are composed of gold and other heavy metals. These nanoprobes are fabricated with organic compounds which serve as linkers to create chemical reactions with the targeted pollutants. The reaction that is formed between the pollutants and nanoprobes create a chemical response which is normally in the form of visual colour change which can be observed with our naked eye or using the assistance of spectrophotometers. We are using molecular modelling to understand the interaction of these organic compounds with the surface of the nanoprobe.
So far we have managed to demonstrate the selective adsorption on nanomaterials on the surface on gold and other nanomaterial. This adsorption mechanism is very critical during the development of colorimetric sensors for detecting pollutants in environmental samples. Lastly, this work would have not been successful without the current support we are getting from CHPC. The CHPC teams have been very supportive by allowing us to use different codes.
Principal Investigator: Dr Mohammad Moghimi Ardekani
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-07-27
Allocation End: 2021-01-28
Used Hours: 410308
Project Name: R&D in Solar Energy in particular Concentrating Solar Power Research
Project Shortname: MECH1137
Discipline Name: Computational Mechanics
This is one of the most suceesful programs in my team which led to several collaborations between University of pretoria and collaborators worlwide in particular in UK. As this topic is one of the most timly topic in our fight with golbal warming crisis and providing green energy resources towrad global net-zero carbon targets by 2050
Principal Investigator: Prof Lyudmila Moskaleva
Institution Name: University of the Free State
Active Member Count: 5
Allocation Start: 2020-07-25
Allocation End: 2021-01-28
Used Hours: 108492
Project Name: Understanding surface reactivity of solids using DFT simulations
Project Shortname: CHEM1294
Discipline Name: Chemistry
We investigate surface reactivity of solids at the atomic level using first-principles quantum-chemical methods, molecular dynamics, statistical theory, microkinetic modelling and thermodynamics. Quantum chemical methods, in particular, those based on density functional theory (DFT), are becoming increasingly popular and powerful. They can be used successfully to achieve a mechanistic understanding at the microscopic level, which is needed to optimize functional materials (such as catalysts, electrocatalysts, semiconductors, optoelectronic materials) with respect to their target properties. We would like to mention two of our recent successful projects. One of them is a computational study on the properties of a hybrid 2D system which comprises in-plane graphene and hexagonal boron nitride (h-BN) components. We have investigated the influence of graphene or h-BN domain size on the atomic geometries, electronic properties and thermodynamic properties of prototypical graphene/h-BN hybrid systems by first-principles calculations. We have demonstrated that the band gap and the thermodynamic properties can be tuned by varying the graphene or h-BN domain size. The results of this study have been very recently published in FlatChem and in C. Another successful project relates to the chemistry of nanoporous gold (np-Au), a versatile material possessing interesting mechanical, optical, and catalytic properties. Our study is focused on the remarkable low-temperature catalytic activity of np-Au and its high selectivity toward partial oxidation reactions. Oxidation of methanol has been studied as a model that could be extended to higher alcohols. Our theoretical study provides a detailed mechanistic picture of a complex reaction energy network on the stepped Au(321) surface from methanol co-adsorbed with O2 all the way to methyl formate partial oxidation product. The mechanism includes over 20 elementary steps. Each elementary step has been characterized by a transition state structure and two minima of the reactants and products. Furthermore, we have studied the effect of Ag and Cu impurities (commonly present in np-Au) on the reaction energies and barrier heights. A manuscript describing this work is currently in preparation. Additionally, in collaboration with the experimental group of Prof Risse (FU Berlin) we applied DFT-based calculation to successfully interpret the observed vibrational spectra of methanol adsorbed at stepped Au surfaces. A relevant publication is currently in preparation.
Principal Investigator: Dr Mervlyn Moodley
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2020-07-27
Allocation End: 2021-01-27
Used Hours: 9187
Project Name: Computational studies of corrosion in transformers
Project Shortname: MATS1120
Discipline Name: Physics
The Computational Studies of Corrosion in Transformers group based at University of Kwazulu-Natal is set to understand the corrosion mechanisms involved in the failure of transformers. The failures of transformers have been linked to the interaction of copper sulphide and copper windings and due to the interaction of silver sulphide on silver surfaces. The copper sulphide is a product of copper particles that react with the corrosive sulphur within the transformer oil. This copper sulphide thereafter deposits on the vacant sites of the copper windings. Density functional theory (DFT) techniques are used in various fields of study and have proved most effective in handling interactions between molecules and surfaces. In this research the DFT techniques are used to understand the interaction of copper sulphide on copper surfaces to obtain energetic, electronic and thermodynamic properties of the system. The interactions of sulphur containing molecules on silver surfaces were also investigated. The understanding of the failures on a computational level would help in creating a model to prevent further failures and to track current failures caused by corrosion. The failures of transformers have also been found to affect both financial and economic sectors due to the high cost in repairing or replacing these failed transformers. This research relies heavily on CHPC resources due to the extensive computational methods needed to understand this complex system. The CHPC provides the Materials Studio Software and a connection to the Lengau Cluster which increases the accuracy of the results and reduces computational time. This project has so far obtained results of the copper sulphide interaction with the copper surface. Upon investigation it was found that more research is required to fully understand the method of corrosion and the interaction of additives in the transformer oil. The CHPC resources are also needed to compute a remedial process to prevent further transformer failures.
Principal Investigator: Prof Linky Makgahlela
Institution Name: Agricultural Research Council
Active Member Count: 6
Allocation Start: 2020-07-27
Allocation End: 2021-01-28
Used Hours: 24637
Project Name: Beef and Dairy Genomics
Project Shortname: CBBI1138
Discipline Name: Bioinformatics
Beef and Dairy genomics team forms part of the Animal breeding and Genetics unit led by Professor ML Makgahlela at the Agricultural Research Council – Animal Production. It comprises of both researchers and post graduate students. The team works along the two large consortiums in South Africa; the Beef Genomics Program (BGP) and the Dairy Genomics Program (DGP) and works towards achieving the goal of generating large genomic data for the South African beef and dairy industry in order to fully implement genomic selection in the future and have the two industries compete at a global level. The work done by the team includes working with commercial and small holder beef and dairy breeders towards collecting a large number of samples for processing, curating and analysing generated genomic data. Thus far, the projects carried out by the team have developed strategies that can be used by breed society's. In addition to the strategies are the research findings that have revealed the genomic structure of the South African beef breeds and underlying genetic factors that are associated with adaptation that warrant the need for conserving these important genetics for future use in times of possible drought. The project has further contributed to capacity building by training experts especially in the field of bioinformatics.
Principal Investigator: Ms Robyn Jacob
Institution Name: SA Sugercane Research Institute
Active Member Count: 2
Allocation Start: 2020-07-28
Allocation End: 2021-01-28
Used Hours: 17396
Project Name: Saccharum Genomics
Project Shortname: CBBI0956
Discipline Name: Bioinformatics
The South African Sugarcane Research Institute (SASRI) is an agricultural research institute located in KwaZulu-Natal. Among pest and disease pressures affecting the South African sugarcane industry, Eldana saccharina (a lepidopteran stem borer) is inflicting the worst damages. We are utilising the compute resources at the CHPC to annotate the transcriptome of eldana-challenged sugarcane in two cultivars which differ in their susceptibility to the borer. This work will complement our previous RNA-seq study in an attempt to differentiate the compatible from the incompatible defense response. The knowledge gained will be used to devise improved breeding methods to deliver more resistant sugarcane varieties to the South African sugarcane industry.
Principal Investigator: Prof Martin van Eldik
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2020-07-28
Allocation End: 2021-01-28
Used Hours: 96492
Project Name: Thermal-Fluid modelling
Project Shortname: MECH1247
Discipline Name: Computational Mechanics
The Thermal-Fluid Modelling research group, is situated in the Faculty of Engineering at the North-West University.
Students using the CHPC currently consists of 1 Masters student and 1 PhD. All students are using Star-CCM+ for their studies.
The research group produced one masters student in 2020 that investigated the thermal fluid modelling of a titanium helically coiled fluted tube. The current Masters student is conducting an aeroacoustic analysis of a glider plane component and how to identify the source and replicate it.
The PhD student is investigating the CFD modelling of a sinter mixing drum to improve the production throughput.
The CHPC makes it possible for the students to be able to complete their work on time, which otherwise would not have been able to.
Principal Investigator: Dr Malebogo Ngoepe
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2020-07-29
Allocation End: 2021-01-25
Used Hours: 17667
Project Name: PROTEA
Project Shortname: MECH1194
Discipline Name: Computational Mechanics
The CFD modelling team within the PROTEA group is focused on developing computational fluid dynamics and related models for studying congenital heart disease.
Improved understanding of disease dynamics, particularly in the African context, can assist with the development of more appropriate solutions.
Our work makes use of reconstructed images taken from patient scans in order to understand flow patterns in specific disease cases. Thus far, we have focused on coarctation of the aorta. Once the images are obtained, comptuational fluid dynamics simulations are run for the cases.
Currently, we are making use of echocardiography to obtain improved boundary conditions. We are also using agent based models to develop growth models that can be coupled to our CFD models.
Principal Investigator: Prof Mwadham Kabanda
Institution Name: University of Venda
Active Member Count: 2
Allocation Start: 2020-07-29
Allocation End: 2021-01-25
Used Hours: 269967
Project Name: Reaction mechanism for atmospheric relevant molecules
Project Shortname: CHEM1161
Discipline Name: Chemistry
This research group consists of two members, the group leader is Prof Kabanda MM, a specialist in the utilisation of theoretical quantum chemical methods to obtain molecular properties; a PhD student, Ms Otukile KP. The research is focused on investigating the kinetics and mechanistic features of selected radical species that are found abundantly in the atmosphere. the outcome of the results would allow an understanding on various reactions taking place in the atmosphere and influencing the purification of the atmosphere.
The work is entirely computational modeling based and for this reason, it requires a lot of computational power. It is for this reason that we rely largely on HPC to provide us with computational power. Publications have already started coming out of the project and for that reason we consider that the project is going well
Principal Investigator: Dr Holliness Nose
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 1
Allocation Start: 2020-08-03
Allocation End: 2021-01-30
Used Hours: 55821
Project Name: Inorganic Computational Chemistry
Project Shortname: CHEM1003
Discipline Name: Chemistry
Our current project involves preparation of photosensitizers for water purification. Water treatment strategies commonly adopted include chlorination, distillation, UV-radiation, boiling and reverse osmosis. While these methods have proved to be effective in water decontamination, they have not been completely efficient in treatment of microbe polluted water. This is attributed to emergence of anti-microbial resistant (AMR) microorganisms such as Methicillin-resistant Staphylococcus aureus and Amphotericin-resistant Candida albican. AMR pathogens find their way into drinking water, causing waterborne diseases. Photodynamic antimicrobial therapy (PACT) provides an alternative and viable method of water disinfections, especially in addressing the anti-microbial resistant bacteria. PACT makes use of a photosensitizer, which when localized in microorganisms can be activated by irradiating it with light of appropriate wavelength to generate a reactive oxygen species (ROS). This ROS is able to destroy or affect biological structures such as cell wall material, nucleic acids, peptides and lipids therefore leading to cytotoxicity. Therefore, this method allows the photosensitizer to bind to the bacterial or fungal cell wall, inhibiting cell growth, with no possibility of recovery or development of resistance against it. My group intends to design and develop the photosensitizers computationally, followed by synthesis of the metal complexes and finally carry-out biological assays to examine their cytotoxicity. This project therefore relies on CHPC heavily as we need to design the photosensitizers theoretically before we go to the laboratory to synthesize them and test their biological activities. This project began on June 1st 2019 and and is currently ongoing. But without the CHPC facilities, we are unable to do this type of research. The project is proceeding on well.
Principal Investigator: Dr Krishna Govender
Institution Name: University of Johannesburg
Active Member Count: 5
Allocation Start: 2020-08-03
Allocation End: 2021-01-30
Used Hours: 184446
Project Name: Computational approaches to design novel anticancer agents
Project Shortname: CHEM0792
Discipline Name: Chemistry
The work conducted focuses on benchmarking with a small component of the allocation devoted to molecular dynamics and quantum mechanical simulations.
The research would not be possible where it not for the HPC facilities provided by the CHPC.
Principal Investigator: Mr Ernest Opoku
Institution Name: Nesvard Institute of Molecular Sciences, Ghana
Active Member Count: 7
Allocation Start: 2020-08-04
Allocation End: 2021-01-31
Used Hours: 301732
Project Name: Molecular Quantum Chemistry
Project Shortname: CHEM1352
Discipline Name: Chemistry
The Molecular Quantum Chemistry Research Group is affiliated with the Department of Basic and Computational Sciences, Koachie Health Systems, Accra, Ghana.
We are a team of young and gifted conscious Africans, who are voluntarily using our skills and expertise to promote Kaochie Health Systems (KHS) through research to help elevate the reputation of Ghana and Africa on the map of scientific research. Our motivation for what we do is that "we want to be part of the patriotic Africans to build Africa for Africans".
Modern chemical and pharmaceutical industries require reactions that are energy efficient and selective towards formation of various relevant compounds. Thus, synthetic designs require the ability to carry out multiple chemical transformations in fewer steps to achieve higher synthetic efficiency. To achieve this, a thorough understanding of the intrinsic steps involved in such chemical transformations and the role of catalysts are crucial. Such information is efficiently obtained using high-performance computers to do extremely demanding calculations. Africa needs scientists with high performance computing expertise coupled with multidisciplinary scientific background to provide a complement to present and future African pharmaceutical and chemical industries. We hope that our objectives will be interesting to young African scientists to voluntarily come on board with their expertise for Africa's overall progress. Multiple projects are currenting ongoing using the CHPC computational resources. Manuscripts are under review and many more are in preparation.
Principal Investigator: Prof Shazrene Mohamed
Institution Name: South African Astronomical Observatory
Active Member Count: 2
Allocation Start: 2020-08-04
Allocation End: 2021-01-31
Used Hours: 78196
Project Name: 3D rad-hydro simulations of the outflows of evolved stars
Project Shortname: ASTR0880
Discipline Name: Astrophysics
The computational stellar astrophysics group (PI. S. Mohamed) is currently based at the South African Astronomical Observatory and the University of Cape Town. The research uses supercomputers, powerful computational machines at the CHPC, to simulate the complex physics involved in the interactions of stars in the final phases of evolution. The interactions include exchanges with a nearby companion star or planet that can lead to the formation of spirals, disks, jets and even violent stellar explosions. By comparing the models with observations from powerful telescopes, these simulations help us understand how solar systems evolve and ultimately, the fate of our own star, the sun.
Principal Investigator: Dr Ndanduleni Lethole
Institution Name: University of Fort Hare
Active Member Count: 3
Allocation Start: 2020-08-04
Allocation End: 2021-01-31
Used Hours: 25132
Project Name: Computational Studies of MxPt1-x (M; Mn, Fe, Co and Ni) alloys for magnetic data storage and biomedical applications.
Project Shortname: MATS1309
Discipline Name: Material Science
The research group is located under the department of Physics, University of Fort Hare. The group started in February 2020 and is composed of the Principal Investigator and one student. Currently, the group entirely depends on the Centre of High Performance Computing (CHPC) facility as it uses Material Studio modelling and simulation environment accessed via the CHPC as its only simulation package. The group aims to grow to at least three students in the year 2021 and also acquire a license for the Vienna ab initio simulation package.
The group is currently undertaking computer simulation studies on the M-Pt (M: Mn, Fe, Co and Ni) alloys for potential application as advanced performance permanent magnets, new storage of ultra-high-density magnetic data and in biomedical applications. The current study is significant since there has been a remarkable increase in data storage density of magnetic disk drives in the past few decades which is projected to be restricted by the "super-paramagnetic limit" (loss of data due to activated fluctuations of magnetization) in the near future. The super-paramagnetic limit can be overcome by designing new magnetic storage materials which are energetical, electronical, magnetical, mechanical and dynamical stable. Thanks to modern simulation packages and sufficient computing resources available at the CHPC, augmentation of various properties of the crystal structure is possible by theoretically calculating the forces acting on the nuclei. Simulations are set up on the local desktop computer using the BIOVIA Materials Studio modelling and simulation environment and submitted to the CHPC computing resources using the CASTEP code. On the negative note, the progress of the project has been disadvantaged by the ongoing lockdown in South Africa. However, few results have been attained. These include; heats of formation, elastic constants, the density of states and band structure on the MnPt alloy.
Principal Investigator: Dr Fabio Mathias Correa
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2020-08-04
Allocation End: 2021-01-31
Used Hours: 2436
Project Name: Evaluation of South African students' in math tests
Project Shortname: CBBI1312
Discipline Name: Other
The project was developed in partnership between Rhodes University and Mars Center for Cocoa Science. The objective was to identify gene expression in plants formed from leaves and to compare with abnormal plants and plants from seeds. The results will make it possible to produce cocoa clones from leaves and will accelerate the delivery of plants to cocoa farms.
Principal Investigator: Prof Jeanet Conradie
Institution Name: University of the Free State
Active Member Count: 5
Allocation Start: 2020-08-05
Allocation End: 2021-02-01
Used Hours: 2809465
Project Name: Computational chemistry of transition metal complexes
Project Shortname: CHEM0947
Discipline Name: Chemistry
This project is concerned with the computational chemistry of transition metal complexes, with special focus on the application of computational chemistry in determining the structure and energy of transition metal complexes, transition states and reaction-intermediates. This is reflected in the outputs of my research group during the period of report. The outputs gave a better understanding of experimental observation and of the factors influencing the reactivity of metal complexes, in order to streamline them for use in different applications, for example in catalysis or energy sources (batteries and solar cells), nonlinear optics, medical applications (eg HIV and anti-leukemia) and antimicrobial activity (anti- bacterial and anti-fungal).
Principal Investigator: Prof Nelishia Pillay
Institution Name: University of Pretoria
Active Member Count: 9
Allocation Start: 2020-08-05
Allocation End: 2021-02-01
Used Hours: 441387
Project Name: Nature Inspired Computing Optimization
Project Shortname: CSCI0806
Discipline Name: Computer Science
The NICOG (Nature Inspired Computing Optimization Group), based at the University of Pretoria, employs machine learning techniques, taking an analogy from nature, to solve real world problems to attain the sustainable development goals defined by the United Nations. This research is solving problems in the health sector, e.g. disease prediction, agriculture, e.g. disease and pest prediction and industry, e.g. logistics, scheduling and classification problems. As we move into the fourth industrial revolution, machine learning is playing a major role in solving these problems. The algorithms used to solve these problems are computationally expensive and hence high performance computing is needed for the implementation of the algorithms. We are at point where we need to make these approaches easily accessible to non-experts. Hence, one of the current foci of NICOG is the automated design of machine learning techniques to produce off-the-shelf tools for non-experts. Such automated design, which is essentially an optimization problem, is also computationally expensive and thus also requires high performance computing.
Principal Investigator: Dr Mary-Jane Bopape
Institution Name: South African Weather Service
Active Member Count: 22
Allocation Start: 2020-08-05
Allocation End: 2021-02-01
Used Hours: 1095351
Project Name: Very Short Range Forecasting
Project Shortname: ERTH1022
Discipline Name: Earth Sciences
Numerical weather and climate activities have historically been limited in Africa in general due the expense associated with supercomputer needed to run these models. In collaboration with the Centre for High Performance Computing, and other HPC hosts in SADC, weather scientists have been working together to learn more about the Weather Research and Forecasting (WRF) model. The model has since been used to conduct sensitivity tests over six SADC countries, and this is resulting in publications in international journals.
Principal Investigator: Prof Peter Teske
Institution Name: University of Johannesburg
Active Member Count: 3
Allocation Start: 2020-08-06
Allocation End: 2021-02-02
Used Hours: 155470
Project Name: Coevolution of mangroves and mangrove-associated crabs
Project Shortname: CBBI0979
Discipline Name: Bioinformatics
Who?
Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg
What?
Analysis of DNA and RNA data from a large portion of animal genomes. Noteworthy developments in 2020 was the publication of the first scientific paper using environmental DNA (eDNA) and transcriptomics (gene expression analysis).
Why?
To improve the management of commercially exploited species, optimise conservation efforts aimed at saving endangered species from extinction, and understand evolutionary relationships in nature.
How?
Genomic data sets generated using massive parallel sequencing technology results can only be assembled by means of supercomputers. Using CHPC, we are able to assemble a huge number of short reads into a meaningful sequence that reflects their order in the animal genome.
Progress?
CHPC and the valuable expertise it has gathered in one place has allowed our small lab to continue punching well above its weight. Despite the challenges related to the lockdown, 2020 was the most productive year in the history of our research group in terms of scientific paper published or submitted. 2021 will be the year when we will publish our most ambitious studies in high-ranking journals, none of which would be possible without the CHPC.
Principal Investigator: Prof Kenneth Ozoemena
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2020-08-06
Allocation End: 2021-02-02
Used Hours: 1708
Project Name: Materials Electrochemistry and Energy Technologies
Project Shortname: MATS1353
Discipline Name: Chemistry
We are using the CHPC to conduct DFT calculations. DFT calculations have been helpful in assisting us to understand the underlying mechanisms of electrocatalysis of some important analytes. For example, it has assisted to understand that the palladium/stannic oxide interfacial chemistry promotes hydrogen oxidation reactions. This was published in ChemElectroChem 2020.
Principal Investigator: Prof Thuto Mosuang
Institution Name: University of Limpopo
Active Member Count: 12
Allocation Start: 2020-08-11
Allocation End: 2021-02-07
Used Hours: 1289
Project Name: Computational studies of various ultra-hard materials
Project Shortname: MATS0875
Discipline Name: Material Science
This is a sensors and energy materials group at the Department of Physics, University of Limpopo. The group has two Doctoral, two Masters students, and two Honours students. Computationally the research projects investigate nanomaterials like copper selenide, gallium nitride, gallium arsenide graphene oxide, and boron nitride. Specifically, electronic, structural, thermodynamic properties are investigated to enhance semi-conductivity. These properties are then mapped with experimental properties for possible gas sensing and energy materials. DL_POLY software through the CHPC is being utilised in the structural, dynamical, and thermodynamic properties. The exciting code also through the CHPC is being utilised in the electronic and excited properties of the materials.
Principal Investigator: Prof Thulani Makhalanyane
Institution Name: Stellenbosch University
Active Member Count: 10
Allocation Start: 2020-08-11
Allocation End: 2021-02-07
Used Hours: 349045
Project Name: Metagenomics of extreme environments
Project Shortname: CBBI1023
Discipline Name: Bioinformatics
Although 2020 was an extremely challenging year, we were able to effectively use the CHPC resources to generate key outputs. Students at MSc and PhD level were able to submit their thesis and will graduate in April 2021. One of these students (Ms. Mancha Mabaso) will obtain her MSc with Distinction. A doctoral student (Dr Taru Badza) graduated in 2020. Two PhD students managed to publish their work in respected international journals (see below) and have inserted acknowledgements to the CHPC.
We have also acquired several new datasets which are currently being processed using CHPC resources. These will be subject to several new students and lead to new projects linked to the program.
1. Phoma, S.B. and T.P. Makhalanyane. Depth-dependent variables shape community structure and functionality in the Prince Edward Islands. Microbial Ecology. https://doi.org/10.1007/s00248-020-01589-4 [Journal Impact factor = 3.862]
2. Kabwe, M.K. Vikram, S., Mulaudzi, K., Jansson, J.K. and T.P. Makhalanyane#. The gut mycobiota of rural and urban individuals is shaped by geography. BMC Microbiology. https://doi.org/10.1186/s12866-020-01907-3 [Journal Impact factor = 3.287].
3. Barnard, S., Van Goethem, M.W., de Scally, S.Z., Cowan, D.A., Jansen van Rensburg, P., Claassens, S. and T.P. Makhalanyane. Increased temperatures alter viable microbial biomass, ammonia oxidizing bacteria and extracellular enzymatic activities in Antarctic soils. FEMS Microbiology Ecology https://doi.org/10.1093/femsec/fiaa065 [Journal Impact factor = 4.09]
4. Bezuidt, O.K., Lebre, P.H., Pierneef, R., León-Sobrino, C., Adriaenssens, E.M., Cowan, D.A., Van de Peer, Y., and T.P. Makhalanyane. 2020. Phages actively challenge niche communities in the Antarctic soils. mSystems DOI: 10.1128/mSystems.00234-20 [Journal Impact factor = 6.519].
Principal Investigator: Prof Rebecca Garland
Institution Name: University of Pretoria
Active Member Count: 15
Allocation Start: 2020-08-07
Allocation End: 2021-02-03
Used Hours: 1050457
Project Name: Development of the first African-based earth system model VRESM and its projections of future climate change over Africa
Project Shortname: ERTH0859
Discipline Name: Earth Sciences
The first African-based Earth System Model (ESM) is under development at the Council for Scientific and Industrial Research (CSIR) in South Africa, through collaboration with the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Australia and South Africa's Centre for High Performance Computing (CHPC). The new ESM is unique in the sense that it is being developed in Africa and through the lens of African and Southern Hemisphere climate processes. That is, the reliable simulation of climate issues critical to Africa, such as the occurrence of drought in in response to El Niño events, wide-spread flooding over Mozambique due to landfalling tropical cyclones and increased occurrences of heat-waves under global warming are key issues in the development of the new model. The model development process is also focussed on the Southern Ocean's role in regulating southern African climate, as well as the global climate through the absorption of carbon dioxide in the ocean. The development and application of an Earth System Model is a computationally extensive endeavour, and was impossible to undertake in South Africa before the Lengau cluster of the CHPC became available in 2018. The CSIR-CHPC partnership towards development of the new model has in 2018 led to the most detailed set of projections of future climate change over southern Africa obtained to date. These simulations have provided new insight into the plausible impacts of climate change in South Africa, including how the frequencies of droughts, heat-waves and landfalling tropical cyclones may change over the next few decades. These projections were key in informing South Africa's Third National Communication on Climate Change, which was published in 2018 under the science leadership of the CSIR. Moreover, the research papers based on the projections have directly informed the Special Report on Global Warming of 1.5 ºC of the Intergovernmental Panel on Climate Change (IPCC).
Principal Investigator: Prof Daniel Joubert
Institution Name: University of the Witwatersrand
Active Member Count: 20
Allocation Start: 2020-08-11
Allocation End: 2021-02-07
Used Hours: 3046295
Project Name: Energy Materials: Numerical explorations
Project Shortname: MATS0800
Discipline Name: Physics
Imagine designing a material atom by atom. Imagine analysing the properties of tomorrow's novel materials before they exist. Computational materials science plays an important role at every of level of the design and engineering of new materials. The rapid advances in computer processing power and memory has given virtual, fundamental, materials design a boost. The first problem faced in designing a virtual material, a material that has not yet been made, is to find the stable configurations in which the atoms in the mix will settle into. The designer must find the configuration of electrons and nuclei, the building blocks of atoms, which result from the interactions among a number of particles that, even for a small piece of material, exceeds the number of particles of sand on all the beaches in the world. This daunting task has a simple solution. Instead of finding the configuration of the real material, the problem is solved for a fictitious material where the constituent particles do not interact. All that is necessary is to find the particle density distribution of the fictitious material, which by design, is the same as that of the real material. A Noble prize was awarded for this idea to the chemists Walter Kohn and John Pople in 1998.
A group of postgraduate students at the University of the Witwatersrand use the computer power at the national Centre for High Performance Computing to conduct virtual experiments on existing and novel materials to examine their potential as energy harvesters. They examine the potential of a selection of materials that can be used as cheap components in solar cells, materials that can generate electricity from waste heat and materials that can be used to split water molecules to extract hydrogen for energy production.
Principal Investigator: Prof Mario Santos
Institution Name: University of Western Cape
Active Member Count: 16
Allocation Start: 2020-08-11
Allocation End: 2021-02-07
Used Hours: 2582477
Project Name: Cosmology with Radio Telescopes
Project Shortname: ASTR0945
Discipline Name: Astrophysics
The Centre for Radio Cosmology (CRC) at UWC aims to fully explore the use of the next generation of radio telescopes for measurements in cosmology, in particular with MeerKAT and SKA. CRC staff is closely involved in the South African and international SKA projects. About 10 postdoctoral researchers and 10 PhD/MSc students are doing their research within the CRC. Our work at the CHPC is mostly focused on running simulations of signals we expect to observe with MeerKAT/SKA and test how well radio telescopes can constrain certain cosmological models. This is a crucial component in the process to use these telescopes for cosmology since we need to understand the signals we are observing. The project include simulations of the hydrogen emission from the early universe, simulations of the contaminants, simulations of the telescope itself and analysis of the constraining power of such telescopes on cosmological models.
Principal Investigator: Mr Jean Pitot
Institution Name: University of KwaZulu-Natal
Active Member Count: 1
Allocation Start: 2020-08-12
Allocation End: 2021-02-08
Used Hours: 2864
Project Name: SAFFIRE Programme
Project Shortname: MECH1121
Discipline Name: Computational Mechanics
The University of KwaZulu-Natal's Aerospace Systems Research Group (ASReG) is at the forefront of rocket propulsion research in academia, both in South Africa and Africa as a whole. Located at the University's Discipline of Mechanical Engineering, ASReG primarily conducts research in the areas of liquid and hybrid rocket propulsion, as well sounding rocket development. The SAFFIRE Programme aims to develop South Africa's first fully-integrated liquid rocket engine, which is being designed for use in a small satellite launch vehicle. The long-term intention of the programme is for the engine to enable the indigenous development of a South African space launch capability. To meet its developmental goals, the programme requires the simulation of complex computational models to predict the fluid dynamic, thermochemical and structural performance of various engine components. These simulations are typically very computationally-expensive, and require extensive computational resources to run within a reasonable time frame. The CHPC offers the only realistic means of obtaining access to such resources. The programme is progressing well, and 2021 has seen the intake of numerous new postgraduate and undergraduate students. In total, 20 postgraduate students are currently involved in ASReG's cutting-edge projects.
Principal Investigator: Prof Paulette Bloomer
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2020-08-14
Allocation End: 2021-02-10
Used Hours: 54820
Project Name: Molecular Ecology and Evolution Programme
Project Shortname: CBBI1030
Discipline Name: Bioinformatics
The Molecular Ecology and Evolution Programme (MEEP) is a research group in the Division of Genetics, Department of Biochemistry, Genetics and Microbiology at the University of Pretoria. We investigate the evolutionary history and current genetic diversity of many vertebrate species (marine and terrestrial), using genetics and genomics tools, and try to link the patterns we see with ecological and human-mediated events. We currently have two projects (Cape buffalo and bowhead whales) that make use of the CHPC resources, with additional projects in the pipeline.
Genomics of Cape Buffalo is a hot topic and is of interest to the general public and wildlife ranchers in particular. Cape buffalo are bred on private game ranchers for a one or a few economically important traits, such as horn length and body size. The effects of this artificial selection, as well as breeding South African buffalo with East African buffalo, is unknown. We can use genomics to evaluate the risks and benefits of these practices for the short and long term (evolutionary) conservation prospects of the species
The genetic work on the bowhead whale uses empirical and simulation data to investigate the effects that different Nearctic human cultures exploiting the whale had on the abundance of the population. This means that genetic data may have more resolution than previously thought and is sufficient to detect subtle changes in population size in relation to exploitation and climate change. This is of great importance as there are many applications. We believe that the work will have sufficient impact to be of interest to the general public in South Africa and internationally.
The development of a new molecular clock calibration method for tropical reef species makes use of simulations for validation. This calibration enables genetic time to be related to chronological time. This method may then be applied to empirical data to identify driving factors for increases in population size of reef dependent species in the tropics.
Principal Investigator: Dr Sarah Blyth
Institution Name: University of Cape Town
Active Member Count: 7
Allocation Start: 2020-08-14
Allocation End: 2021-02-10
Used Hours: 34026
Project Name: LADUMA: Looking At the Distant Universe with the MeerKAT Array
Project Shortname: ASTR1354
Discipline Name: Astrophysics
The LADUMA (Looking At the Distant Universe with the MeerKAT Array) survey is one of the approved Large Survey Projects to be observed on the MeerKAT radio telescope. The team is co-led by Sarah Blyth (University of Cape Town), Andrew Baker (Rutgers University) and Benne Holwerda (University of Louisville) and comprises more than 80 South African and international scientists. The aim of the survey is to observe the neutral hydrogen gas in galaxies over cosmic time to understand how galaxies have evolved since the universe was only one-third of its current age. LADUMA will be the deepest survey of neutral hydrogen emission to date and will enable direct detections of neutral hydrogen well beyond the local universe for the first time. The survey will observe the sky for thousands of hours, generating an enormous radio dataset that will need to be calibrated and turned into 3D data cubes (2D spatial images X 1D frequency information). Achieving this goal will require powerful computers that can process the data in a reasonable time-frame. The CHPC computers are excellent for the kinds of processing required for LADUMA, and the survey team is using its early data and the CHPC computers to test calibration and imaging software and determine the ideal strategy for processing future, much larger datasets. This work is vital to the success of the survey overall and is progressing well, en route to a first science data release during 2021.
Principal Investigator: Prof Oleg Smirnov
Institution Name: Rhodes University
Active Member Count: 7
Allocation Start: 2020-08-12
Allocation End: 2021-02-08
Used Hours: 11224
Project Name: MeerKAT Imaging
Project Shortname: ASTR0967
Discipline Name: Astrophysics
The Radio Astronomy Research Group (RARG) at SARAO conducts research into next generation algorithms for radio interferometry. With the massive data rates of new telescopes such as MeerKAT, and the upcoming SKA, highly parallel and distributed implementations are such algorithms are crucial. We are using the CHPC as a testbed for such algorithms, beginning to process MeerKAT data at scale.
Principal Investigator: Dr Michelle Gordon
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2020-08-18
Allocation End: 2021-02-14
Used Hours: 135008
Project Name: Structural Implications of Mutations in HIV-1
Project Shortname: CBBI0928
Discipline Name: Bioinformatics
Our research group is based at the Nelson R Mandela Medical School at the University of KwaZulu-Natal and focusses on the effects of mutations that cause antiretroviral drug resistance on the structure of HIV-1 proteins. The drugs that patients take as part of their treatment against HIV-1 can stop working because the virus is always changing (mutating). We are looking at how these mutations also change the structure of the virus. To do this, we make a structural model of the affected viral protein using specialised software that uses a lot of computational power. By using the CHPC, I am able to access their high powered server, as well as the software for performing the molecular modelling. With the information gained from this analysis, we can design new drugs that can work against these mutated viruses.
The project is progressing well and three students have already obtained their degrees.
Principal Investigator: Dr Zibo Keolopile
Institution Name: University of Botswana
Active Member Count: 2
Allocation Start: 2020-08-19
Allocation End: 2021-02-15
Used Hours: 122250
Project Name: Physics
Project Shortname: MATS1303
Discipline Name: Physics
Dr Zibo Keolopile, a senior lecturer in the department of physics, university of Botswana. My research group specializes in theoretical modeling using electronic structure models
installed in high performance computer clusters. We study inter molecular interactions on amino acids and other biomolecules. My student, Mr Larona has graduated as an MSC student from the university using this CHPC and he is current doing his PhD and also using the CHPC.
Principal Investigator: Prof Gert Kruger
Institution Name: University of KwaZulu-Natal
Active Member Count: 12
Allocation Start: 2020-08-19
Allocation End: 2021-02-26
Used Hours: 152036
Project Name: CPRU molecular modeling
Project Shortname: HEAL0839
Discipline Name: Health Sciences
(Who) The Catalysis and Peptide Research Unit at UKZN (http://cpru.ukzn.ac.za/Homepage.aspx) is currently working on the mechanism of action on the HIV PR with respect to the natural substrates. (What) We use an quantum chemical/molecular mechanics hybrid (Oniom) approach that gives us high level results on the thermodnamics and kinetics of the reaction. Our model enables us to study application of both electronics and sterics to change the bond strenght and binding energies of new potential inhibitors. The same approach is followed for transpeptidases, essential enzymes for the inhibition of TB. (Why) HIV is a major health threat in SA and new drugs is required due to the constant development of drug resistance. Similarly, TB and TB co-infection with HIV is a mojor health issue. (How) Our theoretical studies will allow us to test a computational model that correctly describes the interactions between the respective enzymes and existing drugs. We are improving our computational model to the extent where are now in a position to make and test new potential drug leads for synthesis. This can only be done with large computational resources provided by the CHPC.
Principal Investigator: Dr Michael Owen
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2020-08-20
Allocation End: 2021-02-16
Used Hours: 136243
Project Name: Industrial heat exchanger simulation and analysis
Project Shortname: MECH1210
Discipline Name: Computational Mechanics
The Thermofluids Division at Stellenbosch University's Department of Mechanical and Mechatronic Engineering has a long history of research in industrial heat exchangers and has conducted pioneering work in the field of dry cooling for large thermal power plants in particular.
Research in this field continues with a focus on understanding and improving the performance of these water conserving cooling systems under a variety of ambient conditions (including strong winds). Work of this nature benefits greatly from the CHPC which allows us to investigate an unprecedented number of scenarios in a short amount of time using computational fluid dynamics (CFD) and parallel computing.
Dry cooling is a key technology for South Africa's energy sector since thermal energy production (coal, nuclear, combined cycle gas and solar thermal) is typically a water intensive process which South Africa can ill afford considering the arid nature of our country. Ensuring robust operation of dry cooling systems can contribute significantly to the sustainability of South Africa's energy production.
Principal Investigator: Prof Evans Adei
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 5
Allocation Start: 2020-08-21
Allocation End: 2021-02-17
Used Hours: 1522947
Project Name: Materials For Energy and Fine Chemicals
Project Shortname: CHEM1046
Discipline Name: Chemistry
There has not been any new development worth reporting since our last feedback
Principal Investigator: Prof Mpho Sithole
Institution Name: Sefaku Makgatho Health Sciences University
Active Member Count: 9
Allocation Start: 2020-08-24
Allocation End: 2021-02-20
Used Hours: 55876
Project Name: Computational modeling of titanium based alloys
Project Shortname: MATS1228
Discipline Name: Physics
Material modeling group at Sefako Makgatho Health Sciences University (SMU) is a new group, almost two years old. The group is interested on Ti-alloys used for biomedical applications and on the development of low cost permanent magnets. Biomedical applications involves development of implants for patients. Permanent magnets are used in devices such as electric motors, disc drives, turbine generators. The project depends on CHPC for calculations. The project is introduced at Hons level to develop students for MSc and PhD levels.
Principal Investigator: Prof Timothy Egan
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2020-08-22
Allocation End: 2021-02-18
Used Hours: 23938
Project Name: Haem chemistry and interactions with antimalarial compounds
Project Shortname: CHEM0935
Discipline Name: Chemistry
The Bioinorganic Research Group at the University of Cape Town, led by Prof. Timothy J. Egan investigates the mechanism of action of potential new antimalarials.
The malaria parasite lives in human blood cells during its blood stage. During this stage it digests large quantities of the oxygen carrier haemoglobin (Hb) that it takes up into a digestive compartment called a digestive vacuole (DV). The amino acids derived from Hb are released from the DV into the rest of the parasite, but the iron-containing haem molecule of Hb, which is potentially highly toxic to the parasite cell is incorporated into a highly insoluble crystalline form called haemozoin (or malarial pigment) that is retained in the DV. The process of haemozoin formation can be targeted by antimalarials.
There is an ongoing pressing need for new antimalarial agents owing to the continuous development of resistance to antimalarials. Currently malaria is responsible for over 400,000 deaths per year and hundreds of millions of infections.
We are using docking methods to search for potential new haemozoin inhibitors as well as enzyme inhibitors. The most promising hit molecules are then purchased or synthesized and tested against malaria parasites grown in culture.
This is currently being done using software licensed to the CHPC that is otherwise too expensive for academic groups as well as using computing resources at the CHPC in the case of more intensive computations where more sophisticated software provides an improvement over low cost software previously employed with considerable success by the Bioinorganic Research Group.
Principal Investigator: Prof Fourie Joubert
Institution Name: University of Pretoria
Active Member Count: 39
Allocation Start: 2020-08-25
Allocation End: 2021-02-21
Used Hours: 2692
Project Name: NGS Bioinformatics
Project Shortname: CBBI0905
Discipline Name: Bioinformatics
The Centre for Bioinformatics and Computational Biology works on the genomics analysis of organisms ranging from viruses, bacteria, fungi, nematodes. insects, plants, animals to humans. The work recently done at the CHPC focused on the clustering of E. coli genomes according to their ability to cause diseases.
A manuscript is currently being written and is entitled: Escherichia coli in aquatic systems in a subtropical environment, with the collaboration of Prof. Fanus Venter, Prof. Emma Steenkamp and Prof. Volker Brözel.
Principal Investigator: Prof Zander Myburg
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2020-08-25
Allocation End: 2021-02-21
Used Hours: 139191
Project Name: Forest Molecular Genetics (FMG) Programme
Project Shortname: CBBI1015
Discipline Name: Bioinformatics
The Forest Molecular Genetics (FMG) Programme at the University of Pretoria focuses on the genetic control of growth and development in fast-growing plantation trees with a view to enhance biomass production and improve wood properties for timber, pulp, paper, and biomaterials production. They work in close collaboration with South African forestry companies through the FMG Consortium (FMGC) to develop capacity and resources for the application of tree biotechnology in operational tree improvement programmes. The group has successfully used a systems genetics approach in an interspecific backcross population of E. grandis x E. urophylla to map key genomic regions affecting gene expression and metabolic profile associated with variation in growth and wood chemistry. They recently embarked on an effort to engineer cell wall traits such as xylan content and structure affecting pulp yield employing new approaches such as CRISPR-Cas9 genome editing. Over the past five years FMG have successfully used a single nucleotide polymorphism (SNP) marker chip with 60,000 DNA markers to genotype over 3000 Eucalyptus trees and recently also established a multi-species SNP genotyping chip for tropical pines. These SNP chips will aid in genome-assisted breeding projects in Eucalyptus and pine where the aim is to fast-track breeding cycles. The programme is also constructing a Genome Diversity Atlas for Eucalyptus and pine species grown in South Africa, laying the foundation for the emerging field of landscape genomics, which combines population genomics with analysis of interactions with environmental factors. Towards this, FMG is undertaking an effort to use long-range single-molecule sequencing to sequence genomes of several hundred Eucalyptus trees, also expanding to other genera including acacia, macadamia and pine.
Principal Investigator: Prof Phuti Ngoepe
Institution Name: University of Limpopo
Active Member Count: 39
Allocation Start: 2020-08-25
Allocation End: 2021-02-21
Used Hours: 7446288
Project Name: Computational Modelling of Materials: Energy Storage
Project Shortname: MATS0856
Discipline Name: Material Science
The Research Group is based in Materials Modelling Centre at the University of Limpopo,
under the leadership of Professor Phuti Ngoepe. Energy Storage Systems: We have, through
simulations on primary particles of LMO spinel, characterized disruptive transition during
discharging; and are currently exploring porosities to enhance capacity of such cathodes. All
manganese NMC primary nanoparticles have been modelled and modified to NMC and the
nature of structural disorder associated with discharging are studied. This will inform the new
manganese rich NMC co-precipitation experiments set up on the UL campus. In addition,
stable O3 structures with enhanced performance, are predicted by doping using 4IR machine
learning methods. Approaches of minimizing anion oxidation at surfaces during discharging
are explored. Some aspects of the beyond lithium ion batteries are continuing in the form of
Li-S,Se, particularly on the S rich side, together with work on catalysts for Li,Na,K,-air
batteries. Mineral processing: After the development on proof of concept pertaining to
agreement of simulations and experiments in the design on reagents for mineral recovery
from complex ore, we have proceeded with the applications to precious metal chacogenides,
where good experimental samples are not readily available. We are exploring applicable
reagents. We have also studied new reagents that are applicable for copper extraction and are
identifying promising candidates. Alloy development: We have continued with phase stability
studies of shape memory alloys using a of combination of energetics, elastic and vibrational
properties. The extension of the study to TiPd alloys is now advanced. Semi-empirical
methods are being employed to explore phase transformations at elevated temperatures. Global
minimisation methods study for nanoclusters of Ti atoms are continuing.
The computational modelling studies, through CHPC, are intended to predict processes that are
essential in pilot and production plants for advanced battery systems, mineral processing and
metal production industries.
Thus far the progress on such studies is excellent and whilst delivering products it is developing
essential human capacity.
Principal Investigator: Prof Scott Hazelhurst
Institution Name: University of the Witwatersrand
Active Member Count: 4
Allocation Start: 2020-08-25
Allocation End: 2021-02-21
Used Hours: 226229
Project Name: Bioinformatics and Experimental Algorithms (BEAT)
Project Shortname: CBBI0930
Discipline Name: Bioinformatics
We are studying the variation in a set of genes that are important in drug metabolism, and particularly variations found in African populations. Small variations can impact both effectiveness and safety of drugs. Prior work of ours did genomic analysis of a large set of novel African genomes sequenced by collaborators in which we identified a number of potentially important variations. We are now studying two very important genes to build structural model models of some of these variations in which we can see how these variations affect the dynamic shape and function of the protein. In order to do this we need to use the Graphical Processing Units at the CHPC since this is extremely computationally expensive. The results will help us understand the impact of variation on drug metabolism. We expect to have results in the next 6 month period.
Principal Investigator: Dr Jaco Badenhorst
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 4
Allocation Start: 2020-08-25
Allocation End: 2021-02-21
Used Hours: 8013
Project Name: Automatic transcription of broadcast data
Project Shortname: CSIR0978
Discipline Name: Other
The Digital Audio Visual Technology (DAVT) Research Group at the CSIR Nextgen Enterprises and Institutions (NGEI) cluster develop speech and language-related technologies for the South African context to enhance access to information and communication. Given the multilingual nature of South Africa, human language technologies (HLTs) can make information and services accessible to a larger proportion of the South African population in a sustainable way, by reaching people in remote locations, people who are not necessarily trained in using technology, or people who are not fluent in English. HLTs can also provide access to information to people with disabilities. HLT can support language diversity and providing of information in multiple languages in an affordable and equitable fashion. The development of all 11 official languages is a national priority, which requires significant attention to HLT in all of these languages. HLT can be of significant economic importance – both by empowering citizens of the country to work more productively, and by forming the core of an exportable set of technologies (since such technologies are currently not available to most of the developing world).
Principal Investigator: Prof Marile Landman
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-08-25
Allocation End: 2021-02-21
Used Hours: 10042
Project Name: Organometallic complexes and surfactants
Project Shortname: CHEM0906
Discipline Name: Chemistry
The Organometallic Chemistry research group at the University of Pretoria is doing research on the synthesis and applications of organometallic complexes, in particular N-heterocyclic carbene complexes. These complexes are applied in the field of catalysis and pharmacology. We use the facilities of the CHPC to study interesting experimental results, for example formation of a specific product instead of the expected molecule. Reaction profiles guide us to understand the formation of the experimental product. We use transition state calculations to determine activation energies and hence energetically we can explain the formation of the preferred complex. We have an ongoing project in catalysis that has resulted in the publication of a few papers related to this topic. For these we have used stand alone computers. Using the CHPC facilities have reduced the calculation times considerably.
Principal Investigator: Prof Andries Engelbrecht
Institution Name: Stellenbosch University
Active Member Count: 15
Allocation Start: 2020-08-25
Allocation End: 2021-02-21
Used Hours: 1199030
Project Name: Computational Intelligence for Optimization
Project Shortname: CSCI0886
Discipline Name: Computer Science
Novel nature-inspired optimization algorithms have been developed to solve optimization problems. These algorithms are all based on very simple models of bird flocking behaviors, and applied to solve complex problems such as portfolio optimization, and developing more efficient machine learning algorithms. New approaches have been developed to understand the characteristics and complexity of optimization problem search landscapes, which allowed the development of automated approaches to predict the best algorithm to use to solve a specific optimization problem.
Principal Investigator: Prof Francois Engelbrecht
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2020-08-28
Allocation End: 2021-02-24
Used Hours: 420198
Project Name: WITS Climate Modelling
Project Shortname: ERTH1200
Discipline Name: Earth Sciences
Researchers from the Global Change Institute (GCI) of the University of the Witwatersrand (Wits) have developed a climate sensitive SIRD model capable of simulating Covid-19 propagation in South Africa (Engelbrecht and Scholes, 2020). The model uses as input detailed climate model simulations of temperature and moisture seasonality at the municipal scale, which were performed on the Lengau cluster of the CHPC. The model is currently providing guidance of the risk of a third wave of Covid-19 infections forming in South Africa in 2021, and at least two high-level publications based on this research are expected to appear in 2021.
Principal Investigator: Dr Rian Pierneef
Institution Name: University of Pretoria
Active Member Count: 10
Allocation Start: 2020-08-31
Allocation End: 2021-02-27
Used Hours: 13853
Project Name: Bioinformatic and Computational Biology analyses of organisms
Project Shortname: CBBI1124
Discipline Name: Bioinformatics
The CHPC has been critical in the successes achieved by the members of this research programme. It has afforded all the users, even those with limited access to sufficient technology and adequate computational resources to perform their research tasks. Access to the CHPC in this reporting period has ensured that 2 students have met the requirements for a PhD degree. This research programme currently supports various research endeavors which include work based on foodborne pathogens, soil health and antimicrobial resistance. Due to the prowess of the CHPC in bioinformatic applications and the computational capacity afforded, future projects involve the analysis of SARS-CoV-2 from wastewater samples and the pathogens with which it co-occurs. The CHPC allows users the peace of mind to embark on big data projects which requires large amounts of computational resources.
Principal Investigator: Prof Ozlem Tastan Bishop
Institution Name: Rhodes University
Active Member Count: 18
Allocation Start: 2020-08-30
Allocation End: 2021-02-26
Used Hours: 6746492
Project Name: Structural Bioinformatics for Drug Discovery
Project Shortname: CBBI0867
Discipline Name: Bioinformatics
Research Unit in Bioinformatics (RUBi) at Rhodes University is specialized in structural bioinformatics research. Structural bioinformatics focuses on the identification and analysis of structure, dynamics and interaction of biological macromolecules in 3D space. While doing so, it aims to make connections between sequence – structure and function of macromolecules. Information on structure is particularly important as you can derive enormous amounts of information.
RUBi's main research interest is early drug discovery. Computer aided drug design technology has greatly revolutionised the drug research and development process. Traditional computational drug discovery approach includes large scale structure based and/or ligand based in silico docking combined with molecular dynamics and binding free energy calculations. All these computationally expensive calculations require to use HPC facilities.
In the last few years, RUBi has been developing some novel protocols by merging computational chemistry, structural bioinformatics and biophysics approaches and combining with traditional methods. These combined approaches also require HPC facilities. We expect that our protocols will advance our and others research. We have already been testing the combined approaches in different cases and a number of hit compounds identified; including identification of South African natural compounds as hits to cancer, malaria, trypanosoma and HIV.
Principal Investigator: Dr Annerine Roos
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2020-08-31
Allocation End: 2021-02-27
Used Hours: 3298
Project Name: DCHS and MRI studies
Project Shortname: HEAL1267
Discipline Name: Health Sciences
The aim of the Drakenstein Child Health Study is to investigate determinants of early child development in a cohort of >1000 mother-child dyads of the Drakenstein district in the Western Cape of South Africa. The communities participating in the study represent a low-middle income country setting that is characterised by high substance abuse, poverty and violence. The Brain imaging subgroup include international collaborators of the Universities of Cape Town, Stellenbosch and Los Angeles, California. We aim to assess longitudinally cognitive, behavioural and neural outcomes in children from birth to 6 years of age, to identify vulnerable groups and key periods for intervention that may optimise development. Evidence show the earlier the interventions, the better the outcomes.
CHPC resources are used by this programme to analyse brain imaging data including structural data, of children with prenatal exposure to substances. Substance exposure is potentially harmful to brain development, but is understudied in young children. These include alcohol, tobacco and methamphetamine that is commonly used in the specific study community. We also aim to elucidate the neural effects of prenatal exposure to maternal depression as this has been shown to affect mother-child bonding and emotional regulation.
Our results are providing clues to brain regions that may be affected by prenatal substance exposure and depression. Numerous papers are currently being drafted for publication using results from CHPC analyses.
Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 4
Allocation Start: 2020-08-31
Allocation End: 2021-02-27
Used Hours: 1570698
Project Name: Computational and statistical methodologies for human and environmental health prediction
Project Shortname: CBBI0818
Discipline Name: Bioinformatics
Our research at CHPC (CBBI0818) is running from the University of Cape Town, South Africa. This research programme is fundamentally aiming 1) to determinate the environment and genetic variation that cause human species to look different, having difference in allergy, drug responses and treatment. 2) to identify and quantify the pattern of inheritance of the observed trait, drug response and treatment variation among human. These are addressed through the design of machine intelligence, artificial intelligent methodologies and statistical approaches to analysis large-scale DNA data of thousands affected/unaffected subjects. In doing so, the use of CHPC in our programme allow us to leverage data science in contributing to human health by increasing understanding of the genetic and environmental underpinnings of complex traits, drug/treatment responses and drug/dosage responses. The accumulation of experimental DNA data in Biology and new high throughput experiments are growing rapidly and give a huge number of data difficult to manage, to store and to analyse existing and future dispersed information. If DNA data are accumulated, become more and more available and large, better the health prediction is, therefore there is a critical need for national life and long -term storage and robust fast accessible memories. Up to today and during lockdown, the use of parallel High-Performance Computing at CHPC has critically increased our researcher portfolio to meet the international standard with respect to large scale genomic era and allow us to apply 2 NIH grants on Data Sciences. This program has already developed of genomic-based software tools that address African genetic variation challenges and provided advanced training around parallel programming with respect to large-scale genomic data to African postgraduate students/researchers.
Principal Investigator: Prof Liliana Mammino
Institution Name: University of Venda
Active Member Count: 3
Allocation Start: 2020-09-01
Allocation End: 2021-02-28
Used Hours: 293936
Project Name: computational study of biologically active molecules of natural origin
Project Shortname: CHEM0959
Discipline Name: Chemistry
WHO?
The group consists of one professor, one M.Sc. student and on Ph.D student, at the University of Venda.
WHAT?
We focus on the study of biologically active molecule, that is, molecules that can have an effect on human organisms and can be potentially interested for drug development. We are currently studying molecules with antidiabetic, anticancer, antimalarial and antiviral properties.
WHY?
We study the properties of the molecules that we are considering.
The pharmaceutical activities of a substance depend on the properties of its molecules. The more we know about these properties, the more we can understand about its pharmaceutical activities; this is important for the design of new molecules with improved activities.
In summary, our studies provide information that is important for specialists who work on further steps of drug development: they can use the information obtained from our studies to select the most suitable molecules, until new improved drugs are built.
Studies contributing to the search for new drugs are important because developing effective drugs is very important for human health.
Drug development is not a fast process (as the current pandemic has painfully revealed to everybody). It needs a lot of contributions from different specialists. Our contributions concern the elucidation of the molecular properties of potential drugs.
HOW?
We use calculations to find the properties of the molecules that we are considered.
There are different approaches for these calculations. The ones that give more reliable results require huge time to complete. Without the use of the CHPC, it would not have been possible to obtain most of the results that we have obtained. That is why using the CHPC is essential for us to be able to conduct our research.
HOW IS THE PROJECT PROGRESSING?
The project is progressing satisfactorily, despite some challenges caused by the pandemic.
Principal Investigator: Dr Adeniyi ogunlaja
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 4
Allocation Start: 2020-09-02
Allocation End: 2021-03-10
Used Hours: 34325
Project Name: Chemistry and Material Science
Project Shortname: MATS1070
Discipline Name: Chemistry
Dr Adeniyi Ogunlaja (Research group -Analytical/Inorganic) at Nelson Mandela University.
Refractory polyaromatic hydrocarbons found in fuels such as dibenzothiophene, quinoline and its alkylated derivatives emits nitrous oxides and sulfur oxides to the environment when combusted, thereby reducing air quality. Desulfurization by means of oxidative desulfurization and adsorptive denitrogenation has been proposed to complement the hydrodesulfurization (HDS) and hydrodenitrogenation (HDN) processes, currently employed to remove sulfur and nitrogen compounds in fuels. At Nelson Mandela University analytical chemistry research group, we design materials that can selectively remove these sulfur and nitrogen compounds. Molecular modelling based upon the density functional theory (DFT) was employed to understand the mode of adsorption (interaction) between synthesised materials and the various compounds to be removed from fuels. Computational study assists with the understanding of the electronic and thermodynamic properties of synthesised materials prior to application. It also gives an insight as to the specific properties to be targeted when designing adsorbents for environmental clean-up. So far, progress has been made around the design and adsorption of some toxic molecules in fuels. HPC assist our group to build models that could be employed in explaining complex phenomena. It has also enabled us to ask big questions around activity of our materials and to test for possible answers computationally. CHPC has created the platform for where researchers like me could assess the HPC and also be assisted when encountering computation problems.
Principal Investigator: Mr Adebayo Azeez Adeniyi
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2020-09-02
Allocation End: 2021-03-01
Used Hours: 219273
Project Name: Drug Discovery Research Using Quantum and Molecular Dynamic Simulation
Project Shortname: CHEM0958
Discipline Name: Chemistry
In addition to our area of research on drug development and electronic properties of small molecules, we have recently expanded our research focus to included vaccine development, photochemistry and polymer chemistry. We make used of several packages that are installed on CHPC for Bioinformatics, Quantum and Molecular Dynamic Simulation. The reason for expanding our research focus is based on the pressing need of the society and global challenges, that lead us into epitopes based vaccine development from the genomes of the pathogens, polymer chemistry, photochemistry of small molecules for application as photoactive compounds and molecular electrochemistry. Our research use theoretical modelling to give rational insight into identified problems which can help in the experimental designs for possible solutions. CHPC is an important facility to our research group, we make use of the facilities and the softwares like Gaussian, Orca, Games and Newchem; also used molecular dynamic packages like Gromacs, Amber and Lammps. We have applied quantum packages to study the chemical and spectroscopic properties of small molecules of which we have been able to reproduced some of the experimental results.
It is obvious that our research progress and achievement revolve around the service of CHPC and many of our research output would not have been possible in without the support from CHPC.
Principal Investigator: Dr Sunita Kruger
Institution Name: University of Johannesburg
Active Member Count: 1
Allocation Start: 2020-09-03
Allocation End: 2021-03-02
Used Hours: 224921
Project Name: Environmental Heat Transfer
Project Shortname: MECH0995
Discipline Name: Computational Mechanics
his research group in the Mechanical Engineering Science Department of the University of Johannesburg is currently focusing on environmental heat transfer. Specifically heat transfer in naturally ventilated greenhouses. Greenhouses are used to protect plants from adverse weather conditions and insects. Ventilation of greenhouses are of vital importance to ensure quality crop production. If temperatures in a greenhouse is too high, poor plant growth may result, and an increased need for frequent watering. A mechanical ventilation system might be required to cool the inside of the greenhouse. Natural ventilation is an alternative option used to ventilate greenhouses. Natural ventilation uses temperature and wind to control the indoor climate of greenhouses. Unfortunately greenhouses are extremely energy intensive. Energy costs are the third highest cost related to greenhouse crop cultivation. Reducing the operating costs of energy associated with greenhouse cultivation may result in a price reduction of greenhouse cultivated crops. Conducting experimental work on ventilation of greenhouses can be costly and cumbersome. Using computational methods such as CFD (Computational Fluid Dynamics) to obtain qualitative and quantitative assessment of greenhouses can reduce costs and time involved. The computer cluster at the Centre for High Performance Computing has been used to conduct the numerical investigation using CFD. Currently research is being conducted on a large commercial greenhouse, as well as a rooftop greenhouse in the city center. Smaller greenhouses containing a single span have also been investigated. Currently, three dimensional models of greenhouses subject to buoyancy driven flow are being investigated.
Principal Investigator: Dr Ernest Odhiambo
Institution Name: University of Nairobi
Active Member Count: 1
Allocation Start: 2020-09-03
Allocation End: 2021-03-02
Used Hours: 115499
Project Name: Computational Modeling of Heat Containment Systems
Project Shortname: MECH1178
Discipline Name: Computational Mechanics
Computational fluid dynamics (CFD) Simulation Laboratories is housed at the department of Mechanical and Manufacturing Engineering at the University of Nairobi. The department is part of the school of engineering. Dr. Ernest Odhiambo, a Thermo-Fluids lecturer is the principal researcher. The other members of the group include; Peter Odhiambo, Anne Kariuki, Kevin Okwach, John Kisilu. All of these members are postgraduate students. Currently Computational Fluid Dynamics is offered at the masters level only although undergraduate students are offered projects with a CFD theme. The group mainly focuses on problems involving fluid dynamics, thermodynamics and heat transfer. In fluid dynamics the focus is on numerical simulation of isothermal fluid and structural interaction (FSI). In the case of thermodynamics and heat transfer numerical simulation of varying temperature environments like fire disasters are considered. In the energy sector, some members of the group are modeling more efficient wind turbine technologies by trying out different blade designs. Additionally, one other research member (Anne) is considering the energy audit of buildings. Anne's work is considered vital in light of the recent UN Climate Change Conference (COP 26) resolutions witnessed in Scotland. The use of CHPC has significantly hastened the obtaining of results, some of which have been useful in the publishing of a journal article discussing the status of energy audit in buildings. The importance of this research cannot be overemphasized, given the negative effects of fossil fuels, which are also used to produce the energy used in buildings. The use of the CHPC clusters enable us to consider different scenarios as would be experienced if a building was on fire. The fire fighting, which would consist of detection, suppression and safe evacuation has been successfully modeled using the CHPC and results obtained are in tandem with expectations. We are grateful to the CHPC staff.
Principal Investigator: Mrs Chantel Niebuhr
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-09-07
Allocation End: 2021-03-06
Used Hours: 807184
Project Name: Hydrokinetic turbine analysis
Project Shortname: MECH1174
Discipline Name: Other
The hydropower and water research group at the University of Pretoria, Civil Engineering Department have consistently made use of the CHPC to complete large scale CFD analysis of water distribution systems. Due to the size and complexity of these models, timely analysis is only possible through the use of a large cluster, as provided by the CHPC.
The work has focused on the analysis of a new design of a locally produced vertical axis hydrokinetic turbine. Successful analysis of the flow through the turbine allowed production of a low cost locally produced product to be used within Canal and river systems in South Africa, producing clean renewable energy for local municipalities. The models specifically allowed an in-depth view of the hydrodynamics around the turbine blades and fixing and re-design of problem areas.
Another project focused on reservoir stagnation zones where the use of the CHPC allowed modelling of the three-dimensional reservoirs as a whole. Modelling the inflow and outflow, whereby analysis of stagnation zones for water quality analysis was possible. The project is progressing well and should be completed by the end of 2021.
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 2
Allocation Start: 2020-09-07
Allocation End: 2021-03-06
Used Hours: 611639
Project Name: Magnetocaloric effect in selected metallic nanoclusters on two-dimensional (2D) substrates, and in selected rare-earths.
Project Shortname: MATS1156
Discipline Name: Material Science
The research study is based at the Department of Physics of the University of South Africa (UNISA). The study concerns fundamental study and potential applications of two-dimensional (2D) nanomaterials in ultrathin refrigeration, air-conditioning system, and in cooling of nanoelectronic devices or any system where nanoscale cooling is needed. Specifically, the research aims to study the phenomenon of magnetocaloric effect (MCE) in metallic nanostructures deposited on various two-dimensional substrates, such as graphene, silicene, and similar 2D materials. Magnetocaloric effect is a property of magnetic materials which could be exploited for refrigeration purposes. While the conventional refrigerator system is based on compression and evaporation of often environmentally unfriendly gases, magnetic refrigeration systems is based on magnetizing and demagnetizing a magnetic material. In the last few years, the focus in magnetocaloric research seems to have shifted toward ultrathin materials. Because of plethora of candidate materials that may be investigated as possible candidates for MCE, performing experimental investigations may be time and resources consuming, and thus, computational studies could provide the lead and narrow the range of materials that could be considered for further experimental investigations. Performing ab-initio density-functional theory (DFT) study to determine the properties of candidate material systems is a viable and state-of-the-art approach which can complement experimental efforts. DFT calculations require specialized softwares as well as high-capacity data storage and memory requirements which are often beyond the capability of desktop computers. Thus, the availability of high-performance computing (HPC) facility is absolutely necessary.
Principal Investigator: Dr Henry Otunga
Institution Name: Maseno University, Kisumu, Kenya
Active Member Count: 2
Allocation Start: 2020-09-07
Allocation End: 2021-03-24
Used Hours: 5163
Project Name: Computational Study of Hematite Clusters
Project Shortname: MATS0888
Discipline Name: Material Science
Sunlight is the most abundant renewable energy resource and considered to be the ultimate solution to address the global energy problem: The Tetrawatt Challenge. However, the vision of solar
energy providing a substantial fraction of global energy infrastructure is still far from being realized. The major challenge is to develop an efficient and cost-effective approach for storing
solar energy that can be used on demand on a global scale. Splitting water photoelectrochemically is a promising way in which solar energy can be harvested and stored through
photocurrent-driven chemical bond rearrangement leading to the formation of molecular hydrogen (2H2O→2H2+O2, E0=1.23 eV, Standard Hydrogen Electrode, SHE), which can be used directly as fuel or as
an intermediate in the production of other fuels.
Hematite (alpha-Fe2O3) has emerged as a candidate photoanode material due to several favorable features: a band gap of about 2.0 eV (which allows for a large fraction of solar spectrum to be
absorbed), excellent stability under aqueous environments, and abundance in nature. Converting energy from the Sun to electricity efficiently via photoelectrochemical splitting of water is based on photo-induced charge separation at an interface (semiconductor/water interface) and the mobility of photogenerated carriers (electron-hole pairs). However, in bulk hematite, the separated charges recombine very fast (very short lifetimes of electron-hole pairs) and have very low mobility, hindering the conversion efficieny. These limitations can be dealt with by nanostructuring hematite, by growing ultrathin films of hematite, and by introducing impurity atoms i hematite. In this work, the structure and energetics of various size clusters of Fe2O3 have been investigated using the plane-wave pseudopotential approach to Density Functional Theory (DFT) and ab initio Molecular Dynamics (MD).
These calculations require a significant amount of compute resources in terms of memory and cpu scaling. In this respect, I am grateful to the CHPC for granting me access to their supercomputing facilities and I hope for more collaboration in future.
This research group is known as The Computational Materials Science Research Group of Maseno University. The members of the research group are
1. Dr. Henry Odhiambo Otunga (PI)
2. Nicholas Ongwen
Principal Investigator: Dr Pieter Levecque
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2020-09-07
Allocation End: 2021-03-06
Used Hours: 12180
Project Name: Non carbon supports for electrocatalyts
Project Shortname: MATS1108
Discipline Name: Material Science
The HySA/Catalysis Centre of Competence in the Department of Chemical Engineering at the University of Cape Town conducts research into new catalysts and components for fuel cells and electrolysers. One main focus is new support materials for catalysts for fuel cells. MAX phases are a new class of materials that can at the same time show properties of ceramics and metals. This means materials can be prepared that show strong corrosion resistance as well as high conductivity which is the properties needed for a good fuel cell catalyst. The purpose of this study is to find a suitable model for MAX phases and their properties so that we can rapidly screen potential compositions and thereby targeting the lab-based preparation as described above. CHPC facilities help us to do the modelling thereby saving significant lab time and expensive chemicals
Principal Investigator: Dr John Mack
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2020-09-07
Allocation End: 2021-03-06
Used Hours: 17971
Project Name: Rational design of phthalocyanine, porphyrin and BODIPY dyes
Project Shortname: CHEM0796
Discipline Name: Chemistry
The Institute for Nanotechnology Innovation (INI) at Rhodes University under director Prof. Tebello Nyokong carries out research related to the use of molecular dyes in biomedical applications, such as cancer treatment through photodynamic therapy, the use of antimicrobial photodynamic chemotherapy for treating hospital superbugs and as sensors for ions that are harmful to human health.
Other applications of interest include wastewater treatment and the development of optical limiters to protect human vision,such as in aviation safety in protecting pilots from the irresponsible use of laser pointers during runway approaches. It is important to understand trends in the electronic and optical properties that make the molecular dyes suitable for these particular applications. The resources of the Centre for High Performance computing help to facilitate this by making it possible to carry out molecular modelling calculations that can be used to predict how changes to the structures of the molecular dyes will modify their properties. The flexibility that CHPC provides where memory allocations are concerned is often vital.
The INI currently has three staff members, fifteen PhD and six MSc students, and three postdoctoral fellows, and usually publishes over forty peer-reviewed publications per year. This rose to a high of sixty-five in 2017 with ten involving the use of CHPC resources.
Principal Investigator: Dr Madison Lasich
Institution Name: Mangosuthu University of Technology
Active Member Count: 16
Allocation Start: 2020-09-07
Allocation End: 2021-03-06
Used Hours: 21381
Project Name: Chem Thermo
Project Shortname: CHEM1028
Discipline Name: Chemical Engineering
Together with the Nuclear Energy Corporation of SA and UKZN, the Thermodynamics-Materials-Separations Research Group (TMSRG) at Mangosuthu University of Technology has developed an accurate model for fluorination reactors, which was recently published in an international journal [Govender, I.; Lokhat, D.; Ramjugernath, D.; Lasich, M; Kock, L. D. Critical analysis of transport phenomena and operational parameters on the performance of an intermediate-scale surface fluorination reactor. Journal of Fluorine Chemistry 2020, 237, 109617]. In addition, a collaboration with the Institute for Systems Science at DUT demonstrated that unusual materials, such as Korteweg fluids, can indeed be modeled using classical simulations, which may be useful for those studying substances as diverse as magma and ultra-cold condensates [Lasich, M.; Zloshchastiev, K. G. Particle size and phase equilibria in classical logarithmic fluid. Journal of Physics Conference Series 2021, 1740, 012042].
Principal Investigator: Prof Robinson Musembi
Institution Name: University of Nairobi
Active Member Count: 2
Allocation Start: 2020-09-08
Allocation End: 2021-03-07
Used Hours: 1518
Project Name: CMCG-UoN
Project Shortname: MATS1321
Discipline Name: Material Science
Condensed Matter Computation Group is a subgroup of the Condensed Matter Research Group at the University of Nairobi. This group hs research interest in materials science as well as computational Biophysics. The following important work is ongoing at the moment:
Prion diseases are undoubtedly fatal neurodegenerative disorders that affect human beings and animals such as cattle, sheep and rabbits. It is believed that these spongiform encephalopathies occur as a result of protein aggregation; and consequently, cause intracellular inclusions or aggregates in specific parts of the brain of humans or animals. Most patients suffering from prion diseases begin developing symptoms in their late fifties. Symptoms include loss of memory, difficulty in speaking, and unsteadiness and lead to progressive dementia, and then death within a few months or years. There is presently no cure or treatment.
These class of neurodegenerative diseases results from a single, tiny mutation in a protein, resulting in it having a wrong shape - through misfolding - then aggregating to form amyloid plaques in the brain. The accumulation of amyloid beta polypeptides in the brain is a cardinal event in the pathogenesis of prion diseases. Notwithstanding the very many research undertakings in this field, the molecular mechanism of protein misfolding and aggregation still eludes us and is poorly understood. Since protein aggregation is a molecular rare event, studying the mechanism of this phenomenon requires a molecular approach rather than using experiments. Molecular dynamics simulations are an indispensable tool for understanding how mutations affect the structure and dynamics of proteins. Since large proteins are modeled atom by atom and require long simulation times, their dynamical behavior must be followed using a large number of computer cores. Such hardware is necessary to run the computational experiments efficiently and get meaningful results.
To achieve our mission, we are relying on the Lengau cluster to help us to assess the structural and dynamics insights of amyloid aggregates that misfold into diseased pathogens by molecular dynamics simulations. In this research, we will show how computer simulations can be used to pinpoint changes in molecular structure that lead directly to prion diseases. It is our opinion that a similar line of investigation should prove beneficial in understanding the origins of prion diseases such as kuru, GSS, and Creutzfeldt-Jakob disease (CJD). Once the origin is understood at molecular detail, strategies to rationally prevent and cure these diseases can be conceived. We hope the ability to model neurodegenerative disorders will inspire better diagnostic tests and, ultimately, treatments to slow down their effects.
Principal Investigator: Prof Malik Maaza
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2020-09-09
Allocation End: 2021-04-22
Used Hours: 679210
Project Name: Modelling of Functional Materials at the Nanoscale
Project Shortname: MATS1306
Discipline Name: Physics
The UNESCO UNISA ITL-NRF Africa Chair in Nanosciences & Nanotechnology (U2ACN2), a trilateral partnership between the UNESCO UNISA & iThemba LABS-National Research Foundation of South Africa, has established a multidisciplinary research program in materials at the nanoscale. The multidisciplinary approach of the U2ACN2 chair cements the several fragmented Africa national efforts in nanosciences and nanotechnology and addresses urgent societal needs in the water, energy, and health sectors in Africa.
Computational research uses complex models in various ways, all of which advance materials science and engineering. These computational models can help researchers understand the outcome of an experiment, identify the most promising avenues for future experiments, and give us insight into processes that cannot be easily explored in the lab. The U2ACN2 center thanks CHPC as an outstanding High-Performance Computing center, which assists our researchers by providing access to computational resources necessary to construct, analyze, and interpret their complex data in the field of nano and materials science.
Our recent projects have been focused on finding an approach via simulation methods to use the coated metal nanoparticles as deliverer with proposed drugs to treat diseases caused by the coronavirus and Malaria insect.
The Modelling computational publication on SARS-COV2 in Nature Scientific Report 2021 has been loaded & publicized on various institutional websites, UNISA, iThemba LABS & NRF. Also, the same publications are now on the open-access platform of Springer & Nature Publishing houses. Likewise, it is intended to use the same approach to investigate if ivermectin & Artemisinin phytoactive compounds can bioconjugate with nanoscaled metallic nanoparticles. The target is to study the efficacy of such bioconjugated nanosystems against Malaria.
In addition, a new series of computations are made on 2D systems in the prediction of enhanced magnetism at room temperature as well as a potential application for water desalination. While in both cases 2D nanosystems are used, their chemical/elemental nature is quite different in nature (Boron nitrides for enhanced nanomagnetism & MoS2 /Graphene in the case of water desalinization.
Principal Investigator: Dr Rose Modiba
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 5
Allocation Start: 2020-09-09
Allocation End: 2021-03-08
Used Hours: 67704
Project Name: Computational modelling of light metals
Project Shortname: MATS1097
Discipline Name: Material Science
The light metals at CSIR who are working on the stability of the materials when alloyed with other transition metals would like to thank CHPC for allowing us to use their facilities. The systematic search for novel materials is hardly achievable only via experimental discovery due to the very large combinatorial space spanned by the crystal structures and chemical compositions for compounds. This difficulty is also connected with eventually high and unstable costs of raw materials on the world market and the time-consuming procedures of synthesis and characterization. It is of great importance for the theoretical search for materials to gain detailed insight into the most relevant physical mechanisms which determine the intrinsic properties of the materials. The CHCP is a very good platform for anyone who would like to do simulation on their materials. Thank you CHPC for the workshops provided to equip us with the most relevant and recent technologies to be able to understand our materials.
Principal Investigator: Dr Saheed Sabiu
Institution Name: Durban University of Technology
Active Member Count: 7
Allocation Start: 2020-09-09
Allocation End: 2021-03-08
Used Hours: 67281
Project Name: Drug Discovery & Development and Viral Metagenomics
Project Shortname: HEAL1361
Discipline Name: Bioinformatics
The HEAL1361: Drug Discovery & Development and Viral Metagenomics Programme is resident at the Department of Biotechnology and Food Science, Durban University of Technology, where the focus is on therapeutic mechanisms of secondary metabolites in communicable and non-communicable diseases while reporting health benefits in a way that will provide valuable data which will lead to new drugs. Besides this, the group is also focusing on molecular dynamics of gut and respiratory viruses using sequencing and computational approaches.
The use of computational approaches relies significantly on CHPC's operations/applications and the programme has been leveraging on this with appreciable progress made to date.
Principal Investigator: Mr Randall Paton
Institution Name: University of the Witwatersrand
Active Member Count: 9
Allocation Start: 2020-09-10
Allocation End: 2021-03-09
Used Hours: 1619702
Project Name: Compressible Gas Dynamics
Project Shortname: MECH0847
Discipline Name: Other
The Flow Research Unit, which was founded in 1990, closed at the end of 2020 with the retirement of its Director, Professor Emeritus Beric Skews. However, the work that the group is doing looking at the effects of rapid, arbitrary acceleration, and specialised geometry on compressible aerodynamics continues under the leadership of long-time Research Officer, Dr Randall Paton. This work is also being extended to examine some effects in space propulsion, and isentropic interactions of compressible flows.
The CHPC is an integral part of this work. It allows for the parametric simulation of these flow fields, which are often impossible to produce experimentally. The current cohort of several Masters and two PhD students all make use of this incredible facility (expertly managed by its tirelessly-dedicated staff) to expand the boundaries of knowledge, leading graduates from the group of all ethnic backrounds and sexes to careers both locally and abroad.
Principal Investigator: Mr Anban Pillay
Institution Name: University of KwaZulu-Natal
Active Member Count: 9
Allocation Start: 2020-09-10
Allocation End: 2021-03-09
Used Hours: 189788
Project Name: Deep Learning Approaches
Project Shortname: CSCI1078
Discipline Name: Computer Science
The Deep Learning research group belongs to the Centre for Artificial Intelligence Research Node at the University of KwaZulu-Natal. The Centre for Artificial Intelligence Research (CAIR) (CAIR.za.net) is a South African distributed Research Network that conducts foundational, directed and applied research into various aspects of Artificial Intelligence.
The research group conducts foundational research in machine learning in general and deep learning in particular. Deep learning projects require substantial computing resources and the CHPC is vital to its success.
The projects involve various area of deep learning that include deep reinforcement learning, convolutional and recurrent neural networks. Application areas include image processing, natural language processing and speech recognition.
Several students are busy with projects at present.
Principal Investigator: Dr Jaap Hoffmann
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2020-09-11
Allocation End: 2021-03-10
Used Hours: 29692
Project Name: Flow through porous media
Project Shortname: MECH1116
Discipline Name: Computational Mechanics
Rock bed is a cheap thermal energy storage medium. However, since rocks shapes are irregular, the flow through a rock bed is not uniform. This work aims to develop more appropriate models to predict flow through, and ultimately, improve the design of rock beds.
Principal Investigator: Prof Michelle Kuttel
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2020-09-11
Allocation End: 2021-03-10
Used Hours: 193587
Project Name: Molecular modelling of microbial polysaccharides and glycoconjugates
Project Shortname: CHEM1242
Discipline Name: Chemistry
This drug discover modelling project is driven by post-doc student Dr Badichi-Akher of Michelle Kuttel's research group at UCT. The project focusses on molecular modelling for medical applications - drug and vaccine design. This work should be useful for the future rational structure-based design of novel drugs and vaccines with improved potency and selectivity.
Principal Investigator: Dr Gavin Gouws
Institution Name: SAIAB
Active Member Count: 7
Allocation Start: 2020-09-11
Allocation End: 2021-03-10
Used Hours: 4597
Project Name: RADseq studies of aquatic biodiversity
Project Shortname: CBBI1274
Discipline Name: Other
The Marine Fish Research Team in the Aquatic Genomics Research Platform at the National Research Foundation - South African Institute for Aquatic Biodiversity employs a variety of genetic tools to understand the evolution and ecology of marine fishes (and marine invertebrates). We are interested in the relationships between species, populations and individuals, and in the movement and migration of individuals, with a view to informing conservation and management. Over the last year, we have conducted studies examining whether the genetic diversity of commercially-exploited marine fishes have changed over time, as a result of harvesting, and whether an endangered line-fish exists as and should be managed as a single population along the South African coast. For the former, SNP genotype data were generated and analysed using applications on the CHPC, while the latter used the CHPC and it's applications to model patterns of migration, dispersal and changes in population size using mitochondrial and nuclear genetic data. Some of this research has recently been published, with additional manuscripts currently being prepared.
Principal Investigator: Prof Bettine van Vuuren
Institution Name: University of Johannesburg
Active Member Count: 5
Allocation Start: 2020-09-11
Allocation End: 2021-03-10
Used Hours: 66504
Project Name: Biocomplexity on sub-Antarctic islands
Project Shortname: CBBI1153
Discipline Name: Bioinformatics
- We are a research group at the Centre of Ecological Genomics and Wildlife Conservation based at the University of Johannesburg, South Africa.
- We are conservation geneticists and are interested in studying spatial and temporal genetic patterns in multiple organisms (plants and invertebrates) on sub-Antarctic islands, with a special focus on Marion Island. We aim to investigate genetic patterns and structure in the context of environmental changes (for example, climate change). We intend on using our study species as proxies for monitoring global change and its impact on biodiversity as a whole.
- We are well aware of the concept of environmental change (such as climate change, which is more pronounced in the sub-Antarctic region). As conservation geneticists, we will investigate the impact that change has on biodiversity. Understanding genetic patterns is crucial, and our results will bring about far-reaching implications for the development of conservation management programs for Marion Island and on a global scale too.
- To do this, we have generated next-generation sequencing (NGS) data using various sequencing chemistries. We will use the CHPC cluster to analyse our NGS data to answer transcriptomic questions, and phylogenomic and population genomic related analyses. The above mentioned data is exceptionally large, and therefore we will not be able to conduct our research without the CHPC resources since no other platforms can handle these large datasets.
- We are in the process of completing three research articles to be submitted for publication soon. In the near future, and based on the work from Daniela and Shilpa, we hope to publish several articles next year.
We are happy with the progress we have made thus far and thank the CHPC for this (the CHPC has been acknowledged in the publications).
Principal Investigator: Dr Samson Khene
Institution Name: Rhodes University
Active Member Count: 5
Allocation Start: 2020-09-14
Allocation End: 2021-03-13
Used Hours: 207557
Project Name: Synthesis, Spectroscopy and Nonlinear Optical Properties of Phthalocyanines
Project Shortname: CHEM0975
Discipline Name: Chemistry
Many of today's optical sensors are based on optical materials in which non-linear optics may play a role. Defects in the cable can have an effect of reducing the light (which carries information) in an optical fiber or cable. This phenomenon is also present in a variety of non-linear active materials or molecules. This nonlinear reduction of light phenomenon can be used as a sensing method for detection and correction of signals that are sent in cables. The aim of our research (at Rhodes University in the Chemistry department) is to make and study molecules which will help improve signal transmission using a nonlinear process. This work will not be possible if it was not supported by CHPC facilities.
Principal Investigator: Dr Babatunde J. Abiodun
Institution Name: University of Cape Town
Active Member Count: 28
Allocation Start: 2020-09-13
Allocation End: 2021-04-21
Used Hours: 2531282
Project Name: CSAG-Atmospheric Modelling
Project Shortname: ERTH0904
Discipline Name: Earth Sciences
The Climate System Analysis Group (CSAG) Atmospheric Modelling project consists of CSAG researchers and students working on model development and applications. Our group is a unique research group within Africa (CSAG http://www.csag.uct.ac.za/). We are a mix of specialties who put the needs of developing nation users at the forefront of everything we do. As a result, we seek to apply our core research to meet the knowledge needs of responding to climate variability and change. In the project, we develop, evaluate, and apply of dynamic and statistical climate models over Africa. Climate models are powerful tools for understanding the complexity of our earth climate system. We use various form of climate model, ranging from uniform-grid Global Climate Models (GCMs), Regional Climate Models (RCMs) and adaptive-grid GCMs (VGCM) that has capability to increase its grid resolution locally over a region of interest. Given the complexity and computational demand of these models we rely on high performance Computers like those at the Meraka CHPC to our models. Our research goal is to understand the dynamics of climate extremes (i.e., droughts, extreme rainfall, heatwaves, and pollution episodes) and the impacts of vegetation changes on regional climate.
The highlights of our recently published research include: the application of the Weather Research and Forecasting (WRF) model to reveal the characteristics of cut-off low (an atmospheric feature known for extreme rainfall and flooding) over the Western Cape (Abba Omar and Abiodun 2020, 2021a and 2021b), analysis of climate geoengineering dataset to show how keeping the global mean temperature at 2020 levels through artificial injection of aerosol to the stratosphere could help lower the future risk of 'Day Zero' level droughts over the Western Cape (Odoulami et al, 2021), and analysis of multi-model ensemble simulations to project the impacts of global warming on crop suitability and planting season in Africa (Egbebiyi et al., 2021). More information on these studies and our other studies can be found on our website (http://www.csag.uct.ac.za/publications_all)
Principal Investigator: Dr ADEDAPO ADEYINKA
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2020-09-14
Allocation End: 2021-03-13
Used Hours: 148618
Project Name: Computational Design of Molecules
Project Shortname: CHEM1221
Discipline Name: Chemistry
The Computational Design of Molecules research group is based at the University of Johannesburg. We aim to design new and improved molecules and materials for applications in Catalysis and renewable energy. Since the availability of energy is one of the main challenges of the African continent, being able to achieve our aims as a group will provide clean energy solutions for the continent. We use computational chemistry software to explore the properties of molecules which is responsible for their activity and then use the knowledge gained to design more efficient and improved materials.
Principal Investigator: Dr Adam Skelton
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2020-09-14
Allocation End: 2021-03-13
Used Hours: 9825
Project Name: Molecular modelling of biomolecules and materials
Project Shortname: CHEM0798
Discipline Name: Chemistry
I am Dr. Adam Skelton and I work at the College of Health Science university of KwaZulu-Natal. I work on understanding the behaviour of biological and material systems on the molecular level.
A particlar interest is in using molecular simulation to direct the rationale design of functionalized nanoparticles for a range of applications such as drug delivery, water treatment and catalysis. In particular, drug delivery is the use of nanoparticles to carry antiviral or antibacterial drugs into parts of the body that are difficult for conventional drugs to reach. Drug-delivery is, therefore, of huge importance in South Africa, especially in the battle against HIV and Tubercolosis.
The research requires running a series of computer simulations, which may take hours at a time. CHPC has had a great impact since it provides me with the facilities to perform such simulations.
Since the project started, my group has published more than 25 papers in international journals and has provided deep insight into biological and material systems on the molecular level.
Principal Investigator: Dr Ouma Moro
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2020-09-15
Allocation End: 2021-03-14
Used Hours: 609259
Project Name: Rational design of novel catalysts using Chemistry 4.0 and 4IR tools
Project Shortname: MATS1365
Discipline Name: Material Science
Chemistry 4.0 is as at the core of material's informatics in the Forth Industrial Revolution (4IR) space. Borrowing from the affordances of the materials genome initiative, machine learning (ML) with(out) deep learning (DL) techniques with neural networks can be used to design the next-generation catalyst(s) for hydrogen evolution reactions, oxygen evolution reactions and hydrogenation and dehydrogenation reactions.
At the core of this project is the application of density functional theory calculations to calculate descriptors that will used as inputs to machine learning models and also for training the ML and DL models. This will facilitate the rapid scaling of material design and design within the continent and also the Republic of South Africa. This because South Africa is well endowed with mineral resources essential for energy storage and catalysis and as governed by the Energy White Paper, this project offers innovative applications and ideas on how the government can scale up technologies related to energy as well as build capacity with the country and continent.
Those working in the project include: Dr Cecil NM Ouma (the Principal Investigator with vast experience in ab initio modelling), Gladys Kingóri (A PhD student at Technical university of Kenya) and Hezbon Ondieki (A prospective PhD student). The HPC resources from CHPC in Cape Town has been at the core of all the research that we have done so far. It is these resources that are both facilitating and mediating Africa's concerted efforts towards catching up with developed nations in terms of research, development and capacity building.
Principal Investigator: Dr Aniekan Ukpong
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2020-09-15
Allocation End: 2021-03-14
Used Hours: 492377
Project Name: Theoretical and Computational Condensed Matter and Materials Physics
Project Shortname: MATS0941
Discipline Name: Physics
The desire to increase the density of stored data and robustness of the magnetic state of stored information against external perturbation underscores our efforts to develop materials for non-volatile random-access memory. Owing to poor scalability of conventional methods of electrical spin injection, alternative ways to generate, transport and detect pure spin currents are being pursued. We have pursued magnetic skyrmions as a carrier of information. Our research group has used the computing capabilities provided at the CHPC to show that the dynamic control of the skyrmion spin texture is realizable when the metal capping layer species of a symmetric magnetic tunnel junction is a heavy metal. We have found that the skyrmion exhibits a unique structural instability as the intensity of the magnetic field is changed. We also found that the time evolution of the spin texture suggests the formation of magnetic skyrmion local structure, which breaks down at low magnetic fields. These results offer insights for developing data storage technologies because it could form the basis for dynamically switchable magnetic bits.
Achievement of carrier transport through field-dependent topological phases such as magnetic skyrmions is a desirable strategy for emerging technologies. For these reasons, we have combined first principles and field-theoretic calculations to study the electrodynamics of carriers at characteristic energies at which distinct topological phase transitions occur in Dirac materials. By including explicit degrees of freedom for nuclear, electronic, and photonic interactions within the quasistatic approximation of time dependent density functional theory, we demonstrate the facile formation of a quantum fluid phase. Data generation are now complete, and two articles have been submitted to Physical Review B and Journal of Physics D: Applied Physics, in each case. We are now addressing the reviewers' comments and criticisms. Once these are completed, the manuscripts will be resubmitted for consideration for publication.
Principal Investigator: Dr Michael Owen
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2020-09-15
Allocation End: 2021-03-14
Used Hours: 18954
Project Name: CFD analysis of low cost MDI spacer
Project Shortname: MECH1367
Discipline Name: Computational Mechanics
The CHPC is being used to perform highly computational intensive transient DPM simulations using ANSYS FLUENT to investigate the effectiveness of makeshift Metered-Dose Inhaler (MDI) spacers for the safe, effective delivery of inhaled medication during the COVID19 pandemic and beyond. In hospitals, inhaled medication is often delivered by means of nebulizers but since these release water vapour into the surrounding air, they pose a serious health risk during the current pandemic since anyone in the vicinity of a COVID19 positive patient using a nebulizer would be highly exposed to the virus. MDIs (like an "asthma pump") are being used instead but these are less effective. MDI drug delivery effectiveness can be improved by using a spacer between the device and the patient but commercial spacers are expensive and therefore not practical considering the number of spacers required at present. A simple and cheap solution has been proposed that makes use of 500ml "cooldrink" bottles to perform the role of the spacer. Our simulations aim to determine the effectiveness of this approach. A model has been created and is currently being validated before the analysis can be completed. While arising during the COVID19 pandemic, the low cost MDI spacer solution being investigated in this project, if proven effective, will be useful in South African medical facilities beyond the pandemic.
Principal Investigator: Prof Yin-Zhe Ma
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2020-09-15
Allocation End: 2021-03-14
Used Hours: 2767
Project Name: Machine learning in 21-cm cosmology
Project Shortname: ASTR1323
Discipline Name: Astrophysics
The Dispersion Measurement(DM) of Fast Radio Burst is proportional to the integral of the electron number density along the line of sight. Combining the neutral hydrogen number density, we can calculate the photon-ionization efficiency of the Intergalactic Medium(IGM) along the way. Since the IGM is ionized by the high energy electron leaked from the galaxy, which is produced during the process of galaxy formation, the study of the photon-ionization efficiency of IGM is an effective way to investigate the process of galaxy formation. The recent stage of our project is to get the mean neutral hydrogen number density from the simulation as a function of redshift. With the DM obtained from observation, we can estimate the photon-efficiency of the IGM. For future experiments, there will be much more FRB data. With these data, we can combine the neutral hydrogen number density got from the other observations, such as the Lyman-alpha observation, then a catalog of photon-ionization efficiency of the IGM at different redshifts located at different directions of the sky would be obtained, which could be used to study the process of galaxy formation of the neighboring galaxies.
Principal Investigator: Mr Theo Fischer
Institution Name: eScience
Active Member Count: 1
Allocation Start: 2020-09-15
Allocation End: 2023-03-15
Used Hours: 104089
Project Name: Acid Deposition
Project Shortname: ERTH0851
Discipline Name: Earth Sciences
The 2010 Mpumalanga Highveld region power station sulphur dioxide emissions amount to 2.2 million tons. After full oxygenation and the addition of cations, this represents an increased total dissolved salt deposition load of 4.6 million tons. This is 23 times higher than the natural annual average TDS load in the runoff from the entire 38 600 km2 Vaal Dam catchment. Although only a fraction of this salt load falls on the Vaal Dam catchment, outfall of only 4% of the anthropogenically emitted sulphur could double the long-term equilibrium salt export of the Vaal Dam catchment. The importance of this investigation arises from the economic and environmental impact of the deposition of anthropogenically emitted salts on water users in the strategic heartland of South Africa on the one hand, and the expensive decisions arising from the location and technology of new power stations and industrial plant on the other. Rational decision making requires evaluation of the high costs associated with both atmospheric deposition impacts and the cost of reducing them.
Principal Investigator: Prof Obodo Kingsley
Institution Name: North-West University
Active Member Count: 5
Allocation Start: 2020-09-16
Allocation End: 2021-03-15
Used Hours: 831376
Project Name: Ab initio modelling of liquid organic hydrogen carriers catalyts and 2D materials
Project Shortname: MATS1366
Discipline Name: Physics
The current research programme "MATS1366: Ab initio modelling of liquid organic hydrogen carriers catalyst and 2D materials" was set up to carry out research activities in the area of catalyst development and other two-dimensional materials. The principal investigator is based in HySA infrastructure center of competence in the North West University, South Africa. To date, the members of the research program include: Kingsley Obodo, Hailouf Houssam, Ijeoma Onyia, and Stella Ogochukwu. The use of the CHPC facility is enabling the members to undertake in their Masters as well as Ph.D research work. The group members are undergoing sufficient progress in the work as can be demonstrated by the novel research generated, which is currently under-review and submitted for publication. Some of the systems studied during the reporting period are Sn3C2 monolayer with Transition Metal Adatom as well as the dopant complexes and the pristine Ti3N2 MXene monolayer using spin-polarized density functional theory calculations with van der Waals correction.
Principal Investigator: Mr Steven James
Institution Name: University of the Witwatersrand
Active Member Count: 4
Allocation Start: 2020-09-17
Allocation End: 2021-03-16
Used Hours: 169653
Project Name: Learning abstract representations for high-level planning
Project Shortname: CSCI1368
Discipline Name: Computer Science
We are a research group working in artificial intelligence as part of the RAIL Lab at the University of the Witwatersrand. Our work looks at how robots can use their sensory observations to learn symbolic concepts of their environment in a way that is similar to humans. For example, when planning, humans reason about the world using higher-order concepts, which allow us to ignore the unimportant details and construct long-term plans. The ability to plan far into the future is a key aspect of human intelligence and is something that must be achieved if we are to deploy robots in the real world.
Our approach relies on the robot being equipped with a set of skills, and then autonomously learning high-level concepts to support planning with those skills. Our work allows these robots to transfer these concepts to new unseen environments, which is an important step towards creating flexible robots capable of solving a variety of tasks. Ultimately, we envision our approach being used to create robots capable of operating in multiple environments, such as kitchens, hospitals and warehouses, reducing the need to develop costly, single-purpose robots.
Our approach relies on the CHPC's cluster to run numerous experiments with varying amounts of data to measure how efficiently we can construct these higher-order concepts. These results are further averaged over many trials to improve the statistical significance of our results and ensure that the outcome was not simply a fluke. We have currently reached a stage where the first phase of the project is complete - experiments in simulated environments have validated our approach. Our next step is to deploy our work on a real, physical robot to demonstrate its real-world applicability.
Principal Investigator: Prof Jan Jacobs
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2020-09-22
Allocation End: 2021-04-07
Used Hours: 177776
Project Name: Machine-learning-based modeling of electromagnetic and sound devices and applications
Project Shortname: MECH1317
Discipline Name: Other
The research group of Professor Pieter Jacobs in the Department of Electrical, Electronic and Computer Engineering at the University of Pretoria is, broadly speaking, concerned with the machine-learning-based modeling of electromagnetic and sound (specifically music) related phenomena. Currently, CHPC allocated resources have been targeted at antenna (i.e. electromagnetic) deep learning modeling. While various regression methods (e.g., neural networks, Gaussian processes, support vector machines) have previously been used for the modelling of antenna characteristics, deep learning methods have remained relatively unexplored. Fast, accurate models of antenna responses are essential for the efficient optimization of antenna structures, and could significantly reduce the time required to design antennas by reducing the time spent on highly computationally expensive electromagnetic simulations. Use of the CHPC has made it possible to train, analyze and compare thousands of different deep learning model architectures based on neural networks, deep kernel learning, and deep Gaussian processes (the first time that such an exhaustive comparison has been carried out). The CHPC enabled for these models to be trained and analyzed in parallel, which greatly decreased the time required to compare different models. In addition, a novel antenna modelling technique, based on deep kernel learning and knowledge-based neural networks, has been developed. It is envisaged that two journal papers will result from the above work.
Principal Investigator: Dr Zaid Kimmie
Institution Name: NICD
Active Member Count: 23
Allocation Start: 2020-09-23
Allocation End: 2021-04-07
Used Hours: 16802
Project Name: Covid-19 Decision Support
Project Shortname: CBBI1319
Discipline Name: Data Science
The research team contains members from the MRC, CSIR, University of Witwatersrand and University of Pretoria. The aim of the exercise is to develop a model of Covid-19 that takes into account the spatial nature of the spread of the disease and the spatial variation in factors that affect the disease. We believe that ignoring spatial effects will undermine the long-term effectiveness of Covid-19 models.
Implementing stochastic spatial models is computationally expensive and would not be possible without the parallel processing resources provided by the CHPC.
Principal Investigator: Dr Vuyani Moses
Institution Name: Rhodes University
Active Member Count: 20
Allocation Start: 2020-09-23
Allocation End: 2021-03-22
Used Hours: 1672063
Project Name: Bioinformatics and Computational Chemistry Applications
Project Shortname: CBBI1122
Discipline Name: Bioinformatics
We are a newly created research group which falls under the Rhodes University Research Unit in Bioinformatics (RUBi). Our interests are using computational techniques to solve biological problems such as drug discovery and biofuel production.
In our research group we use the CHPC resources to perform Molecular docking in-order to identify natural compounds with the potential to inhibit a wide variety of drugs targets from various diseases such as HIV and Malaria. To validate these potential compounds, Molecular Dynamics (MD) simulations are performed. Due to complex nature of these calculations, they tend to be quite computationally expensive. As result we are heavily reliant on the CHPC for the computational power required for such calculations.
The CHPC has been an integral part of our research as most of our work is 100 % computational. Therefore our students are highly reliant on the facilities and resources offered by the CHPC to complete their research projects in due time. MSc Students which were enrolled in our one year MSc programme have successfully gone through the examination process and will be graduating next year. Of these students, most are still with us pursuing PhD degrees with research projects which are still heavily reliant on the CHPC.
As a result, access the CHPC cluster is crucial to the proper functioning of our research programme.
Principal Investigator: Prof Matthew Adeleke
Institution Name: University of KwaZulu-Natal
Active Member Count: 11
Allocation Start: 2020-09-25
Allocation End: 2021-03-24
Used Hours: 162312
Project Name: Computational and Evolutionary Genomics
Project Shortname: CBBI1231
Discipline Name: Bioinformatics
Quantitative and Computational Genomics is a research group in the Discipline of Genetics at the University of KwaZulu-Natal, Durban South Africa. We employ Quantitative Genetics, Bioinformatics, metagenomics to detect pathogens (parasites and bacteria), understand their diversity and how it contributes to adaptation, drug resistance and control/prevention. Computational approach is also being used to characterize vaccine candidates against these pathogens.
Metagenomics as well as identification and characterization of the vaccine candidates require working with large sequence data and genomes of these pathogens. Some of the softwares required for manipulating the genomic sequences are available on CHPC in addition to the high computing power required for the analysis which is available again on CHPC.
The work on vaccine development using computational approach is still in formative stage 2 MSc students already submitted their dissertation for examination and 3 masters student are in their second year masters. We hope that this approach will lead to reduction both in price and period relative to traditional vaccine development methods.
Principal Investigator: Dr Steve Peterson
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2020-09-24
Allocation End: 2021-06-09
Used Hours: 157900
Project Name: Development of a Prompt Gamma Imaging Device
Project Shortname: PHYS0830
Discipline Name: Physics
The UCT Prompt Gamma Imaging (PGI) Group is a part of the Measure Research Unit based in the Department of Physics at the University of Cape Town. PGI is a new form of imaging that will be used in conjunction with proton radiation therapy cancer treatments. The protons that are used to attack the cancer cells produce gamma-rays that we are detecting and using to produce images of the dose deposited in the patient. PGI is still a technology in development and relies heavily on computing resources for both detector design and image reconstruction..
Principal Investigator: Prof Sanushka Naidoo
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-09-23
Allocation End: 2021-03-22
Used Hours: 1571
Project Name: Eucalyptus and Pine Pathogen Interactions
Project Shortname: CBBI1057
Discipline Name: Environmental Sciences
The Eucalyptus and Pine Pathogen Interactions research group, from the University of Pretoria, focuses on investigating the molecular interactions of economically important forest tree species with pests and pathogens of interest to the South African forestry industry. One of the most pressing threats to global pine cultivation is the pitch canker fungus, Fusarium circinatum, which can have a devastating effect in both the field and nursery. Many strategies are currently employed to manage F. circinatum in the field and nursery, with limited success. Investigation of the host-pathogen interaction between Pinus spp. and F. circinatum is crucial for development of effective disease management strategies. To this end, RNA-sequencing data was generated for six pine species, with varying levels of resistance, during F. circinatum challenge. As with many non-model organisms, however, investigation of host-pathogen interactions in Pinus spp. is hampered by limited genomic resources. Fortunately, advances in bioinformatics has made it possible to leverage the inherent redundancy in next generation sequencing data to assemble the reference transcriptome. A transcriptome assembly and annotation work-flow was established on the CHPC using data for Pinus pinaster. The CHPC is an essential platform that allows access to the tools needed for the generation of high quality transcriptomes and the analysis of differential gene expression. The established work-flow for P. pinaster was used to investigate host responses for the remaining species to allow comparison of host responses between species and has also been applied to Pinus nigra challenged with Diplodia pathogens.
Principal Investigator: Mr Darren Martin
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2020-09-23
Allocation End: 2024-04-02
Used Hours: 26978
Project Name: New Method for Measuring Telomeres at High Resolution
Project Shortname: CBBI1262
Discipline Name: Bioinformatics
Zoe Gill a PhD student atthe university of Cape Toown is using long-read sequencing to explore the lengths and sequence deiversity of human telomeres - the bits of DNA that cap chromosomes. She has discovered that there exists substantial diegrees of variation among people within thee regions which have previously been aassumed to be mostly identical between different people.
Principal Investigator: Dr Thishana Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2020-09-25
Allocation End: 2021-03-24
Used Hours: 83705
Project Name: Combined kinetics,quantum-chemical investigation of reaction mechanisms involving catalysts
Project Shortname: CHEM0821
Discipline Name: Chemistry
The TS Computational Chemistry Research Group (University of Kwazulu-Natal, School of Chemistry and Physics) carries out quantum chemical modelling of homogenously catalysed organic reactions in the inter-domain field of Physical-Organic Chemistry. Computational Chemistry can be classified as 'Green Chemistry' as it is sustainable and does not generate chemical waste. The focus of this research group has shifted from catalytic asymmetric synthesis. Currently, the focus is on bioactive molecules where we are attempting to compare the chemical reactivity properties of bioactive molecules for drug delivery. Computational nutraceutics which is often referred to as conceptual DFT is a new concept for predicting the molecular structure, spectroscopy, and chemical reactivity of nutraceuticals by means of computational chemistry and molecular modelling. Using this methodology, the aim is to perform a combined electronic and structure investigation to understand enzyme-inhibitor interactions that can aid in the synthesis and strategic design of novel drugs for the treatment of various infectious diseases.
The CHPC provides the facilities: hardware, in the form of the Lengau cluster and software programs such as Gaussian16, amongst many others. In 2020 our projects yielded three publications.
Principal Investigator: Prof Richard Tia
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 31
Allocation Start: 2020-09-26
Allocation End: 2021-03-25
Used Hours: 2642001
Project Name: Computational Chemistry and Materials Science
Project Shortname: CHEM1044
Discipline Name: Chemistry
The work being conducted in this research programme involves the development of active and selective catalysts for conversion of greenhouse gases like carbon dioxide into useful fuels and fine chemicals, the depolymerization of lignin, an abundant resource in plant biomass, into value-added chemicals and fuels and studies on the computer-aided synthesis of organic molecules of applications in medicine.
With increasing interest of the scientific community and government agencies on the mitigation of rising carbon dioxide levels and the attractiveness of using carbon dioxide as a feed-stock for industrial processes, this work has direct benefit for humanity.
Our research activities fall under two broad areas, namely;
1. Molecular modeling - Exploring the mechanisms of organic, inorganic and organometallic reactions.
These studies afford important molecular-level mechanistic details of industrially-relevant chemical reactions that are difficult, if not impossible, to obtain experimentally. Molecular level understanding enable chemical reactions to be guided quickly and efficiently along desirable pathways, with the effect of producing the right product with minimal energy consumption and minimal environmental impact. A key aspect of this work is the development of homogeneous transition metal catalysts for the depolymerization of lignin, an abundant natural resource, for fuel.
2. Materials modeling
The atomic- and molecular-level mechanistic insight gained from these studies are useful for the design of novel catalysts for the conversion of CO2 and other green-house gases as well as stranded gases from the petroleum refining into useful fuels. This addresses the problem of global warming as well as providing an environmentally friendly alternative sources of fuel.
The research objectives described here are very computationally-demanding and using the CHPC resources is highly beneficial. Without that, we would not be able to carry out some of these calculations.
Principal Investigator: Dr Lucy Kiruri
Institution Name: Kenyatta University, Nairobi, Kenya
Active Member Count: 6
Allocation Start: 2020-09-28
Allocation End: 2021-03-27
Used Hours: 161211
Project Name: KU Computational Chemistry Research Group
Project Shortname: CHEM1032
Discipline Name: Chemistry
CHEM1032: Kenyatta University Computational Chemistry Research Group
The areas of research include Molecular modeling, namely quantum mechanics, Molecular Mechanics and Molecular Dynamics. Dr. Shadrack is in biophysics and his work involves molecular docking and molecular dynamics of natural products and FDA-approved drugs against covid-19. He uses GROMACS 2020 and plumed plug in for his calculations. Dr Lucy on the other hand works does quantum mechanical calculations of metal complexation with modified cellulose moiety and DFT/TDDFT calculations on Dye-sensitized solar cells (DSSCs) using Gaussian 2016. We are thankful and grateful to the CHPC in fast-tracking our work since we were using core i5 desktop before where calculations would take much longer. Since the start of using the CHPC, we have made much progress on our research work. We have published a paper on the Journal of Molecular Graphics and Modelling: Ensemble-based screening of natural products and FDA-approved drugs identified potent inhibitors of SARS-CoV-2 that work with two distinct mechanisms. We look forward to more publication this year.
Principal Investigator: Prof Graham Jackson
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2020-09-28
Allocation End: 2021-03-27
Used Hours: 7067
Project Name: Insect neuropeptides
Project Shortname: CHEM1101
Discipline Name: Chemistry
Work is progressing on the design of species specific insecticides. Using molecular modelling of the insect near-receptor, we are designing compounds which will inhibit the receptor and prevent the insect from flying. Today we have worked on the malaria mosquito, the migratory locust, 3 species of fly and nematodes responsible for leishmania.
Principal Investigator: Dr Brigitte Glanzmann
Institution Name: Stellenbosch University
Active Member Count: 18
Allocation Start: 2020-09-28
Allocation End: 2021-03-27
Used Hours: 483145
Project Name: SAMRC Precision Medicine African Genomics Centre
Project Shortname: CBBI1195
Discipline Name: Bioinformatics
The advent and evolution of next generation sequencing (NGS) has considerably impacted genomics research. High-throughput technology currently allows for the generation of billions of short DNA or RNA sequence reads within a matter of hours. This becomes extremely important when studying specific diseases or when trying to identify susceptibility alleles in patients and animals, which may contribute to disease development. All of the NGS technologies lead to "big data" generation which require extensive bioinformatic and computational resources which is often beyond the scope of many research laboratories. Computational life sciences therefore relies on the implementation of well-structured data analysis pipelines as well as high-performance computing (HPC) for large-scale applications.
Principal Investigator: Dr Njabulo Gumede
Institution Name: Walter Sisulu University
Active Member Count: 1
Allocation Start: 2020-09-28
Allocation End: 2021-03-27
Used Hours: 6250
Project Name: Computer-Aided drug design for cancer therapy
Project Shortname: CHEM1058
Discipline Name: Chemistry
The Computer-Aided Drug Design for Cancer Therapy group is located at Mangosuthu University of Technology, in the Department of Chemistry. I am collaborating with Professor Winston Nxumalo from University of Limpopo. I am co-supervising one of his MSc in Chemistry students. My focus is on assisting his student with computational chemistry aspects. He has now completed his MSc successfully.
The work that I do simple involves the use of pharmacophore modeling, density functional theory, molecular docking and free energy perturbation methods. These methods helps to design new drug-like molecules and predict their binding modes and their binding affinities important for their structure activity relationships.
The White paper in higher education envisaged in 1996 stipulates that University have autonomy to perform research and development for the public good. In keeping up with that notion this research is aimed at providing solutions for the public good. Hence, the use of public resources if fitting because the end product is earmarked for people diagnosed with prostate and breast cancer.
Essentially, these cancers when they have progressed to late-stage they are aggressive and mortality rates are high. Since, drug therapies for this patient population become ineffective after three years of therapy. This is due partly to mutations and off-target interactions. Therefore, a need has grown to design drugs that will effectively inhibits various mutants that render current drug therapies ineffective.
The project is progressing very well. However, I have not utilized the GPU cluster as CHPC is currently sourcing them. I would then be able to optimize the drug-like molecules with known binding affinities to yield new derivatives with predicted relative binding affinities. Then I will synthesize them, perform in vitro bioanalytical experiments and lastly in vivo experiments. The idea is to yield potent inhibitors.
Principal Investigator: Dr Gurthwin Bosman
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2020-09-28
Allocation End: 2021-05-26
Used Hours: 14997
Project Name: Quantum computations for photoinduced reactions
Project Shortname: CHEM1126
Discipline Name: Physics
The research group is one of the arms of the Laser Research Institute in the Department of Physics of Stellenbosch University. Laser Research Institute of the Stellenbosch University, boasts of ongoing formidable research projects in the fields of ultrafast science, spectroscopy and laser diagnostics, laser development, trapped ion quantum control, and biophotonics and imaging, with a number of laboratories housing ultra-modern equipment. Our research group is focused on ultrafast transient absorption spectroscopy on chemical compounds ranging from simple molecules to polymers. Experimental setups for ultrafast transient absorption spectroscopy have been thoroughly developed over the years by different masters, doctoral and postdoctoral students. The research projects conducted in the ultrafast laboratory had produced masters' and doctoral theses, as well as peer-reviewed publications.
Scientific observations being made by experiments in our research group need to be properly understood and interpreted for proper communication to the general community. Therefore, a level of theoretical simulation which will allow deeper insights is needed. Part of this theoretical simulation is the density functional calculation, a theory well accepted to interpret molecular and/or structural dynamics we observe experimentally. The calculations can take forever if run on a single computer. This is where the Centre for High-Performance Computing (CHPC) comes in.
Centre for High-Performance Computing (CHPC) offers a wide range of theoretical coding and simulation with the advantage of supercomputing on parallel computers. This enables users' jobs submission to run on a faster scale. Our research group is privileged to have access to these supercomputing capabilities and the provision of simulation software for our calculations.
We are running series of density functional calculations ranging from simple molecules to polymers using Gaussian 09 that is provided by CHPC.
Principal Investigator: Dr Quinn Reynolds
Institution Name: Mintek
Active Member Count: 5
Allocation Start: 2020-09-29
Allocation End: 2021-03-28
Used Hours: 184811
Project Name: Computational Modelling of Furnace Phenomena
Project Shortname: MINTEK776
Discipline Name: Applied and Computational Mathematics
Look around you as you're reading this. Do you see any steel, aluminium, copper, silicon, precious metals, or similar materials? The odds are good that you're sitting in a room filled with the products of pyrometallurgy, the ancient art of using fire to extract metals from raw materials which is still the cornerstone of our modern industrialised society.
At Mintek, we are working hard on creating the next generation of technology in Pyrometallurgy 2.0. Our researchers are busy developing new high-temperature metallurgical processes which leverage renewable energy, carbon-free chemistry, efficient energy reuse, complex ore treatments, recycled wastes as ores, and similar technologies for the pyrometallurgical furnaces of the future.
A key component in these advanced process designs is engineering digitalisation - by using CHPC's powerful computers to rapidly build software and models for numerical experiments and virtual prototypes, we are able to work with our technology partners to transfer new ideas from concept to testing to industry better, faster, and cheaper than ever before.
Principal Investigator: Prof Juliet Hermes
Institution Name: SAEON
Active Member Count: 4
Allocation Start: 2020-09-30
Allocation End: 2021-03-29
Used Hours: 32818
Project Name: SAEON Coastal and Regional Ocean Modelling Programme
Project Shortname: ERTH1103
Discipline Name: Earth Sciences
The South African Environmental Observation Network (SAEON) provides data and knowledge on the state of the ocean and changes within it. Because it is so vast and dynamic, in situ monitoring arrays need to be complemented with numerical model simulations to 'fill the gaps'. The models being produced within this project provide information about how the ocean is changing and allow us to investigate why it is important and how it might impact future ecosystems, society and climate. Because the numerical models are large and require significant computing resources, the CHPC is an essential to this project. The project is doing well, a number of lower resolution simulations have been tested and now we are developing the high resolution verision (~3km horizontal grid).
Principal Investigator: Prof Veikko Uahengo
Institution Name: University of Namibia
Active Member Count: 6
Allocation Start: 2020-09-30
Allocation End: 2021-04-22
Used Hours: 22512
Project Name: Solar Materials
Project Shortname: MATS1043
Discipline Name: Material Science
The group is working on Solar materials, based at the University of Namibia (UNAM). The group is targeting local available materials with photocatalytic properties used for the development solar materials. The raw materials such as zinc oxides and copper oxides are used nowadays in the applications of harvesting energy from the sun or for phtocatalytic purposes, upon smart engineering of their band gaps. The minerals are currently exported in their raw form without even a single percentage of value addition. Importantly, energy has become critical in our ever fast growing societies which are becoming highly dependent on energy for technological advancement. Thus, local available resources must be exploited for value addition and to provide solutions to our own problems, for the benefits of the societies. The CHPC has become a powerful intermediator making life much easier for researchers, in predicting which system is suitable for a certain functionalities, then the simulations can be used to guide experimental work, by eliminating those that are not good enough for a particular functionality. This saves money in chemicals and solvents along the way. Thus far, the progress of the projects have ran smoothly and achieved milestones, that could not be possible without this Facility.
Principal Investigator: Prof Rebecca Garland
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2020-10-01
Allocation End: 2021-03-30
Used Hours: 130362
Project Name: Simulating atmospheric composition
Project Shortname: ERTH0846
Discipline Name: Earth Sciences
Air pollution can have large negative impacts on human health, agriculture, ecosystems, visibility and climate. In South Africa, although ambient air quality is regulated, many areas are out of compliance with the National Ambient Air Quality Standards. In order to protect human health and mitigate impacts, it is critical to improve air quality. The Constitution provides that everyone has a right to have an environment that is not harmful to their health. The Atmospheric Composition Focus Area (ACFA) in the CSIR Climate and Air Quality Modelling research group aims to provide the evidence base to quantify the impacts of air quality and to improve air quality.
The group uses the CHPC to run an air quality model to simulate urban and regional air quality at high resolution. This chemical transport model simulates the physics and chemistry of the atmosphere. The processes represented within the model are complex, and thus computationally intensive, which makes use of the CHPC facility a necessity. The CSIR ACFA is the only group in South Africa routinely running a chemical transport model to simulate air quality for management purposes.
Using the CHPC resources, the team has been able to simulate the impact of policy interventions on air quality in cities. Additionally, the team has simulated the health risk from air pollution regionally in South Africa. In the past, this has been done using monitoring station data only, which then limits the analysis to only those living directly around the station. The team has also simulated the impact of climate change on air pollution. These simulations use the climate projections from the CSIR's CCAM-CABLE, which is also run at CHPC, to provide meteorology input into the air quality model.
These outputs directly provide the evidence base needed for decision makers to draft and implement policies and interventions to effectively improve air quality as well as understand its impacts, now and into the future.
Principal Investigator: Prof Mohsen Sharifpur
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2020-10-01
Allocation End: 2021-03-30
Used Hours: 336427
Project Name: Computational Heat transfer
Project Shortname: MECH1073
Discipline Name: Computational Mechanics
Our research group is from the department of mechanical aeronautical engineering at the University of Pretoria. The main research field of our research group is related to improve heat transfer systems and investigation on a new generation of heat transfer fluids. Because nowadays energy plays a key
role in human being's life, and nowadays energy demands are increasing. But for modelling this kind of problems using high-performance computing is essential because of its high computational costs.
Principal Investigator: Dr Anna Bosman
Institution Name: University of Pretoria
Active Member Count: 9
Allocation Start: 2020-10-05
Allocation End: 2021-04-03
Used Hours: 33199
Project Name: Deep Learning and Neural Network Research at CS UP
Project Shortname: CSCI1166
Discipline Name: Computer Science
The research program of the Computer Science Department, University of Pretoria (UP), is headed by Dr Anna Bosman, and forms a part of the Computational Intelligence Research Group (CIRG) at UP. The focus of the program is on the following research topics: fitness landscape analysis of neural networks and real-life applications of deep learning. The following deep learning applications are currently investigated: (1) convolutional neural networks for satellite image analysis; (2) evolution of long short-term memory network architectures; (3) convolutional neural networks for image segmentation; (4) convolutional neural networks applied in the entomology domain.
Studying fitness landscapes of neural networks deepens our general understanding of the fundamental principles of neural network research, and enables progress in fundamental artificial intelligence. Deep learning applications allow us to apply modern artificial intelligence techniques in the South African context. Thus, the usage of CHPC helps us strengthen machine learning and artificial intelligence research in South Africa. Sampling and estimation techniques for fitness landscape analysis are used to probe the error surfaces of the deep and shallow neural networks. The research is of empirical nature, and entails heavy sampling of the search space. Such experiments would not be feasible without access to a computer cluster. Deep learning applications benefit significantly from being run on a GPU, therefore, access to the GPUs allows us to upscale the experiments to real-life applications. Recently, a journal article and a conference paper resulting from the experiments run on the CHPC were published. This indicates that the research program is productive, and delivers academic outputs.
Principal Investigator: Dr Mehdi Mehrabi
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2020-10-04
Allocation End: 2021-04-02
Used Hours: 59765
Project Name: Modeling of heat transfer characteristics and pressure drop of nanofluids in micro and mini tubes.
Project Shortname: MECH1086
Discipline Name: Other
Clean Energy Research Group in the Department of Mechanical and Aeronautical Engineering at the University of Pretoria is one of the leading research groups in computational fluid dynamics (CFD). In our research group, different projects are investigated numerically, and the project that I am working on is focused on heat transfer in micro and mini channels. Miniaturization has made most devices smaller than just a few years ago, which has created a challenge of thermal management. This project aims to understand the heat transfer process better and design more effective cooling devices. Due to this project's complexity, a large capacity of computational power is required, and it is where CHPC helps us decrease the time needed from weeks to few days. The project is on its middle stages, some sections of the research has been done. One master student has been graduated and one journal paper has been published so far.
Principal Investigator: Prof Hasani Chauke
Institution Name: University of Limpopo
Active Member Count: 9
Allocation Start: 2020-10-05
Allocation End: 2021-06-24
Used Hours: 205121
Project Name: Computational Modelling of Minerals, Metals and Alloys
Project Shortname: MATS1047
Discipline Name: Material Science
The minerals, metal and alloy development programme (MATS1047), led by Professor Hasani Chauke (primary investigator, PI) is amongst others one of the major strategic research niche at the Materials Modelling Centre (MMC), University of Limpopo. The work employ first-principles quantum mechanical approaches and molecular dynamics based methods, which employs various academic and commercial software's with different types of interfaces. These computers based software's are linked to local servers (MMC) and the Centre for High Performance Computing (CHPC). The programme continue to receive enormous support from the CHPC, particular to run large scale calculations at a more reasonable time. The programme constitute and support about ten postgraduate students at masters and doctoral level.
Principal Investigator: Prof Arnaud Malan
Institution Name: University of Cape Town
Active Member Count: 6
Allocation Start: 2020-10-05
Allocation End: 2021-04-03
Used Hours: 24089
Project Name: UCT CFD
Project Shortname: MECH1314
Discipline Name: Computational Mechanics
InCFD is a research group based within the department of Mechanical Engineering at the University of Cape Town (UCT). The prime objectives are to develop state-of-the-art computational fluid dynamics (CFD) modelling tools and CFD based innovation for the express support of industry. This is done via the uncompromising pursuit of innovation through fundamental research which carries the hall mark of excellence. InCFD is home to the South African Research (SARChI) Chair in Industrial CFD.
InCFD is a leading partner in the EU H2020 project SLOWD. SLOshing Wing Dynamics (SLOWD) aims to investigate the use of fuel slosh to reduce the design loads on aircraft structures. This goal will be achieved through investigating the damping effect of sloshing on the dynamics of flexible wing-like structures carrying liquid (fuel) via the development of
experimental set-ups complemented by novel numerical and analytical tools.
InCFD used CHPC to do several simulations of sloshing tanks to compute the forces and slosh damping using their in-house software Elemental. Elemental's excepational capability was proven via simulating two violent slosh experiments viz. lateral and verticle slosh in the presence of gravity. Particularly high accuracy was demonstrated, where the L2 error norm in the latter case is less than 2%. It is further shown that accounting for gas compressibility in a weak sense reduces predicted pressure peaks by up to 50% while the solver is 7 times faster to run. This is seen as a key development for more effective slosh impact design.
Principal Investigator: Dr Aijaz Ahmad
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2020-10-06
Allocation End: 2021-04-04
Used Hours: 16624
Project Name: Molecular modelling and drug design
Project Shortname: HEAL1257
Discipline Name: Health Sciences
We do combine work means we do in-silico work and validate it with in vitro. For in-silico work, we use the CHPC resources.
Principal Investigator: Prof Ponnadurai Ramasami
Institution Name: University of Mauritius
Active Member Count: 5
Allocation Start: 2020-10-08
Allocation End: 2021-04-15
Used Hours: 246463
Project Name: Computational Chemistry Methods to Study Structural and Spectroscopic Parameters
Project Shortname: CHEM1290
Discipline Name: Chemistry
I am the group leader of the Computational Chemistry Group in the Department of Chemistry of the University of Mauritius. The research interest of the group ranges from fundamental to applied chemistry. One of the research interests is to predict structural and spectroscopic parameters of novel compounds. In this context, we are currently predicting the structures of two-dimensional nanomaterials prior to their synthesis. We are also studying the electronic structure of metal oxide nanoparticles. These projects involve the use of Quantum Espresso.
We are also collaborating with experimentalists, mainly organic and inorganic chemists from African countries. From the organic chemistry perspective, we are studying cycloaddition reactions to provide insights into the reaction mechanism so as to explain the formation of the observed products. From the inorganic chemistry aspects, we are studying inorganic complexes using computational method so as to complement the experimental research in terms of structural and spectroscopic parameters. However, in some cases, where experimental data are not available, the computed parameters are useful to the experimentalists for the interpretation of results. For these projects, we are using Gaussian software. In order to test the reliability of results, we are also doing higher level calculations using ORCA software.
Without the use of the CHPC facility, it would not have been possible to carry out high level computations for the projects that we have planned. This facility is allowing us to aim at carrying out high level research and to eventually have good publications in high impact factor journals. We completed three projects and the manuscripts are currently under review.
Principal Investigator: Prof Rotimi Sadiku
Institution Name: Tshwane University of Technology
Active Member Count: 7
Allocation Start: 2020-10-09
Allocation End: 2021-04-07
Used Hours: 16749
Project Name: NANOCOMPOSITE FOR ENERGY STORAGE
Project Shortname: MATS1376
Discipline Name: Material Science
This research group is made up of masters and doctoral student across different fields of engineering and are supervised by Prof. Rotimi Sadiku, Prof. Suprakas S. Ray, Prof. Hamam, and Prof. Bonex.
The group is mandated with the development of high-performance energy storage system. Therefore, to successfully design and develop such material, the research team needs the use of High-Performance Computing resources. This is necessary in order to simulate at the atomistic level and understand the transport properties of the metal ions in the anode and how these ions arrange within the anode during charging and discharging. Without having proper understanding of the behavior of this material using computational studies, the experimental work will simply be costly.
As such, this research study will employ atomistic and multiscale modelling to investigate the ion transport, absorption energy, diffusion barrier kinetics for metal ion intercalation, the specific capacity, voltage profile, power density, charging and discharging cycle of the material to be developed for high performance storage.
Principal Investigator: Prof Cornie van Sittert
Institution Name: North-West University
Active Member Count: 26
Allocation Start: 2020-10-08
Allocation End: 2021-04-20
Used Hours: 2441466
Project Name: Computational Chemistry within LAMM at NWU (Potchefstroom)
Project Shortname: CHEM0778
Discipline Name: Chemistry
Since 1880 the main source of energy for South Africa was coal, and at present, coal provides 77% of South Africa's primary energy needs. However, electricity comes at a very high cost, namely air pollution and the influence of air pollution on human health. In 2004 the South African government reformed the legislation about air pollution. To contribute to the management of air quality, new energy sources must be investigated. These new energy sources must be affordable, clean and renewable. Some of these alternative energy sources are fuel cells and batteries. Electricity from fuel cells and batteries is obtainable through electrochemistry, where free energy of spontaneous reactions is transformed into electricity. A potential replacement form of energy is the hybrid sulphur (HyS) cycle. The HyS cycle is a two-step water-splitting process, which could be used for the production of hydrogen. In the HyS cycle, the anode material used is platinum. However, because platinum is a rare and expensive metal, it is not an economically viable option for long-term and large-scale hydrogen production. Hence, various attempts to reduce or eliminate the platinum content while not compromising the process performance has been made. To understand the electrochemistry of the anode and make informed decisions on the type and amount of metal to be used in various platinum alloys, investigations on a fundamental level are needed. These type of investigations could be classified as computational chemistry. The resources needed for these type of investigations, namely various types of hardware and software is of cardinal importance. Although resources are available at NWU, it is not nearly enough to fully support the research covered in the Laboratory of Applied Molecular Modelling (LAMM). So if we, as researchers within the LAMM, did not have access to the CHPC resources, the progress of our research will be much slower.
Principal Investigator: Dr Eric Maluta
Institution Name: University of Venda
Active Member Count: 11
Allocation Start: 2020-10-12
Allocation End: 2021-04-22
Used Hours: 413170
Project Name: Energy Material Modeling in the Application of different Photovoltaic Technologies
Project Shortname: MATS0827
Discipline Name: Physics
The Department of Physics at the University of Venda is working on the understanding of the properties of different materials for application in renewable energy technologies through the density functional theory simulations as performed under the CHPC cluster. The main aim is to reduce the cost of the material used in renewable energy technologies for the future use and mitigate climate change through energy supply. We are also building capacity of the rural students on the postgraduate studies and skill development. The CHPC is a gateway for the department of Physics of the University of Venda as an institution situated in the rural area to produce researchers and to publish research work. There is a growing number of students research work from honours to the PhD level. Several student are getting their masters and PhD degree through these initiatives.
Principal Investigator: Prof Stefan Ferreira
Institution Name: North-West University
Active Member Count: 5
Allocation Start: 2020-10-13
Allocation End: 2021-04-11
Used Hours: 1054368
Project Name: Astrospheres
Project Shortname: ASTRO1277
Discipline Name: Astrophysics
The project aims to simulate the astrosphere around a star. These astrospheres consists of the outblowing stellar wind and like our local heliosphere shields planets from interstellar cosmic ray radiation. In this project we aim to run advanced codes to simulate astrospheric evolution and particle transport within. We were recently contacted by an European group to provide benchmarks and tests between our results and their results.
Principal Investigator: Dr Gerhard Venter
Institution Name: University of Cape Town
Active Member Count: 7
Allocation Start: 2020-10-13
Allocation End: 2021-04-11
Used Hours: 481992
Project Name: Simulation of Ionic Liquids
Project Shortname: CHEM0791
Discipline Name: Chemistry
Dr Venter's research group is part of the Scientific Computing Research Unit at the University of Cape Town and uses computer simulation to study the chemical and physical properties of biopolymers in a special class of solvents, called "ionic liquids". These simulations provide insight into the intermolecular interactions and chemical behaviour that control the dissolution and subsequent reactivity of these naturally occuring polymers. A better understanding of these processes can lead to the rational design of new, environmentally friendly solvents systems that can dissolve biomass and enhance its reactivity. The dissolution of biomass is the first step in converting naturally occuring polymers to biofuels and other platform chemicals.
High performance computing is required for all research conducted in this group and without the resources and infrastructure provided by the Centre for High Performance Computing (CHPC), the research will not be possible.
Principal Investigator: Dr Luna Pellegri
Institution Name: University of the Witwatersrand
Active Member Count: 1
Allocation Start: 2020-10-14
Allocation End: 2021-04-12
Used Hours: 7074
Project Name: Developing of new techniques for real-time verification in proton-therapy
Project Shortname: PHYS1327
Discipline Name: Physics
One of the most critical issues in proton-therapy is the real-time verification of the dose delivered during the treatment. An approach for monitoring the treatment planning system accuracy during the irradiation is investigated in this project. The methodology is based on enhancing the production of characteristic prompt-gammas in the tumour. The work is performed by Dr L. Pellegri and Ms S. Hart from the University of the Witwatersrand and iThemba LABS in collaboration with the group of Prof. C La Tessa from the University of Trento (Italy). The first part of the project consisted in the verification via GEANT4 simulations of the feasibility of the project. Due to the heavy computing power that these simulations require, the use of the CHPC Lengau Cluster was crucial. The preliminary results show that the gamma ray response is sensitive to the doping nucleus investigated if in used in pure concentration. The simulations performed will be compared with experimental data collected at Proton Therapy Center Trento (Italy).
Principal Investigator: Prof Chris Meyer
Institution Name: Stellenbosch University
Active Member Count: 5
Allocation Start: 2020-10-14
Allocation End: 2021-04-12
Used Hours: 386341
Project Name: Development of CFD models
Project Shortname: MECH1077
Discipline Name: Computational Mechanics
The research activity is led by Prof CJ Meyer from Stellenbosch University and is focused on developing computational models of industrial thermo- and fluid dynamic processes. There is a specific emphasis on the use of free software under the GNU General Public License. The industrial processes under consideration are those relevant to specific segments of industry in South Africa most notably power generation. Current projects include the simulation of large-scale air-cooled condensers as well as detailed simulations concerning the flow through axial flow fans used in the energy sector. The cohort of students are making excellent progress.
Principal Investigator: Prof Rosemary Dorrington
Institution Name: Rhodes University
Active Member Count: 9
Allocation Start: 2020-10-14
Allocation End: 2021-04-12
Used Hours: 14882
Project Name: Marine Natural Products Research
Project Shortname: CBBI0963
Discipline Name: Bioinformatics
Marine Natural Products Research Group, Department of Biochemistry and Microbiology, Rhodes University
The Marine Natural Products (MNPs) Research Platform covers the broad field of marine biodiscovery, focusing on the potential of bioactive secondary metabolites produced by marine organisms endemic to the Agulhas Bioregion as lead compounds for drug discovery. More than half of new pharmaceutical drugs on the market or in clinical trials are natural products and their derivatives and the majority of these are now coming from marine macrofauna and their associated microbiomes.
The MNPs research programme is active across the broad field of marine biodiscovery, focusing on exploring the potential of marine invertebrates and their associated microorganisms as sources of novel bioactive small molecules. Research projects include: (1) Biodiversity mapping of benthic habitats in the Agulhas bioregion, focusing on invertebrates, ascidians, soft corals and their associated microbiota; (2) Isolation and characterization of bioactive secondary metabolites of marine organisms; (3) screening marine natural product libraries for anti-viral, anti-cancer and antibacterial activity and (4) elucidating the metabolic pathways that result in the production of lead compounds to pave the way for engineering recombinant systems for their production for the pharmaceutical industry. Associated projects focus on the application of high throughput metagenomic and analytical chemistry technologies to map patterns and processes in marine ecosystems. These "omics" approaches e.g. next generation DNA and RNA sequencing and high resolution tandem mass-spectrometry generate very large and complex datasets, the analysis of which requires the high performance computing capacity provided by the CHPC.
Principal Investigator: Prof Sybrand van der Spuy
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2020-10-14
Allocation End: 2021-04-12
Used Hours: 610900
Project Name: CFD simulation of turbomachinery
Project Shortname: MECH1187
Discipline Name: Computational Mechanics
The turbomachinery research group at Stellenbosch University has been making use of the CHPC for their CFD simulation work during the past three years. The use of the CHPC enables the accurate and detailed modelling of aspects like gas turbine combustion and fan noise. The results achieved to date have been world class.
Principal Investigator: Dr Fabio Cinti
Institution Name: NITHEP
Active Member Count: 4
Allocation Start: 2020-10-15
Allocation End: 2021-04-13
Used Hours: 238316
Project Name: Quantum Monte Carlo for ultra-cold atoms
Project Shortname: PHYS0892
Discipline Name: Physics
This project aims to boost the operational temperature of bistable magnetic molecular materials, called Single Molecule Magnets (SMMs), by identifying, understanding, and eventually overcoming the two main problems related to the hysteretic properties of these materials (e.g. the disappearance of hysteresis at high temperature and the butterfly-like shape of the hysteresis curves). The target application of these materials is the storage of information at the molecular level.
The main goal will be reached by achieving a series of sub-objectives:
• Characterizing the electronic structure and the static and dynamic magnetic properties of a series of lanthanide-based complexes.
• Developing a code that reproduces and models the experimental data
• Understanding the main reasons behind the quench of hysteretic behaviour at high temperature/low fields and consequently identifying the right strategy to design high
performances SMMs.
Principal Investigator: Prof Bruce Bassett
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 2
Allocation Start: 2020-10-15
Allocation End: 2021-09-09
Used Hours: 20305
Project Name: Machine Learning for Astronomy
Project Shortname: ASTR1157
Discipline Name: Astrophysics
MeerKAT and the SKA will provide a wonderful opportunity to discovery completely new kinds of astronomical sources. However, automatically discovering new classes of objects is very difficult since algorithms do not know what to look for. The research group of Prof. Bruce Bassett has been working actively on developing more human-level algorithms to detect such anomalies. The challenge is to help the algorithm adaptive identify good features that identify anomalies accurately and separate them from standard, well-known classes.
On the other hand we have been working on neural machine translation for African languages for which there is typically very little available translation data. We will explore the use of multilingual learning - in which one trains a machine translation model simultaneously on multiple languages - for African languages which exploits the linguistic similarities between languages in the same family.
A part of this exploration will be the use of monolingual data to help circumvent the lack of translation training data. The end goal is to build translation models for African languages for which there are currently no support from services such as Google translation.
CHPC facilities will be important since training deep learning neural machine translation models is computationally very expensive.
Principal Investigator: Dr Ryno Laubscher
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2020-10-16
Allocation End: 2021-04-14
Used Hours: 98639
Project Name: University of Cape Town Applied Thermal-Fluid Research Unit
Project Shortname: MECH1279
Discipline Name: Computational Mechanics
The ATProM research group, who forms part of UCT's Mechanical Engineering Department, specializes in thermofluid modelling of energy conversion processes such as heat exchangers, combustion systems and power cycle components. The simulation techniques range from process modelling to using artificial intelligence methods such as neural networks. Currently, one of the main focuses of the group is the development of computationally efficient simulation models of complex energy conversion systems. These types of models can be used to perform in-situ condition monitoring, optimization and fault finding. Developing such models requires simulation result databases which is typically generated using large computing facilities such as the CHPC. Once the simulation database is created, a surrogate model is developed using data-driven techniques. Currently, the project is progressing well and have already resulted in numerous international publications.
Principal Investigator: Prof Kevin Naidoo
Institution Name: University of Cape Town
Active Member Count: 12
Allocation Start: 2020-10-16
Allocation End: 2021-04-14
Used Hours: 925870
Project Name: Reaction Dynamics of Complex Systems
Project Shortname: CHEM0840
Discipline Name: Chemistry
The Scientific Computing Research Unit (SCRU) directed by Prof Kevin Naidoo is built from the following laboratories:
Computation & Modelling Laboratory
Cancer Translational Science Laboratory
Informatics & Visualisation Laboratory
All three laboratories make direct or indirect of CHPC resources to develop diagnostics for Cancer or Therapeutics in Biomedicine. Of national interest is the collaboration between the SCRU laboratories and the CHPC to make advance computation more easily accessible to South African researchers in the fields of Biology and Chemistry through the CHPC's hosting of the Galaxy Biomolecular Reaction Interaction Dynamics Global Environment (BRIDGE). Prof. Naidoo's research groups are mostly interested in the development and applications of methods useful to Life Scientists. He is a domain specialist in code development for Free Energy methods, Molecular Dynamics and unsupervised Machine Learning. Flagship codes developed by Prof Naidoo and his students are the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF), Free Energy Force Induced (FEFI) coarse grained molecular dynamics and the Denoising Autoencoder Self Organising Map (DASOM). The SCRU Cancer Translational Science Laboratory links the computation and informatics technologies with laboratory experiments to provide models for cancer research scientists aiming to achieve Translational Research goals cancer care.
Principal Investigator: Dr Caroline Kwawu
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 12
Allocation Start: 2020-10-15
Allocation End: 2021-04-13
Used Hours: 587075
Project Name: Renewable Energy Materials
Project Shortname: MATS1146
Discipline Name: Material Science
The research group is a computational materials group. We are into the study and identification of new and novel energy materials for CO2 conversion and biomass conversion to fuel. We are also interested in photo-absorbers for sunlight conversion into electricity.
The research is very crucial to combat Climate change by reversing CO2 into useful forms. We are optimistic at the rate we are going to inspire our students to venture into this field. We are investigating novel modified transition metals, homogeneous catalysis and metal organic frameworks for renewable energy production. We employ theoretical techniques based on the DFT theory to simulate chemical reactions. The CHPC is currently the only computing resource available to my group to conduct research and has been very instrumental to the progress of my work. So far 4 publications were made possible because of the CHPC facility. We hope to publish much more soon.
Principal Investigator: Dr Winfred Mulwa
Institution Name: Egerton University, Egerton, Kenya
Active Member Count: 8
Allocation Start: 2020-10-19
Allocation End: 2021-04-17
Used Hours: 752857
Project Name: Magnetic Refrigeration
Project Shortname: MATS1181
Discipline Name: Physics
Who: MATS1181 under PI Winfred Mulwa from Egerton University Kenya: Magnetic refrigeration. What: Magnetization and demagnetization of magnetic materials known as magnetic refrigeration that rely on magnetocaloric effect (MCE). In cooling technology, magnetic refrigeration which depends on magnetocaloric effect is commonly used in refrigerators to achieve exceptionally low temperatures. Why: . Magnetic refrigeration does not rely on the uses of harmful and ozone-depleting coolant gases. How: This work is done computationally. We use the Quantum Espresso code (Density Functional Theory). This purely depends on CHPC because all the calculations have to be done in CHPC. Thanks to CHPC. How is the project progressing: We have achieved all the objectives. The project is as planned. Two of my MSc students are graduating in June 2021.
Principal Investigator: Prof Zenixole Tshentu
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 9
Allocation Start: 2020-10-19
Allocation End: 2021-04-17
Used Hours: 105530
Project Name: Metal-ligand, anion-cation interactions and protein-ligand studies
Project Shortname: CHEM0864
Discipline Name: Chemistry
The group at NMU Chemistry Department under the leadership of Prof Tshentu is engaged in developing selective chemistry for beneficiation of chemical resources. The work on developing reagents that are selective for precious metals has made gains and continues to produce reliable materials that could have industrial applications. The work on desulfurization and denitrogenation of fuel has contributed to the search for selective methods for removal of contaminants from fuel (N and S compounds) and is therefore contributing to upgrading of fuel towards a zero-sulfur level. Theoretical studies contribute to the smart design of selective reagents and functional materials. We are grateful to CHPC for the computational chemistry facilities.
Principal Investigator: Prof Eno Ebenso
Institution Name: North-West University
Active Member Count: 5
Allocation Start: 2020-10-19
Allocation End: 2021-04-17
Used Hours: 329359
Project Name: Theoretical Investigations of Corrosion Inhibition Activities of Organic Compounds
Project Shortname: CHEM1176
Discipline Name: Chemistry
Our research group, Materials Science Innovations and Modelling Research Focus Area is domiciled at the Mafikeng Campus of North-West University.
The group conducts research activities on materials design and applications. Specific research focus includes but not limited to the design of corrosion inhibitors and electrochemical sensors. Other areas of interest are thermodynamics of solutions, materials for environmental remediation, reaction mechanism monitoring. The group utilizes computational chemistry software such as Gaussian and Materials Studio. Computational studies conducted in the group are mostly used to corroborate experimental results to ensure comprehensive scientific findings.
Using computational studies, we have been able to predict corrosion inhibition mechanisms of many organic compounds. We recently developed Artificial Neural Network (ANN) model that could aid the design of novel corrosion inhibitors. Our continuous access to CHPC facilities has assisted us in timely execution of research plan and results acquisition. We have been able to achieve significant improvement in calculation speed when compared to our previous experience using PC.
Principal Investigator: Dr Lonnie van Zyl
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2020-10-21
Allocation End: 2021-04-19
Used Hours: 41000
Project Name: Engineering bacterial pyruvate decarboxylase for increased thermostability
Project Shortname: CBBI1265
Discipline Name: Bioinformatics
Dr. Leonardo van Zyl at the The Institute for Microbial Biotechnology and Metagenomics (IMBM) at the University of the Western Cape is investigating which portions of an enzyme contribute to its stability at high temperatures. The enzyme being investigated is called pyruvate decarboxylase (PDC) that catalyzes the conversion of pyruvate, a central metabolite in bacterial cells, to acetaldehyde. Through the action of a second enzyme called alcohol dehydrogenase, the acetaldehyde is converted to ethanol. This makes the enzymes useful in engineering bacterial strain to enable them to produce ethanol from renewable resources such as plant waste material. Bacteria which grow at high temperatures (60C), called thermophiles, have been identified as possible candidates for ethanol production, as ethanol production at these elevated temperatures has benefits for the process. The PDC enzymes are only found in organisms that grow at moderate temperatures and thus cannot withstand the high temperatures during the fermentation process. This research aims to identify the areas of the protein susceptible to high temperatures and engineer the enzyme to cope with the higher temperature. The protein crystal structures for the least- and most thermostable versions of PDC have been solved, and we can use computer simulations of the movement of these proteins at various temperatures to identify where the structure fails and address it by incorporating chemical bonds that are not so easily broken thereby retaining its functionality. A general thermostabilizing feature has not been identified for all proteins, and there is exists a huge demand for thermostable variants of a wide range of proteins globally. Should this work be successful it may suggest a general workflow for the engineering of thermostable proteins as well as shed new light on thermostabilizing features of proteins. Dr. van Zyl used the CHPC Lengau cluster to perform 250 nanosecond simulations of these medium sized (240000 atoms) protein systems at 25C and 60C to establish how temperature affects these proteins. This work should help South Africa grow its knowledge economy, display the talents of its researchers and possibly help it be a global competitor in the biofuels market through the use of publicly funded computational resources.
Principal Investigator: Dr Gebremedhn Gebreyesus Hagoss
Institution Name: University of Ghana
Active Member Count: 5
Allocation Start: 2020-10-23
Allocation End: 2021-04-21
Used Hours: 84143
Project Name: Atomistic simulations and condensed matter
Project Shortname: MATS1031
Discipline Name: Physics
The condensed matter research group at the Department of Physics, University of Ghana is focused on the study of the structural, electronic, magnetic, and optical properties of 2D and bulk materials. Computational simulations of the properties of these materials are studying using density functional theory and extended Hubbard functionals, GW approximation of many-body perturbation theory (MBPT), and the Bethe-Salpeter equation (BSE).
Our computational work would not be possible without the enhanced computing resources available at the CHPC in South Africa. Typically, we prepare our input files in our laptops and works stations and submit the job to the CHPC cluster. The job is monitored at least once a day and the results downloaded when completed.
The main focuses of our research are on transition metal oxides, perovskite materials, and ruthenates. These materials are very useful for energy harvest and storage. The following are topics of researches in my group.
1. Electronic, magnetic, structural, and optical properties of transition-metal oxides. First principle calculations were carried out to study the structural, electronic, optical, and magnetic properties of transition metal oxides. The results are compared to our experimental results.
2.Perovskite Materials for energy applications The accurate description of the structural, Electronic, and optical properties of low-temperature phase perovskite are not yet well established. In this project, we focus on the investigation of structural, electronic, dielectric, and vibrational properties of low-temperature phase perovskite materials using density functional theory with the inclusion of the onsite and inter-site Hubbard correction (DFT+U+V).
3. Two-dimensional Materials Research The 2D transition metal dichalcogenides are compounds that we are interested to study in this project, have a chemical formula MX2 (where M = Ti, Mo, Nb, W, Hf, Re, etc. and X = S, Se, and Te). In particular, we focus on controlling the excitonic properties of 2D HfS2 monolayer via lanthanide substitutional doping using GW and BSE. 4. Ruddlesden-Popper perovskite ruthenates The Ruddlesden-Popper perovskite ruthenates have a chemical formula (Sr, Ca)n+1RunO3n+1. The magnetic and electronic properties of these materials depend on the layer number and the structural distortions. In this project, we focus on investigating the structural, electronic, magnetic, and optical properties of Sr4Ru3O10 using DFT with the inclusion of the onsite Hubbard correction (DFT+U) and spin-orbit coupling.
Principal Investigator: Dr Chris Barnett
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2020-10-26
Allocation End: 2021-04-24
Used Hours: 70288
Project Name: Analysis of disease related polymers
Project Shortname: CBBI1063
Discipline Name: Bioinformatics
I investigate the shapes, structures, and properties of molecules by using computational modelling techniques. I'm particularly interested in complex sugars (glycans), which are interesting to study because they are involved in intricate molecular recognition processes in cells, for example, playing a role in cell signalling, adhesion, and immunity. Further understanding of these molecules and the complex systems they are involved in may lead to the generation of additional diagnostic markers and inhibitors that can be used to combat disease. The CHPC provides a platform for being able to run large-scale and highly parallel simulations which is a great help in making rapid progress towards solving research questions. The CHPC is also a test bed when carrying out computation on and developing algorithms for large datasets.
Principal Investigator: Dr Pedro Monteiro
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 16
Allocation Start: 2020-10-26
Allocation End: 2021-05-05
Used Hours: 217519
Project Name: Southern Ocean Carbon - Climate Observatory SOCCO
Project Shortname: ERTH0834
Discipline Name: Earth Sciences
SOCCO is a CSIR-led and DSI co-funded programme that uses the comparative geographical advantage that South Africa has in the Southern Hemisphere to contribute to the global research challenge of understanding the role of the Southern Ocean in global and regional climate. The SOCCO research niche is to explore the role played by fine scale ocean dynamics in improving the climate sensitivity of ocean and coupled numerical models with a special focus in understanding the Southern Ocean's role in the CarbonClimate links. To address the scales of dynamics in the ocean, we primarily use the coupled NEMO-PISCES model in a hierarchy of resolutions from 200 km to 2 km - using the models as experimental platforms. The finer the resolution, the greater the number processes that contribute to ocean-atmosphere carbon exchange. This understanding contributes to reducing model biases in process models and climate projections as well as the development of a South African Earth Systems Model (ESM). This work advances research in global climate change based on the importance of feedbacks of the Southern Ocean dynamics on the carbon-climate system. Additionally, the ESM will be used to explore how the climate sensitivities of the Southern Ocean evolve over the 21st century as well as being South Africa's first submission to the 6th Assessment Report of the IPCC. ESM will be the basis for the medium to long term climate projections in Africa which will then support societal needs in health, water resource planning, agriculture, biodiversity management and more broadly in economic development in the region. From regional, forced ocean models to fully-coupled earth system models comprising of interacting ocean, ice, atmosphere, land, ocean biogeochemical models, numerical modelling of earth system components require massively parallel computing resources. The size and complexity of these models are such, that for SOCCO's work, the CHPC is indispensable for the resources and service it provides.
Principal Investigator: Prof Marla Trindade
Institution Name: University of Western Cape
Active Member Count: 1
Allocation Start: 2020-10-28
Allocation End: 2021-04-26
Used Hours: 30354
Project Name: Microbial genomics
Project Shortname: CBBI1149
Discipline Name: Bioinformatics
Microorganisms carry a wealth of potential in their genomes. They can produce enzymes for industry and small molecules that could be antibiotics, anti-cancer drugs, anti-inflammatories and a host of other medically useful compounds as well as being used as whole cell biocatalysts. For humans to better understand how to best use this potential we need to unlock the genetic code in order to take advantage of what they can offer humanity. At the Institute for Microbial Biotechnology and Metagenomics (IMBM) we have isolated thousands of bacteria and their viruses from a variety of environments which we test for their ability to produce such proteins and compounds and determine how they function. One of our successes is the isolation of a novel ornithine lipid synthase from a oil contaminated site using a special technique called metagenomics. This gene allows for the production of a biosurfactant which are compounds which can replace chemically synthesized surfactant in future products. To get to grips with the molecular mechanism by which ornithine lipid synthase (OlsB) couples the non-proteinogenic amino acid ornithine to a fatty acid chain we are in the process of determining the three dimensional structure of the protein which should shed light on how it does this. To complement the analysis of the static 3D structure, modelling and molecular dynamic simulations will be performed to clarify how the enzyme functions. A second project aims to understand the mode of action of novel lanthipeptide found in a marine bacterium. Lanthipeptides are well known antibiotics and are often used in food preservation, but can also have other bioactivities. They normally exert their bactericidal activity by self assembling into pores in bacterial cell membrane leading to leakage of the cytoplasm and cell death. Molecular dynamic simulation of the new lanthipeptide in a cell membrane may give clues as to how the newly discovered peptides are similar or different to those that have been previously characterized. Currently IMBM does not have the resources to simulate these 100000+ atom systems for the length of time it requires to see meaningful changes in the protein itself or interaction with substrates. The CHPC's Lengau cluster is the fastest computer on the African continent, which supports GPU-based computation. The software (NAMD) used to model and simulate these dynamics was expressly written to take advantage of the massively parallel computing capabilities offered by GPU-compute and is one of the software packages offered by CHPC to researchers. We therefore now have access to a system which allows us, through simulation, to see these molecular interactions that may lead to robust designer enzymes for industry or altered enzymes for the production of bespoke small molecules.
Principal Investigator: Dr Joseph Mutemi
Institution Name: University of Nairobi
Active Member Count: 3
Allocation Start: 2020-10-28
Allocation End: 2021-05-05
Used Hours: 82391
Project Name: Numerical weather and climate modeling, prediction, forecasting and change projections for Africa and sub regions
Project Shortname: ERTH1131
Discipline Name: Earth Sciences
The ERTH1131 is led by Dr. Joseph Mutemi, Senior Lecturer at the University of Nairobi, Department of Meteorology, Kenya. The research group is addressing knowledge gaps in the science of weather and climate predictions alongside long term projections over East Africa and the socio-economic implications. The group is using the physical science of weather and climate aided by higher performance computer modeling and information processing from large data sets. Many areas in East Africa including Kenya are affected by frequent disasters induced by weather extremes whose long term manifestations are unfavourable climate impacts. Communities and policy makers need information on these extremes in advance of their occurrence to make decisions which help society to cope and build resilience.
Good examples modeled using the CHPC facilities are the devastating weather conditions and floods in Kenya during 2018 which had many catastrophic consequences. Further, the period 2019 has also been modeled. While tropical cyclone Idai and Kenneth afflicted Southern Africa, the conditions across Kenya was total failure during March to May season. Even though end of 2019/ early 2020 was remarkably wet over Kenya, drought set in parts northern Kenya during from mid 2020 to April 2021 (minutes 5.52 to 19.44 in https://www.youtube.com/watch?v=oWLb86vZZA8). The 2021 drought in northern Kenya has led to massive loss of livestock among the pastoralists communities.
The modeling work is also an opportunity for scientific capacity building in Kenya in the University of Nairobi. Early career researchers at masters and doctorate are levels are conducting in-depth climate research using the CHPC facilities for computational work, namely script development and analysing large global models and observations including satellite data sets.
Ongoing research is about 25% complete, so there remains work to understand and better develop techniques to advance early warning as a way to adapt to the current climate related challenges in East Africa.
Principal Investigator: Prof Ignacy Cukrowski
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2020-11-02
Allocation End: 2021-05-01
Used Hours: 552084
Project Name: Understanding chemistry from QM study of molecular systems
Project Shortname: CHEM0897
Discipline Name: Chemistry
Activities in chemistry (in science in general) can be seen as made of two distinctive approaches: 1) development of new theories and methodologies that should lead to better understanding of concepts and chemical process (reactions) and 2) practical implementation of known or new methodologies that should lead to routine and highly efficient experimental/computational operations. Our research group in the Department of Chemistry, University of Pretoria (Prof. Ignacy Cukrowski (the leader), Dr. Jurgens de Lange, several PhD, MSc and Honours students as well as a postdoctoral Fellows) is involved in fundamental studies. Our focus is primarily on understanding fundamentals governing inter-atomic and inter-fragment interactions from the electron density distribution throughout a molecule, or molecular system in general. For instance, there are many kinds of chemical bonds but still there is no an ultimate general theory of bonding. Hence, there are various approximate quantum chemical models that are being used to describe and explain just a specific kind of bonding. In our group we prefer to interpret classical chemical bonding, regardless of its kind, as an interaction governed by universal laws of physics. This allows us to expend the concept of interactions from classical 2-atom approach (a chemical bond) to poly-atomic interactions involving fragments of a molecular system. Such approach proved to be very useful in modelling reaction mechanisms to understand (on atomic and molecular fragment level) how and why new compounds are or are not formed as planned by a synthetic (in)organic chemist. Full understanding of successful and failed synthetic processes is of great importance as it must aid the development of, e.g., new drugs needed for treatment of (i) highly contagious diseases, such as tuberculosis, HIV/AIDS, or (ii) Alzheimer, a disease with reported cases growing rapidly throughout the world. It is important to realize that such theoretical work requires, due to the size of molecular systems under investigations, dedicated and expensive computational facilities, such as CHPC, with a dedicated staff to ensure that research groups can access and make use of computational centre 24/7.
Principal Investigator: Prof Edet Archibong
Institution Name: University of Namibia
Active Member Count: 3
Allocation Start: 2020-11-03
Allocation End: 2021-05-02
Used Hours: 7667
Project Name: (1) Computational Study of Semiconductor Clusters. (2) Computational Study of Bio-active Molecules Extracted from Plants
Project Shortname: CHEM0969
Discipline Name: Chemistry
The service provided by CHPC has made it possible for two MSc students working at the Computational Chemistry Laboratory of the University of Namibia to complete their research work successfully. Mr. Owen Puley and Ms. Elizeth Humba will graduate with MSc degree (Chemistry). Their projects were done using the CHPC Lengau machine. The work of Elizeth Humba allow understanding of how properties of doped titanium clusters vary with chain length. This work potentially has useful application in the semiconductor industries. The work of Owen Puley estabilished that the structures and properties of primary ozonides which are formed when ozone reacts with phenolic compounds are similar in the gas phase and in aqueous solution. The latter result is important with regards to our knowledge of the interaction of ozone with phenolics in water and in the atmosphere.
Both theses rightly acknowledged the service and assistance provided by CHPC. Without the latter, it will be impossible to conduct the research projects at the level they were done.
Principal Investigator: Dr Geoff Nitschke
Institution Name: University of Cape Town
Active Member Count: 11
Allocation Start: 2020-11-03
Allocation End: 2021-05-02
Used Hours: 1042042
Project Name: Evolving Complexity
Project Shortname: CSCI1142
Discipline Name: Computer Science
The research aims to invesigate the efficacy of completely new robot designs to solve problems in environments that humans cannot easily reach (e.g. deep-sea beds and space) -- this robot design is automated ina complex 3D physics-based simulation, when the environment and task is fed in by the user - what the simulation outputs is the design for new robots that can potentially be physically constructed by engineers to solve these same problems in the real-world.
Principal Investigator: Dr Phillip Nyawere
Institution Name: Kabarak University, Nakuru, Kenya
Active Member Count: 6
Allocation Start: 2020-11-06
Allocation End: 2021-05-13
Used Hours: 252109
Project Name: Barium Floride and Perovskites
Project Shortname: MATS0996
Discipline Name: Physics
Our team of Barium-Perovskite is a team of computational physics simulation base in Kenya and in various universities. As the lead investigator, I have worked with CHPC since my postgraduate until attaining my PhD in the year 2013. I have mentored others through this resource and so far graduated one PhD student, Elicah Wabululu in the year 2020. Another student Truphena Kipkwarkwar has successfully defended her MSc thesis at Kabarak University and is expected to graduate later this year.
Our work is involved in simulation and characterization of materials for purposes of photovoltaic application and other related research including superconductivity. These are areas of interest currently both in theoretical and technological applications.
Training of students is critical because it provides human resource necessary for training in our universities. We also look forward to partnership with industry to provide important information in the application of the materials being improved through property-application relations.
Our work is done through computer simulation. Using various mathematical algorithms which are installed in the CHPC machine as computer codes necessary for achieving these goals.
So far our process has covered sizeable grounds in equipping our students as future technocrats. We expect more graduations in the next two years culminating into a new cohort of researchers that will form the next generation of researchers,
Principal Investigator: Dr Ndumiso Mhlongo
Institution Name: University of KwaZulu-Natal
Active Member Count: 15
Allocation Start: 2020-11-09
Allocation End: 2021-05-08
Used Hours: 71022
Project Name: Biomolecular Modelling Research Unit
Project Shortname: HEAL1002
Discipline Name: Health Sciences
Biomolecular Modelling Research Unit is located at the University of KwaZulu-Natal, Howard College Campus and headed by Dr Ndumiso N. Mhlongo. This research group employs CHPC resources to conduct molecular dynamics simulations to analyse the dynamical properties of macro-molecules such as folding and allosteric regulations; ligand-receptor interactions; atom-to-atom interactions; protein-protein interaction;virtual screening and molecular docking of molecules for the design and development of inhibitors against diseases and disorders. Through the use of CHPC resources, we have designed potential inhibitors against M. tuberculosis and cancer treatment. These have made contributions to discovery new inhibitors & new knowledge which could directly translate into real health benefits of the society.
Principal Investigator: Prof Walter Schmitz
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2020-11-09
Allocation End: 2021-05-08
Used Hours: 5015
Project Name: Particle segregation
Project Shortname: MECH1258
Discipline Name: Computational Mechanics
The Pulverized Coal (PC) used in a coal-fired boiler consists of fine powder crushed and grinded from raw coal chunks of about 50 mm in diameter down to particles of about 100 microns and smaller. The presence of foreign material other than carbon particles contributes to a multitude of problems including wear of mill internals, boiler tube leaks, poor combustion and production of harmful emissions. The removal of unwanted non-carbon particles from PC (also called coal beneficiation) is therefore much needed in the quest for clean coal combustion.
The segregation of solid particles in an air Fluidized Bed (FB) as described in this paper finds application in the coal beneficiation industry. Two application stages are considered; Firstly raw crushed coal with particle size range between 1 and 15 mm ready to enter the mill and secondly inside the mill where particles with a size range between 0.1 and 1 mm is targeted. Particle segregation in a FB is based on a sink / float principle. Particles ending up at the bottom is called Jetsam and those at the top Flotsam. Particles segregate due to combinations of density and size differences. With particles of similar density the large size particles will tend to sink while small size particles will rise. With similar size particles the denser particles will sink and lighter particle will rise. Complication may arise however with particles mixtures consisting of small dense particles and larger less dense particles.
In order to optimally employ differences in particle density and size for the purpose of segregation a thorough understanding is needed of the segregation mechanisms involved. Towards this end numerical analysis is used to replicate some previous experiments and then to apply it to the application of coal beneficiation above. The multi-phase Computational Fluid Dynamics (CFD) code Neptune_CFD is used. The numerical simulations are carried out on the supercomputer at the Centre for High Performance Computing (CHPC) in Cape Town.
Principal Investigator: Prof Giuseppe Pellicane
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2020-11-09
Allocation End: 2021-05-11
Used Hours: 626373
Project Name: Computational Study of Structure-Property Relationships in polymer blends relevant to OPV devices
Project Shortname: MATS0887
Discipline Name: Physics
Polymers are organic materials present in energy devices based on renewable and non-polluting sources, where they can be used as the active photovoltaic component. By the scientific point of view, polymers are also widely used as a potential nano-carrier for drugs in nano-medicine and for pharmaceutical applications. The group leader is Dr G. Pellicane, who is a (honorary) associate professor at UKZN and NRF C1 rated scientist. Members include Mr. S. Mamba (PhD student), Prof. Tsige (Full Professor of Polymer Science at the University of Akron, US) and Prof. Workineh (Associate Professor at Bahir Dar University, Ethiopia. Our research focus is on theoretical and computational studies of complex fluids, and within this project we mainly use density functional theory calculations and molecular dynamics simulations. We published several articles in scientific journals within the framework of this project, and presented our results in international conferences/workshops, that will allow for sharing and diffusion of vital knowledge with the international scientific community. We are deeply grateful to the skilled and resourceful staff members at CHPC (Dr Anton Lopis), and for the generous allocation of computational resources granted to us by them, which are instrumental to fulfill the goals of this project.
Principal Investigator: Prof Rasheed Adeleke
Institution Name: North-West University
Active Member Count: 14
Allocation Start: 2020-11-10
Allocation End: 2021-05-21
Used Hours: 1948
Project Name: Environmental and Agricultural Microbiology
Project Shortname: CBBI1183
Discipline Name: Environmental Sciences
North-West University, Potchefstroom continues to advance the understanding of microbial communities across different soils and agroecosystems. Our core interest is towards soil and plant health. We seek to generate novel solutions that address critical global issues, including environmental sustainability, green energy and food security. Currently, our research projects utilize state of the art sequencing technologies to decipher the whole genome of novel microorganisms, and to understand the composition and functional repertoire of microbial community in different environments, including soil, water and plants. Such data can only be analysed using large computer hardware/resources. Thus, we are very reliant on the CHPC's server to execute most of our bioinformatics analysis and/or pipeline. Our research programme currently boasts of several postgraduate students at honours, masters, PhD and postdoc level.
Principal Investigator: Dr Nikiwe Mhlanga
Institution Name: Mintek
Active Member Count: 13
Allocation Start: 2020-11-10
Allocation End: 2021-05-13
Used Hours: 451067
Project Name: Hydrogen Storage Materials and Catalysis
Project Shortname: MATS0799
Discipline Name: Material Science
MATS0799 is a Mintek computational cluster. It mostly constitutes of Mintek Advanced Materials members. The cluster was initiated mainly for the hydrogen storage project. This entailed the synthesis, screening, and modeling of solid-state hydrogen storage materials (carbon nanotubes, metal hydrides, and metal-organic frameworks) to support the national HySA (Hydrogen South Africa) program. Over the years more members with different interests from hydrogen storage joined the cluster, broadening the group's interest. The development of Surface-enhanced Raman Scattering biosensors is one of the projects. DTF studies are done on SERS substrates to enhance experimental SERS substrates. Alloys systems for high temperature are also simulated and their envisioned application is in the Aluminium smelting industry. We need CHPC for a number of reasons: to access the different computational codes the group uses for simulations; to enable the calculation of even larger clusters which characterizes the type of simulations we do; the valuable support and guidance we get from the CHPC staff with problems related to our simulations.
Principal Investigator: Dr Hezekiel Kumalo
Institution Name: University of KwaZulu-Natal
Active Member Count: 15
Allocation Start: 2020-11-11
Allocation End: 2021-05-10
Used Hours: 272654
Project Name: Molecular modeling and computer aided drug design
Project Shortname: HEAL1009
Discipline Name: Health Sciences
The group covers a wide range of computational and molecular modelling research areas with the main focus on biological systems and drug design approaches. The main interest is related to the design and study of biologically and therapeutically oriented targets. This is achieved by employing the applications of computational methods to the study of problems of chemical and biochemical reactivity, with particular focus upon the transition state, environmental effects on mechanisms, the origins of catalysis, and the interpretation of kinetic isotope effects. This includes mechanistic pathways and transition states for reactions in enzyme and solutions; design of enzyme inhibitors and exploring the binding and catalytic theme of the designed targets and adopting sophisticated computational approaches to understand protein structures and functions. We have involved in projects such as Understanding drug resistance mechanisms via different computational tools QM/MM MD simulations Quantitative Structure-Activity Relationship (QSAR) Conformational Analysis of biomolecules Bioinformatics tools applications Development Projects Approaches to enhance binding free energy calculations results in Developing parameters for biomolecules: on-going projects Software implementations: on-going projects. All the projects that we do in the group contribute to the training of pharmaceutical scientists with specific skills for both the pharmaceutical industry and academia. This has the potential of stimulating the local pharmaceutical industries in South Africa to manufacture pharmaceuticals of quality, excellence and affordability for optimum and cost-effective patient health, instead of being dependent on multinational pharmaceutical companies. We are still a small yet fast-growing group however funding is a problem, therefore for the resources at CHPC allows us to generate hypotheses for subsequent experimental testing in a much quicker manner and higher throughput than using experiment alone to generate hypotheses that you'd like to test. It has given us an opportunity to be able to explain experimental data we could not explain easily such as the binding landscapes of different enzymes and the mechanism of action for different inhibitors
Principal Investigator: Dr Roelf Du Toit Strauss
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2020-11-10
Allocation End: 2021-05-09
Used Hours: 3595995
Project Name: Computational Space Weather
Project Shortname: PHYS0918
Discipline Name: Physics
One of the biggest hurdles faced by manned exploration of space is the high levels of natural radiation present in the solar system. This is not only an important consideration faced by future astronauts on board spacecraft, but also by future colonizers of Mars, and inhabitants of future moon bases and space stations. This important risk is acknowledged by both SpaceX and NASA, and planned bases and spacecraft try to accommodate so-called "space storm shelters", where space dwellers can hide from dangerous radiation levels. At the Centre for Space Research of the North-West University, South Africa, we are doing our part to mitigate these possible harmful effects by developing state-of-the-art numerical models that can simulate and predict the levels of harmful natural radiation. To simulate the intensity of these so-called "cosmic ray" particles, complicated and large-scale numerical models are run on large scale computer clusters, such as the Lengau cluster of the Centre for High Performance Computing (CHPC) in Cape Town, South Africa
Principal Investigator: Dr Kiprono Kiptiemoi Korir
Institution Name: Moi University, Eldoret, Kenya
Active Member Count: 6
Allocation Start: 2020-11-12
Allocation End: 2021-05-19
Used Hours: 805571
Project Name: Thermal characterization of MoS2 nanostructures: an ab initio study
Project Shortname: MATS0868
Discipline Name: Material Science
This research group draws its members from Moi University, Computational Material Science Group (CMSG), in addition, we have collaborators: Dr. Haffad of University of Beijaia- Algeria, and Dr. Re Fiorentin of Istituto Italiano di Tecnologia (IIT) Italy. Our research activities focus mainly on materials for energy, optoelectronics, and ultra-hard industry.
ZnO nanowires have been proposed as potential photo-anode materials for photo-electrochemical water splitting due to their low toxicity, simple synthesis, and easy modification routes. However, ZnO suffers from low PEC activity and photo-corrosion effects, and therefore, the application of ZnO nanowires in PEC water splitting still awaits the development of effective design and synthesis strategies to improve its PEC efficiencies to commercially viable levels.
The predictive approaches used in this work are anchored on the principles of quantum and classical mechanics and require huge computational effort to solve the mathematical formulas, such as Schrödinger and Newtonian equations. For this reason, availability of the state of the art High-Performance Computing facility, such as CHPC is a critical component for the implementation of this work.
For example, in our recent work, using ab initio Density Functional Theory calculations considering 3d transition metal doping as a potential route towards the attainment of ZnO nanowires with superior PEC activity. Our results showed that the stability of 3d transition metal dopants in ZnO NWs is dependent on the d character of the transition metal dopant as well as their concentration and doping site, with most transition metal atoms being energetically most favorable at the Zn substitutional site both in O-rich and Zn-rich conditions. In addition, the band alignment relative to the redox potential of water revealed that the valence band maximum of Sc, V, Ni, and Cu doped ZnO NWs remains strongly positive above the oxidation potential of O2/H2O, while their reduction potential remains negative below the reduction potential of H+/H2, favouring PEC applications.
Principal Investigator: Dr Samuel Iwarere
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2020-11-12
Allocation End: 2021-05-11
Used Hours: 468492
Project Name: Understanding Plasma-Liquid Interaction
Project Shortname: MECH1107
Discipline Name: Chemical Engineering
The research is being carried out under the guidance of the Thermodynamics Research Unit based in the School of Chemical Engineering at the University of KwaZulu-Natal. The understanding of plasma-liquid interactions is of prime importance in the context of environmental remediation and wastewater treatment applications. Plasma treatment of wastewater involves complex chemical and physical phenomena, which makes the comprehensive modelling of phenomena such as gas phase reaction, turbulence and heat transfer a difficult task. To gain insight into the complex processes associated with the use of plasma wastewater treatment, Computational Fluid Dynamics (CFD) will be used to study the relevant chemistry and fluid dynamic effects at the plasma-liquid interface. The Centre for High Performance Computing (CHPC) allows for calculation within realistic time frames, allowing the researchers to determine the accuracy of the simulations encountered in plasma physics. Simulation of the plasma arc has progressed well, with the researchers working in conjunction with other scientists in the plasma field. We will now be entering a challenging phase of the research which will investigate the plasma discharge coming into contact with liquid water.
Principal Investigator: Prof Alan Christoffels
Institution Name: University of Western Cape
Active Member Count: 3
Allocation Start: 2020-11-12
Allocation End: 2021-05-11
Used Hours: 29510
Project Name: Bioinformatics and Public Health
Project Shortname: CBBI0819
Discipline Name: Bioinformatics
The CHPC infrastructure was used to support Dr Diallo's PhD thesis, where he investigated olfaction in Glossina fuscipes fuscipes (Tsetse), vector of trypanosomiasis. The study showed that Tsetse is equipped with diverse olfactory sensilla; basiconic, trichoid and coeloconic, and exhibit sexual dimorphism in types and number. Putative receptors for tsetse repellent components and 1-octen-3-ol (attractant odour) were identified using a multidisciplinary approach; behaviour, molecular biology, electrophysiology and bioinformatics. Additionally, using dsRNAi silencing method proved the direct role of Tsetse odorant binding proteins in the detection and perception of 1-octen-3-ol. The study significantly contributes to the understanding of tsetse olfaction and to the development of olfactory based tools for controlling the spread of trypanosomiasis.
Principal Investigator: Prof Enrico B Lombardi
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2020-11-13
Allocation End: 2021-06-09
Used Hours: 690481
Project Name: Defects in wide-bandgap semiconductors and 2D materials
Project Shortname: MATS1160
Discipline Name: Material Science
• The materials research group of Prof Lombardi at the University of South Africa (UNISA) focuses on defects in wide band gap semiconductors and 2 dimensional (2D) materials. This research group is exploring a range of defects 2D materials which affect their functionality and efficiency, for applications ranging from next generation spintronics devices, to nano-electronic an opto-electronic devices. As in all solid state materials systems, point defects are inevitable, and is particularly important in new chemically grown 2D materials due to the imperfection of the growth process, including, amongst others, 2D transition metal chalcogenides. Our group has contributed to the understanding of fundamental defects and defect processes in these 2D materials, predicting the properties of intrinsic point defects and other likely defects, and the conditions under which they are likely to occur. These results provide insight to the physics of defects that are grown via chemical vapour deposition, as well as in electron irradiated materials. These defects are responsible for large variation of electric and optical properties, while they may also act as efficient electron or hole traps, which strongly influence transport and optical properties of semiconductors, in turn strongly impacting their applicability to next generation devices. This research is performed using the state-of-the-art density functional theory, and has made extensive use of CHPC compute resources.
Principal Investigator: Prof Phuti Ngoepe
Institution Name: University of Limpopo
Active Member Count: 29
Allocation Start: 2020-11-16
Allocation End: 2021-05-15
Used Hours: 7360230
Project Name: Computational Modelling of Materials: Energy Storage
Project Shortname: MATS0856
Discipline Name: Material Science
The Research Group is based in Materials Modelling Centre at the University of Limpopo,under the leadership of Professor Phuti Ngoepe.
Energy Storage Systems: We have, through simulations on primary particles of Lithium manganese oxide (LMO) spinel, characterized disruptive transition during discharging; and are currently exploring porosities to enhance capacity of such cathodes. All nickel manganese cobalt (NMC) primary nanoparticles have been modelled and modified to NMC and the nature of structural disorder associated with discharging are studied. This will inform the new manganese rich NMC co-precipitation experiments set up on the UL campus. In addition, stable O3-type layered structures with enhanced performance, are predicted by doping using 4IR machine learning methods. Approaches of minimizing anion oxidation at surfaces during discharging are explored. Some aspects of the beyond lithium ion batteries are continuing in the form of Li-S,Se, particularly on the S rich side, together with work on catalysts for Li,Na,K,-air batteries.
Mineral processing: After the development on proof of concept pertaining to agreement of simulations and experiments in the design on reagents for mineral recovery from complex ore, we have proceeded with the applications to precious metal chacogenides, where good experimental samples are not readily available. We are exploring applicable reagents. We have also studied new reagents that are applicable for copper extraction and are identifying promising candidates.
The computational modelling studies, through CHPC, are intended to predict processes that are essential in pilot and production plants for advanced battery systems, mineral processing and
metal production industries.
Thus far the progress on such studies is excellent and whilst delivering products it is developing essential human capacity.
The CHPC has thus far contributed immensely to the progress made in all these projects and has assisted with allocation of adequate computing power that cannot be acquired for individual researchers on our local servers
Principal Investigator: Dr Evans Benecha
Institution Name: University of South Africa
Active Member Count: 11
Allocation Start: 2020-11-17
Allocation End: 2021-05-16
Used Hours: 448825
Project Name: Defect engineering in novel 2-D materials
Project Shortname: MATS1025
Discipline Name: Physics
The research programme titled "Defect engineering in novel 2-D materials" focuses on investigation of the properties of defects in single layered materials - usually one atom thick, as well as other material systems in the nanoscale dimension. The group spearheading this research is headed Dr Evans Benecha and it consists of senior researchers, postdocs and graduate students from the University of South Africa. nano materials possess interesting properties as opposed to their bulk counterparts. For example, graphene – which is a single layer of carbon atoms –enables electrons to flow much faster than silicon, is the world's strongest material, harder than diamond, yet lightweight and flexible. This unique combination of superior properties makes it a credible material for new technologies in a wide range of fields. Some of the envisaged applications of graphene as well as other single atom layered materials include making of medical implants, solar cells, stronger sports equipment, and batteries; just to name a few. However, the properties of these materials are not well understood for these applications to be realized. Dr Benecha and his group's approach towards understanding these materials involves use of large computational resources, and access to the CHPC computing facility has significantly reduced the time needed to generate and analyze data. The results from this project will not only assist in the current understanding of the role of defects in these materials, but will also help to reveal potential new functionalities.
Principal Investigator: Dr Parvesh Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2020-11-17
Allocation End: 2021-05-16
Used Hours: 199867
Project Name: Molecular dynamics and docking studies of organic compounds
Project Shortname: CHEM0795
Discipline Name: Chemistry
I am currently an Associate Professor in the School of Chemistry at the University of KwaZulu Natal (http://scp.ukzn.ac.za/Schoolleadershipandstaff2/ParveshSingh.aspx). My research group is involved in the designing of new heterocyclic assemblies with potential applications in anticancer, antibacterial, anti-TB, and anti-diabetic research. Specifically, we employ molecular docking, pharmacophore modeling and molecular dynamics simulations to predict novel chemical assemblies with potential activity against the diseases. The identified lead molecules are subsequently synthesized in our synthetic laboratory and tested in vitro for their biological activities. All the computer simulations are performed on the CHPC cluster. This supercomputing facility has been very useful to gather useful information that was almost impossible to get should this facility was not available for us to use. Running these jobs on normal computers would have taken months to finish or would die in middle. With this supercomputing facility in our hands, we not only managed to run complex calculations but obtained constructive scientific explanations for our experimental results. Consequently, we managed to publish this compiled data in reputed chemistry journals. Moreover, my post-graduate students have had the opportunity to learn different computational programs installed on CHPC that are being used in the drug design and drug discovery field.
Principal Investigator: Prof Rajshekhar Karpoormath
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2020-11-17
Allocation End: 2021-05-16
Used Hours: 75181
Project Name: Design of small novel organic compounds as potential drug candidates
Project Shortname: HEAL0835
Discipline Name: Health Sciences
Prof Rajshekhar Karpoormath completed his B.Pharm and M. Pharm from Karnataka University and Rajiv Gandhi University of Health Sciences, India respectively. He then obtained his PhD in Organic Chemistry (2013) from the University of KwaZulu-Natal (UKZN). In 2010 he joined UKZN as a lecturer and currently Associate Professor in Pharmaceutical Chemistry. He is also Academic Leader of Research in College of Health Sciences, UKZN and a National Research Foundation-South Africa (NRF-SA) - Rated researcher.
Prof Karpoormath started his independent research group (Synthetic and Medicinal Chemistry Research Group) in 2014. Over the years he has successfully secured several national and institutional grants worth over 6.5 million Rand (500,000 USD). These funds were utilized in establishing a well-equipped Drug Discovery Laboratory at UKZN and productive research collaboration with national and international universities as well as research institutes. His main research focus areas are Target-based drug design and synthesis of small molecules as potential anticancer and antimicrobial agents, Methodology development and development of electroanalytical methods to trace biological, organic species by fabrication/modification of electrodes with nanomaterials. His research group has published more than 100 peer-reviewed articles in international journals, two book chapters and two patents, just in a span of 7 years (2014-2021). He has successfully graduated with 21 postgraduate students (10 Ph.Ds. and 11 Masters) since 2014. He is one of the top researchers at UKZN and was the recipient of several awards in recognition of his achievements.
Principal Investigator: Dr George Manyali
Institution Name: Masinde Muliro University of Science and Technology, Kakamega, Kenya
Active Member Count: 10
Allocation Start: 2020-11-18
Allocation End: 2021-05-17
Used Hours: 201458
Project Name: Ab Initio study of Thermoelectric Materials
Project Shortname: MATS0712
Discipline Name: Material Science
The Computational and Theoretical Physics (CTheP) Group at the Department of Physics, Masinde Muliro University of Science and Technology, comprised of a team of researchers and students dedicated to the development and application of computational modeling to outstanding problems in materials science. In general, the group seeks a deeper understanding of quantum-mechanical descriptions of interacting electrons and nuclei in order to predict and design properties of materials and devices using density functional theory as a tool for the first-principles simulation. This kind of simulations generates volumes of data which cannot be handled by the common desktop computers. High-performance computing provides the computational environment that includes parallel processing, large memory, and storage of the big data. Therefore, Center for High-Performance Computing facility in Cape Town, South Africa, plays a vital role in providing the resources that aid the discovery of new materials and accelerates its application in the industry, an achievement that would have been in vain with desktop computers. Some specific projects for our group include characterization of already known thermoelectric materials. The information gained from this project is used as identifiers in search for new thermoelectric materials with the tailored figure-of-merit. Such materials are used to enhance the efficiency of thermoelectric generator power system for renewable energy. Such outcomes of our projects have an impact on the livelihood of the rural communities in Kenya, and generally, supports the Agenda Four of the Kenyan economic blueprint that was recently availed by the president of the Republic Kenya.
Principal Investigator: Prof Ashwil Klein
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2020-11-23
Allocation End: 2021-05-22
Used Hours: 9184
Project Name: Molecular dynamic simulation
Project Shortname: CHEM1241
Discipline Name: Bioinformatics
For the various studies we used in silico and molecular approaches including docking and MD simulation study to achieve project objectives. The tools used from the Schrodinger suite are not freely available and formed an integral part of our data analysis, therefore access to CHPC cluster was of paramount importance. Significant progress was made with this project and the data generated from these studies resulted in a few manuscripts that are under review in reputable science journals with an significant impact.
Principal Investigator: Prof George Amolo
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 13
Allocation Start: 2020-11-20
Allocation End: 2021-05-19
Used Hours: 2436227
Project Name: Properties of Materials for Green Energy Harnessing
Project Shortname: MATS862
Discipline Name: Material Science
The MATS862 is a Kenyan materials modeling group consisting of mainly young faculty and graduate students based at the School of Physics and Earth Sciences, The Technical University of Kenya, Nairobi. Some students and team members are based outside Nairobi. One PhD student is based in the Democratic Republic of Congo.
We use scientific codes written to simulate the properties of materials based on fundamental principles of chemistry, physics, mathematics and computer science. The work is focused on materials that have potential socio-economic values to the community with regard to new or more efficient materials and hence better devices for energy conversion. This has in the last 6 months extended to new areas beyond our initial focus and now includes drug design in chemistry and high pressure physics. The later has brought in a new collaborator from Case Western University in USA who has the-state-of-the-art high pressure facility in experimental physics
The work is being done to create capacity in skills and knowledge to handle new and emerging societal needs in the energy sector by complementing experimental research groups as well as providing useful information to guide product development.
Known information about elements is placed in an input file and submitted to the supercomputer to enable reproduction of independent information obtain by other techniques. Once this is done successfully, combinations of similar or new elements are tested to check if additional or new value can be obtained.
The CHPC comes in to provide computational resources that allow calculations to be done in a short time. We are doing very well based by the number of numbers of publications, graduation rate, attendance of conferences as well as invited talks.
Principal Investigator: Prof Serestina Viriri
Institution Name: University of KwaZulu-Natal
Active Member Count: 15
Allocation Start: 2020-11-25
Allocation End: 2021-05-24
Used Hours: 98398
Project Name: Deep Learning in Medical Image Analysis
Project Shortname: CSCI1229
Discipline Name: Computer Science
The CHPC is providing state-of-the-art High-Performance Computing which enables to conduct of current innovative research. Powerful parallel computation processing capabilities are required in every research especially in this era of Big Data. In our case, we have used this platform to conduct the life-saving type of research through Medical Imaging Analysis. Some of the positive results achieved are Accurate Skin Lesion Segmentation, Classification of Osteoarthritis Severity from Knee X-ray Images Using CNN, and even beyond medical analysis to remote sensing, etc.
Principal Investigator: Dr MC du Plessis
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 3
Allocation Start: 2020-11-25
Allocation End: 2021-05-24
Used Hours: 4035
Project Name: ACO Routing for OBS Networks
Project Shortname: CSCI1211
Discipline Name: Computer Science
Optical Burst Switching (OBS) is a next-generation paradigm which holds the promise of improved capacity on fibre optic networks. However, there is a gap for effective, efficient and responsive network resource management algorithms, to ensure that OBS can fulfil its promise. Research is being done at the Nelson Mandela University, Centre for Broadband Communications by postgrad computer science students, Joshua Oladipo and Francois du Plessis, under the supervision of Prof M.C. du Plessis from the department of computer science and Prof Tim Gibbon from the department of physics to apply the machine learning algorithm known as Ant Colony Optimisation to this problem. The CHPC has been crucial to the research by providing computational resources for long running network simulations which are used to study the performance of the algorithms.
Principal Investigator: Dr Lynndle Square
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2020-11-27
Allocation End: 2021-05-26
Used Hours: 4609
Project Name: Exploring poly(2,5)benzimidazole enhanced with carbon nanotubes for space applications
Project Shortname: MATS1088
Discipline Name: Physics
In this project, we will look at materials for space applications. We are considering a specific polymer that has also been used for hydrogen fuel cells, Now we are exploring it, based on the already but limited reported success of it for space. We will enhance it with carbon nanotubes. The project itself has an experimental component and uses expertise across two institutions (NWU-UWC). We will explore ion bombardment, for which we will use a second national facility. The computational component for this project explores multiple scales of modelling, including fluid dynamics, Nano-scale modelling and molecular dynamics. The molecular dynamics will investigate the mechanical properties, which will be accompanied by experimental work and a second project will explore the surface ion interaction using LAMMPS. This project relies on the Material Studio license provided by CHPC and the without the computing power it provides the project would have to reconsider its approach.
Principal Investigator: Prof Catharine Esterhuysen
Institution Name: Stellenbosch University
Active Member Count: 11
Allocation Start: 2020-11-27
Allocation End: 2021-06-24
Used Hours: 190147
Project Name: Computational chemistry analysis of intermolecular interactions
Project Shortname: CHEM0789
Discipline Name: Chemistry
The Computational Supramolecular Chemistry group at Stellenbosch University investigates the intermolecular interactions involved in a range of compounds in order to determine the relationship between the structures and properties of the materials. In particular, we focus on understanding the nature and origin of the sorptive properties of porous materials with respect to the compound being adsorbed. For instance, gases such as CO2 or solvents like water undergo differing intermolecular interactions with the porous framework that can be probed through calculations performed using the CHPC's computational facility. These allow us to understand the role of intermolecular interactions in the mechanisms of sorption in order to design materials with improved properties, particularly with regard to the uptake of greenhouse gases such as CO2. Such materials can thus be used to reduce the impact of the industrial carbon footprint, with the further aim of then catalysing the CO2 sequestrated within the porous framework to produce useful chemical products. Since these processes happen at molecular level that cannot fully be probed using experimental techniques. For instance, with the computational facilities provided by the CHPC we can directly follow the motion of individual gas molecules within the frameworks to explain sorption behaviour, which would be impossible using any other technique. The CHPC's facilities thus allow us to obtain a thorough understanding of the sorption behaviour that we not be able to achieve otherwise.
Principal Investigator: Dr Rendani Mbuvha
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2020-11-27
Allocation End: 2021-05-26
Used Hours: 178044
Project Name: Bayesian Methods for Neural Networks
Project Shortname: CSCI1332
Discipline Name: Data Science
We are part of a research group that is lead by Prof Tshilidzi Marwala at the Universities of Johannesburg and Witwatersrand. The group focuses on bayesian methods in machine learning. Bayesian methods allow for a principled understanding of the uncertainty around the parameters of complex methods like neural networks. Bayesian inference frequently requires the use of computationally intensive methods such as markov chain monte Carlo - that require CHPC resources to accelerate experimental time through extensive parellization. The work has results in two publications as well as numerous works in progress
Principal Investigator: Dr Jan Buys
Institution Name: University of Cape Town
Active Member Count: 8
Allocation Start: 2020-11-27
Allocation End: 2021-05-26
Used Hours: 269201
Project Name: Deep Learning for Low-resource Natural Language Processing
Project Shortname: CSCI1335
Discipline Name: Computer Science
The University of Cape Town Natural Language Processing group is a research group under the UCT Department of Computer Science that performs research on various topics related to the automated processing of language. The research group is led by Dr. Jan Buys and currently consists of 4 Masters students and 2 PhD students. Some undergraduate and honours students are also involved with the research.
The main focus is on developing methods for text generation in low-resource settings. Recent advances in Artificial Intelligence have been driven by the development of large neural networks that can "learn" how to perform various tasks by processing very large datasets - this is referred to as deep learning. For text generation, for example, deep learning systems have been developed that can automatically write realistic-looking news articles or other short pieces of text. However, deep learning techniques perform less well in settings where only small amounts of data are available. While text generation systems can perform well in English, similar systems for other South African languages (such as Nguni languages) are much less accurate or don't exist at all. In this research project, we are performing foundational research to determine how we can adapt deep learning models to perform well in low-resource settings where only small amounts of data are available. Deep learning models are computationally intensive, even on small datasets, so they are trained on Graphical Processing Units to speed up the computations. We have developed language models, which are the models underlying deep learning text generation systems, for multiple South African languages, investigating which type of neural network is most appropriate. Our approach can automatically subdivide words into smaller units in order to enable modelling words that did not appear in the training data. We have also shown that training a model on multiple related languages, can improve performance. Currently, we are developing automatic translation systems for South African languages. We are also developing language processing models for a number of other low-resource problems: Predicting clinical outcomes from doctor's notes, answering complex questions from documents, and rewriting the style of text passages.
Principal Investigator: Dr Uljana Hesse
Institution Name: University of Western Cape
Active Member Count: 3
Allocation Start: 2020-11-28
Allocation End: 2021-06-09
Used Hours: 131629
Project Name: Medicinal Plant Genomics
Project Shortname: CBBI1133
Discipline Name: Bioinformatics
My name is Dr Uljana Hesse, I work at the Department of Biotechnology at the University of the Western Cape in Bellville, South Africa. My research program focusses on the establishment of genome analyses of endemic South African medicinal plants locally. The program encompasses 1) generation and analysis of genome and transcriptome data from diverse endemic South African medicinal plants; and 2) development of novel computational tools for efficient storage and mining of plant sequencing data. Rooibos (Aspalathus linearis) represents the pilot plant species for the establishment of laboratorial and computational protocols. Our rooibos transciptomes have recently been published. Current research focusses on the assembly of the rooibos genome, which involves the analysis of "big data". We have completed computational analyses of our short-read Illumina sequencing data (amounting to approximately 1Tb of data and 200x genome coverage), which included evaluation of diverse assembly programs. To improve contiguity of the assembly, we have generated 0.5Tb of long read sequencing data using Oxford Nanopore Sequencing Technologies (MinION) and are in the process of evaluating assembly strategies for joint assembly of Illumina and MinION datasets. These analyses require extensive CPU resources locally only available at CHPC. Joint assembly is expected to significantly improve the rooibos genome assembly, and permit downstream analyses such as repeat masking, gene prediction and subsequent biological analyses
Principal Investigator: Dr Shankara Radhakrishnan
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2020-11-30
Allocation End: 2021-06-24
Used Hours: 176624
Project Name: Solar energy and CO2 Reduction
Project Shortname: CHEM0869
Discipline Name: Chemistry
The research group aims at the catalytic activity of variety of macrocycles / metal-complexes on electrochemical reduction of CO2 whereby one can produce liquid fuels such as Methanol, ethanol and other useful chemicals. Hence such computational work and facility is of extreme importance as they help us in computing heavy chemical structures which require longer computational time. With the facility at CHPC we are able to do such calculations with shorter time and ease.
Principal Investigator: Dr Sharon Moeno
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2020-12-01
Allocation End: 2021-05-30
Used Hours: 21513
Project Name: Drug Design, Delivery and Bioactivity of Small Phenolic Compounds
Project Shortname: CHEM1287
Discipline Name: Chemistry
My group is comprised of members of the Materials unit within the Department of Oral Biological Sciences (part of the School of Oral Health Sciences) in the Faculty of Health Sciences at Wits University. Our group engages in the design of small compounds derived from phenolic compounds. The design of compounds undertakes computational analysis and in silico screening as a means of determining whether compounds possess adequate drug likeness. As part of our research activity in the unit, promising compounds are synthesized, characterized and elucidated. Finally, the bioactivity of prepared compounds is ascertained by way of conducting antimicrobial and cytotoxicity studies. This research work is conducted in an effort to identify lead compounds for possible use as antimicrobial, anticancer, and wound healing agents. The use of the CHPC clusters facilitates the in silico and computational analyses conducted by our group on a regular basis. Docking and modelling studies enabled by the use of the Lengau cluster of the CHPC enables our group to understand the interaction of the designed and prepared compounds with the identified target proteins. The current project is in its very early stages but we are hopeful that it will soon gain traction.
Principal Investigator: Dr Richard Walls
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2020-12-03
Allocation End: 2021-06-01
Used Hours: 76006
Project Name: Fire Engineering Research
Project Shortname: MECH1148
Discipline Name: Computational Mechanics
The Fire Engineering Research Unit at Stellenbosch University (FireSUN) are seeking to understand the influence of fire on society and develop tools for improving fire safety. Work has focussed on modelling the spread of fire in informal settlements such that large-scale tools for predicting spread can be developed. Recent work has focussed on understanding how we can test an certify construction products in standard fire testing furnaces. There are many unknowns in fire test furnaces and this work will help in enhancing their operation along with the assessment of whether products tested are actually safe.
Principal Investigator: Dr Stefan du Plessis
Institution Name: Stellenbosch University
Active Member Count: 12
Allocation Start: 2020-12-04
Allocation End: 2021-06-02
Used Hours: 9379
Project Name: Shared Roots
Project Shortname: HEAL0793
Discipline Name: Health Sciences
Shared Roots is a collaborative research project undertaken by researchers from the departments of psychiatry, neurology and genetics at Stellenbosch University and researchers from the South African National Bioinformatics Institute (SANBI). It is a MRC Flagship funded study and the principal investigator on the study is the executive head of the department of psychiatry Professor Soraya Seedat. Dr Stéfan du Plessis is responsible for the neuroimaging component. Our study included participants with posttraumatic stress disorder (PTSD), schizophrenia or Parkinson's disease. It is known that individuals with mental illness as well as other common brain disorders have higher rates of heart disease and stroke than the general population. It is not clear why this is the case. Our study therefore aims to collect information about all the potential factors that can play a role, to better understand the increased risk and enable the development of treatment strategies. To achieve this goal we will combine state-of-the-art research techniques such as genetic evaluations and the latest neuroimaging techniques. This will be combined in analysis with information evaluating the brain disorders, general health and lifestyle factors.
For our neuroimaging component, we scanned over 600 participants using Magnetic Resonance Imaging (MRI). Here we investigate potential brain changes associated with increased metabolic risk. We proceeded to calculate precise measurements of around 70 known brain regions using the MRI scans, which will be compared between cases and healthy controls. Processing takes around 24 hours for each scan. To finish in a timely manner, we used the Centre for High Performance Computing Rosebank, Cape Town, Sun Intel Lengau cluster.
Principal Investigator: Prof Hadley Clayton
Institution Name: University of South Africa
Active Member Count: 3
Allocation Start: 2020-12-07
Allocation End: 2021-06-05
Used Hours: 72282
Project Name: Bioorganometallic Chemistry of Transition Metals
Project Shortname: CHEM1288
Discipline Name: Chemistry
The Inorganic Research Group at UNISA uses the CHPC resources for the computational study of the geometric and electronic parameters of bio-organometallic complexes with potential biological applications as metallodrugs. The computational data is used to support experimental data from single crystal X-ray diffraction studies and bioassays.
Principal Investigator: Prof Thirumala Govender
Institution Name: University of KwaZulu-Natal
Active Member Count: 8
Allocation Start: 2020-12-08
Allocation End: 2021-06-17
Used Hours: 44719
Project Name: IN SILICO EVALUATION OF NANO DRUG DELIVERY SYSTEMS
Project Shortname: MATS0816
Discipline Name: Material Science
The Novel Drug Delivery Unit (NDDU) at the University of KwaZulu-Natal is led by Professor Thirumala Govender, a Professor of Pharmaceutics, Head of the UKZN NanoHealth Pillar and Evaluator on the Medicine Control Council of South Africa. The NDDU currently focuses on developing advanced medicine formulations to overcome antibiotic resistance. Antibiotic resistance is considered a global crisis currently, affects the development of human society and has high-cost implications to the government in terms of finances and resources.
Our group has designed various types of novel pharmaceutical materials as well as advanced and new generation "smart" nano-drug delivery systems such as nanomicelles, nanoplexes, polymersomes etc. with superior architectural designs which have been prepared by our team and have shown superior activity against sensitive and resistant bacteria. The group philosophy is to use a multidisciplinary integrated approach that will minimize the cost of research and maximize therapeutic outcomes.
Hence the facilities provided by CHPC allows our group to integrate molecular modelling with our research that involves extensive in vitro and in vivo animal evaluation of our novel medicines and is being recognized locally and internationally for excellence.
Principal Investigator: Dr Richard Klein
Institution Name: University of the Witwatersrand
Active Member Count: 9
Allocation Start: 2020-12-08
Allocation End: 2021-06-06
Used Hours: 262197
Project Name: PRIME
Project Shortname: CSCI1340
Discipline Name: Computer Science
PRIME is a research lab in the School of Computer Science and Applied Mathematics at Wits University. We focus on Machine Learning and Artificial Intelligence techniques for Perception and Representation Learning. The AI models that we train are very large and require weeks of computing to learn. The primary goal of this research is to be able to learn good representations of data that is unlabelled. This means that in the future, AI can learn from large unlabelled datasets which are cheaper to create, and then fine-tune their understanding of the world on smaller, more expensive, labelled dataset.
Principal Investigator: Mr kirodh Boodhraj
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 2
Allocation Start: 2020-12-09
Allocation End: 2021-06-07
Used Hours: 5978
Project Name: Geospatial modelling regarding satellite imagery, oceans and coastal areas using machine learning, ODC and STAC
Project Shortname: CSIR1266
Discipline Name: Earth Sciences
The Blue Economy is gaining momentum. It serves to create or modify methods and processes for which we use the oceans resources in a sustainable way alongside increasing economic growth while preserving the oceans health. There are many aspects to achieve this and they all start with understanding and anticipating the oceans. One way of achieving this is by numerical models of the oceans and coastal areas.
These projects target understanding the oceans and coastal areas from numerical simulations. The oceans project focuses on creating ocean forecasts and the coastal projects aim at getting higher accuracy results in the coastal domain.
The NextGen Geospatial Modelling and Analyses group with the Data Sciences group within the CSIR are pooling resources to achieve the goals intended.
If significant progress is made on the projects, then this will feed into the public sector and will add value there by integrating into the current services and also creating new services. So far the projects are on track and progress satisfactory. Note that these projects are multiyear projects as their scope is large.
Principal Investigator: Dr Nana Ama Browne Klutse
Institution Name: Ghana Space Science and Technology Institute
Active Member Count: 2
Allocation Start: 2020-12-15
Allocation End: 2021-06-24
Used Hours: 40615
Project Name: Regional Climate modeling over Africa
Project Shortname: ERTH1087
Discipline Name: Earth Sciences
The climate change science research team of Ghana located at the University of Ghana focuses on climate research over Africa. The research involves the use of climate models to understand climate variability, changes and climate impact on water resources, energy, agriculture and health. Modelling is a major part of this research. I supervise students from different countries and institutions in Africa. Our research demands computing facilities which are not available in our various countries. The support of the South African government, the management, and the technical team of the CHPC afford the climate change science research team the opportunity to work from Ghana and other countries in West Africa successfully without having to travel. The project is progressing successfully.
The team is grateful to the South African Government.
Principal Investigator: Dr Lawrence Borquaye
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 5
Allocation Start: 2020-12-18
Allocation End: 2021-06-16
Used Hours: 182198
Project Name: Biomolecular Computations
Project Shortname: HEAL1382
Discipline Name: Chemistry
This is the Borquaye Research group in the Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi-Ghana. Our research group focuses on bioactive molecules such as natural products, peptides, essential oils and/or small molecules and their biological activities. We also make use of molecular docking and molecular dynamics tools to unravel potential modes of action of bioactive compounds, predict their preferred binding targets and explore events that mediate biomolecule-ligand interaction over a specified time period. The goal is to unearth compounds that could potentially be developed into drugs and to understand how these compounds work in biological systems. Our molecular docking and molecular dynamics projects require high performance computing, which we are able to access at the CHPC (Lengau). We have made significant progress and we are currently wrapping up the last set of experiments needed for a publication. We have been able to get a clear understanding of how certain natural products interact with their specific protein targets in the malaria parasite and effect their action.
Principal Investigator: Prof Titus Msagati
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2020-12-26
Allocation End: 2021-07-14
Used Hours: 59829
Project Name: Metabolomics, Proteomics and Biochemistry
Project Shortname: CHEM1089
Discipline Name: Chemistry
CHPC Pretoria is more professional and cautious in helping academics to engage the current scientific world. CHPC allows us to quickly analyze extremely large data sets. Analyzing large data sets are not so easy, it takes more time (which is not possible with our own computer) and more memory. CHPC provides both memory and storage for the whole research team and makes an easy way for the analysis. In recent days, biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. CHPC is the only platform provides us data management, analysis, and high integration of big data. Thank you CHPC and we need your support.
Principal Investigator: Prof Nicola Mulder
Institution Name: University of Cape Town
Active Member Count: 13
Allocation Start: 2020-12-26
Allocation End: 2021-06-24
Used Hours: 9182
Project Name: H3ABioNet
Project Shortname: CBBI0825
Discipline Name: Bioinformatics
The imputation project aims to evaluate different tools and panels to impute genetics data for human samples to improve the datasets from which we can derive knowledge on genetic relation to diseases. The metaproteomics data analysis is also being done on samples of biomedical interest. These studies are aiming to determine the role of the microbiome in diseases as well as in the susceptibility to sexually transmitted diseases, including HIV. The pneumococcal project will increase our understanding of prevalent strains and how some strains are able to cause diseases Again, this has the potential to facilitate novel discoveries for diseases in Africa and to identify biomarkers of disease which could be used to develop better diagnostics.
Principal Investigator: Prof Abu Yaya
Institution Name: University of Ghana
Active Member Count: 8
Allocation Start: 2020-07-31
Allocation End: 2021-06-03
Used Hours: 297993
Project Name: DFT modeling of weak interactions; a case study for Carbon nanosystems
Project Shortname: MATS0990
Discipline Name: Material Science
The research group is made of members from the Department of Materials science and Engineering, University of Ghana, Legon and Department of Physics, University of Agriculture, Abeokuta, Nigeria.
The pace at which materials are being developed and process for useful applications has been made possible by the use of computers in trying to mimic what experimentalist could expect before embarking on expensive experimental procedures, which have drastically reduced the cost of running experiments. This has therefore made supercomputers such as the CHPC in South Africa, an indispensable tool for our research work on gas sensing; toxic gases which can become weapons for terrorist and hence the need for a robust system to sense their presence using CHPC Lengau computers from South Africa.
Our quest to use materials for man's survival and comfort has been a central theme of the human condition. Humans have always pushed the cutting edge of discovering new materials. This is evident as man used natural materials such as wood, clay, skins, bone and stone. Gold was refined and used for ornamentation. Alloys such as brass and steel were used for warfare and then the use of ceramics to plastics and finally, the discovery of semiconductor materials led to the digital revolution. The Discovery of new materials has mostly been accidental and slow. However, an improvement of the understanding of the theory of materials from the level of the atom and the advent of improved computational resources led to our ability to systematically discover new materials and predict their behaviour. This ushered in the birth of the science of using computers to predict materials properties which are now known as Computational Materials.