Press Releases
Principal Investigator: Prof Yin-Zhe Ma
Institution Name: Stellenbosch University
Active Member Count: 6
Allocation Start: 2023-01-03
Allocation End: 2023-06-05
Used Hours: 301011
Project Name: Machine learning in 21-cm cosmology
Project Shortname: ASTR1323
Discipline Name: Astrophysics
CHPC is a wonderful server. It provides us a place to do large computation, such as simulation and MCMC. This broadens our study methods. It also has many software installed. For example, openmpi, cfitsion, anaconda and so on. This results in that we don't need to install them by ourselves. For an unprofessional person, some software may require l long time to install correctly.
Dr. Guo-Jian Wang is a Postdoc of our group at UKZN. He focuses on 21-cm data analysis and applications of machine learning methods in solving problems in cosmology and astrophysics. He is currently working on the identification of radio frequency interference based on the HERA experiment, and he is also working on cosmological parameter estimations with machine learning methods using 21-cm observations. In his research, he needs to do many simulations to train network models, which should be conducted on professional GPU machines. Therefore, his research needs to use public resources like the CHPC. In his research, he simulated data using the CPU nodes on CHPC and trained network models using the GPU nodes. Based on the CHPC, he has finished two papers published (or submitted) to AAS journals, and there are another two papers under preparation.
Principal Investigator: Dr Joseph Mutemi
Institution Name: University of Nairobi
Active Member Count: 6
Allocation Start: 2023-01-04
Allocation End: 2023-06-06
Used Hours: 12393
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 Earth and Climate Sciences, Kenya, is focused in addressing key research questions in East Africa. One research article was published at Climate Dynamics showing the value of soil moisture in controlling the climate over Eastern Africa, as well as other parts of the continent including the Sahel and southern Africa. Further, ongoing experimental work has highlighted important aspects of how land use patterns influence weather processes over East Africa. Further, land surface representation has been revealed as a key area of focus, since different representations not only affect the lower atmosphere processes, but these signatures are revealed in all-atmosphere and land variables, including soil moisture, humidity and rainfall. Upcoming results envisions understanding best model configurations options and providing guidelines towards improvement of operational weather and sub-seasonal forecasting systems in East Africa.
Principal Investigator: Prof Josua Meyer
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2023-01-09
Allocation End: 2023-07-31
Used Hours: 1294049
Project Name: Fundamentals of forced and mixed convection in heat exchangers
Project Shortname: MECH1094
Discipline Name: Computational Mechanics
In April 2022, Professor Josua Meyer was appointed as a professor at Stellenbosch University in the Department of Mechanical and Mechatronic Engineering, having previously held the same position at the University of Pretoria. Throughout his tenure, he served as the Head of Mechanical and Aeronautical Engineering for 20 years and as the Chair of the School of Engineering for 17 years. The School of Engineering is recognized as one of the world's largest engineering schools, and Prof. Meyer led one of the largest heat transfer research groups globally.
Prof. Meyer holds an A-rating from the NRF, denoting his status as an esteemed scientist acknowledged by peers for exceptional international scholarship in their respective field. His recent research outputs have demonstrated high quality and significant impact. Currently, he is establishing a new research group with a primary focus on the thermal sciences, particularly in the area of heat exchangers. His work in this domain centers on fundamental investigations of internal forced convection and transitional flow regimes, with applications in thermal-solar, wind, and nuclear energy.
As part of his ongoing endeavors, Prof. Meyer is engaged in a program involving the generation of computational fluid dynamics (CFD) data. These data complement experimental measurements and facilitate the identification and quantification of several previously unrecognized flow phenomena. Specifically, the comparison of experimental and CFD data obtained from water flowing through a circular tube with different Reynolds numbers and heat fluxes has revealed four significant phenomena that were previously unidentified. These include the distribution of wall temperature in simultaneous hydrodynamic and thermal developing boundary layers, the presence of a tube recirculation region at the tube inlet, a non-linear fluid temperature gradient during flow development, and the need for a new definition of "fully developed flow."
In summary, Prof. Meyer's appointment at Stellenbosch University marks his transition from the University of Pretoria, where he held prestigious positions within the Department of Mechanical and Mechatronic Engineering. His influential research and leadership in the field of heat transfer have contributed to the growth and recognition of his research group. Through his investigations of thermal sciences, particularly heat exchangers, Prof. Meyer has uncovered significant flow phenomena that were previously unexplored.
Principal Investigator: Dr Caleb Kibet
Institution Name: International Centre of Insect Physiology and Ecology, Nairobi, Kenya
Active Member Count: 10
Allocation Start: 2023-01-09
Allocation End: 2023-07-10
Used Hours: 297645
Project Name: Insect Genomics
Project Shortname: CBBI1470
Discipline Name: Bioinformatics
The program explores transcriptional gene regulation of chemosensory genes in insect vectors, including tsetse and mosquitoes. The program also uses whole genome assembly to understand the vectors. This research entails analysing massive genomic data including, protein binding microarrays, ChIP-seq, and whole-genome sequences. In this research, we build machine learning models to scan whole genomes for potential binding sites, use multiple evidence lines to understand how olfaction is regulated. This information will allow us to design better vector management tools. Genome assesbly and annotation provide critical scientific knowledge to facilitate the design of vector control strategies.
Principal Investigator: Prof Juliet Pulliam
Institution Name: Stellenbosch University
Active Member Count: 19
Allocation Start: 2023-01-10
Allocation End: 2023-07-10
Used Hours: 171568
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 Zeno Apostolides
Institution Name: University of Pretoria
Active Member Count: 17
Allocation Start: 2023-01-10
Allocation End: 2023-07-10
Used Hours: 19134
Project Name: Receptomics
Project Shortname: CBBI0926
Discipline Name: Bioinformatics
The Complementary and Alternative Medicine (CAM) group in the department of Biochemistry, Genetics and Microbiology at the University of Pretoria is led by Professor Zeno Apostolides. The group comprises of eight post-graduate students who research medicinal plants for possible anti-diabetic properties. Diabetes affects about 10% of the global population and is aggravated by diets that are high in starchy foods for example, maize, wheat, rice and potatoes. The enzymes amylase and glucosidase in the small intestine hydrolyse the starch to produce glucose that is readily absorbed into the blood stream and circulated to all the organs. In healthy persons, the high blood concentration of glucose in the blood stimulates the pancreas to secrete insulin. Insulin stimulates muscle and fat cells to absorb glucose from the blood. However, in type 2 diabetic patients, only low amounts of insulin is produced and hence muscle and fat cells absorb glucose slowly causing prolonged high blood glucose concentrations. One possible therapy for diabetes is to partially inhibit the amylase and glucosidase enzymes in the small intestine so that the starch is hydrolysed slowly and hence glucose is produced slowly. Several medicines in clinical use e.g. acarbose, target the amylase and glucosidase enzymes but these medicines have adverse side effects and are not affordable to poor people who rely on starch rich diets. Our aim is to investigate the medicinal plants, herbs and spices that are claimed to have anti-diabetic properties for inhibition of the amylase and glucosidase enzymes. The biochemical compounds in these plants are screened for binding to amylase and glucosidase in computer simulations at the CHPC. Compounds that bind tighter to these enzymes than acarbose are tested in laboratory-based enzymes assays. Future work will test the best compounds from laboratory in small animal studies and eventually in clinics.
Principal Investigator: Dr Vuyo Mavumengwana
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2023-01-10
Allocation End: 2023-07-10
Used Hours: 38204
Project Name: Microbial symbionts bioactive compounds and their virtual screening
Project Shortname: CBBI1434
Discipline Name: Bioinformatics
The Vuyo Lab is comprised of current 3 Ph.D. students, and 3 masters and honors students. The group is affiliated to the Stellenbosch University, Tygerberg Medical Campus. Our research aim is to mine bioactive natural products from microbial symbionts found in extremophilic environments and marine organisms. The bioactive natural products are screened in-vitro, in-vivo, and virtually against pathogens infectious diseases, and cancers. The work contributes to the fight against infectious diseases and cancer via producing targeted therapeutic solutions. As mentioned above we perform virtual screening of natural products via molecular dynamics simulations of complex biological systems. The simulations require robust computational power which is offered by the CHPC. This enables us to obtain results quicker and accelerates our drug discovery process. Furthermore, due to the reliability and efficiency of CHPC we have performed more simulations in a short space of time and currently drafting research papers.
Principal Investigator: Dr Lucy Kiruri
Institution Name: Kenyatta University, Nairobi, Kenya
Active Member Count: 7
Allocation Start: 2023-01-11
Allocation End: 2023-07-06
Used Hours: 137665
Project Name: KU Computational Chemistry Research Group
Project Shortname: CHEM1032
Discipline Name: Chemistry
CHEM1032: Kenyatta University Computational Chemistry Research Group
CHEM1032 was created in June 2017 and since then we have been able to run our calculations on the Lengau CHPC cluster. Currently, there are 7 members and only 4 who are active. Our research area is in Molecular dynamics (protein-ligand interactions, nanomedicine, Tuberculosis and COVID-19); and density functional theory (structure and catalysis). We use GROMACS and Gaussian 16 to carry out our research.
Dorothy Nganga is a second year student and her project is on derivatives of chitosan as a nanoparticle carrier for curcumin. She is using MD simulationsvto examine the structural stability and thermodynamic properties, and behavior of chitosan and curcumin in a neutral environment. The MD simulation has revealed strong binding affinities and significant intermolecular interactions (hydrogen bonding and van der waals interactions) between curcumin and the N,O- carboxymethyl chitosan. This indicates its great potential to be the preferred derivative of chitosan to be used in controlled drug release systems for hydrophobic bioactive compounds.
Joseph Auka is in his advanced stage pf second year at Kenyatta University. His research is on natural products compounds which shows high potency as inhibitors of against Protein Kinases A and B in Mycobacterium tuberculosis. His work entails geometry optimization of the natural products compounds using gaussian16. The molecular dynamics of about 100 ns is done and the trajectory analyzed for protein-ligand stability and free energies. The MD is done using GROMACS 2020. Joseph has made some progress as his first manuscript is under review.
Currently, Lucy and Daniel are working on drug discovery for infectious and non-infectious diseases like Parkinson diseases. Our research on Parkinson is motivated by the discovery of small molecules (natural products) whose activity was observed to be high in vitro and in vivo, however, the actual model and mechanisms of actions remains not well explored. We have employed computational approach to understand the mechanisms of action. Although our preliminary results are promising and helps to explore the underlying mechanisms, we are still exploring many other mechanisms of actions of the drug like molecules. All members are grateful to CHPC, SA for according us computing time.
Principal Investigator: Dr John Mack
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2023-01-11
Allocation End: 2023-07-27
Used Hours: 11874
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, seven MSc and three Honours students, and one postdoctoral fellow, 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 Didam Gwazah Adams Duniya
Institution Name: BIUST
Active Member Count: 1
Allocation Start: 2023-01-11
Allocation End: 2023-06-26
Used Hours: 75747
Project Name: Cosmological Probes of Gravity, Dark Energy, and Large Scale Structure
Project Shortname: ASTR1480
Discipline Name: Astrophysics
Lead by Dr. Duniya (Botswana International University of Science and Technology) research is currently being done, in collaboration with several researchers, on cosmological probes of gravity.
The imprint of interacting dark energy needs to be correctly identified in order to avoid bias in
constraints on interacting dark energy, on the largest scales. One of the papers investigates the large-scale imprint of interacting dark energy in redshift space distortions. Moreover, beyond-Horndeski gravity model provides a single, unified formalism of gravity theories. It allows placing observational constraints on a range of models at once, rather than constraining individual models. Two of the papers study the imprint of beyond-Horndeski gravity on very large scales: in the cosmic magnification, and in redshift space distortions, respectively (among other papers). These studies will reveal how gravity affect the large-scale structure of the Universe.
Progress is currently being made in performing the numerical analyses and producing the necessary results, using the excellent Lengau HPC.
Principal Investigator: Dr Nangamso Nyangiwe
Institution Name: Tshwane University of Technology
Active Member Count: 2
Allocation Start: 2023-01-11
Allocation End: 2023-09-21
Used Hours: 10747
Project Name: Application of density functional theory in engineered nanoparticles
Project Shortname: MATS1427
Discipline Name: Material Science
Our research group in the physics department at the Tshwane University of Technology focuses on computational materials modelling. We use density functional theory (DFT) and molecular dynamics (MD) to model and predict novel properties of different materials for various applications. The team works closely with experimentalists to complement the computational research work. Our current projects include understanding the behaviour of atoms on the surface of a metal, the adsorption and diffusion of atoms on metal surfaces using first-principles calculations, modelling graphene and related carbon-based materials and their interaction with phosphate ions, the experimental and computational study of optical and electrical properties of mixed halide perovskites and modelling the effects of environmental factors on photovoltaic materials. Without the CHPC resources, it is impossible to do this kind of research, we are so grateful to HPC. We use CHPC resources to run our calculations to obtain the properties we want.
Principal Investigator: Dr Lynndle Square
Institution Name: North-West University
Active Member Count: 6
Allocation Start: 2023-01-11
Allocation End: 2023-08-17
Used Hours: 494692
Project Name: Exploring poly(2,5)benzimidazole enhanced with carbon nanotubes for space applications
Project Shortname: MATS1088
Discipline Name: Physics
The work from this group considers materials for space applications in Low Earth Orbit (LEO)in the Centre for Space Research at North West University. To date, poly(2,5)benzimidazole composites are investigated using computational physics and experimental techniques for radiation shielding consideration. Publications for this year, 2023, thus far be found at https://pubs.aip.org/aip/apm/article/11/7/071103/2900822/ABPBI-MWCNT-for-proton-radiation-shielding-in-low and in the conference proceedings with ISBN: 979-8-3503-3346-6/23. The computational methods used consider different scales, computational fluid dynamics to model the deposition process published recently in IEEE Transactions on Plasma Science ( Volume: 50, Issue: 12, December 2022), molecular dynamics, reactive molecular dynamics and density functional theory. All of these give vital information about the polymer, composites and preliminary work on interactions with the LEO environment. The work is complemented, guided and verified using various experimental techniques and national facilities, for example, iThemba labs Gauteng, for which different ion bombardments were investigated. The multiple studies explored under the supervision of the PI, Dr Square, in PhD, MSc, and BSc honours projects have shown encouraging results. The computational work depends on the national license made available by the CHPC and its infrastructure for parallel computing.
Principal Investigator: Prof Penny Govender
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2023-01-12
Allocation End: 2023-09-21
Used Hours: 34589
Project Name: Design of MOFs-based sorbent materials for capturing carbon dioxide
Project Shortname: CHEM0797
Discipline Name: Material Science
"The computational chemistry research group is at the University of Johannesburg led by Prof Penny Govender. The research group currently focuses on material science, environmental sciences, reaction mechanisms and medicinal chemistry. Density functional theory (DFT) calculations using materials studio CASTEP module at CHPC is 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. 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. Environmental and energy problems are important topics globally due to the fast development of urbanization; huge population increases and industrialization. Recently, water pollution has resulted as a major issue in developing countries, particularly in regions where people rely on groundwater for domestic and drinking purposes in Africa. 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 carbon dioxide, 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 and therefore the ongoing need to focus via theoretical methods to continuously investigate.
Principal Investigator: Dr Holliness Nose
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 5
Allocation Start: 2023-01-12
Allocation End: 2023-07-13
Used Hours: 273012
Project Name: Inorganic Computational Chemistry
Project Shortname: CHEM1003
Discipline Name: Chemistry
Dr. Holliness Nose is currently a lecturer at the Technical University of Kenya and has expertise in Inorganic and Computational Chemistry.
She is one of the few Computational Chemistry faculty in Kenya as may be confirmed by her status of a Principal Investigator at the Centre for High Performance Computing (CHPC-South Africa) and has been a leader in the creation of a MSc program in Computational Chemistry at the School of Chemistry and Materials Science.
She has authored/co-authored five research papers in experimental and theoretical chemistry in referred peer-reviewed journals.
Her objective is to build a career as a research scientist in the field of catalysis and drug design and development so as to be able to solve challenging problems in health for Africa and the world at large.
Principal Investigator: Prof Fernando Albericio
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2023-01-12
Allocation End: 2023-07-13
Used Hours: 6305
Project Name: Peptide chemistry and Organic chemistry
Project Shortname: CHEM1102
Discipline Name: Chemistry
We are Peptide Science Group at UKZN in School of Chemistry and Physics, Westville campus. The project was brought up with an intend to learn computational chemistry, in order to understand the underlying mechanism of reaction. The project involves synthesis of several organic molecules towards application in organic 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 and higher level of computing is in progress. We expect to be going ahead with these results for further analysis towards prediction of reaction mechanism.
Principal Investigator: Dr Krishna Govender
Institution Name: University of Johannesburg
Active Member Count: 16
Allocation Start: 2023-01-12
Allocation End: 2023-07-13
Used Hours: 389802
Project Name: Computational approaches to design novel anticancer agents
Project Shortname: CHEM0792
Discipline Name: Chemistry
The primary objective of the Computational Chemistry and Molecular Modelling Group at the University of Johannesburg is to develop novel drug candidates that can be used in the treatment of cancer. The group focuses primarily on utilization of available molecular modelling software packages in order to achieve their goal, but inevitably we will develop our own workflows and custom scripts that can achieve the desired goals.
All work conducted in the group is heavily dependent on HPC resources, without which results would not be generated in the short time frames that we have become accustomed to.
Principal Investigator: Dr Clement Agoni
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2023-01-12
Allocation End: 2023-07-13
Used Hours: 45569
Project Name: Structural Modelling and In-Silico Peptide Design Research
Project Shortname: HEAL1524
Discipline Name: Health Sciences
The structural modelling and In-Silico Peptide Design Research project is based in the College of Health Sciences at the University of KwaZulu Natal. The team explores drug-target interactions of novel small molecule inhibitors against diseases of global concern such as tuberculosis, malaria, cancer, and viral infections using molecular modelling techniques. The second aspect of the research involves the structural modelling of peptides toward the discovery of bioactive peptides from natural sources for therapeutic purposes, with a central question of whether structural modelling can accelerate the development of bioactive peptides. Resources from CHPC allow our group to perform computationally intensive processes such as Molecular Dynamics simulations and Machine Learning which hitherto would have been very expensive and time-consuming using local computers with limited capacities. So far we are have successfully published the finding of some of the research investigations in the project in reputable journals even as we continue to explore the research domain
Principal Investigator: Prof Ray Everson
Institution Name: North-West University
Active Member Count: 2
Allocation Start: 2023-01-12
Allocation End: 2023-07-31
Used Hours: 554829
Project Name: CO2 Capture in Circulating Fluidized Beds
Project Shortname: MECH0866
Discipline Name: Chemical Engineering
The Research Programme is a collaboration between NWU and VUT focused on emissions reduction and sustainability with a broader focus on CO2 and SO2 capture and management. The current use of the CHPC systems has been on modelling SO2 capture in Flue Gas Desulphurization. The work is part of the ongoing efforts by the Eskom Power Plant Engineering Institute (EPPEI) specialization centre for Emissions Control at the North West University in assisting Eskom to meet both national and global environmental regulations with respect to CO2 and SO2 emissions. In spray-dry scrubbing, hot flue gas is contacted with a spray of an alkali slurry in order to remove SO2 from the gas stream. The advantage of this process is the generation of dry product, eliminating the need for slurry handling and reducing the overall water usage and waste-water production of the desulphurization process. In this work, successive modelling of the three key phenomena occurring in spray-dry scrubbing, which entail Hydrodynamics modelling, Evaporation/Drying modelling and SO2 absorption modelling, including Chemical reaction modelling, is implemented in a computational fluid dynamics platform (Starccm+). The process itself is a multiscale, multiphase and multiphysics problem requiring high computing systems to solve the complex differential equations defining these phenomena, which has been made possible by the CHPC. The spray drying process has been successfully modelled using the CHPC and validated with experimental data; we are currently working at fine-tuning some data for publication and the ambition is to have this completed by the end of August. We are also busy with the next section of the project wherein the desulphurization model will be concluded, deployed on the CHPC and the results validated with experimental data.
Principal Investigator: Dr Fortunate Mokoena
Institution Name: North-West University
Active Member Count: 6
Allocation Start: 2023-01-13
Allocation End: 2023-07-13
Used Hours: 22427
Project Name: Protozoan parasites and cancer drug discovery
Project Shortname: CBBI1293
Discipline Name: Bioinformatics
We work predominately on Schrodinger Maestro. Although we have plans to do some gromacs and potentialy trinity of NGS analysis. We hope for more tokens to be able to do some molecular dynamics simulations through Desmond. It has been particularly useful for my group to be able to do these and would be great if we could be able to conduct MMGBSA on the last MDS snapshop but we remain absolutely greatful to CHPC for the allocated hours (which are quite generous) and truly greatful for the support when it comes to adressing queries.
Principal Investigator: Dr Hamilton Ganesan
Institution Name: Inqaba Biotec
Active Member Count: 2
Allocation Start: 2023-01-16
Allocation End: 2024-01-16
Used Hours: 83125
Project Name: General Analysis
Project Shortname: CBBI0843
Discipline Name: Bioinformatics
Assistance might be required hereWe at inqaba biotec, a private biotechnology company based in Pretoria, Muckleneuk with subsidiaries in East and West Africa and multiple sattelite offices across Africa, have been in the business of producing Next Generation Sequencing data for our wide client base for over twenty years. Throughout this time in operation, we have seen a significant increase accessibility to Next Generation Sequencing technologies thus fuelling the need for DNA to be sequenced at ever increasing speed.
Concomitant with the the rapid advancement in the speed of DNA sequencing technologies is the production of increasingly large data sets. This two-fold increase has had an impact on our operations because naturally, our digital storage capacity and compute resources has now become crucial with many of our clients requiring data storage and data analysis in some form or another.
Therefor, the compute resources made available at the CHPC has provided invaluable infrastructure in order for my company, inqaba biotec, to function optimally. In many cases, larger data sets such as human genome sequences need to be analyzed and due to its sheer size, requires considerable compute resources. Without access to the CHPC compute resources, the delivery time on many these projects would be extended to an unreasonable and unecceptably long period.
In the realm of personalized medicine, driven primarily by genomic data, the need to quickly transfer and analyze data has a direct impact on speed of diagnosis and understanding of a clinical case. This alone is a solid case in point to highlight the crucial service of High Performance Computing in our sphere.
Being a biotechnology company however, means we deal with sample types across a broad range including animal, plant, medical, veterinary & mining research to name a few. This of course means, our compute needs and software needs are broad too, leaving us even more indebted for a resource such as the CHPC.
I am truly thankful for the various staff that have a generally helpful and knowledge imparting attitude to its users, contributing to a thriving scientific environment in SA.
Principal Investigator: Prof Shazrene Mohamed
Institution Name: South African Astronomical Observatory
Active Member Count: 5
Allocation Start: 2023-01-17
Allocation End: 2023-06-17
Used Hours: 59821
Project Name: 3D rad-hydro simulations of the outflows of evolved stars
Project Shortname: ASTR0880
Discipline Name: Astrophysics
Energetic explosions are a common occurrence in the universe. With new and upcoming observational facilities, we will be able to detect millions of these events in the night sky; we thus need a way to distinguish them from one another. The events range from dying stars exploding as supernovae, to the exciting and now well-known neutron star mergers that led to the detection of gravitational waves in 2015. In this work, we focus on another type of explosion – those produced by collisions between stars. Just as big cities have greater traffic than cities in the countryside, some regions in space have a larger number of stars in a relatively small volume. In these regions, e.g., the centers of galaxies and globular clusters, the high concentration of stars increases the probability for collisions. We investigate specifically the collisions between main-sequence stars and white dwarfs. Main-sequence stars are average stars similar to the Sun and consist primarily of hydrogen and helium with small amounts of heavier elements such as carbon, nitrogen and oxygen. White dwarfs are produced when stars at the end of their lives (billions of years old) shed their outer envelope and leave behind a core consisting of carbon and oxygen. White dwarfs are more exotic than the Sun, since they can weigh about half the mass of our sun, whilst squeezing all that mass into 2% of the Sun's radius – roughly the size of the earth. This implies that these objects have extreme densities, which should lead to interesting interactions when colliding with other objects. White dwarfs and main-sequence stars can collide at velocities of 10^6 - 10^7 mph, releasing ~ 10^27 times more energy than an atomic bomb in less than a thousand seconds. Using 3D supercomputer simulations with detailed physics, we can model a variety of these collisions and make predictions for the energy that will be released during the event, as well as the chemical composition and the future evolution of the surviving star.
Principal Investigator: Dr Pritika Ramharack
Institution Name: Medical Research Council
Active Member Count: 16
Allocation Start: 2023-01-17
Allocation End: 2023-07-18
Used Hours: 486889
Project Name: Phytomedicine in Metabolic disorders
Project Shortname: HEAL1387
Discipline Name: Health Sciences
The aim of my new Molecular modeling and Bio-computation research group within the Biomedical Research and Innovation Platform (BRIP), SAMRC, is to conduct predictive biological target identification, compound physio-chemical descriptions, molecular modeling, molecular docking and molecular dynamic simulations that are required for the enhancement of current therapeutic regimens in various metabolic disease conditions. These techniques may also be implemented in identifying and optimizing vaccine developments against SARS-CoV-2 variants amidst the Covid-19 pandemic. The group is currently still being established, with students currently being recruited for the 2021/2022 academic cycles. The work will focus on the use of the Schrodinger suite for the design and characterization of newly synthesized compounds and co-crystals, as well as the use of Glide for molecular docking. The use of the Amber suite will also be utilized to simulate a theoretical experimental environment that will be programmed using specialized chemical forcefields, thus allowing for molecular interactions and free-binding energy of the complexes to be analysed. This will provide critical information on the potential structural mechanisms of action of the compounds, as well as the structural dynamics of enzymes, with particular interest on mutational modifications. To perform these studies, the use of the CHPC will be critical in accessing the Schrondinger and Amber suites and to perform large scale molecular simulations. The successful use of the CHPC in my research is documented in various studies that are evidenced in 22 internationally peer-reviewed Journal articles (https://orcid.org/0000-0001-5850-6782?lang=en). My goal is continue utilizing this platform to facilitate and expand computational chemistry capacity development within South Africa, focusing on previously disadvantaged universities. The collaborative work within the SAMRC, using CHPC, will also provide key genomic and proteomic insights on new and circulating SARS-CoV-2 variants detected in South Africa.
Principal Investigator: Dr Sunita Kruger
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2023-01-17
Allocation End: 2023-07-31
Used Hours: 278324
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 and fluid-structure interaction. Specifically heat transfer in naturally ventilated greenhouses, and the modelling of rock drills. 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 rooftop greenhouse. Smaller greenhouses containing a single and multi-spans have also been investigated. Currently, three dimensional models of greenhouses subject to buoyancy driven flow are being investigated, as well as the fluid-structure interaction to improve the efficiency of rock drills.
Principal Investigator: Dr Fabio Cinti
Institution Name: NITHEP
Active Member Count: 4
Allocation Start: 2023-01-18
Allocation End: 2023-08-31
Used Hours: 64550
Project Name: Quantum Monte Carlo for ultra-cold atoms
Project Shortname: PHYS0892
Discipline Name: Physics
Our group (led by Fabio Cinti, associate professor at University of Johannesburg) studies pattern formation of special structures like stripe phases, cluster crystals, quasicrystals and curved surfaces in a quantum regime. Presently these structures can understand a large amount of fascinating phenomena in soft matter, superconductivity, nonlinear optical systems, and long-range interacting systems. Quasicrystals are one of the most intriguing examples, as particles self-assemble in a long-range ordered pattern which is at the same time non-periodic, thus been able to exhibit forbidden crystalline ordering. Many studies observed cluster quasicrystals in soft macromolecular systems at finite temperatures by using this type of interactions. While a recent theoretical work have surprisingly revealed the stability of those structures also at zero temperature for a particular case, the extent to which classical cluster quasicrystals can be stable in the absence of thermal fluctuations is a matter of debate.
We investigate quantum cluster quasicrystals by imposing external quasi-periodic potentials or, alternatively, building a disordered-free extended hardcore-boson Hubbard model on two-dimensional quasicrystalline lattices. Interestingly, the competition of interactions and quasiperiodicity generate a wide range of phases, such as supersolidity and Bose glasses. We also observe superfluidity in a model relevant to quantum cluster quasicrystal. By using state-of-the-art quantum Monte Carlo approaches, it was found that moderate quantum fluctuations make dodecagonal structures to persist, leading to a small but finite local superfluid phase.
Finally we are also interested to probe quantum many-body systems in curved geometry. we are focusing on the existence of a supersolid phase on the sphere by using numerical methods. We also investigate the nature of the superfluid phase on the sphere. The dynamical properties of shell-trapped bosons are another open problem that we are delve into.
Principal Investigator: Dr Nicolette Chang
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 18
Allocation Start: 2023-01-18
Allocation End: 2023-07-18
Used Hours: 606232
Project Name: SOCCO Academy
Project Shortname: ERTH1488
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 Carbon - Climate links. Through a combination of in situ experiments, observations and model simulations, we advance process knowledge and understanding of model biases in representing these processes. We are also examining the skills needed to analyse increasingly large datasets from model simulations, observational platforms such as satellite and high resolution platforms as well as the skills to improve the computational efficiency of our simulations and the algorithms driving them.
Principal Investigator: Prof Gerard Tromp
Institution Name: Stellenbosch University
Active Member Count: 14
Allocation Start: 2023-01-19
Allocation End: 2023-07-19
Used Hours: 84626
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. SATBBI also has an important educational and training mandate. The CHPC is a vital resource for these activities.
Principal Investigator: Dr Chris Oosthuizen
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2023-01-23
Allocation End: 2023-07-24
Used Hours: 62829
Project Name: Bayesian Integrated Population Modelling of Southern Elephant Seals
Project Shortname: CBBI1533
Discipline Name: Environmental Sciences
Understanding the drivers of population dynamics is a fundamental problem in ecology, and an important ingredient in efforts to mitigate current, global declines in biodiversity. It is therefore essential that robust methods are available to quantify population growth rates and the demographic forces shaping them. The current state-of-the-art consists of transient Life Table Response Experiments (tLTRE) coupled with Integrated Population Models. We used more than 30 years of mark-recapture and population count data to estimate the demographic contribution of immigration and other vital rates to population growth in southern elephant seals. Our analysis compared the effects of three different combinations of multi-variate priors on our IPM-tLTRE estimates, and found that the estimated tLTRE contribution of immigration was sensitive to these priors. In a simulation study, our model both overestimated small contributions and underestimated larger contributions of immigration, reiterating the challenge of robustly estimating the demographic contribution of immigration. Thanks to the computational resources of the CHPC, we have been able to validate our model's performance using simulation. This would have been demanding using 'standard' IPMs, but we have pioneered the use of even more computationally demanding Gaussian Process priors in this field. One of the key efficiency gains made possible by our modelling language, Stan, and the CHPC, is the ability to parallelise expensive likelihood calculations across multiple cores. It appears we may have been the first group to run Stan on the CHPC. We will surely not be the last.
Murray Christian has been the driving force of this research during his Post-doctoral fellowship within the Marion Island Marine Mammal programme at the University of Pretoria, with the Centre for Statistics in Ecology, the Environment and Conservation at the University of Cape Town being the partner institute. This work will be submitted to Ecological Applications in July 2023.
Principal Investigator: Dr Emmanuel Dufourq
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 7
Allocation Start: 2023-01-23
Allocation End: 2023-07-24
Used Hours: 17817
Project Name: Machine Learning for Ecology
Project Shortname: CSCI1563
Discipline Name: Data Science
The Machine Learning for Ecology Research Group is part of the African Institute for Mathematical Sciences. The group focuses on research and scientific discoveries for conservation ecology using advancements in machine learning. By harnessing the capabilities of machine learning, we can process and interpret data from various sources, such as passive acoustic recordings and camera traps.
The world has witnessed a distressing decline in biodiversity, brought about by various factors such as resource overexploitation, deforestation and climate change. Despite numerous species being on the International Union for Conservation of Nature's Red List for several years, further conservation efforts are still crucial to ensure the survival of the remaining individuals. The urgency of this matter has been reiterated by the Intergovernmental Panel on Climate Change (IPCC), which has called for immediate action to be taken. These challenges necessitate an abundance of information and more sophisticated solutions. While it is evident that the populations of threatened species are declining, significant conservation efforts have been implemented to counteract this trend.
Researchers and rangers actively monitor these populations using various methods, including the use of microphones and cameras in the environment, and analysing the recorded media for evidence of species of interest. Passive acoustic monitoring (PAM) is a non-invasive approach for studying soundscapes. However, analysing thousands of hours of recordings poses a challenge in terms of manual processing. Nonetheless, PAM has provided new insights into the study of endangered species that are challenging to directly observe.
Artificial intelligence has been successfully employed to develop classification models capable of automatically detecting animal vocalisations. This approach has been successfully applied in studies of various species. Through the use of high performance computing, our group is focusing on developing methods to address wildlife monitoring and work on critical species that are under threat of extinction both locally and internationally.
Principal Investigator: Dr Uljana Hesse
Institution Name: University of Western Cape
Active Member Count: 8
Allocation Start: 2023-01-24
Allocation End: 2023-07-24
Used Hours: 89720
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 focuses 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.
To date, we have generated a high quality rooibos genome assembly, finalised gene predictions using short and long rooibos transcriptome data as supporting evidence, and completed functional annotation of the rooibos genes. For long read DNA and RNA sequencing, we have established Oxford Nanopore (MinION) technologies at UWC. We are also finalising a Convolutional Neural Network algorithm trained to identify and classify transporter genes, which can be adapted for the analysis of any other protein family. All computational analyses, which require substantial computational power and prowess, are being conducted locally at CHPC. This proves that Medicinal Plant Genomics can be completed entirely in South Africa, strengthening the countries independence in the bioprospecting of its natural resources, including the native flora and fauna.
Principal Investigator: Prof Mwadham Kabanda
Institution Name: University of Venda
Active Member Count: 3
Allocation Start: 2023-01-24
Allocation End: 2023-08-08
Used Hours: 57431
Project Name: Reaction mechanism for atmospheric relevant molecules
Project Shortname: CHEM1161
Discipline Name: Chemistry
The research group is lead by Prof MM Kabanda of the Department of Chemistry at the University of Venda. The students involved in the research group are Nesane Tshimangazo, Gift Masuku and Tshedza Sithuba. The research work involved investigation of the molecular species with potential atmospheric, environmental and biological applications. The computational work included here is compared with experimental work that is done to try and understand the use of the chosen molecules towards solving problems associated with climate change, water purification and medicinal potential. The calculations are computationally expensive if performed on person computer or laptop. In this way, HCP is crucial is reducing the computational time for the work. The work is progressing successively as we have been able to publish five article in the current six month period. The articles are included under the publication section.
Principal Investigator: Prof Lyudmila Moskaleva
Institution Name: University of the Free State
Active Member Count: 10
Allocation Start: 2023-01-24
Allocation End: 2023-08-24
Used Hours: 868738
Project Name: Understanding surface reactivity of solids using DFT simulations
Project Shortname: CHEM1294
Discipline Name: Chemistry
The group of Prof Moskaleva at the University of the Free State uses advanced computational methods to investigate the surface reactivity of solids at the atomic level. These methods include first-principles quantum-chemical methods, molecular dynamics, statistical theory, microkinetic modelling and thermodynamics. Such modeling studies can reveal the microscopic mechanisms of reactivity, which are essential to optimize functional materials for various applications, such as catalysis, electrocatalysis, semiconductors, and optoelectronics. We would like to highlight two of our successful projects that rely on HPC resources provided by the CHPC center.
One of these projects conducted in cooperation with German scientists and funded by the German Research Foundation (DFG), is a computational study on nanoporous gold (np-Au), a versatile material with interesting mechanical, optical, and catalytic properties. Our study focuses on the remarkable low-temperature catalytic activity of np-Au and its high selectivity toward partial oxidation reactions. We use CO and methanol oxidation as model reactions. We study the dynamic behavior of the catalytic surface, including diffusion and restructuring processes, with the help of ab initio molecular dynamics simulations. These simulations are very computationally demanding and require HPC resources to perform. We were able to show how O atoms self-organize into chains on a stepped Au surface, a process accompanied by surface coarsening, while no chain formation is found on a flat Au(111) surface. These O chains can participate in catalysis by accommodating and activating adsorbates at O vacancies and by supplying reactive O atoms. They could also be responsible for the selectivity of partial oxidations.
Another project funded by National Research Foundation (NRF) is a computational study on hydrocarbon combustion chemical reactions using density functional theory (DFT) and high-level ab initio quantum chemistry methods. The objectives of this study are to determine valuable information such as geometric, thermodynamic, and kinetic properties of some of the important elementary combustion reactions. Together with our cooperation partners from TIFR, India we are performing benchmarking calculations on these systems with very accurate W1U, CCSD(T)-DLPNO and various DFT methods with the goal of performance evaluation and choosing an optimal method for future use in generating a training set for Machine Learning. A manuscript has been submitted for publication. The results will be collected in a dataset MOLDIS: https://moldis-group.github.io/
We are grateful to the CHPC for providing us with excellent computational resources and support that are essential for our research programme.
Principal Investigator: Dr Chika Nnadozie
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2023-01-25
Allocation End: 2023-07-25
Used Hours: 1314
Project Name: Campylobacteroisis
Project Shortname: CBBI1446
Discipline Name: Bioinformatics
This research group is hosted at the Institute for water research (IWR), Rhodes University, Grahamstown, Eastern Cape. IWR is a renowned research and innovation center specializing in environmental water quality research. The freshwater microbial ecology research group has just completed one of their projects funded by the Water Research Commission, South Africa Project No. K5/2886. The result of the study suggests Livestock grazing around the river is the most bacterial pollution contributor to the Bloukrans River
Principal Investigator: Dr Nikhil Agrawal
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2023-01-25
Allocation End: 2023-07-31
Used Hours: 36221
Project Name: Molecular Modeling of proteins using different computational tools
Project Shortname: HEAL1189
Discipline Name: Health Sciences
The molecular Modeling research group is based at the University of KwaZulu-Natal, Durban South Africa. In our research group, we use a computational modeling tool to investigate the dynamics of biomolecules such as proteins, and membranes at the atomic level.
The project has made remarkable progress so far. Through their simulations, we have identified specific key residues involved in the stable binding of Aβ fibrils to cholesterol-rich cell membranes. This discovery provides promising insights for developing targeted inhibitors, potentially leading to groundbreaking therapies against Alzheimer's disease.
Principal Investigator: Prof Warren du Plessis
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2023-01-25
Allocation End: 2023-07-31
Used Hours: 3101
Project Name: Electronic Warfare (EW) Technologies
Project Shortname: MECH0989
Discipline Name: Electrical Engineering
The electronic warfare (EW) programme has not made significant use of CHPC capabilities over the last 6 months. The work that was conducted during this time was preparation for continuing research that should lead to more significant outputs in the next reporting period. This will change at some point in the future, but the precise timing is unclear.
Principal Investigator: Prof Mahmoud soliman
Institution Name: University of KwaZulu-Natal
Active Member Count: 49
Allocation Start: 2023-01-26
Allocation End: 2023-07-26
Used Hours: 1725838
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 a 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 are employed in performing the molecular dynamic calculations and the corresponding post-molecular dynamic simulation analysis
Principal Investigator: Dr Molemi Rauwane
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 5
Allocation Start: 2023-01-26
Allocation End: 2023-07-27
Used Hours: 3182
Project Name: Molecular Biology and Bioinformatics of plant-pathogen interactions
Project Shortname: CBBI1564
Discipline Name: Bioinformatics
Project ID CBB11564: Molecular Biology and Bioinformatics of Plant-Pathogen Interactions
The research group of Molecular Biology and Bioinformatics of Plant Pathogen interactions is led by Dr Molemi Rauwane from Nelson Mandela University, in collaboration with UNISA and the Agricultural Research Council.
The group focuses on the use of molecular biology techniques and bioinformatics tools to identify characterize and understand/unravel mechanisms of plants in response to biotic and abiotic stress. Our group focuses on understanding plant-pathogen interactions as well as plant-abiotic (heat and drought) stress in crops of economic importance such as wheat, beans, cassava, and sweet potatoes, among others. Other projects from different collaborators also work on understanding plant-pathogen interactions in vegetable crops such as tomato and okra.
These studies are done for breeding crops with resistance/tolerance to multiple stress caused by climate change. The crops can then be planted anytime without challenges of loosing them because of biotic or abiotic stress, or both stresses combined. This can go a long a way in alleviating poverty.
With the crops been exposed to different biotic and abiotic stress daily, understanding their response to these factors enable the development of improved varieties with resilience to biotic and abiotic stresses. CHPC platform helps in analysing the data generated from NGS system, so as to interpret the data that entails response of plants to biotic and abiotic stress. This plays a role in decisions made in terms of improving important varieties of crops of economic importance.
Currently, two manuscripts are currently in progress for publications in peer-reviewed journals, and a conference poster is in preparation for conference attendance.
Principal Investigator: Prof Eric van Steen
Institution Name: University of Cape Town
Active Member Count: 7
Allocation Start: 2023-01-26
Allocation End: 2023-08-03
Used Hours: 654414
Project Name: Lateral interactions on surfaces
Project Shortname: CHEM0780
Discipline Name: Chemistry
Heterogeneous catalysts are complex solids that contain the actual catalyst, but also other materials with different functionalities. The actual catalysis takes place on the surface of the catalytically active material, and to maximize the surface of this material nano-sized particles are used. These particles are put on a support, and some more additives are added to enhance its functionality (promoters). Putting these catalysts together has been a black art for a long time. The group led by Prof. Eric van Steen at the University of Cape Town studies the function of the support and these additives using computational models. For instance, cobalt as a catalytically active material functions particularly well when supported on titania. Here we show using DFT-calculations on the CHPC that the support not only carries cobalt, but actually participates in the catalytic reaction. Furthermore, we show that platinum, which is often added to ensure that cobalt is present in its metallic form, is also altering the electronic structure of cobalt and thus improving the reaction.
Principal Investigator: Dr Madison Lasich
Institution Name: Mangosuthu University of Technology
Active Member Count: 7
Allocation Start: 2023-01-26
Allocation End: 2023-07-27
Used Hours: 418019
Project Name: Chem Thermo
Project Shortname: CHEM1028
Discipline Name: Chemical Engineering
The Chem Thermo project is led Dr Madison Lasich and includes her post-doctoral scholar Dr Victoria Adeleke and current Masters candidate Mr Themba Ngcobo. The group collaborates with researchers at MUT, UKZN, and DUT. Recently the research group has contributed to and published several notable studies. A combination of different computational physics and molecular simulation methodologies yielded insights into the behaviour of Korteweg fluids, a class of fluids exhibiting strong capillarity. These results were published in an international journal and this class of fluids includes substances as diverse as magma and superfluid helium. Details on the intermolecular interactions between various estrogenic pollutants and a common 3D printing polymer, poly(lactic acid), were computed using a combination of molecular simulation and the classical Flory-Huggins theory. These results were published in an international journal and may be useful in the design of both detection and treatment systems that handle these emerging contaminants. The group also contributed to a project to design a multiepitope vaccine for Toxoplasma gondii for chickens and to another project to assess the antioxidant properties of carvacrol. In all of these studies, the high performance computing resources of the CHPC are vital to undertake computationally intensive calculations and simulations employing a variety of computational techniques.
Principal Investigator: Dr Annerine Roos
Institution Name: University of Cape Town
Active Member Count: 12
Allocation Start: 2023-01-27
Allocation End: 2023-08-02
Used Hours: 11397
Project Name: DCHS and MRI studies
Project Shortname: HEAL1267
Discipline Name: Health Sciences
We are a group of neuroscientists and clinicians in the field of psychiatry who investigate brain correlates of psychiatric and neurological disorders. The Universities of Cape Town and Stellenbosch collaborate with international brain imaging groups in this work. The aim is to find out what goes wrong in the brains of people suffering from such disorders, to inform suitable interventions and treatment. We for instance, image young children using MRI and follow them over time with repeat scans, to determine how environmental influences such as prenatal substance exposure or maternal depression may impact neural development. Such projects are crucial to identify vulnerable groups and key periods for intervention to optimise development. Evidence shows the earlier interventions, the better the outcomes. We also investigate disorders in adults such as obsessive-compulsive-and-related disorders and Parkinson's disease, to gain a better understanding of underlying neural issues. CHPC enables us to analyse brain data that requires powerful technical resources. Brain data comes with very large files and programs need to have the computer capacity to process the data. If it was not for CHPC, it would have taken months to produce certain output on one's own computer; it takes less than a month to do the same work on CHPC that uses multiple computers at the same time. We upload the raw imaging data from the scanner onto CHPC's system, and subject it to programs that conduct specific steps to produce results. Results may include files on the size and thickness of brain regions, and the intactness of brain tracts interconnecting such regions. We are presenting and publishing numerous pieces of work using this output.
Principal Investigator: Prof Yoshan Moodley
Institution Name: University of Venda
Active Member Count: 7
Allocation Start: 2023-01-29
Allocation End: 2023-07-29
Used Hours: 197638
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.
Principal Investigator: Prof George Amolo
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 16
Allocation Start: 2023-01-30
Allocation End: 2023-08-24
Used Hours: 1061984
Project Name: Properties of Materials for Green Energy Harnessing
Project Shortname: MATS862
Discipline Name: Material Science
The MATS862 is largely a group based in Kenya, at the Technical University of Kenya, but has among its team membership, researchers from other national institutions as well as those from other parts of Africa. The majority of the members are graduate students and early career PhDs.
While the group has dealt with properties of hard materials as well as materials for energy conversion for more than a decade now, we have in the last few years embraced multidisciplinary work in water treatment and drug design within chemistry. This move is to enhance research on what directly involves needs of the community around us. Calculations of properties in the core of the earth where there are minerals has also taken root from external collaborations as will be listed on progress made.
Computational modeling, whether from first principles or from empirical approaches in an essential part of modern scientific and technological investigations as it enriches the outcome. Almost all aspects of our lives will eventually benefit from aspects of computational modeling from fundamental science to aspects that now require artificial intelligence. With access to HPC resources, decision support to guide productivity in industry is now real.
Materials in bulk, surfaces and at a nanoscale can be prepared its properties tested without assumptions, which is the basis of the first principle approach. Such materials would have spatial formation, which is used by special computer codes to determine properties of interest. Due to accuracy and the fact that it can take time to obtain properties of interest, the CHPC has dedicated computing resources that are available 24-7 to accomplish the needs of running calculations without interruption and saving as well as storing the output for a period of time.
We have made good progress and continue to attract partners as per the attachments.
Principal Investigator: Prof Fourie Joubert
Institution Name: University of Pretoria
Active Member Count: 43
Allocation Start: 2023-01-30
Allocation End: 2023-09-10
Used Hours: 17914
Project Name: NGS Bioinformatics
Project Shortname: CBBI0905
Discipline Name: Bioinformatics
The facilities at the CHPC have been used for investigating the genomics of a symbiont of a woodwasp, which plays a significant role in the forestry industry. This led to the paper: Queffelec J, Postma A, Allison JD, Slippers B. (2022) Remnants of horizontal transfers of Wolbachia genes in a Wolbachia‑free woodwasp. BMC Ecology and Evolution 22(36):1-14. 10.1186/s12862-022-01995-x PDF.
Additionally, a bacteria of agricultural interest was characterized, leading to the paper: NandaKafle G, Blasius LA, Seale T, Brözel VS. Escherichia coli Strains Display Varying Susceptibility to Grazing by the Soil Amoeba Dictyostelium discoideum. Microorganisms. 2023 May 31;11(6):1457. doi: 10.3390/microorganisms11061457. PMID: 37374960; PMCID: PMC10304320.
Principal Investigator: Dr Ruben Cloete
Institution Name: University of Western Cape
Active Member Count: 12
Allocation Start: 2023-01-30
Allocation End: 2023-09-12
Used Hours: 506309
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 possibly 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 improved 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 protein structures is key. Therefore, large scale computing resources are required to run large protein systems. Currently, we received SAMRC funding to computationally investigate SARS-CoV2 coronavirus protein targets to identify drugs and purchase the compounds to test them experimentally.
Principal Investigator: Prof Thuto Mosuang
Institution Name: University of Limpopo
Active Member Count: 13
Allocation Start: 2023-01-30
Allocation End: 2023-08-24
Used Hours: 55127
Project Name: Computational studies of various ultra-hard materials
Project Shortname: MATS0875
Discipline Name: Material Science
The research group is based in the Department of Physics, University of Limpopo. We are now consisting of three (3) Doctoral, and two (2) Honours students in our group. Computationally the research projects investigate various materials such as molybdenum disulphides, molybdenum diselenides, copper sulphides, copper selenides, gallium nitride, gallium arsenide, graphene oxide, boron nitride, gold, silver, nickel, and copper nanoparticles. The gold, silver, nickel, and copper nanoparticles are probed for possible toxicity/non-toxicity when ingested in human tissues. Molybdenum disulphides, molybdenum diselenides, and boron nitrides are investigated for possible chemical sensing. Specifically, electronic, structural, optical, 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 is useful on the structural, dynamical and thermodynamics properties. The exciting code is informative on the electronic, excited states and transport properties of these materials. Now lately, Materials Studio also through CHPC is being used to understand precious metal – protein molecules interactions.
Principal Investigator: Dr ADEDAPO ADEYINKA
Institution Name: University of Johannesburg
Active Member Count: 12
Allocation Start: 2023-01-30
Allocation End: 2023-07-30
Used Hours: 941996
Project Name: Computational Design of Molecules
Project Shortname: CHEM1221
Discipline Name: Chemistry
The Computational Design of Molecules Research group is based located within the Department of Chemical Sciences at the University of Johannesburg. We aim to design and simulate new or improved molecules, and nanomaterials for applications in Catalysis, Renewable energy, and nanotechnology. 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 various 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. We rely on computational resources from the Centre for High-Performance Computing to carry out our computational work efficiently in order to achieve our goals. To date, we have been able to computationally design various unique molecules which have demonstrated great potential as adsorbents for greenhouse gases as well as for application in electrocatalysis. Several articles have been published in top journals as output from the various projects under this research program.
Principal Investigator: Prof Selwyn Mapolie
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2023-01-30
Allocation End: 2023-08-24
Used Hours: 1458
Project Name: Computational investigations of multinuclear metal complexes with macromolecular materials
Project Shortname: CHEM1527
Discipline Name: Chemistry
The Organometallic Chemistry Research Group at Stellenbosch University is interested in developing new metal-containing drugs for cancer treatment. This involves designing, synthesizing, characterizing and testing these compounds. To this end, we have identified a series of binuclear palladium-containing complexes that have shown excellent activity against breast cancer cell lines while displaying less toxicity than the conventional chemotherapeutic agents. However, to better understand how these compounds work, we need to investigate the interactions of the compounds with biologically relevant molecules, like DNA and blood proteins. While we have done this experimentally, using a computational chemistry approach to complement our results has provided significant insights and allowed us to better visualize the processes these drugs are involved in. Without the use of the CHPC's resources, we would not have been able to determine that these compounds interact with DNA through various mechanisms. Furthermore, the computational results have highlighted the importance of a specific part of the molecules that directly affect the interaction of the compounds with DNA, which can be manipulated for future research endeavors.
Principal Investigator: Dr Marilize Le Roes-Hill
Institution Name: Cape Peninsula University of Technology
Active Member Count: 1
Allocation Start: 2023-01-31
Allocation End: 2023-08-01
Used Hours: 24673
Project Name: Actinobacterial genomics/metagenomics
Project Shortname: CBBI1347
Discipline Name: Other
The Applied Microbial and Health Biotechnology Institute (AMHBI) is a newly formed research institute based at the Cape Peninsula University of Technology. The institute aims to perform research that covers the full innovation chain - from fundamental to experimental to applied research, with the end goal being the development of new products. Certain components of our research also focus on biodiversity and how biodiscovery is driven by it. In order to understand what is happening within a specific environment, we often look at what we can culture from the environment (in order to access new products such as antibiotics and novel enzymes) but are typically guided by the total population structure as determined by metagenomics. As such, in order to analyse large data sets generated through next generation sequencing, we have made use of the resources of the Centre for High Performance Computing (CHPC) for the processing of the data. The outcome of the analyses has highlighted the great degree of bacterial diversity in South African environments; especially the great diversity of specific antibiotic-producing bacteria, the actinobacteria. With the worldwide increase in the number of drug- and multidrug-resistant pathogens, there is a continued need for the discovery of novel antibiotics. This study therefore contributes to our current knowledge base as to where we can potentially source these novel antimicrobial agents, while also focusing on the discovery of novel microorganisms often not cultivated during culture-based studies.
Principal Investigator: Prof Malik Maaza
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2023-02-01
Allocation End: 2023-09-04
Used Hours: 277093
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.
Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 6
Allocation Start: 2023-02-06
Allocation End: 2023-08-06
Used Hours: 133502
Project Name: Computational and statistical methodologies for human and environmental health prediction
Project Shortname: CBBI0818
Discipline Name: Bioinformatics
Computational risk prediction and Artificial Intelligence for multi-omics-driven human health challenges is running from my research group and continue to support several African researchers and students via several African universities and H3African and DS-I African consortia. This research programme is fundamentally aiming:
1) to determinate the environment and genomics 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 humans.
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 Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 9
Allocation Start: 2023-02-06
Allocation End: 2023-08-06
Used Hours: 164011
Project Name: African Multi-Omics Data Science
Project Shortname: CBBI1039
Discipline Name: Bioinformatics
Training in computational risk prediction and Artificial Intelligence for multi-omics-driven human health challenges is running from my research group as joint appointment from the University of Kinshasa, DR Congo, and Northumbria University, Newcastle, UK and continue to support several African researchers and students via several African universities and H3African and DS-I African consortia. This research training programme is fundamentally aiming:
1) to provide students with experience and training in computational cost tasks and large-scale data analysis
2) to determinate the environment and genomics 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 humans.
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: Dr Thipe Modipa
Institution Name: University of Limpopo
Active Member Count: 4
Allocation Start: 2023-02-06
Allocation End: 2023-08-07
Used Hours: 7059
Project Name: Speech Technology
Project Shortname: CSCI1440
Discipline Name: Computer Science
The University of Limpopo's Telkom Center of Excellent Speech Technology group conduct research focusing on the following areas: automatic speech recognition, text-to-speech, natural language processing. The center's focus is to promote the languages spoken in the Limpopo province and contribute to the development of digital resources for under-resourced languages. The development of such resources requires massive computational resources. The Department of Computer Science does not possess such resources and relies on the services provided by the CHPC. The service provided by the CHPC has benefited the center since of the MSc students was able to generate the much-anticipated results. The center will continue to use the services of the CHPC since more students require such services given nature of their research projects.
Principal Investigator: Dr Brigitte Glanzmann
Institution Name: Stellenbosch University
Active Member Count: 21
Allocation Start: 2023-02-06
Allocation End: 2023-08-06
Used Hours: 82729
Project Name: SAMRC Precision Medicine African Genomics Centre
Project Shortname: CBBI1195
Discipline Name: Bioinformatics
The South African Medical Research Council's Genomics Centre had quite humble beginnings where we sequenced the first 6 human genomes on the African continent. Since then, we have had a 124% increase in the number of samples that have been sequenced at this facility, and these have been for both local and international researchers. Every sample that comes through the Genomics Centre, and which is sequenced, is processed on the CHPC. We are highly reliant on the resources provided to us by the CHPC and this platform has also been used to train young researchers to process their research data,
Principal Investigator: Prof Mario Santos
Institution Name: University of Western Cape
Active Member Count: 21
Allocation Start: 2023-02-06
Allocation End: 2023-08-08
Used Hours: 446963
Project Name: Cosmology with Radio Telescopes
Project Shortname: ASTR0945
Discipline Name: Astrophysics
An array of 350 radio telescopes in the Karoo desert of South Africa is getting closer to detecting "cosmic dawn" — the era after the Big Bang when stars first ignited and galaxies began to bloom.
In a paper accepted for publication in The Astrophysical Journal, the Hydrogen Epoch of Reionization Array (HERA) team reports that it has doubled the sensitivity of the array, which was already the most sensitive radio telescope in the world dedicated to exploring this unique period in the history of the universe.
While they have yet to actually detect radio emissions from the end of the cosmic Dark Ages, their results do provide clues to the composition of stars and galaxies in the early universe. In particular, their data suggest that early galaxies contained very few elements besides hydrogen and helium, unlike our galaxies today.
Principal Investigator: Dr Samuel Atarah
Institution Name: University of Ghana
Active Member Count: 3
Allocation Start: 2023-02-06
Allocation End: 2023-09-07
Used Hours: 161604
Project Name: Ab initio studies of electronic and magnetic properties of selected elements
Project Shortname: MATS1162
Discipline Name: Physics
Perovskite material are the fastest growing of the new material targeted for energy harvesting applications. In particular lead free perovskites are the preferred material for this application due their environment friendly nature.
We are a part of the Condense Matter research group of the Department of Physics, at the Unversity of Ghana. The study of Pb-free perovskites as candidate material is our current focuse and it done computationally using among others the Quantum Espresso suite. Cells of perovskites are pretty large requiring computational power. This is what make the CHPC a very important resource to our study. In fact, for sure it would be hard to get about the study without the CHPC facility so generously offered.
We have not seen the anticipated progress in our work this time due to very long waiting times for jobs to be computed. We anticipate better luck in the coming times.
Principal Investigator: Prof Markus Boettcher
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2023-02-06
Allocation End: 2023-08-08
Used Hours: 59422
Project Name: Modeling time-dependent emission from blazar jets
Project Shortname: ASTRO1535
Discipline Name: Astrophysics
This program is conducted by the group of Prof. Markus Boettcher at North-West University, Potchefstroom. Specifically, it is part of the Ph.D. research of NWU student Hannes Thiersen. The project studies a particularly enigmatic class of active galaxies called blazars, in which mass accretion onto a supermassive black hole in the center of a galaxy leads to the ejection of streams (jets) of gas propagating at almost the speed of light. In blazars, these jets are oriented closely aligned with our line of sight. Blazars are emitting radiation across the entire electromagnetic spectrum, from radio waves to high-energy gamma-rays, and, among other properties, their radiation is known to be variable on a large range of time scales, from minutes to years. The causes of such variability and correlations between the variations in different wavelength bands are poorly understood and do not show any predictable patterns. This project studies this multi-wavelength variability through a suite of numerical simulations in which stochastic variability patterns are introduced into the input parameters of a commonly used emission model for blazars. Due to the stochastic nature of the variability, robust conclusions concerning standard diagnostics of variability patterns can only be drawn by a large, statistically meaningful sample of realizations, requiring thousands of individual variability simulations. This would not be feasible without large-scale computing facilities like the CHPC. Significant progress has been made, but continued service interruptions due to load shedding as well as prioritisation of requests by the National Weather Service have led to interruptions of simulations, which needed to be re-started, and has therefore slowed the progress down. Nevertheless, the results should be ready for publication before the end of 2023.
Principal Investigator: Dr James Sifuna
Institution Name: The Catholic University of Eastern Africa, Nairobi, Kenya
Active Member Count: 6
Allocation Start: 2023-02-06
Allocation End: 2023-09-07
Used Hours: 292233
Project Name: Ab initio study on novel materials for novel functionalities.
Project Shortname: MATS1424
Discipline Name: Material Science
The Theoretical Condensed Matter Group at the Catholic University of Eastern Africa, has two leaders and a couple of students. We have common interests in material discovery. I head the group at the moment and we have had a perfect rapport with every member.
Recently we had a team from CHPC that visited us in Nairobi and it was very fantastic sharing with them.
The research group has a very high affinity for new novel materials that are alternatives to fossil energy.
We Employ DFT as a tool in our calculations as implimented in SIESTA and Quantum ESPRESSO codes.
CHPC is critical in the sense that it gives us computing facilities we cant achieve within our university. We study large systems that will always need plenty of CPU hours to converge. Thanks to CHPC.
At the moment, we have achieved almost half of the set objectives and we are thankful to CHPC and its technical team.
Principal Investigator: Dr Stefan du Plessis
Institution Name: Stellenbosch University
Active Member Count: 15
Allocation Start: 2023-02-07
Allocation End: 2023-08-08
Used Hours: 37780
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.
Principal Investigator: Dr Saheed Sabiu
Institution Name: Durban University of Technology
Active Member Count: 21
Allocation Start: 2023-02-07
Allocation End: 2023-08-08
Used Hours: 499680
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 Kevin Colville
Institution Name: Centre for High Performance Computing
Active Member Count: 6
Allocation Start: 2023-02-01
Allocation End: 2023-08-01
Used Hours: 11264
Project Name: Workshops
Project Shortname: WCHPC
Discipline Name: Other
The CHPC runs workshops. See www.chpc.ac.za and wiki.chpc.ac.za for more info.
Principal Investigator: Dr Lonnie van Zyl
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2023-02-08
Allocation End: 2023-08-08
Used Hours: 4907
Project Name: Engineering bacterial pyruvate decarboxylase for increased thermostability
Project Shortname: CBBI1265
Discipline Name: Bioinformatics
In 2023 the Institute for Microbial Biotechnology and Metagenomics (IMBM) at the University of the Western Cape were awarded one of the Biodiversity Biobanks of South Africa (https://bbsa.org.za/) given their extensive microbial collection assembled over two decades from a variety of exotic locations. As part of their service offering IMBM would not only provide users access to the bacterial cultures, but are also aiming to provide the genome sequence data for all bacteria in their collection, as is done by the leaders in the field such as the American Type Culture Collection or Deutsche Sammlung von Mikroorganismen und Zellkulturen. To do so, they have partnered with the DSI funded DIPLOMICS working group to purchase an Oxford Nanopore Technologies genome sequencer capable of sequencing 60 bacterial genomes at a time with the goal of sequencing at least 500 of the bacteria in their collection, as a start. Apart from being useful to clients who work on the bacteria themselves, this data could also be mined independently to inform on the factors affecting how and why bacteria exploit certain environmental niches as well as be mined for enzymes or metabolic pathways of interest.
Principal Investigator: Dr Hezekiel Kumalo
Institution Name: University of KwaZulu-Natal
Active Member Count: 16
Allocation Start: 2023-02-09
Allocation End: 2023-08-09
Used Hours: 101136
Project Name: Molecular modeling and computer aided drug design
Project Shortname: HEAL1009
Discipline Name: Health Sciences
Our research group, situated at the UKZN Durban Medical School campus and closely affiliated with the University of KwaZulu-Natal in South Africa, focuses extensively on the intricate realm of biological systems within the domain of drug design. Utilising computational and molecular modelling as our guiding compass, we delve into the depths of scientific inquiry. Our primary mission centers on the precise design and thorough investigation of targets with profound biological and therapeutic implications. Employing advanced computational methods, we gain insight into complex chemical and biochemical reactivity, emphasising aspects such as the transition state, environmental influences on reactions, catalysis origins, and kinetic isotope effects. Within the sphere of enzymatic reactions, our research plumbs the depths of mechanistic pathways, transition states, and the development of enzyme inhibitors. We also explore the intricacies of evolved targets' binding and catalytic properties. Our methodology relies on advanced computational techniques, including Quantum Mechanics/Molecular Mechanics (QM/MM) MD simulations, Quantitative Structure-Activity Relationship (QSAR) analyses, and bioinformatics tools. This approach enables us to deepen our understanding of molecular interactions, dynamic behaviours, and binding free energy calculations. Beyond the confines of academia, our efforts extend to nurturing pharmaceutical scientists equipped with specialised skills. This prepares them to seamlessly navigate the pharmaceutical industry and academia, bolstering the local pharmaceutical landscape. Despite fiscal challenges often faced by emerging research groups, our partnership with the Center for High-Performance Computing (CHPC) accelerates our progress. The CHPC provides invaluable resources, enabling us to rapidly formulate and scrutinise hypotheses and elucidate complex experimental data, including the binding landscapes of enzymes and the mechanisms of various inhibitors. In summary, our research group is dedicated to pursuing scientific enlightenment, training future pharmaceutical scientists, and growing South Africa's pharmaceutical industry. While specific project progress details remain undisclosed, our unwavering commitment to these objectives underscores our academic dedication.
Principal Investigator: Prof Rajshekhar Karpoormath
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2023-02-09
Allocation End: 2023-08-09
Used Hours: 75541
Project Name: Design of small novel organic compounds as potential drug candidates
Project Shortname: HEAL0835
Discipline Name: Health Sciences
For the Academic year 2022, my research group, Synthetic Medicinal Chemistry Research Group (SMCRG), at the University of KwaZulu Natal, was awarded the top 30 research groups in UKZN.
We generate a library of small molecules and carry out molecular docking and molecular simulation studies to validate our experimental work. It gives credibility to our findings and, in most cases, helps reduce cost and time.
We have filed a second patent on the anti-TB lead molecule, and a third patent on the broad-spectrum antibiotic molecule is in progress. Our various projects are ongoing, and the CHPC resources have been tremendously helpful.
Principal Investigator: Dr Collins Obuah
Institution Name: University of Ghana
Active Member Count: 3
Allocation Start: 2023-02-09
Allocation End: 2023-08-24
Used Hours: 44783
Project Name: Bioinorganic Chemistry
Project Shortname: CHEM1351
Discipline Name: Chemistry
We the computational group at the University of Ghana, Department of chemistry are researching into the improvement of the compounds which are used in solar panels. Power is the backbone for every economy. The effective and clean production of power is the goal of every country. There are compounds which are used in solar panels to produce electricity. However, they need further improvement in their efficiency. Our research looks into modifying these compounds to improve the efficiency. We are using the CHPC facility to predict the efficiency of tetrazine base compounds that we have designed. So far we have been able to show that these compound are effective for their use are solar cell materials. Results from this work is been put as manuscript for publication soon.
Principal Investigator: Dr Jaco Badenhorst
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 6
Allocation Start: 2023-02-10
Allocation End: 2023-08-11
Used Hours: 2823
Project Name: Automatic transcription of broadcast data
Project Shortname: CSIR0978
Discipline Name: Other
The Voice Computing (VC) 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: Dr MC du Plessis
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 3
Allocation Start: 2023-02-10
Allocation End: 2023-09-19
Used Hours: 70807
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 Thishana Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2023-02-07
Allocation End: 2023-08-09
Used Hours: 56194
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) currently, uses computational chemistry as a tool in the field of Green Chemistry to compare the chemical reactivity properties of bioactive molecules for drug delivery. Conceptual DFT which is often referred to as 'computational nutraceutics' is a concept used to predict the molecular structure, spectroscopy, and chemical reactivity of nutraceuticals (food or part of a food that provides medical/health benefits, including the prevention/treatment of diseases) 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.
Principal Investigator: Prof Craig Law
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2023-02-13
Allocation End: 2023-09-14
Used Hours: 8668
Project Name: Aerothermodynamics with vortices, vorticity and shear
Project Shortname: MECH1532
Discipline Name: Other
The Aerothermodynamics research programme at the University of the Wtiwatersrand is headed by Prof. Craig Law. He and his team investigate the flow of fluids. This can include topics as diverse as understanding why an owl is so efficient in flight or an investigation of the shape of a Hydrogen-Oxygen combustor nozzle for a rocket engine. This recently revealed how to reduce the length of a combustor by 50%. This revealed challenges associated with the way we model combustion which is being investigated further. We are also working to understand how to design a fluidic control system for a rocket aerospike nozzle. We are using rocket engine combustors and nozzles to learn how to better model the combustion of hydrogen accurately. The lessons learned hear can be used to investigate how best to use hydrogen combustion in future power, industial and aerospace applications. This knowledge will be critical as we seek alternatives to fossil fuels and need to better understand the viability of hydrogen as a means to store energy.
The investigation started with the numerical modelling of a single nozzle combustion chamber that has become a benchmark and validation case for this type of work. The models were compared to published data and the results produced using the CHPC are much better than anything published so far. As our understanding of the modelling and flow improves we plan to build small scale experimental rigs to validate our numerical predictions and hopefully further improve or numerical models.
The use of numerical models allows for a fairly cost effective and safe means to explore the effect of combustor and nozzle geometries on the flow fields. This can reduce the overall number of experiements required to demonstrate a concept and allows for these experiments to be done without the risk of building a rocket engine and test cell. The flow fields that are being investigated are typically constantly changing with time and require a lot of computing resources to model successfully. The CHPC is an invaluable partner in providing the computational support that makes the numerical aspects of these investigations possible. Progress has been slow so far, but it is anticipated that this should begin to improve over the next 12 months as more postgraduate students join the programme.
Principal Investigator: Prof Graham Jackson
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2023-02-13
Allocation End: 2023-09-19
Used Hours: 81515
Project Name: Insect neuropeptides
Project Shortname: CHEM1101
Discipline Name: Chemistry
Insect pesticides are non-specific and often harmful to beneficial insects like the honey bee, and humans. In this study, by the Jackson group at the University of Cape Town, we are aiming to develop species specific insecticides against the mosquito, the desert locust and several fly pests. Insect physiology is under hormonal control with different insects having different but closely related hormones. By using computational means, in silicon screening, molecular dynamics, we are designing and testing different compounds that will block the hormone receptor and hence disrupt the insect physiology, in particular its ability to fly. The large computing power of the CHPC is necessary to screen our large databases (>10000000) of potential compounds. The GPU cluster is necessary for the molecular dynamics of our large system which consists of the hormone bound to the receptor, imbedded in a membrane. By following the dynamics over several hundred nanoseconds activation of the receptor can be followed. We have now identified 3 new compounds to be tested as species specific insecticides
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 14
Allocation Start: 2023-02-13
Allocation End: 2023-09-14
Used Hours: 3686710
Project Name: Structural, electronic, magnetic properties and anisotropy energy in some metallic and non-metallic heterostructures
Project Shortname: MATS0988
Discipline Name: Material Science
The last two decades have witnessed efforts at discovering materials with novel properties for specific applications such as in electronic and magnetic devices. The discovery of new materials are sometimes accompanied by previously unknown physical, chemical or electronic processes which necessitate the use of advanced theoretical approaches. One of the aims of our research therefore, is to discover novel materials via computational methods and to exploit the unique properties of these materials for potential technological applications. Ultimately, our research is theory-led discovery of novel materials underpinned by DFT method. The numerical implementation of the latter is computational intensive, requiring several computational hours, large data storage and memory requirements, beyond the capacity of ordinary table-top computers. Therefore, 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 10 postgraduate students of various nationalities working in various aspects of the project.
The research is borne out of a collaboration between Dr. Raji (UNISA, South Africa) and the group of Dr. Brice Malonda (Marien Ngouabi University, DRC). 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, harmful gas sensors, catalysis and renewable energy. The study employs density-functional theory (DFT) to investigate these materials. We aim to modify the pristine properties of selected solid crystals, including their surfaces through defect engineering, material heterostructures, alloying and interface engineering.
This research has enabled collaboration between South Africa based academic researchers and colleagues in Congo, Germany, Mexico and Italy. The scope of the project will guarantee regular postgraduate students training who are able to undertake cutting-edge research and contribute to scientific development of South Africa and the rest of Africa continent. Also, the research aim to continuously produce high-impact research publications.
Principal Investigator: Prof Matt Hilton
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2023-02-14
Allocation End: 2023-08-16
Used Hours: 1878
Project Name: Cosmology and astrophysics from Sunyaev-Zel'dovich selected galaxy clusters
Project Shortname: ASTR1534
Discipline Name: Astrophysics
At the Wits Centre for Astrophysics, Prof. Matt Hilton and his research group are using CHPC to analyse data on galaxy clusters, the largest gravitationally bound structures found in the universe. In one project, CHPC is being used to analyse maps of the sky produced by the Atacama Cosmology Telescope (ACT), in order to measure the abundance of galaxy clusters over a 10 billion year span of cosmic history. CHPC is also being used to simulate the ACT cluster survey and measure cosmological parameters, such as the amount of dark matter and dark energy in the universe. In another project, CHPC is being used to process radio data from MeerKAT on clusters detected by ACT. The aim of this work is to determine the nature and evolution of the mysterious diffuse radio emission in galaxy clusters, which is produced when clusters collide. Such cluster mergers are the most energetic events in the universe since the Big Bang. High performance computing resources, such as those provided by CHPC, are crucial to allow the large datasets involved to be processed efficiently.
Principal Investigator: Prof Jaco Dirker
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2023-02-15
Allocation End: 2023-08-31
Used Hours: 60445
Project Name: Heat Transfer Enhancement in Thermal Systems
Project Shortname: MECH1029
Discipline Name: Computational Mechanics
The Clean Energy Research Group (CERG) in the Department of Mechanical and Aeronautical Engineering at the University of Pretoria is involved in experimental and numerical heat transfer research focussed on clean energy applications. We have a number of world-class experimental facilities focused on heat transfer, balanced by a Computational Fluid Dynamics (CFD) division. Currently, work is ongoing in two-phase microprocessor cooling applications such as CPU cooling. This is because current cooling techniques are not effective enough for the high heat flux outputs of current electronic devices. These techniques experience what is known as early dry-out regions, which prevent boiling and thus reduce heat transfer. We investigate different fluids, known as self-rewetting fluids, to help prevent the onset of these dry-out regions. This is possible due to the unique surface tension characteristics of these self-rewetting fluids. Where normal fluids experience a linearly decreasing relationship between the surface tension and fluid temperature, self-rewetting fluids experience a non-linear relationship where, after a certain fluid temperature, the surface tension increases with rising fluid temperature. This is important as surface tension controls the motion of fluids at a two-phase interface, meaning that an increased surface tension will draw fluid between bubbles, formed by boiling, and the heated surface (CPU), wetting the surface and delaying the dry-out regions. To investigate this, two-phase flow simulations need to be performed which are famous for being computationally expensive, requiring a lot of processing power and time. On a powerful 8-core personal computer, small two-dimensional domains require more than 30 hours to solve a single simulation indicating the need for a high-performance computing service such as the CHPC to effectively investigate larger two-dimensional domains as well as three-dimensional domains. The current project is near its end, with more than 60% of the simulations conducted. All model validations have been concluded and now additional explorative research has begun.
Principal Investigator: Dr Ndanduleni Lethole
Institution Name: University of Fort Hare
Active Member Count: 5
Allocation Start: 2023-02-16
Allocation End: 2023-09-07
Used Hours: 263937
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 in the Department of Physics, University of Fort Hare. The group started in February 2020 and comprises the Principal Investigator and one MSc student as of 2023. Currently, the group entirely depends on the Centre of High-Performance Computing (CHPC) facility as it uses the Materials Studio simulation package and computing resources provided by the National Integrated Cyberinfrastructure System CHPC. The group aims to grow to at least two BSc Honours and two MSc students in 2024. The group is currently undertaking two main projects; namely (1) 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 (2) Quest for New Cathode materials for Calcium, Lithium, Magnesium and Zinc ions Batteries. Both projects employ the first principles approach and use computational simulations.
The research work on magnetic materials is significant since there has been a remarkable increase in the 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, magnetic, mechanical and dynamical stable.
With the recent resurgence of plugged-in electric and hybrid electric vehicles and rechargeable electronic devices such as laptops, smartphones, tablets, smartwatches, etc, there is a need for more alternative energy storage battery chemistries. The development of these storage devices is inherently dependent on the type of cathode (charge host structure) material employed and the electron transfer reactions between the alkali metal atoms and host structure lattice along with their consequent electrochemical insertion/removal voltage of alkali metal atoms.
Principal Investigator: Prof Linky Makgahlela
Institution Name: Agricultural Research Council
Active Member Count: 10
Allocation Start: 2023-02-16
Allocation End: 2023-08-17
Used Hours: 1502
Project Name: Beef and Dairy Genomics
Project Shortname: CBBI1138
Discipline Name: Bioinformatics
The ARC-Animal Production, Animal Breeding and Genetics unit is based in Irene, Pretoria. Our research activities aim to develop knowledge on the animal genetic resources of South Africa, and apply traditional and genomics technologies for improved climate-smart production in the livestock industry while preserving animal biodiversity. The growing global population threatens food security, and half of this growth is expected in Africa. Climate change will reduce available natural resources needed for agriculture. We need to produce 100% more food, than today, in the next 30 years, and with limited natural resources. Genomic technological innovations promises to deliver genetic diversity, efficiency, product quality, food safety and public health, animal health and welfare and environment, all interlinked. Current research develops strategies for characterization, conservation and utilization of indigenous animal (cattle, sheep & goats) genetic resources. These are adapted genotypes that will survive global warming. Combine advance genomic technology data (DNA markers and whole genome sequence) and traditional animal pedigrees and longitudinal performance data, and develop statistical models for national genetic evaluations estimated breeding values. The use of genomic enhanced breeding values will speed up the rate of identifying the breeding stock and food production in cattle, sheep and goat sectors. All research activities are carried out in collaboration with partners e.g. SA Universities, Commodity groups and Government departments. Post-graduate students are linked to the research as the bloodline for capacity building. The Beef and Dairy Genomics project graduates several post-graduate students annually, and in the reporting period Ms Kooverjee Bhaveni graduated her MSc. in April 2023, and went further to register for a PhD at the University of the Free State. Research for two PhD students (Mr Mafolo, Ms Kgari and Mr Ramoka) and two MSc students (Ms Mabunda and Ms Monchusi) is on going.
Principal Investigator: Prof Charalampos (Haris) Skokos
Institution Name: University of Cape Town
Active Member Count: 10
Allocation Start: 2023-02-17
Allocation End: 2023-08-31
Used Hours: 355100
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 Edwin Mapasha
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2023-02-20
Allocation End: 2023-09-07
Used Hours: 228991
Project Name: Studies of defects in two dimensional materials such as graphene and tin disulphide for technological applications.
Project Shortname: MATS1429
Discipline Name: Physics
Institution: University of Pretoria Research group: Theoretical and computational solid state research group Project title: Studies of defects in two dimensional materials such as graphene and tin disulphide for technological applications. Semiconducting silicon has been one of the primary materials used in the microelectronic industry for the past several decades. The silicon-based technology is nearing the limits of its use since current technologies require vastly scaled down devices. Because of this, there is a search for new, novel materials mainly two-dimensional materials that can meet this demand. Some of such two dimensional material are graphane and tin disulphide. The peculiar properties of graphane and tin disulphide include high quality crystalline, large surface area, high charge carrier mobilities and wide energy band gap to mention few. These unique properties ignited a large interest as a potential alternative to silicon and a candidate for various new technological applications. Some of the applications include the use of graphane for micro electronic devices, hydrogen storage (fuel cells) and as a lithium-ion battery anode. The aim of this project is to use the density functional theory methods implemented in the Quantum Espresso Package to optimize the electronic performance of graphane and SnS2 in order to facilitate its viable use in microelectronic applications. To efficiently produce reliable results we heavily rely on the higher performance computers. The paper published by Mr Craig Bekeur under the journal of electrochemistry featured in the newsletter of NiThecs for the month of June.
Principal Investigator: Prof Monde Ntwasa
Institution Name: University of South Africa
Active Member Count: 5
Allocation Start: 2023-02-20
Allocation End: 2023-08-22
Used Hours: 10906
Project Name: Anti-Cancer Drug Discovery
Project Shortname: HEAL1237
Discipline Name: Health Sciences
This research programme is based on anti-cancer drug discovery work done at the University of South Africa (Unisa). We use computational biology to screen, model and develop lead molecules for disease eradication purposes. The work we do focuses on but is not limited to cancer, thus making it very significant as cancer cases are on the rise in south africa and the world. We heavily rely on CHPC resources, particularly in the preliminary stages of our research, which entails the screening and discovery of new and novel compounds. Currently, the projects are going well and we hope to do even more before the end of this year.
- Charmy Twala
Principal Investigator: Dr Thokozani Justin Kunene
Institution Name: University of Johannesburg
Active Member Count: 1
Allocation Start: 2023-02-20
Allocation End: 2023-08-21
Used Hours: 117373
Project Name: TurboMagFluids
Project Shortname: MECH1573
Discipline Name: Applied and Computational Mathematics
The Turbomag flow group (postgraduate students) from the University of Johannesburg in the Mechanical and Industrial Engineering Technology department aims to provide technology inputs, advancements, contributions, and learning through numerical approaches and experimental work.
We investigate turbo and hydraulic machines. The use of magnetism in fluid flow is also our specialisation by means of computational studies and experiments.
The programme is making good progress in its first year of establishment. We have postgraduate recruits who are learning how to use CHPC resources and code. These are some commercial and open-source computational fluid dynamics and molecular dynamics codes.
How? (give a very brief and superficial description of the process, and how it relies on the CHPC)
How is the project progressing?
Principal Investigator: Prof Liliana Mammino
Institution Name: University of Venda
Active Member Count: 0
Allocation Start: 2023-02-21
Allocation End: 2023-08-21
Used Hours: 148879
Project Name: computational study of biologically active molecules of natural origin
Project Shortname: CHEM0959
Discipline Name: Chemistry
WHO WE ARE
A professor and postgraduate students at the University of Venda.
THE NATURE OF OUR RESEARCH
We study biologically active molecules of natural origin computationally.
Biologically active molecules are molecules that can cause some effects in the organism. We study molecules whose effects can help in the treatment or prevention of diseases.
We choose molecules of natural origin because their effects are already known from traditional medicine; therefore, they are ideal for the development of more powerful drugs.
WHY IT IS INTERESTING TO STUDY MOLECULES COMPUTATIONALLY
The biological activity of a substance depends on the properties of its molecules. Computational studies enable us to know the properties of a molecule. Knowing them helps understand how they relate to the molecule's activity.
For instance, we can study a certain number of molecules having anticancer activity and compare their properties. Then we can study how each of them can attach itself into a certain area (active site) of a protein that is important for a cancer to grow, and block its function; we can compare the ways and strength with which each molecule interacts with that protein and know which ones are more effective.
HOW MOLECULES ARE STUDIED COMPUTATIONALLY
The calculation of the properties of molecules is very demanding in terms of computer power. Performing calculations on normal computers would require enormous amounts of time, and the most demanding ones would not manage to complete. Using the CHPC enables us to obtain results in a reasonable time, and to perform also the most demanding ones; it is therefore essential for us to conduct our research effectively.
HOW THE PROJECT IS PROGRESSING
We are currently studying molecules with antimalarial, anticancer and antioxidant properties. We have already published some of our results, and we are in the process of obtaining new ones.
Principal Investigator: Prof Hadley Clayton
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2023-02-21
Allocation End: 2023-08-21
Used Hours: 11836
Project Name: Bioorganometallic Chemistry of Transition Metals
Project Shortname: CHEM1288
Discipline Name: Chemistry
Clayton Organometallic Research Group at the University of South Africa. Computer applications are used to investigate the bioorganometallic chemistry of transition metal complexes and their derivatives. This includes density functional methods which are applied to investigate chemical and physical properties of new transition metal complexes synthesized and molecular docking software which is used to study metal complex-protein interactions. The research contributes to the development of structure-activity theories which guides the development of new drugs with potential for the treatment of cancer, rheumatoid arthritis, diabetes and malaria. We have recently reported our finding on the potential use of zinc metal complexes as SARS-CoV-2 viral entry and replication inhibitors.
Principal Investigator: Prof Abram Madiehe
Institution Name: University of Western Cape
Active Member Count: 1
Allocation Start: 2023-02-21
Allocation End: 2023-08-22
Used Hours: 515331
Project Name: Nanobiotechnology
Project Shortname: CBBI1572
Discipline Name: Bioinformatics
The Nanobiotechnology Research Group at the University of the Western Cape performs research on the development of point-of-care diagnostics for both infectious disease, such as HIV, TB, SARS-Cov-2 and ebola; and non-communicable diseases, such as type 2 diabetes, and therapeutics for cancer and obesity. These reagents will use aptamers (single-stranded oligonucleotides) as replacement for antibodies. The students have used the HPC to isolate and select aptamers against their modelled proteins for these diseases. All students have been successful in obtaining aptamers, that they will use on the next phase of their project, which is to develop the devices for disease diagnosis.
Principal Investigator: Mr Ernest Opoku
Institution Name: Nesvard Institute of Molecular Sciences, Ghana
Active Member Count: 12
Allocation Start: 2023-02-21
Allocation End: 2023-08-21
Used Hours: 266275
Project Name: Molecular Quantum Chemistry
Project Shortname: CHEM1352
Discipline Name: Chemistry
Nesvard Institute of Molecular Sciences is an African-focused private nonprofit research and educational institute in Ghana founded in 2019 and incorporated in 2021 under the companies Act, 2019 (Act 992). The liability of its members is limited by guarantee. Our broader objective is to propagate a new paradigm in molecular science education and research to complement the African development project.
Our vision is to advance molecular sciences in Africa through free and open world class education, training, advocacy, research, and collaboration to prepare the next generation of native African molecular scientists to solve African problems.
We aim to provide fundamental requisite skills that are less common to obtain from traditional educational institutions in Africa to complement further education. We collaborate with laboratory researchers in industry, nonprofit, government, or academic laboratories across Africa and beyond.
And even more than that, our goal has been to teach, mentor and collaborate with younger, but also more experienced native African scientists, on how to set up and perform good scientific research, write good scientific articles, and give them a springboard for further education in rewarding molecular sciences disciplines in more prestigious institutions.
Research works at Nesvard Institute of Molecular Sciences focus on wide area of molecular sciences. We employ techniques of basic and advanced theoretical and computational chemistry and molecular modeling such as (but not limited to) elementary and advanced Hartree-Fock theory, electron correlation methods, density functional theory (DFT), models and concepts of chemistry, linear algebra, symmetry, and group theory, classical and statistical thermodynamics to study molecular properties and associated features.
Through CHPC generous computational time and resources, multiple research projects are completed with several currenting ongoing.
Principal Investigator: Prof Irene Barnes
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2023-02-21
Allocation End: 2023-08-22
Used Hours: 3860
Project Name: Irene Barnes TPCP
Project Shortname: CBBI1575
Discipline Name: Bioinformatics
The Tree Protection and Cooperative Programme group has achieved a numerous amount by making use of the CHPC server facilities. Research on pests and diseases of pine, eucalypts and wattle is conducted by the TPCP team. A wide variety of techniques are used to study plant pathology and entomology in an effort to produce world class results. Research includes the identification of new pests and pathogens, as well as the biology and genomic investigation of these organisms to inform and guide management strategies to avoid economic losses. Bioinformatic analyses on some of these pests are being done using the CHPC facilities. These include the investigation of pest/pathogen populations using genetic markers to trace ancestry and pathogen movement globally. More in-depth analyses of these pests and pathogens are also being conducted by analysing mitochondrial genomes and identifying gene clusters that may play a role in pathogenicity. These projects are progressing well and some students will be completing their masters degrees this year.
Principal Investigator: Dr Sphelele Sosibo
Institution Name: North-West University
Active Member Count: 8
Allocation Start: 2023-02-21
Allocation End: 2023-08-22
Used Hours: 4139
Project Name: Molecular Dynamics of target enzymes
Project Shortname: HEAL1414
Discipline Name: Chemistry
The synthesis and biocomputations research group belongs to the North-West University's Materials Science Innovation and Modelling (MaSIM) entity.
The research group focuses of on drug discovery to find new drugs leads using already existing approved drugs.
Modern health science has improved the quality of life today and continue to improve the life expectancy. However, the process of drug discovery is lengthy and expensive. We use the CHPC to fasten the drug discovery process.
The programme has resulted in the dissemination of knowledge to postgraduate students from previously disadvantaged groups as a skill to achieve their project objectives such as graduations. We have produced about eight honours and 1 MSc. A PhD candidate has submitted and further training 1 MSc and 1 honours candidate.
Principal Investigator: Dr Rian Pierneef
Institution Name: University of Pretoria
Active Member Count: 18
Allocation Start: 2023-02-22
Allocation End: 2023-08-02
Used Hours: 151027
Project Name: Bioinformatic and Computational Biology analyses of organisms
Project Shortname: CBBI1124
Discipline Name: Bioinformatics
The CHPC research programme "Bioinformatic and Computational Biology analyses of organism" is a collection of researchers and students with the Principal Investigator based at the University of Pretoria. This research group focusses on the application of bioinformatic and computational biology analyses across a wide variety of organisms and environments to better understand the complexities of life. The data used in these endeavors are large in size and complex in format and as such requires a suitable computational platform such as the CHPC. This research programme is continuously expanding and evolving all based in part on the ability to access the state of the art computational resources hosted by the CHPC. Thank you CHPC!
Principal Investigator: Dr Njabulo Siyakatshana
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 21
Allocation Start: 2023-02-22
Allocation End: 2023-08-22
Used Hours: 98392
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 have been instrumental in informing climate reporting to the UNFCCC, as well as applications for climate adaptation in climate-change impacted industries such as agriculture and logistics as well as for policy-making.
Principal Investigator: Prof Joke Buhrmann
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2023-02-24
Allocation End: 2023-09-13
Used Hours: 12545
Project Name: Operations Research
Project Shortname: CSCI1538
Discipline Name: Applied and Computational Mathematics
The Operations Research and Data Science research group is based at the North-West University, Industrial Engineering. The focus of the group is on advance optimisation algorithms. In Operations Research we look at the performance of algorithms solving NP-complete and NP-hard problems like the Traveling Salesman problem. In this programme, complex large-scale operations research problems are investigated. High performance computing is also used to run Operational Research optimisation and numerical simulations, to realise improved performance of various systems. While time complexity is of essence when solving large-scale combinatorial problems, parallel computing, as provided by the CHPC, can also improve performance by allowing numerous metaheuristic search algorithms to run in parallel threads. This could significantly reduce the amount of time needed to solve complex NP-complete and NP-hard problems optimally. We also recently launched research collaboration on the optimisation of thermo-fluid systems using simulation together with the University of the Witwatersrand. If you are interested in doing postgraduate research in Operations Research and Data Science using high performance computing, please contact Prof Joke Bührmann, joke.buhrmann@nwu.ac.za for more details.
Principal Investigator: Prof Catharine Esterhuysen
Institution Name: Stellenbosch University
Active Member Count: 9
Allocation Start: 2023-02-27
Allocation End: 2023-09-21
Used Hours: 278885
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. CO2 uptake by different tBu-calixarene polymorphs (see figure) differs as a result of varying intermolecular interactions. Calculations performed using the CHPC's computational facility thus allow us to explain the role that intermolecular interactions play in 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: Prof Robinson Musembi
Institution Name: University of Nairobi
Active Member Count: 12
Allocation Start: 2023-02-27
Allocation End: 2023-08-29
Used Hours: 210913
Project Name: CMCG-UoN
Project Shortname: MATS1321
Discipline Name: Material Science
The Condensed Matter and Material Science Computation Research Group (Monolith Research Group) carries out a variety of research projects, primarily focusing on materials for optoelectronic applications and one member studying degenerative prion disease. When illuminated with light of the proper wavelength that can excite them to respond, optoelectronic materials including solar cells, photosensors, photodiodes, and actuators typically work by producing electrical current. There are numerous uses for optoelectronic materials in everyday gadgets, with photovoltaics being the most prevalent. Under light, photovoltaic solar cells generate an electrical current, and the majority of nations have accepted these technologies as alternate energy sources. The layer that the study team is focusing on is responsible for absorbing sunlight, which is a component of solar cells and other devices that rely on light to produce electrical current. On a different note, one PhD student is carrying out research for drug discovery to study prion disease. Prion diseases are neurodegenerative illnesses that are lethal in both humans and other animals like sheep, cattle, and rabbits. The majority of prion disease sufferers start to exhibit symptoms in their late fifties. Memory loss, trouble speaking, shakiness, increasing dementia, and mortality within a few months or years are all symptoms. For this illness, there is currently no cure or effective treatment. These kinds of neurodegenerative disorders are caused by a single, minute change in a protein's structure, which leads to misfolding and results in an improper shape for the protein, which then assembles to form amyloid plaques in the brain. Studying the process of protein aggregation requires a molecular approach rather than experiments because it is an uncommon molecular event. The CHPC compute facility is an important equipment to the research group without which our research group won't have been able to do the work the group has been able to accomplish so far. The research group currently is using software installed at the facility including Quantum Espresso, GROMMACS, and Python. Recently members of the group have expressed interest in using LAMMPS and ORCA, this will enable the research group members to tackle different kinds of problems using different types of software. The group remains greatly indebted to the CHPC facility for being granted access and technical expertise provided by the CHPC staff who are always prompt.
Principal Investigator: Prof Mpho Sithole
Institution Name: Sefaku Makgatho Health Sciences University
Active Member Count: 9
Allocation Start: 2023-02-27
Allocation End: 2023-09-07
Used Hours: 5848
Project Name: Computational modeling of titanium based alloys
Project Shortname: MATS1228
Discipline Name: Physics
The research group is based at Sefako Makgatho Health Sciences University. The group is collaborating with researchers at council of scientific and industrial research at CSIR, Pretoria and generation enterprises and intuitions cluster. The group rely on the CHPC facilities for calculation of data. The research projects are based on investigating the properties of Titanium alloys for biomedical applications, permanent magnets for electronic applications and the stability of the shape memory alloys. The method employed is the first principle approached using CASTEP in material studio, based on DFT. The group is currently training 1 PhD, 5 MSc and 1 Hons students.
Principal Investigator: Dr Rose Modiba
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 4
Allocation Start: 2023-02-27
Allocation End: 2023-09-07
Used Hours: 16174
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 Eno Ebenso
Institution Name: North-West University
Active Member Count: 6
Allocation Start: 2023-02-27
Allocation End: 2023-08-31
Used Hours: 227107
Project Name: Theoretical Investigations of Corrosion Inhibition Activities of Organic Compounds
Project Shortname: CHEM1176
Discipline Name: Chemistry
Our research groups, Centre for Materials Science at the University of South Africa (UNISA) and Materials Science Innovation and Modelling (MaSIM) Research Focus Area at the North-West University developed quantitative-structure-property-relationship (QSPR)/artificial neural network (ANN) models for the prediction of corrosion inhibition potentials for pyrimidine-based compounds. The work involved the use of molecular and electronic structure parameters of the pyrimidine molecules to develop linear and non-linear mathematical models that could predict the corrosion inhibition efficiencies of future pyrimidine derivatives. The study was conducted with the view to establishing a simple, cost-effective model for screening a large array of potential corrosion inhibitors to identify the best performing candidate before embarking on wet experiments. This approach saves time, cuts costs and reduces the amount of work-up chemicals that get into the environment through voluminous synthesis and experimental measurements. In this work, forty (40) pyrimidine derivatives were selected and subjected to density functional theory (DFT) calculations. The DFT calculations were aided by the CHPC resources, which sped up acquisition of results. Geometry optimization and frequency calculations were carried out on the 40 selected pyrimidine derivatives using B3LYP/6-31G + (d,p) level theory and IEFPCM for implicit solvent consideration. The calculations were carried out with on Gaussian 09 software licensed in CHPC. Quantum chemical parameters such as global harness, softness, electronegativity, ionization potential, electron affinity, and fraction of electrons transferred were derived for the optimized structures and fitted into linear and non-linear QSPR models. The computational studies that led to the derivation of these parameters relied on CHPC resources. The best model was determined based on statistical indicators. The best-performing model was trained with new set of pyrimidine derivatives and found to give satisfactory results. The outcome of this project was communicated as a published article in Journal of Molecular Modeling (2022) 28: 254 (https://doi.org/10.1007/s00894-022-05245-1).
Principal Investigator: Dr Anna Bosman
Institution Name: University of Pretoria
Active Member Count: 32
Allocation Start: 2023-02-28
Allocation End: 2023-09-27
Used Hours: 366597
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 led 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: loss 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 image analysis and segmentation; (2) evolution of recurrent network architectures; (3) automated software testing; (4) biologically plausible machine learning. Studying loss landscapes of neural networks deepens our general understanding of the fundamental principles of neural networks, and enables progress in fundamental artificial intelligence. Sampling and estimation techniques for loss 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 allow us to apply modern artificial intelligence techniques in the South African context, as well as to explore novel algorithmic ideas in this field. 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. The research program yields annual publications in highly ranked international journals and conferences. This indicates that the research program is productive, and successfully delivers academic outputs. Thus, the usage of CHPC helps us strengthen machine learning and artificial intelligence research in South Africa.
Principal Investigator: Prof Daniel Joubert
Institution Name: University of the Witwatersrand
Active Member Count: 19
Allocation Start: 2023-03-01
Allocation End: 2023-10-05
Used Hours: 581163
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 and collaborators 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 Ignacy Cukrowski
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2023-03-01
Allocation End: 2023-09-28
Used Hours: 26053
Project Name: Understanding chemistry from QM study of molecular systems
Project Shortname: CHEM0897
Discipline Name: Chemistry
Science, including Quantum Chemistry, provides a platform to explore and challenge our orthodox concepts on how the universe of chemistry works. A chemical bond is at heart as the central concept in chemistry. One must realize, however, that chemical bonding is not a quantum mechanical-defined physical property; hence, it is a subject of endless and often fruitless debates. Moreover, having so many and very different models of chemical bonding without knowing what this really is does not make it easier.
There is, however, a general agreement that concentrating electron density (ED) in and delocalizing ED to internuclear region is always associated with minimizing system's energy and synonymous with chemical bonding. Recently developed by us Fragment, Atomic, Localized, Delocalized, and Interatomic (FALDI)-based the total electron density decomposition involves entire space occupied by a molecule. FALDI quantifies localized and delocalized by all atoms ED at any point of the 3D space occupied by a molecule. Each atom and atom-pair contributions of delocalized density are quantified to reveal major players in the all-atom chemical bonding. Importantly, each individual contribution to the total ED is computed without an artificial and non-physical partitioning of a molecule meaning that at each stage of calculation the chemical integrity of a molecule (its structure) and characteristic for this molecule electron density distribution if fully preserved.
This unique concept of bonding (without bonds) was developed by research group lead by Prof Cukrowski in the Department of Chemistry, University of Pretoria. We continuously explore the power and applicability of the molecular-wide and electron density-based (MOWED) concept of bonding on numerous chemical systems. To this effect, we make an extensive use of computational resources provided by the Centre for High Performance Computing (CHPC) in Cape Town as well as our own codes.
Principal Investigator: Dr Lawrence Borquaye
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 15
Allocation Start: 2023-03-03
Allocation End: 2023-08-03
Used Hours: 956000
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 be developed into drugs and understand how these compounds work in biological systems. Recently, we have begun investigating the interactions of various peptides with model membranes to predict peptide bioactivity and toxicity. 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 understand how certain natural products interact with their specific protein targets in the malaria parasite and effect their action.
Principal Investigator: Dr Samuel Egieyeh
Institution Name: University of Western Cape
Active Member Count: 8
Allocation Start: 2023-03-03
Allocation End: 2023-09-03
Used Hours: 65479
Project Name: Computational (Cheminformatic and Bioinformatic) Drug Discovery, Design and Development for Infectious Diseases
Project Shortname: CBBI1212
Discipline Name: Health Sciences
Our research focuses on computational drug discovery and design, analysis and interpretation of chemical and bioactivity data using Cheminformatics, Bioinformatics, Machine Learning and Biostatistics techniques in conjunction with relevant in-vitro bioassays in order to discover, design and develop novel drug candidates, especially from natural products, for infectious diseases.
Principal Investigator: Prof Zander Myburg
Institution Name: University of Pretoria
Active Member Count: 7
Allocation Start: 2023-03-04
Allocation End: 2023-09-04
Used Hours: 9732
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. The group has successfully used systems genetics approaches in interspecific hybrid populations of Eucalyptus grandis x E. urophylla to map key genomic regions affecting gene expression and metabolic profiles associated with growth and wood chemistry traits. Over the past five years, the FMG Programme has successfully used single nucleotide polymorphism (SNP) chip technology to genotype thousands of Eucalyptus and pine trees. These SNP chips 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, the FMG Programme has obtained funding from the US-Dept of Energy to sequence the genomes of over 2000 E. grandis trees to study woody biomass formation, carbon drawdown and genotype by environment interactions. This capacity is already being extended to genera such as Acacia, Macadamia and pine. The programme has strong collaborations with the Bioinformatics and Computational Biology Centre at the University of Pretoria (Prof Fourie Joubert) where they have access to a few servers and a cluster. They are also collaborating with Prof Jill Wegrzyn at the University of Connecticut, and have access to the cluster at UConn. Emerging work in the Programme will rely on high-throughput processing of DNA sequence data and applying machine learning towards genomic prediction of breeding values in trees.
Principal Investigator: Prof Nelishia Pillay
Institution Name: University of Pretoria
Active Member Count: 10
Allocation Start: 2023-03-07
Allocation End: 2023-09-25
Used Hours: 1705007
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 and optimization 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, crop modelling and streamflow prediction and industry, e.g. logistics, scheduling and classification problems, as well as innovation in industry, e.g. routing, packing, recommender systems. 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 Jaap Hoffmann
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2023-03-07
Allocation End: 2023-09-30
Used Hours: 96024
Project Name: Flow through porous media
Project Shortname: MECH1116
Discipline Name: Computational Mechanics
The Solar Thermal Energy Research Group at Stellenbosch researches applications of solar energy across multiple industries. These technologies are particularly important to South Africa, as the country has one of the highest solar resources in the world. Due to the intermittent nature of the resource, energy storage plays an important role in ensuring that energy is available on demand. Rock bed energy storage is one of the least expensive energy storage options, but the existing theory covers mostly plug flow. In contrast, megawatt-scale energy storage facilities call for a mixed-flow design. Due to the nature of crushed rock particles, when they pack down, the pressure drop and heat transfer coefficient in the bed show a directional influence. The aim of this project is to characterize the directional effect of pressure drop and heat transfer in order to design packed beds for industrial applications. The project started with isothermal pressure drop simulations, that culminated in the PhD of Mr Hassan. Bar validation, out heat transfer work are coming to an end and should be finished by the end of 2024 when one of my master's students graduates. Lastly we need to quantify the effect of the particles on the production and destruction of turbulence in the bed, as the porous medium approach essentially defines the porous zone as a fluid, and the effect of the particles are introduced via source terms.
Principal Investigator: Dr Maya Makatini
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2023-03-09
Allocation End: 2023-09-12
Used Hours: 20290
Project Name: Wound healing and Antimicrobial peptides
Project Shortname: CHEM1406
Discipline Name: Chemistry
As the Peptide synthesis group at Wits University, we have benefited immensely from the academic facilities provided by the CHPC. We can describe our experience with the CHPC as follow.
The facilities provided by the CHPC help visualize and process data in a manner that any scientist could easily interpret. The programs provided by the CHPC reduce the cost and time associated with conducting extensive experimental trials. Working with highly skilled CHPC staff members makes using computational software to interpret and visualize data a very easy task, even for those who do not have prior knowledge of computers and the various software provided by the CHPC.
The CHPC has revolutionized the scientific world through state-of-the-art technology and infrastructure. Peptide synthesis for pharmaceutical purposes is a challenging task, therefore, the use of CHPC resources has helped us to limit our synthesis to peptides that are proposed to have pharmaceutical properties by various software provided by the CHPC.
Principal Investigator: Prof Koop Lammertsma
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2023-03-09
Allocation End: 2023-09-12
Used Hours: 228909
Project Name: ChiralCat
Project Shortname: CHEM1410
Discipline Name: Chemistry
The ChiralCat project is conducted at the University of Johannesburg under the direction of Prof. K. Lammertsma with Prof. A. Muller as co-supervisor and Dr. G. Dhimba as computational chemist and with PhD and MSc students performing experimental studies.
ChiralCat is about chiral-at-metal catalysis in which the chirality of the transition metal catalysts is maintained during a chemical reaction. The rational design of such catalysts capable of effecting enantioselective chemical transformations is of paramount importance to satisfy the increasing industrial demand for chiral fine chemicals. ChiralCat is an innovative approach in asymmetric catalysis, requiring a detailed understanding to advance the field. So far, asymmetric catalysis is dominated by catalysts carrying expensive chiral ligands. Such conventional catalysts require exhaustive screening of the chiral ligand pool to obtain products with high enantiomeric excess. Not only is this a tedious and costly process, also the chiral ligands are often far more expensive than the transition metals. ChiralCat explores instead the use of abundantly available transition metals with readily available simple ligands to compose catalysts that are inherently chiral and that keep their chiral integrity during the catalytic reaction.
To provide these insights and assist experimentalist in synthesizing chiral-at-metal catalysts requires insight in the molecular behavior of the catalysts and their catalytic reactions. Computational chemistry is by far the best and most effective means to provide this insight, which may well simplify many industrial processes. Because of the available and indispensable compute power of CHPC we could make much progress with this project showing the feasibility of asymmetric epoxidation of olefins and hydrogenation of ketones with a simple molybdenum catalyst.
Principal Investigator: Mr Mogesh Naidoo
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 4
Allocation Start: 2023-03-09
Allocation End: 2023-09-15
Used Hours: 82860
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 still 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 Gert Kruger
Institution Name: University of KwaZulu-Natal
Active Member Count: 14
Allocation Start: 2023-03-09
Allocation End: 2023-09-12
Used Hours: 105400
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 Phuti Ngoepe
Institution Name: University of Limpopo
Active Member Count: 28
Allocation Start: 2023-03-10
Allocation End: 2023-10-19
Used Hours: 2651574
Project Name: Computational Modelling of Materials: Energy Storage
Project Shortname: MATS0856
Discipline Name: Material Science
The Energy Storage Cluster is part of the three clusters at the Materials Modelling Centre, University of Limpopo under the leadership of Professor Phuti Ngoepe. In the past 6 months, we have been working mostly on generation of interatomic potentials using various machine learning approaches. These are mostly interatomic potentials to help molecular dynamics simulations of doped cathode materials i.e. mostly lithium manganese oxide cathode materials. The second crucial aspect 7is the engineering of coating materals for these high-energy-density electrodes.
The other milestone was that there was a research workshop hosted in Honour of our Principal Investigator Prof PE Ngoepe on the 03-04 August 2023, during which a number of talks were delivered from local and international delegates and the work at executed at CHPC was presented. The theme of conference is modelling of minerals, alloys and energy materials in line with work that Prof Ngoepe has done in the areas of minerals, alloys and battery storage materials. The computational modelling studies, through CHPC, were presented by students as poster presentations and progress on the clusters was presented by staff members during oral presentation slots
Principal Investigator: Dr Phindile Khoza
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2023-03-10
Allocation End: 2023-09-28
Used Hours: 53199
Project Name: Macrocyclic Molecules and Nanomaterials for Solar Energy and Environmental Remediation
Project Shortname: MATS1481
Discipline Name: Chemistry
Our focus is on the Synthesis of materials – nano, and micro for applications in solar energy, cancer, and water treatment. There is a dire need for the discovery of materials that will be applicable in different areas. Cancer, wastewater treatment, and solar energy research are all very much important fields requiring attention to come up with novel materials that'd be efficient and effective. Computational modeling of organic and/or inorganic novel materials before going to the lab saves time and affords you the opportunity of developing compounds with superior properties; this is where CHPC comes in, giving us the opportunity of virtually 'seeing' and developing a compound. This is an ongoing project, and it started last year. We have managed to publish two articles in peer-reviewed journals. The computational method used is a relaxed potential energy surface scan (PES) with selected dihedral angles constrained to 4 steps of 90 degrees, using the TD-DFT (up to 50 excited states for each scan) at the B3LYP/6-31G level.
Principal Investigator: Dr Mpho Ngoepe
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 1
Allocation Start: 2023-03-13
Allocation End: 2023-09-13
Used Hours: 1640
Project Name: DSI-Mandela Nanomedicine
Project Shortname: HEAL1547
Discipline Name: Health Sciences
DSI-Mandela nanomedicine platform based at Nelson Mandela University is a research group focusing on the synthesis of nanomaterials. Nanomedicine has the potential to revolutionize healthcare by developing new and more effective ways to diagnose, treat, and prevent diseases. The nanomaterials are designed to combat against infectious disease, airborne pathogen, cancer and diabetes. Due to increasing number of emerging pathogens that are hard to manage such as novel viruses and antibiotic resistance bacteria there is a need to discover need therapeutic strategies. Based on the World Health Organization, cancer is a leading cause of death worldwide, accounting for nearly 10 million deaths in 2020, or nearly one in six deaths. Many cancers can be cured if detected early and treated effectively. Prevalence of diabetes has been rising more rapidly in low- and middle-income countries than in high-income countries. Diabetes is a major cause of blindness, kidney failure, heart attacks, stroke and lower limb amputation. Diabetes can be treated, and its consequences avoided or delayed with diet, physical activity, medication and regular screening and treatment for complications. For both diabetes and cancer treatment, current strategies have been found to ineffective in some patient's due side effects associated with therapeutics used. Nanomedicine had aid improve patient compliance and bioactivity of the therapeutics used. Supercomputing available at CHPC can be used to simulate the behaviour of nanomaterials and nanodevices at the atomic and molecular level. This can help scientists to design and develop new nanomedicine technologies. A molecular dynamics simulation of a protein with 100,000 atoms can take weeks or months to complete on a traditional computer. However, a supercomputer can complete the same simulation in a few hours or days.
Principal Investigator: Prof Jeanet Conradie
Institution Name: University of the Free State
Active Member Count: 9
Allocation Start: 2023-03-13
Allocation End: 2023-09-12
Used Hours: 2301419
Project Name: Computational chemistry of transition metal complexes
Project Shortname: CHEM0947
Discipline Name: Chemistry
The Conradie-Reseach group currently consists of prof Conradie, 1 MSc, 1 PhD and 2 post doctoral fellows, of which Dr Malloum is an active CHPC user. In addition prof Conradie co-supervise students from Wits (Me Teimouri and mr Bailey) and Camaroen (Mr Tcheombe). Prof Conradie has active computational chemistry colaborators in Norway (prof Ghosh) and Camaroen (prof Nya, prof Fifen, dr Tabouli). The CHPC resources made it possible for my research group and colaborators to understand and shed light on experimental observation. The theoretical calculated results also make it possible to predict experimental behaviour. For example, it was possible to obtain a relationships between experimental redox potentials and DFT calculated energies for different series of electronically altered iron(II)-terpyridine derivatives. These relationships enable the prediction of redox behaviour for related complexes, which is important in many fields such as electro- and photocatalytic applications involving reduction of CO2 and H2O, and dye-sensitized solar cells (DSSC). Furthermore the UV-vis-properties of thiophene-containing Cu(β-diketonato)2 complexes are evaluated using TDDFT, for possible application of these molecules as dyes in Dye Sensitized Solar Cells.
Principal Investigator: Dr Leigh Johnson
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2023-03-13
Allocation End: 2023-09-13
Used Hours: 13420
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 impact of different HIV programmes on trends in HIV incidence.
Principal Investigator: Prof Hasani Chauke
Institution Name: University of Limpopo
Active Member Count: 16
Allocation Start: 2023-03-13
Allocation End: 2023-11-02
Used Hours: 391539
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 employs first-principles quantum mechanical approaches and molecular dynamics based methods, which employs various academic and commercial software with different types of interfaces. These computer-based softwares are linked to local servers (MMC) and the Centre for High Performance Computing (CHPC). The programme continues to receive enormous support from the CHPC, particularly to run large scale calculations at a more reasonable time. The programme supports about six (06) postgraduate students at honours, masters, doctoral level and Two (02) post-doctoral fellows and one senior researcher. At least one doctoral and one masters students graduated in 2023.
Principal Investigator: Dr Babatunde J. Abiodun
Institution Name: University of Cape Town
Active Member Count: 33
Allocation Start: 2023-03-13
Allocation End: 2023-09-14
Used Hours: 213174
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 variability (that usually induce weather and climate extremes like droughts, extreme rainfall, heatwaves, and pollution episodes), the impacts of climate change at regional scale, and how to mitigate climate change impacts in the future.
Understanding the space-time variability of surface solar radiation is essential for skillful prediction solar (photovoltaic) energy production. Our recent paper (Tang, C. et al., 2023) examined the variability of surface solar radiation over the Reunion, a tropical island in the South-West Indian Ocean. We showed that:
(i) surface solar radiation anomalies are larger on the windward side (at the east or southeast) of Reunion island and in the summer season, and smaller on the leeward side (at the west or northwest) and in the winter season.
(ii) the island-scale "cloudy" condition, that correspond to low solar PV output, can typically last 1 or 2 days.
(iii) Tropical cyclones can reduce surface solar radiation by up to 50%, depending on their distance to Reunion, intensity and most importantly, their longitudinal position relative to the island.
(iv) the synoptic convective regimes and the Madden-Julian Oscillation (MJO) at intraseasonal timescale can modulate surface solar radiation by up to 13% and 5% in Reunion respectively, depending on their phases of convective activities.
Principal Investigator: Prof Paulette Bloomer
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2023-03-15
Allocation End: 2023-10-05
Used Hours: 24516
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 several projects (Wildebeest, red roman, Cape buffalo and different birds including falcons and Houbara) that make use of the CHPC resources, with additional projects in the pipeline.
Principal Investigator: Dr Gerhard Venter
Institution Name: University of Cape Town
Active Member Count: 9
Allocation Start: 2023-03-15
Allocation End: 2023-09-21
Used Hours: 337731
Project Name: Simulation of Ionic Liquids
Project Shortname: CHEM0791
Discipline Name: Chemistry
Gerhard Venter's research group uses quantum chemistry, classical molecular dynamics computer simulation and machine learning methods to study and predict the properties ionic liquids. Ionic liquids are molten salts consisting of organic or inorganic ions that have low melting points such that they are liquids at ambient temperature. Green and sustainable chemistry calls for solvents that minimize harmful waste products and environmental hazards and ionic liquids are important candidates that can fulfil this role.
A better understanding of the physical and chemical properties of ionic liquids can lead to improved rational design of new, environmentally friendly liquids with applications as electrolytes in next-generation batteries and as energetic materials. Computer simulations not only provide first-principles characterization of ionic liquids and solutes, but also form the basis of models that aim to use machine learning for the prediction of thermodynamic properties.
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 Regina Maphanga
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 11
Allocation Start: 2023-03-15
Allocation End: 2023-11-02
Used Hours: 762152
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 Adebayo Azeez Adeniyi
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2023-03-15
Allocation End: 2023-09-19
Used Hours: 245025
Project Name: Drug Discovery Research Using Quantum and Molecular Dynamic Simulation
Project Shortname: CHEM0958
Discipline Name: Chemistry
The feasibility and progress of our research work depend mostly on the available CHPC facilities. The progress of our research work depends mostly on the availability of CHPC facilities. Using CHPC facilities has led to a significant research impact and has enhanced our productivity. Using CHPC facilities has led to a significant research impact and has enhanced our productivity. Besides many of our ongoing works, we have also published an additional article since the last report in March. With the available facilities from CHPC, we have been able to expand our research focus to include machine learning. Deep neural network, vaccine development, photochemistry and polymer chemistry in addition to our area of research on drug development and electrochemical properties of small molecules. We made use 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 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 uses theoretical modeling 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 software like Gaussian, Orca, Games and Newchem; also use 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 reproduce some of the experimental results.
It is obvious that our research progress and achievement revolve around the service of CHPC and much of our research output would not have been possible without the support from CHPC.
Principal Investigator: Dr Adam Skelton
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2023-03-15
Allocation End: 2023-09-19
Used Hours: 79006
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 Frederick Malan
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2023-03-15
Allocation End: 2023-10-05
Used Hours: 16646
Project Name: Proton-Responsive Metal Complexes as Catalysts for Sustainable Hydrogen Production and Storage
Project Shortname: CHEM1358
Discipline Name: Chemistry
The research of the Malan Inorganic Chemistry Research group, led by Dr Frederick Malan (University of Pretoria), revolves around the design, economic synthesis, and characterization of new transition metal compounds with a purpose. The catalytic activity associated with these compounds is evaluated mainly from a homogeneous catalysis point of view. Additional electrochemistry, computational chemistry, and single crystal X-ray diffraction studies aid in the understanding of the working of these catalysts. The aim of investigation of the role of proton-responsive ligands in carbon dioxide and nitrogen fixation processes is to efficiently make use of these cheap building blocks as an entry point to fuel and other fine chemicals, as well as to curb the effect of greenhouse gas pollution. Catalysts reduce the activation energy by which a reaction takes place, and therefore the calculation and prediction thereof (via the CHPC) is important in this research. To date, promising results have been obtained with two PhD projects and several honours projects, with more results (especially from a computational point of view) which includes geometry optimization, reaction outcome prediction using reaction energetics, as well as frontier orbital and electrochemical insights obtained. Currently, QM methods including DFT studies using mainly B3LYP coupled with 6-311G* and def2tzvpp basis sets are typically employed. More results from current and future students are pending.
Principal Investigator: Dr Johannes Pretorius
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2023-03-16
Allocation End: 2023-09-30
Used Hours: 50586
Project Name: Thermo-fluid simulation of natural and forced draft heat rejection systems
Project Shortname: MECH1510
Discipline Name: Computational Mechanics
We are part of the Solar Thermal Energy Research Group (STERG) under the Department of Mechanical and Mechatronic Engineering at Stellenbosch University. We are currently investigating two research topics: The performance of natural draft direct dry cooling systems, and the performance of forced draft cooling systems for supercritical carbon-dioxide (sCO2) applications. We do this by one-dimensional (1D) calculation and three-dimensional (3D) Computational Fluid Dynamics (CFD) simulations.
For the natural draft dry cooling systems: To evaluate the performance of the system, the equations for fluid flow and heat transfer are solved at millions of points across the geometry of the system (consisting of a large dry cooling tower) – which is where we need the computing resources of the CHPC. The natural draft direct dry cooling system is a unique system, typically used as part of power generation applications, that aims to combine the advantages of two traditional cooling methods to achieve a more cost-effective solution. Our research should establish how competitive this system is compared to current alternatives, and potentially improve power generation efficiency while maintaining water conservation. To date we have successfully modelled the plant performance with one-dimensional calculations under no-wind conditions, as well as simulated the performance under steady conditions for no-wind and windy conditions. Our next step will be to simulate the performance of the system under conditions which change with time.
For the forced draft cooling system for sCO2 applications: Again, the equations of fluid flow and heat transfer are solved at millions of points across the system geometry, requiring the CHPC's resources. In this case, we simulate a complete 8-bladed fan, while modelling the heat exchanger as a porous zone. The flow of supercritical CO2 inside the tubes of the heat exchanger is modelled using a 1D Python program, while the flow over the outside of the heat exchanger tubes is modelled using CFD. The two programs will be coupled such that they solve simultaneously, to obtain accurate solutions on the interaction between the fan and the heat exchanger. To date we have successfully completed investigations a sensitivity study on the configuration of the fan and heat exchanger for cold-flow conditions. Next, we will introduce heat into the simulation by coupling the sCO2-side Python code to the air-side CFD program.
Principal Investigator: Dr Geoff Nitschke
Institution Name: University of Cape Town
Active Member Count: 16
Allocation Start: 2023-03-17
Allocation End: 2023-09-18
Used Hours: 524307
Project Name: Evolving Complexity
Project Shortname: CSCI1142
Discipline Name: Computer Science
Agent-based Models (ABM) are computational simulations that are used to investigate emergent phenomena that arise from interacting entities often called agents. ABM are used across many fields ranging from Medicine and Economics to Archaeology and Biology. Creating an ABM is not an easy task. They can be complex, hard to analyse and particularly hard to develop for non-Computer Scientists. As such, several platforms, have been created. While these platforms may be useful, they are limited in that they are essentially their own development ecosystems. This project produces a platform enabling users to create their own ABMs for a wide range of experimental disciplines and applications.
Principal Investigator: Prof Rotimi Sadiku
Institution Name: Tshwane University of Technology
Active Member Count: 11
Allocation Start: 2023-03-20
Allocation End: 2023-10-17
Used Hours: 1435157
Project Name: NANOCOMPOSITE FOR ENERGY STORAGE
Project Shortname: MATS1376
Discipline Name: Material Science
Who: The research group, based at TUT led by Prof. Sadiku, is focused on developing advanced nanocomposite materials for energy storage applications in the automotive industry.
What: The team is working on creating a groundbreaking pseudocapacitive electrode material with exceptional electrical conductivity and high energy density, vital for next-generation automotive energy solutions.
Why: This research addresses a critical need for energy-efficient and sustainable transportation solutions. The work conducted at TUT is at the forefront of advancing technology for a cleaner and more sustainable future.
How: This project relies on cutting-edge computational simulations facilitated by the CHPC, enabling precise modeling and prediction of material behavior under various conditions using quantum mechanics techniques.
Progress: The project is progressing exceptionally well, with significant strides made in understanding the material's properties, which is crucial for its successful implementation in energy storage applications.
Principal Investigator: Prof Michelle Kuttel
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2023-03-20
Allocation End: 2023-10-12
Used Hours: 9764
Project Name: Molecular modelling of microbial polysaccharides and glycoconjugates
Project Shortname: CHEM1242
Discipline Name: Chemistry
The vaccine group at the University of Cape Town South Africa comprises Prof. Michelle Kuttel of the Department of Computer Science and Prof. Neil Ravenscroft of the Chemistry Department. Our primary research focus is on computational glycochemistry: using molecular modelling to predict the conformation and interactions of microbial surface carbohydrates that play key roles in infection, in order to inform the development of anti-microbial vaccines.Carbohydrate molecules are of particular scientific interest because they play key roles in microbial infection processes. However, they are challenging to model accurately because they are extremely structurally diverse and very flexible. Although the quality of current additive all-atom force fields for simulating carbohydrate molecules has been demonstrated in many applications, occasional anomalies reported for the behaviour of specific polysaccharides is a cause for concern. A more accurate polarizable "Drude" force field that simulates electronic polarization has been developed to address deficiencies in the current force fields. However, this model has not been tested across a wide variety of simulations. In this project, we are doing an extensive comparison of the additive and Drude polarizable CHARMM force fields for simulating carbohydrate molecules, using the NAMD simulation software. These complex simulations are only practicable if run on supercomputers, which is why access to the CHPC is so useful to our group.
Principal Investigator: Dr Anthony Pembere
Institution Name: Jaramogi Oginga Odinga University, Bondo, Kenya
Active Member Count: 2
Allocation Start: 2023-03-20
Allocation End: 2023-10-19
Used Hours: 181555
Project Name: Investigating electronic and photovoltaic properties of organic semiconductors
Project Shortname: CHEM1540
Discipline Name: Chemistry
Our research group is called computational material science. We are based at the Department of Physical Science, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Bondo – Kenya, and collaborate closely with colleagues at the Department of Pure and Applied Chemistry, University of Calabar. We use computational methods to probe the dynamics, kinetics, chemical bonding and reactivity of novel inorganic and organic materials for applications in catalysis, solar cells, adsorption and drug delivery. Being given access to the CHPC facilities has been of great benefit to us, since it has enabled us complete the work that previously had been impossible due to limited computational facilities.
Principal Investigator: Dr Foster Mbaiwa
Institution Name: BIUST
Active Member Count: 2
Allocation Start: 2023-03-27
Allocation End: 2023-09-27
Used Hours: 57948
Project Name: Computational study of oxidative dehydrogenation of fatty acid methyl esters
Project Shortname: CHEM1461
Discipline Name: Chemistry
Professor Foster Mbaiwa's research group at the Botswana International University of Science and Technology is currently investigating how diesel produced from plant-based oils (like used sunflower oil), called fatty acid methyl esters, can be modified to resemble diesel from fossil fuels. This is important because diesel from plant oils, although it is environmentally friendlier, is heavier than normal diesel and its continuous use on cars can damage the fuel pump. In our research we employ computational chemistry techniques to streamline the design of catalysts that can be used to convert the fatty acid methyl esters to fossil based diesel. Mainly we use the LAMMPS molecular dynamics code, thanks to the Center for High Performance Computing (CHPC), to simulate the reactions in the gas phase over a surface of a catalyst. These simulations are computationally demanding hence the need for high performance computers such as the one we use at the CHPC. This part of the work is performed by Mbaiwa's doctoral student, Maipelo Nyepetsi.
Principal Investigator: Dr Adeniyi ogunlaja
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 7
Allocation Start: 2023-03-27
Allocation End: 2023-09-27
Used Hours: 8867
Project Name: Chemistry and Material Science
Project Shortname: MATS1070
Discipline Name: Chemistry
Dr Adeniyi Ogunlaja (Research group -Analytical/Inorganic) research at Nelson Mandela University crosses many themes including Bio-materials, Nanomaterials and Catalysis. Three research questions guided my research. The first one asks about the conditions and approaches that can be adopted for oil recovery, detection of organosulfur compounds in fuel oils and purification of fuels such as adsorptive-catalytic treatment of fuels (denitrogenation and desulfurization methods). The second question focuses on tackling global warming by turning carbon dioxide into fuel, what levels of CO2 can be converted to fuels? The third question looks into potential antimicrobial and anticancer properties of metal complexes and cocrystals. Generally, findings show that redox properties of both metals complexes and cocrystals offer unusual routes for new mechanisms for antimicrobial and anticancer therapy. In all projects, the understanding of catalysts and new drugs electronic properties is very important, hence the need for computation study. 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: Prof Tjaart Krüger
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2023-03-27
Allocation End: 2023-09-27
Used Hours: 84344
Project Name: A DFT study of bio-inspired organic solar cells
Project Shortname: MATS1498
Discipline Name: Material Science
Using a new approach to study aggregation types in conjugated polymers.
Conjugated polymers have found broad applications in light-emittingGreat progres diodes and organic solar cells and breakthroughs in both technologies have been obtained in the last five to ten years. A deep understanding of the underlying photophysical parameters of these systems can push the technologies even further. One of the crucial parameters lacking understanding is how aggregates are formed in such devices.
Prof. Tjaart Krüger from the University of Pretoria has teamed up with Dr Newayemedhin Tegegne from Addis Ababa University to shed more light on aggregate formation in organic polymers. Dr Tegegne's team synthesised their own polymers and performed detailed experimental and computational studies. The experimental results served as an important reference for the computations. Their unique combination of three computational methods is a new but powerful approach to determining the aggregation types in polymers and serves as a platform for investigating numerous other types of polymers. In particular, they showed that their type of polymers are mainly H-aggregates, a formation that is key to producing high-performance solar-cell devices.
Due to the complexity of the organic polymer systems, the authors relied on a powerful computer cluster to execute the necessary calculations and are therefore grateful for the availability and capabilities of the CHPC to enable this work.
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 5
Allocation Start: 2023-03-28
Allocation End: 2023-10-03
Used Hours: 190217
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 Center for Augmented Intelligence and Data Science (CAIDS) of the University of South Africa (UNISA) and is being led by Dr. Abdulrafiu Raji. The study focus is on computational studies of two- and three-dimensional (2D) crystals, surfaces, nanocrystals, organic semiconductors for potential applications in spintronics and catalysis. Other applications being envisaged are ultrathin refrigeration and air-conditioning systems, and any nanoarchitecture where cooling may be needed. The research aims to induce novel electronic and magnetic interactions in nanostructured materials which could be exploited for practical applications. For example, 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. This motivates our interest in computational studies of relevant bulk crystals, surfaces and material heterostructure not only for their magnetocaloric effect, but also for other potential applications such as in water purification, thermoelectricity and superconductivity. Thermoelectric materials convert heat to electricity while a superconducting material conduct direct current (DC) electricity without energy loss when they are cooled below a critical temperature. Such a property allows electrical energy to be transferred between two points with perfect efficiency, losing nothing to heat.
Because of plethora of candidate materials that we are investigating and since experimental synthesis of candidate materials are prohibitive in time and human resources, large-scale computational studies is a better alternative. Indeed, 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 an ordinary desktop computer. The softwares have been made available on the CHPC platform. The CHPC administrators also maintain the softwares and provide different kinds of technical supports to students involved in the projects. Thus, the availability of high-performance computing (HPC) facility is absolutely necessary. The project currently have postgraduate students working on its several aspects.
Principal Investigator: Dr Phillip Nyawere
Institution Name: Kabarak University, Nakuru, Kenya
Active Member Count: 10
Allocation Start: 2023-03-29
Allocation End: 2023-11-07
Used Hours: 67524
Project Name: Barium Floride and Perovskites
Project Shortname: MATS0996
Discipline Name: Physics
MATS0996 Barium and Perovskites materials is a group based in Kenyan university. The Principal investigator is Dr. Phillip Nyawere of Kabarak University who is a Computational Materials graduate trained at International center for Theoretical Physics in Italy. At Kabarak University, MSc in Physics is at the department of Physical and Bilogical Sciences and a number of my students in this department are beneficiaries of CHPC both in the past and current ones.
Currently the group has thriteen members amongst which three have graduated and four are graduating in December 2023. The research group comprises of both Master of Science in Physics and PhD in Physics.
Our work involves use of computational code implemented in quantum espresso which is a free open source software useful for this work. We also use Siesta Code which is another Density Functional Theory to calculate the properties of materials for applications in areas such as solar cells fabrication and superconductivity studies.
Dr Elicah Wabululu who is a beneficiary of HPC is currently a faculty member in one of universitiy's in Kenya and is a co-supervisor. It is through this resources that our work has progressed to the current levels.
The project that begun as PhD research work with intention of developing good energy materials, has grown into several MSc in Physics research titles benefiting students in three different universities. Some of the students are now preparing to register for their PhD programmes from early next year.
This work is being done by students who have no funding for their research work. It would have been very expensive to pay for computational resources if CHPC was not available. The computational hours used here converted into money is immense.
This computational work requires fast computers because personal computers do not have capacity in terms of memory to do huge calculations. It is in this interest that CHPC has become handy to our project.
These allocated hours are very important to these students because without these computational time their projects would not be completed. But since the world has become a global village and due to generosity of the funders, it has become possible to submit our work to CHPC which is thousands of kilometers away from Kenya and get results just as from a laboratory within our campus.
Our project has expanded and is attracting more students each year. This is because our students are using their personal computers without having to travel to South Africa and yet get quality results at a fast rate. The completion rate of these students have been impressive thanks to CHPC.
Online submission of our work is easy and fast. The computational time is good enabling the students to progress fast.
Principal Investigator: Prof Nosipho Moloto
Institution Name: University of the Witwatersrand
Active Member Count: 9
Allocation Start: 2023-03-30
Allocation End: 2023-10-03
Used Hours: 3374
Project Name: Wits Quantum Dots
Project Shortname: MATS1284
Discipline Name: Material Science
Pioneering Computational Approaches in Renewable Energy Research at the University of the Witwatersrand
The University of the Witwatersrand's groundbreaking research group, "Nanomaterials for Water, Energy, Biomedical, and Sensor Applications" (NanoWEBS), is at the forefront of scientific efforts to address the energy crises in South Africa. NanoWEBS, based in the School of Chemistry within the Faculty of Science, specializes in cutting-edge research related to renewable energy technologies. Specifically, our work centres on the modelling of quantum dots and nanomaterials for various energy applications. These materials exhibit remarkable potential in transforming how we harness and utilize energy, from enhancing solar cells to developing catalysts for green hydrogen production. The importance of this work cannot be overstated. South Africa faces critical challenges in energy sustainability, and we are committed to pioneering innovative solutions. Renewable energy, particularly in the form of advanced materials, holds immense promise for achieving a sustainable future in this sector.
Our research team comprises both experimentalists and computational experts. While experimentalists focus on the synthesis and characterization of nanomaterials, computational specialists employ advanced models to explain our experimental findings. These computational simulations provide valuable insights into the properties and behaviours of nanomaterials, aiding our quest to unlock their full potential. As our research progresses, we anticipate an increasing need for computational resources. This is where the Centre for High-Performance Computing (CHPC) facilities play a pivotal role. They provide the computational power required for in-depth analyses and simulations, helping us gain a deeper understanding of these transformative materials. Our project is off to a promising start, with a clear trajectory toward further breakthroughs. The impact of our research extends to renewable energy, water resources, biomedical applications, and sensor technologies, offering real-world solutions to the challenges facing South Africa.
Principal Investigator: Dr Eric Maluta
Institution Name: University of Venda
Active Member Count: 14
Allocation Start: 2023-03-30
Allocation End: 2024-03-19
Used Hours: 110417
Project Name: Energy Material Modeling in the Application of different Photovoltaic Technologies
Project Shortname: MATS0827
Discipline Name: Physics
The university of Venda, Department of Physics, Energy Material Modelling Group now under the Centre of Excellence in Renewable Energy Research works on understanding different properties of materials to enhance the efficiency of different Photovoltaics technologies. As a group we have worked on different semiconductors materials for improving the efficiency of the, Perovskites, Dye Sensitized Solar Cells, and Sodium Ion batteries for energy storage. We hope that as the county is going through the energy crisis, our research can give solution to this situation if we are able to get a better solar radiation harvesting technology and better energy storage. The Centre for High Performance Computing plays an important role as it give the group a platform to perform all the calculations. The UNIVEN group depend on the support of calculation hours given by CHPC and all other training on the Material Studio software which we are using.
The group uses the density functional theory methodology to understand the properties of this materials. The Materia studio package we are using for the calculations is available and provided free at CHPC for all researchers in South Africa. Since the beginning of the project we have been able to produce more than Ten MSc and 3 PhD thesis for student graduations.
Principal Investigator: Prof Rasheed Adeleke
Institution Name: North-West University
Active Member Count: 16
Allocation Start: 2023-04-03
Allocation End: 2023-10-03
Used Hours: 7331
Project Name: Environmental and Agricultural Microbiology
Project Shortname: CBBI1183
Discipline Name: Environmental Sciences
Our research programme at the Unit for Environmental Sciences and Management, North-West University, Potchefstroom continues to advance the understanding of microbial communities across different environments and agroecosystems such as plants, food, water and soils. Our core interest is towards soil and plant health. We are actively investigating the microbial endophytes associated with ready-to-eat vegetables with the aim of identifying novel and efficient endophytes and their roles in improving plant and human 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 such as, food, soil, water and plant. 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 level.
Principal Investigator: Prof Soraya Bardien
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2023-04-03
Allocation End: 2023-10-03
Used Hours: 35566
Project Name: Parkinson's disease Research Group
Project Shortname: HEAL1381
Discipline Name: Health Sciences
The Parkinson's disease Research Group at Stellenbosch University is the only one of its kind in South Africa since we are the only group in the country to study the genetic causes of Parkinson's disease. We use various approaches to generate masses of genetic data on our study participants. Resources at the CHPC are needed to be able to analyse these large datasets. Our work to date has shown that South African individuals do not have the common Parkinson's disease-associated variants and possibly have novel variants. We collaborate with a large international consortium known as the Global Parkinson's Genetics Program (GP2; https://gp2.org/) whose goal is to the understand the genetic contribution to Parkinson's disease on a global scale. The collaboration with GP2 is ongoing and once completed, we hope to be able to determine who of our over 600 study participants have a genetic cause for their disorder. This finding will significantly impact clinical management of these individuals and for their families.
Principal Investigator: Dr Thierry Hoareau
Institution Name: University of Pretoria
Active Member Count: 10
Allocation Start: 2023-04-03
Allocation End: 2023-10-03
Used Hours: 108979
Project Name: Reneco Conservation Genomics
Project Shortname: CBBI1504
Discipline Name: Environmental Sciences
Researchers at Reneco, a conservation organization working in collaboration with the University of Pretoria are dedicated to preserving natural populations of falcons, and are utilizing whole genome sequencing technologies to better understand the genomics of sakers, peregrines, and gyrfalcons. These falcons are at the core of the falconry practice in the Middle East region. The aim of the research is to preserve the natural populations of falcons and manage captive breeding flocks.
The team's recent work focuses on the phylogenomics of gyrfalcons, population genomics of peregrine subspecies used in falconry, genetics of migration of Asian houbara, and annual genetic investigations to identify the geographic origin of sakers and peregrines from the Sheikh Zayed Falcon Release Programme. They are also characterizing the genomics of captive gyrfalcons from the ECWP Falcon breeding programme in Morocco and captive sakers from the reintroduction and reinforcement programmes in Bulgaria and Kazakhstan, respectively.
By studying the genomics of both wild and captive falcons, the research team is building a foundational genomic resource that is currently lacking for natural populations. Using these genomic tools, they can identify the best sites for the release programmes and maintain genetically healthy captive breeding flocks with low inbreeding levels and the absence of hybrids or introgressed individuals.
The team's research focusses on falcon conservation using whole genome sequencing technologies. The programmes relies on the CHPC to analyse large datasets more efficiently. The CHPC cluster has provided the computing resources needed to conduct the research efficiently and effectively.
Principal Investigator: Dr Nicolette Chang
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 19
Allocation Start: 2023-04-04
Allocation End: 2023-04-20
Used Hours: 33799
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 Carbon - Climate links. Through a combination of in situ experiments, observations and model simulations, we advance process knowledge and understanding of model biases in representing these processes. We are also examining the skills needed to analyse increasingly large datasets from model simulations, observational platforms such as satellite and high resolution platforms as well as the skills to improve the computational efficiency of our simulations and the algorithms driving them.
Principal Investigator: Prof Evans Adei
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 35
Allocation Start: 2023-04-04
Allocation End: 2023-10-03
Used Hours: 2813658
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 opened our 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) Safo, M.A., et al., (2023) doi.org/10.1016/j.jmgm.2023.108515.
(ii) Adomako, S., et al., (2023) doi.org/10.1155/2023/6375973
(iii) Amankah, G., et al. (2023) doi.org/10.1016/j.comptc.2023.114138.
(iv) Arhin, R., et al., (2023) doi.org/10.1016/j.jmgm.2023.108451
(v) Abdulai, A. Y., (2023) doi.org/10.1016/j.jmgm.2023.108421.
(vi) Afugu, A., et al. (2023) doi.org/10.1007/s00214-023-03001-z
(vii) Amankwah, G., et al., (2023) doi.org/10.1016/j.jmgm.2023.108418.
(viii) Mensah, M.., et al. (2023) doi.org/10.3390/catal13040757
The highlighted first co-authors are all undergraduate students. Most of our publications come from undergraduate students' research work and the potential or aptitude for future Basic research work of some of our Second Class (Lower Division) students could not have been evident had it not been for the considerable generosity of CHPC CPU resources to enable us to accommodate them in our Laboratory.
Principal Investigator: Prof Eric K. K. Abavare
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 7
Allocation Start: 2023-04-04
Allocation End: 2023-10-26
Used Hours: 303425
Project Name: Atomic and Electronic structures of semiconductor interface systems
Project Shortname: MATS1159
Discipline Name: Physics
16TH OCTOBER 2023
PRESS RELEASE, CHPC SOUTH AFRRICA
The Frontier Science Group (FSG) in the Department of Physics, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana is proud to be associated with the Centre for High Performance Computing (CHPC) in South African. We atomistic, electronic and magnetic properties of materials using quantum mechanical approaches based on first principles calculations in the framework of density functional theory (DFT).
Our researches basically focus on the study of interface and magnetic materials spintronic application. 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. Again, we also investigate 2D-materials of group element with transition and rare earth metals.
Experimentally, several important semiconductor materials are grown based, as a consequence complete understanding of how these growths 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, for the magnetic materials, we concentrate on doping of the -2D materials; that is the doping of the single layer of group IV materials.
SiC and GaN 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. Similarly, the search for spintronic materials is another interesting field. Spintronics takes advantage of electron spin degree of freedom for device application through magnetic coupling. We search for new novel materials properties for use.
By careful special crystal orientation, the materials SiC and GaN involve 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 forward the frontiers of this area for mankind in our quest for the pursuit of scientific achievement and better human life through technology.
Principal Investigator: Dr Francis Opoku
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 7
Allocation Start: 2023-04-11
Allocation End: 2023-10-26
Used Hours: 775250
Project Name: High-Throughput theoretical design of two-dimensional materials as an ultrasensitive toxic gas sensor
Project Shortname: MATS1423
Discipline Name: Chemistry
Two−dimensional materials can be stacked to generate van der Waals heterostructures (vdWH), which is a valuable strategy for practical application in optoelectronics and renewable energy sources. Using first−principles DFT calculations and taking into account the impact of in−plane biaxial strain, we thoroughly explore the optical, electronic, mechanical, transport, and photocatalytic properties of 2D vdWH. All the simulations were done using the resources provided by the Centre for High Performance Computing (CHPC), Rosebank, Cape Town. The Quantum ESPRESSO code package, norm−conserving pseudopotentials, and the Perdew–Burke–Ernzerhof of the generalized gradient approximation were used as exchange−correlation functional to perform DFT calculations. Because it is a dependable functional, the Heyd−Scuseria−Ernzerhof hybrid functional with the conventional mixing parameter of α = 0.25 and screening parameter of 0.2 Å is employed to get a more precise bandgap and optical properties. The AIMD simulation has been calculated based on the canonical ensemble through the Nose−thermostat algorithm. The phonon dispersions calculation was used to check the dynamic stability through the density functional perturbation theory method as implemented in Quantum Espresso by utilizing the PHonon code. The Thermo_pw package is used to determine the elastic constants. The optical properties were calculated from the frequency−dependent dielectric response using epsilon.x binary within the random−phase approximation. It is worth noting that the vdWH is sensitive to in−plane biaxial strain, which offers important theoretical guidance for the development of next−generation optoelectronics, thermoelectric and renewable energy devices.
Principal Investigator: Dr Aniekan Ukpong
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2023-04-11
Allocation End: 2023-10-10
Used Hours: 49648
Project Name: Theoretical and Computational Condensed Matter and Materials Physics
Project Shortname: MATS0941
Discipline Name: Physics
Breakthrough Research Unveils New Approach for Understanding Quantum Phase Transitions
A ground-breaking research at the University of KwaZulu-Natal (UKZN) has recently revealed a novel approach to understanding quantum phase transitions (QPTs) and quantum critical points (QCPs) using the Grüneisen ratio (Γ) as an entanglement compass. This innovative theoretical formalism, developed by a team of international researchers, promises to shed new light on the entanglement of quantum states in macroscopic many-body systems.
Traditionally, the Grüneisen ratio has been a fundamental tool for exploring finite-temperature and QCP phenomena. However, for genuine quantum phase transitions, where thermal fluctuations are absent, the thermodynamic Grüneisen ratio is inadequate. The newly proposed approach leverages Γ in the context of quantum 1D Ising models with a transverse field, employing Kane's quantum computer to navigate the intricate landscape of quantum entanglement.
One of the most exciting outcomes of this research is the demonstration of the breakdown of the Hellmann-Feynman theorem, showcasing its potential to revolutionize our understanding of quantum materials. By applying this approach, the team has uncovered intriguing emergent phenomena, including dynamic slowing down and the creation of mass in materials when they approach QCPs/QPTs.
This research also holds promise for unraveling the mysteries of quantum spin liquids (QSLs), an enigmatic state of quantum matter where spins do not conform to ordered, long-range patterns even at absolute zero temperature. The highly entangled state of disordered spins and strong quantum fluctuations in QSLs make them intriguing candidates for the development of quantum communication and topological quantum computation technologies.
Understanding the ground state of QSLs is crucial because their host materials offer potential building blocks for cutting-edge technologies. Spinons, anyons, skyrmions, and topological order within QSLs are all subject to topological braiding statistics, opening up new avenues for quantum innovation.
This groundbreaking research program is set to reshape our understanding of quantum phase transitions and their applications in emerging quantum technologies. The findings offer a glimpse into a future where quantum entanglement becomes a powerful compass guiding us through the uncharted territories of quantum matter.
Moreover, the CHPC's resources will eventually be required to investigate the efficacy and effectiveness of our proposed Grüneisen ratio as a probe of the many-body quantum entanglement in candidate materials that may host the QSL ground state. Prominent examples of such materials include κ-(BEDT-TTF)2Cu2(CN)3, 1T-TaS2, α-RuCl4, among others.
For media inquiries, please contact:
Dr Aniekan Ukpong,
School of Chemistry and Physics,
University of KwaZulu-Natal
Email: aniekan.ukpong@ukzn.ac.za
Tel: 033 260 5875
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2023-04-12
Allocation End: 2023-10-31
Used Hours: 60018
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 is continuously validated using test cases from literature.
Principal Investigator: Dr Quinn Reynolds
Institution Name: Mintek
Active Member Count: 7
Allocation Start: 2023-04-13
Allocation End: 2023-10-31
Used Hours: 454544
Project Name: Computational Modelling of Furnace Phenomena
Project Shortname: MINTEK776
Discipline Name: Applied and Computational Mathematics
Look around you, right now. How many of the items in your modern life contain metals? From the aluminium and iron in your car to your stainless steel cutlery, and even the silicon in the processor running the electronic device that you're reading this on, the vast majority of it had to go through a metallurgical furnace before it got to you. It doesn't matter if the metal came from raw ore or recycled sources, it had to be processed in the molten state before it could be refined and used to make the technology we take for granted today.
The problem is, processes at such high temperatures demand massive amounts of energy - and that does not always come cheap or clean. By working with resources made available to us by CHPC, researchers at Mintek are able to build powerful models and simulations that help us to untangle the complex physics and chemistry that work in concert to make smelting furnaces function correctly, and from there, optimise them to be more efficient and less damaging to the environment.
Principal Investigator: Dr Anand Krishnan
Institution Name: University of the Free State
Active Member Count: 1
Allocation Start: 2023-04-14
Allocation End: 2024-02-07
Used Hours: 10876
Project Name: Design and development of PROTACs based therapeutics for antitumor therapy: a novel approach in drug discovery
Project Shortname: HEAL1578
Discipline Name: Health Sciences
Dr. Krishnan Anand, a Senior Lecturer in the Department of Chemical Pathology, University of the Free State, Bloemfontein. He holds a Y1 NRF rating and has gained recognition as one of the world's leading researchers in applied biochemistry.
Dr. Anand, is carrying out cutting-edge research in life-saving metabolic medicines. The nature of work is in nanoscience, particularly in translational research. His team investigates the biological functions of extracellular vesicles, and the role of circulating biomarkers in disease progression. It focuses the therapeutic area of antiviral, antibacterial, anticancer, etc.
Their work involves a dynamic team of seasoned scientists focusing on areas such as antiviral, antibacterial, and anticancer. Because these are the devastating diseases at this moment in the world. This research is crucial as it addresses significant public health challenges and has the potential to yield transformative therapies. Utilizing public resources for this work is justified as it promises to advance medical science, improve patient outcomes, and ultimately reduce the societal and economic burdens of these debilitating diseases.
The process of the research project involves advanced computational resources from CHPC to revolutionize drug development. These resources enable intensive computational simulations and analyses, providing insights into complex biological interactions and guiding experimental efforts. By integrating CHPC computational and experimental methodologies, researchers aim to target key disease-related proteins effectively, potentially leading to breakthrough treatments for conditions like antiviral, antibacterial, and cancer.
Overall, the research group is on a promising trajectory, making meaningful contributions to medical science and positioning itself as a leader in innovative drug development.
Principal Investigator: Prof Obodo Kingsley
Institution Name: North-West University
Active Member Count: 0
Allocation Start: 2023-04-18
Allocation End: 2023-11-16
Used Hours: 987892
Project Name: Ab initio modelling of liquid organic hydrogen carriers catalyts and 2D materials
Project Shortname: MATS1366
Discipline Name: Physics
The research program "MATS1366: Ab initio modeling of liquid organic hydrogen carriers' catalyst and 2D materials" is conducted at the HySA infrastructure center of competence at North-West University, South Africa. Led by Kinglsey Obodo the principal investigator, this program includes other researchers such as Asres, Georgies Alene, Hailouf Houssam, Okonkwo, Ifeanyichukwu, etc. They utilize the CHPC facility for both master's and Ph.D. research work, making significant progress in their field. Notably, the research group work includes the development of a dehydrogenation catalyst, an ab initio study of structural and electronic properties of Pt/Pd-based alloys, and research on hydrogenation of furfural-to-furfuryl alcohol over La-based inorganic perovskites.
This research program leverages density functional theory, implemented through software packages like CASTEP, Quantum Espresso, GPAW, and VASP, to carry out complex calculations. Additionally, the research group is working on other projects, including catalyst development for liquid organic hydrogen carriers (LOHCs) dehydrogenation and catalysts for water electrolysis, a process that breaks down water into hydrogen and oxygen. The team's innovative research is currently under review and pending publication, contributing to advancements in the field of hydrogen and catalyst development.
Principal Investigator: Dr Gavin Gouws
Institution Name: SAIAB
Active Member Count: 5
Allocation Start: 2023-04-18
Allocation End: 2023-10-18
Used Hours: 2711
Project Name: RADseq studies of aquatic biodiversity
Project Shortname: CBBI1274
Discipline Name: Other
The PI and his team of students and collaborators, mostly involving the National Research Foundation - South African Institute for Aquatic Biodiversity (NRF-SAIAB), employ a variety of genetic tools to understand the evolution and ecology of marine and freshwater fishes and 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 biodiversity conservation and fisheries management.
Over the last year, we have conducted studies to investigate the genetic structure and patterns of population connectivity in a commercially-exploited and previously-overharvested marine fish (the slinger, Chrysoblephus puniceus). In particular, this research assessed the connectivity between Marine Protected Areas and unprotected areas along the east coast of South Africa, to determine whether these form an efficient network to protect stocks of this species, and to investigate spill-over and resource provision from conservation areas to those areas where fishing is allowed. Additionally, we examined patterns of relatedness in juvenile fishes and attempted to determine likely parental populations to identify areas which seed both MPAs and unprotected areas. This information is important for the management of the fishery dependent on this species and provides a template for the study of other linefishes. Additional studies concerned the invasion pathways of freshwater crayfish and the movement patterns of freshwater crabs in and among river systems.
Although this research is yet to be published, the students involved (Samantha Ockhuis) has completed and submitted her PhD dissertation.
Principal Investigator: Dr Tshepo Khoza
Institution Name: 0 Other
Active Member Count: 16
Allocation Start: 2023-04-19
Allocation End: 2023-10-31
Used Hours: 58183
Project Name: Application of high performance computing at the Council for Geoscience
Project Shortname: ERTH1227
Discipline Name: Earth Sciences
The Council for Geoscience (CGS) was established under the Geoscience Act (Act No. 100 of 1993), as amended in 2010. The organisation is listed as a schedule 3A public entity in terms of the Public Finance Management Act (No. 1 of 1999). The principal act mandated the Council for Geoscience to generate, curate and publish world-class geoscience knowledge products and to render geoscience-related services to the South African public and industry. The mandate for the CGS includes basic geoscience research into the nature and origin of rocks, ores, minerals, formations, the history and evolution of life and the formation of the earth with a view to understanding the geological processes of the past and present and to compile and publish such research findings nationally and internationally to contribute to the understanding of the earth, its evolution and its resources. For the CGS to fulfil its mandate and advance the geoscience field in South Africa and beyond, it adopted modern software packages, among other approaches, that require high computing power, which a normal laptop or desktop cannot provide. For this reason, the CGS sought access to the Centre for High Performance Computing (CHPC) for the purpose of expanding its computing resources. The CHPC research programme entails running high-performance computer programs for geophysical modelling, seismological data processing, geological modelling, and any other packages that are currently not suitable for desktop computing. This program covers research in the many scientific operations of the CGS including infrastructure and land use, water and environment, and minerals and energy.
Principal Investigator: Dr Barbara Huyssen
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2023-04-19
Allocation End: 2023-10-31
Used Hours: 2886
Project Name: Aerodynamics of Interfering Flow
Project Shortname: MECH1546
Discipline Name: Computational Mechanics
The University of Pretoria and Sysdel CC collaborated on an aerodynamic investigation for a pod integration on a jet aircraft.
Computational simulations are done to determine the aeromechanical loads of a redesigned aerodynamic payload for a fast jet aircraft. The integration of the payload onto the aircraft is done and funded by a government institution ARMSCOR. The computational resources were used to conduct computational fluid dynamic simulations for the preliminary design of the payload. The research was successfully concluded in October 2023 with a promising new pod's design.
Principal Investigator: Dr Thobani G. Gambu
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2023-04-20
Allocation End: 2023-11-02
Used Hours: 229481
Project Name: BET/Catalysis: Catalysis on responsive substrates - towards dynamic catalytic theory
Project Shortname: MATS1516
Discipline Name: Chemical Engineering
The utilization of carbon dioxide with green hydrogen to form clean fuels or chemicals is of paramount importance. The primary objective of this project is to generate new systems for the conversion of this greenhouse gas.
My new group at the University of Cape Towns, Catalysis Institute, aims to utilize dynamic electric fields and light eradiation to improve catalytic performance of ferroelectric based catalyst materials for this reaction. The CHPC resources are key in (i) identifying candidate catalyst systems with required properties and (ii) generating energetic data for microkinetic modelling necessary for the study of the catalytic performance under dynamic conditions. These models will enable us to gain insight into how these systems behave. Such insights will aid our primary goal of developing practical systems for these reactions under dynamic conditions.
Thus far, the project has focused on establishing a baseline by studying MoC and Cu based systems for the same application under static conditions. The work on MoC has provided key insights into the role and function of the catalyst. This work has been presented at two international conferences, North American Catalysis Conference (NAM23, USA) and Syngas Convention (SYNGAS4, RSA). The next phase will now model surfaces of ferroelectric materials as well as the properties of metal nanoparticles adsorbed on these surfaces. This will be achieved using the CHPC resources and will be used to corroborate experimental observations anticipated from the experimental efforts which are ran in parallel.
Principal Investigator: Prof Tien-Chien Jen
Institution Name: University of Johannesburg
Active Member Count: 25
Allocation Start: 2023-04-20
Allocation End: 2023-11-09
Used Hours: 1436252
Project Name: Developing an Innovative Metal Matrix Composite Membrane for Hydrogen Purification
Project Shortname: MATS0991
Discipline Name: Material Science
Hydrogen stands out as a remarkable energy carrier due to its impressive combustion enthalpy and its minimal environmental footprint. Its versatility enables direct application in a wide array of transportation vehicles, including cars, ships, and aircraft. While there are numerous challenges associated with implementing hydrogen technology, there is a prevailing belief that hydrogen will play a pivotal role in our energy landscape in the 21st century.
The central objective of this endeavor is the creation of a novel composite metal membrane (CMM) capable of achieving exceptionally high hydrogen separation efficiency while meeting the durability standards established by the U.S. Department of Energy (DOE). To achieve this aim, a collaborative research team, composed of experts from the University of Johannesburg (UJ), the Council for Scientific and Industrial Research (CSIR), and Hydrogen South Africa (HySA), will employ a diverse range of experimental techniques, including atomic layer deposition (ALD), sol-gel, and spin coating. The envisaged CMM will effectively address challenges such as hydrogen embrittlement and catalyst failure, circumventing the complexities associated with forming a flawless, ultra-thin catalyst layer on the substrate surface.
Additionally, a crucial aspect of this project involves theoretical analysis and computations pertaining to the intricate catalyst structure and the interaction between novel materials and the decomposition of hydrogen molecules into hydrogen atoms through a diffusion transfer mechanism. A simulation-based approach, employing techniques like density functional theory (DFT), computational fluid dynamics (CFD), and molecular dynamics (MD) simulation, will make use of CHPC resources, such as VASP, ANSYS, and LAMMPS code, to scrutinize the decomposition process of hydrogen molecules and the transmission of hydrogen atoms through the newly developed catalytic material. This research promises to enhance our comprehension of the fundamental hydrogen atom transfer processes within hydrogen production and purification catalysts, shedding light on the critical factors for optimization.
Principal Investigator: Prof Almuth Hammerbacher
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2023-04-20
Allocation End: 2023-10-19
Used Hours: 7503
Project Name: Microbiomics, transcriptomics and spectral sensing to assess resistance in forestry trees
Project Shortname: CBBI1588
Discipline Name: Bioinformatics
The overall aim of the current study will be to catalogue the diversity of gut microbial communities of the Eucayptus snout beetle and to determine how their degradative and biosynthetic processes affect digestion, nutrition, plant secondary metabolite detoxification and immunity. To achieve this aim, the microbial communities of the leaves from two different Eucalyptus genotypes, gut and frass of beetles reared on these Eucalyptus genotypes will be catalogued using MiSeq Next Generation sequencing. Secondly, to determine the functional roles of the Gonipterus gut microbial community, a comparative metatranscriptomic analysis will be performed on the gut microbial communities of beetles reared on susceptible and resistant Eucalyptus hosts. Thirdly, to investigate the potential for microbial biotransformation of Eucalyptus essential oils, a metabolomic analysis will be performed on cultured gut microbial communities supplemented with Eucalyptus essential oils. Lastly, to determine if Gonipterus sp. n. 2 utilises Eucalyptus secondary metabolites in sequestration against microbial pathogens, metabolomic and culture based methods will be used to identify their potential for antimicrobial activity. Early investigations show that the transcriptome data has potential, but requires significant additional work to deliver a high quality product.
Principal Investigator: Dr Marina du Toit
Institution Name: North-West University
Active Member Count: 2
Allocation Start: 2023-04-21
Allocation End: 2023-10-31
Used Hours: 21609
Project Name: Nuclear safety of PAR, new nuclear fuel development and hydrogen internal combustion
Project Shortname: MECH1507
Discipline Name: Computational Mechanics
Scientists in the energy field are focused on discovering alternative energy sources to replace fossil fuels. Future energy sources must meet certain criteria including suitability for transportation fuel, ease of conversion into other forms of energy, high utilization efficiency, safety throughout the fuel lifecycle, environmental friendliness, and affordability. Hydrogen energy is considered one of the most promising future energy carriers as it satisfies many desirable characteristics. However, the use of hydrogen energy remains a safety concern. During a hypothetical case of a severe accident in a nuclear power plant, hydrogen refueling station, or any other hydrogen infrastructure, a large amount of hydrogen can be released in the facility (confined or enclosed environment). Due to the wide range of the flammable concentration (4-75 vol.% hydrogen in air at STP), the hydrogen-air mixture can pose a significant danger of deflagration or explosion. In order to mitigate an accidental hydrogen release, dispersion, and explosion, the air ventilation systems or/and PAR can be considered for use. Air ventilation systems are generally installed where hydrogen infrastructure is present. PAR's operation is based on the principle of exothermic reaction of H2/O2 on platinum (Pt) catalyst. Computational Fluid Dynamics (CFD) is the numerical approach used to solve challenging problems related to fluid mechanics, heat transfer, chemical reactions, etc. The advent of CFD has been a significant advancement in studying the progress of chemical processes using the principles of similitude theory and modelling of chemical reactions, as well as heat and mass transfer.
Principal Investigator: Prof Ponnadurai Ramasami
Institution Name: University of Mauritius
Active Member Count: 4
Allocation Start: 2023-04-24
Allocation End: 2023-10-24
Used Hours: 17574
Project Name: Computational Chemistry Methods to Study Structural and Spectroscopic Parameters
Project Shortname: CHEM1290
Discipline Name: Chemistry
Prof Ponnadurai Ramasami is the leader of the Computational Chemistry Group in the Department of Chemistry, Faculty of Science of the University of Mauritius. He also holds a UNESCO Chair in Computational Chemistry. The research group focuses on the use of computational methods to solve chemistry and interdisciplinary problems.
The research areas of interest are:
• Study of molecules and clusters in vacuum and solution phases.
• Study the structures and conformations of the molecules and clusters.
• Spectroscopic parameters derived from infrared, Raman and NMR spectra.
• The energetic of molecules and clusters.
• Reaction mechanisms
• Global warming species
During the past 6 months, the Gaussian and ORCA software were used on CHPC to perform computations to mainly study reaction mechanism of atmospheric relevance. We are currently working on two manuscripts related to the reaction of hydrofluoroolefins and their contribution to ozone depletion. Without the use of the CHPC facility, it would not have been possible to obtain reliable results. This facility is allowing us to aim at carrying out high level research and to eventually have good publications in high impact factor journals.
The URL of the website of his research group is https://sites.uom.ac.mu/ccuom/
Principal Investigator: Dr Lamla Thungatha
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 1
Allocation Start: 2023-04-24
Allocation End: 2023-10-24
Used Hours: 11903
Project Name: Computational chemistry of energetic materials
Project Shortname: CHEM1378
Discipline Name: Chemistry
CSIR Landward refers to the research and development undertaken by the Council for Scientific and Industrial Research (CSIR) in Landward Sciences. This involves studying the effects of explosive events and developing protective interventions, particularly for vehicles and other assets. The CSIR operates specialised facilities, such as the Detonics, Ballistics, and Explosives Laboratory (DBEL), to conduct experiments with explosives and weaponry, aiming to enhance safety and efficiency for operators in the field. Additionally, CSIR Landward Sciences has access to a laboratory in Kloppersbos, north of Pretoria, for the formulation and characterisation of energetic materials.
In designing new energetic materials or explosives there is a need to simulate these in order to understand their sensitivity and performance, CHPC assists in conducting research on new developments of energetic materials. The results give important information before we actually go to the lab experiments. We are a chemist group which is at the initial stages, with the aim to fully have a functional computational package as well as the lab.
Principal Investigator: Dr RAMONTSHENG RAPOLAKI
Institution Name: South African Weather Service
Active Member Count: 6
Allocation Start: 2023-04-24
Allocation End: 2023-10-13
Used Hours: 112180
Project Name: ARC-NRE Agrometeorology
Project Shortname: ERTH1556
Discipline Name: Earth Sciences
The ARC-NRE Agrometeorology research programme is comprised of researchers, interns and students working in the Agrometeorology Division of the Agricultural Research Council. Our research activities and our activities utilising the CHPC are strongly focused on weather and climate modeling for South Africa's agricultural sector. On the CHPC our activities are predominantly focused on utilising the Weather Research and Forecasting (WRF) model to dynamically downscale selected Coupled Model Intercomparison Project Phase 6 (CMIP6) global climate models to develop a high-resolution climate projections dataset for southern Africa. We are undertaking this massive task to ultimately provide South Africa's agricultural industry with agriculturally-relevant data on climate changes and climate change impacts, with the goal of facilitating a resilient agriculture sector across South Africa. Our activities for this began in May 2023, and to date we have progressed substantially because of the vast resources offered by the CHPC.
Principal Investigator: Dr Ryno Laubscher
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2023-04-26
Allocation End: 2023-10-31
Used Hours: 68476
Project Name: CFD Programme for R Laubscher
Project Shortname: MECH1466
Discipline Name: Computational Mechanics
In 2023 the research group successfully branched into cardiovascular modelling and have developed a dynamic FEA model of a human aortic heart valve. Furthermore, this model was validated using a design, built and commissioned human cardiovascular pulse duplicator experiment.
Principal Investigator: Other Christo Venter
Institution Name: North-West University
Active Member Count: 7
Allocation Start: 2023-05-02
Allocation End: 2023-11-23
Used Hours: 8371
Project Name: Astrophysical Calculations and Data Analysis
Project Shortname: ASTR1245
Discipline Name: Astrophysics
Who? Several astrophysicists from the North-West University, along with international collaborators.
What? We are studying pulsars via complex numerical models and multi-wavelength data fitting.
Why? Pulsars have been an enigma since their discovery in 1967. Much progress has been made over the past decades, with the latest breakthroughs coming from the Fermi Large Area Telescope and ground-based Cherenkov telescopes that detected pulsars in the GeV to TeV energy range. We will continue to use the latest high-energy data to constrain our cutting-edge models and thus improve our understanding of pulsars. Broadly speaking, this contributes to highly skilled graduates who can make an impact in industry as well as communicate basic science to the public.
How? We are running large parallel codes on the CHPC in order to compute and fit models to data.
How is the project progressing? The progress has been steady and several publications are in view.
Principal Investigator: Dr Nicolette Chang
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 17
Allocation Start: 2023-05-02
Allocation End: 2023-11-17
Used Hours: 588242
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. Our approach is to set up and run a hierarchy of Southern Ocean models resolutions from 200km, 100km, 50km 10km and 2 km to explore these research questions - using the models as experimental platforms. For this we primarily use the coupled NEMO - PISCES model. We will then use this understanding to contribute to reducing model biases in the CSIR Variable Resolution Earth Systems Model (VR-ESM) which is presently under development. Part of this development will be inter comparison runs, changes to the parameterisations, and coupling of the PISCES biogeochemical model to the PCOM ocean model in VR-ESM. This model 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 contribution to the 6th Assessment Report of the IPCC due in 2019.
Principal Investigator: Prof Joanna Dames
Institution Name: Rhodes University
Active Member Count: 6
Allocation Start: 2023-05-02
Allocation End: 2023-11-02
Used Hours: 4807
Project Name: Mycorrhizal Interactions
Project Shortname: CBBI0966
Discipline Name: Bioinformatics
Arbuscular mycorrhizal (AM) fungi form mutually beneficial relationships with many plants. Exploiting these benefits for agriculture requires a sustainable approach. Using molecular sequencing techniques and the CHPC platform for analysis, representatives from four AM fungal families were detected in cultivated wheat soils. Soil nitrogen and phosphate influenced AM fungal diversity, and different crop rotations, such as wheat followed by canola, impacted species abundance and diversity. Enhancing AM fungal soil diversity requires a reduction in inorganic fertilizer applications, particularly P, and promoting crop rotations which include legumes.
A similar study of the AM fungal communities in maize soils under different cultivation practices used molecular techniques to determine AM fungal diversity and abundance. Members of the Glomeraceae were detected in all soils but were most abundant in soils employing conservation agricultural practices. Crop residue, tillage management and soil phosphate were responsible for functional shifts in the AM fungal community. Fifty percent of molecular sequences obtained were unclassified, indicating novel AM fungal species requiring further investigation.
Principal Investigator: Prof Francois Engelbrecht
Institution Name: University of the Witwatersrand
Active Member Count: 4
Allocation Start: 2023-05-02
Allocation End: 2023-05-16
Used Hours: 142500
Project Name: WITS Climate Modelling
Project Shortname: ERTH1200
Discipline Name: Earth Sciences
The GCI has launched the biggest climate change downscaling experiment ever undertaken on African soil, namely the downscaling of a large ensemble of CMIP6 global climate model projections over Africa.
Principal Investigator: Prof Marlo Moller
Institution Name: Stellenbosch University
Active Member Count: 10
Allocation Start: 2023-05-03
Allocation End: 2023-11-08
Used Hours: 280049
Project Name: Tuberculosis Host Genetics
Project Shortname: HEAL1360
Discipline Name: Health Sciences
Although approximately 25% of the world's population is infected with Mycobacterium tuberculosis, the vast majority will never develop any clinical tuberculosis (TB). Inter-individual variation in the immune response plays a major role in determining different clinical outcomes in infected persons. The Tuberculosis Host Genetics group based at Stellenbosch University aim to identify these unknown host genetic factors influencing immunity. Our investigations of the genetic contribution of the human host to individual and population susceptibility to tuberculosis span the full continuum of TB susceptibility, ranging from those extremely susceptible to disease to those seemingly resistant to infection. We have focused on TB genome-wide associations studies, host genes and strain interactions, the role of sex and ancestry in disease, TB "resisters", tuberculous meningitis and primary immunodeficiencies (PIDD) presenting with an increased TB susceptibility. Our experience in the genetic diagnosis of PIDD has allowed us to expand to the diagnosis of other rare genetic diseases by using the pipelines initially developed for PIDD. We also take the work to the cellular level by studying the function of the TB susceptibility genes discovered, with a specific interest in autophagy. Our insights into the latest genetic analyses available have allowed the work on genetic susceptibility to TB to benefit from population genetic analyses and next generation sequencing. Our work leverages the complex ancestry of South Africans, especially the unique genes from KhoeSan ancestry, to find novel genes and pathways involved in TB resistance or susceptibility, as shown by our admixture mapping. We are currently supervising a ground-breaking project on the sequencing and de novo assembly of an admixed South African genome and establishing recombination maps to African groups. Our chief strength is on putting a uniquely African emphasis on the current highly computational field of genetics as it impacts on human disease, while exploring the downstream functional effects. The findings of our work could in future contribute to the development of host-directed therapies. Moreover, we are contributing to diagnosing rare diseases, including primary immunodeficiencies, in a developing country.
Principal Investigator: Dr Bubacarr Bah
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 10
Allocation Start: 2023-05-04
Allocation End: 2023-11-20
Used Hours: 26175
Project Name: Large Scale Computations in Data Science
Project Shortname: CSCI0972
Discipline Name: Applied and Computational Mathematics
The is the Data Science research group at AIMS South Africa. We build and evaluate deep learning models for prediction problems coming from varies real-life applications including agriculture, health, and renewable energy. These applications are very important to society. These models are trained to learn from data from these different application areas. These datasets are huge and cannot typically be store in the storage of a standard desktop or laptop. Neither can the required computation be done using such devices, hence we require the CHPC. With the CHPC projects of students of the group have being progressing well. One PhD student successfully defended his PhD in October 2023.
Principal Investigator: Dr Michael Owen
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2023-05-08
Allocation End: 2023-11-30
Used Hours: 22919
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 Ozlem Tastan Bishop
Institution Name: Rhodes University
Active Member Count: 9
Allocation Start: 2023-05-08
Allocation End: 2023-11-08
Used Hours: 3028832
Project Name: Structural Bioinformatics for Drug Discovery refresh
Project Shortname: CBBI1436
Discipline Name: Bioinformatics
Main research interest of RUBi is on computational drug discovery. In the last couple of years, the focus has been on analysis of missense mutations and understanding the mechanisms of these mutations in drug resistance and potential hit compound identification. We have published two key articles on SARS-CoV-2 drug target, Mpro protein. In these articles we reported how the mutations of evolving virus is effecting the structure and function of the protein drug target.
We also developed a web based tool to analyze proteins and their mutant forms: MDM-TASK-web: https://mdmtaskweb.rubi.ru.ac.za/
Principal Investigator: Prof Kenneth Ozoemena
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2023-05-09
Allocation End: 2023-11-07
Used Hours: 7577
Project Name: Materials Electrochemistry and Energy Technologies
Project Shortname: MATS1353
Discipline Name: Chemistry
Prof Kenneth Ozoemena leads the SARChI Chair in Materials Electrochemistry and Energy Technologies (MEET) at the University of the Witwatersrand.
Our research involves batteries, fuel cells, electrolysers, and sensors. The CHPC is assisting (and continues to assist) us in our theoretical calculations (DFT) which allow us to understand the behaviour of our electrocatalysts, thus complementing our experimental findings.
The research has progressed well this year. The students are in the process of submitting their publications and theses. We should be able to provide these outputs in 2024.
Principal Investigator: Prof Mark Tame
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2023-05-11
Allocation End: 2023-11-14
Used Hours: 180223
Project Name: Quantum simulation
Project Shortname: MATS1555
Discipline Name: Physics
The group at Stellenbosch consists of Prof. Mark Tame and his postgraduate students. We are working on simulating a variety of quantum systems on the classical computers available at the CHPC – from simulating small molecules using quantum chemical methods to simulating large systems of interacting atoms using quantum trajectories methods. The work we do is essential in the development of quantum algorithms that may eventually be run on quantum computers, as well as the realization of quantum systems for sensing and imaging purposes that have the potential to provide an enhancement in measurement precision. We make use of various software available on the CHPC – Gaussian, Schrodinger and Python – and hardware in the form of multiple computational processor units with very large RAM capacity, as well as graphics processor units. The projects are at an early stage, but they are coming along, with some initial positive results expected to be published in international journals soon.
Principal Investigator: Prof Kgomotso Sibeko-Matjila
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2023-05-09
Allocation End: 2023-11-09
Used Hours: 63067
Project Name: Theileria research
Project Shortname: CBBI1517
Discipline Name: Bioinformatics
The Theileria Research Group at the Department of Veterinary Tropical Diseases, University of Pretoria aims to study the unique properties of Theileria parva parasites and find new ways to control the infection.
This work attempts to find novel drug targets and drug candidates so that alternative treatments are available upon the expected emergence of drug resistant Theileria parva strains.
This is done by taking the 3D structures of Theileria parva proteins and using intensive computational methods to find drug-like molecules that can bind to their active site and inhibit their activities. The powerful computing facilities at the CHPC are very useful in speeding up these calculations, as well as being able to run on reliable backup power during loadshedding.
We have performed these calculations for 6 distinct protein targets.
Principal Investigator: Dr Zipporah Muthui
Institution Name: Chuka University, Chuka, Kenya
Active Member Count: 4
Allocation Start: 2023-05-12
Allocation End: 2023-11-21
Used Hours: 4303
Project Name: Electronic Structure and Magnetic Properties of Heusler Compounds
Project Shortname: MATS1112
Discipline Name: Physics
The MATS1112 group is composed of physics graduate students Bonface, Gabriel and Jane. Currently, Bonface and Gabriel have successfully completed their MSc final thesis defense and are awaiting the graduation ceremony on 24th November, 2023. Jane is awaiting to defend her PhD proposal at the faculty level, having successfully done so at the department level. Their research focuses on manipulation of material properties at the atomic level to provide alternative, environment friendly, green energy sources. Bonface dealt with modifying sodium bismuth titanate for piezoelectric applications, while Gabriel dealt with modification of molybdenum disulphide monolayer for visible light applications. Jane is dealing with modifications of TiO2 and ZrO2 for solar active photocatalytic applications. The PI, Dr. Zipporah Muthui has been working on a spin-gapless Heusler system for spintronic applications. These jobs require HPC resources as they involve supercells that require sufficient computing resources. Without the HPC resources provided, all these work would not have been possible.
Principal Investigator: Dr Richard Klein
Institution Name: University of the Witwatersrand
Active Member Count: 7
Allocation Start: 2023-05-12
Allocation End: 2023-11-13
Used Hours: 46635
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 RAGUPATHI RAJA KANNAN RENGASAMY
Institution Name: North-West University
Active Member Count: 1
Allocation Start: 2023-05-15
Allocation End: 2023-11-15
Used Hours: 22509
Project Name: Marine Drug Discovery
Project Shortname: HEAL1559
Discipline Name: Bioinformatics
As a Professor at North-West University, my research group working on the discovery of marine resources for novel drug discovery. South Africa has a wide range of marine resources and is still not yet explored for their health-beneficial potential. Hence my research on marine drug discovery will be much valid. The output of our research will be benefits to the society.
For our research programme, we extensively utilize computational platforms to screen the marine leads through the Schrodinger suite. The High-Performance computing facility at CHPC is giving much more support to our research, and we are very happy and express our deep appreciation to CHPC for rendering their computational resources for our research.
Principal Investigator: Prof Matthew Adeleke
Institution Name: University of KwaZulu-Natal
Active Member Count: 12
Allocation Start: 2023-05-16
Allocation End: 2023-11-16
Used Hours: 59696
Project Name: Computational and Evolutionary Genomics
Project Shortname: CBBI1231
Discipline Name: Bioinformatics
The Quantitative and Computational Genomics research group at the University of KwaZulu-Natal, is using computational and genomic approach to understand how probiotics modulates the rumen microbiome for improved health and productivity of small stock in South Africa. Furthermore, our group seeks to understand genetic and antigenic diversity of coccidian parasites for designing anticcodial vaccines and in general control measures for improved animal welfare and increased productivity. Part of the study's focus is to utilize computational approach to understand selection signature and explore comparative genomics to vaccine candidates. Samples are usually collected for DNA extraction. Genetic markers of interest are then amplified and the product is then sent for sequencing. The CHPC platform is very critical to process and analyse huge sequence data being generated in our research group.
Principal Investigator: Dr Njabulo Gumede
Institution Name: Walter Sisulu University
Active Member Count: 2
Allocation Start: 2023-05-17
Allocation End: 2023-11-21
Used Hours: 9159
Project Name: Computer-Aided drug design for cancer therapy
Project Shortname: CHEM1058
Discipline Name: Chemistry
This research group is relatively new and deals with the design of new chemical entities that are synthetically tractable for advanced prostate cancer at Walter Sisulu University. I have recruited a Post-Doctoral fellow-Dr L. Segauke who will be involved in this project. This year, I will also be joined by an MSc student at WSU, that has just completed her Honours project. We use various molecular modelling techniques such as docking, free-energy perturbation, classical MD simulation, IFD-MD, Watermap, AutoQSAR, QM/MM to study the binding of a small molecule into a receptor. It can be in a primary, secondary or an allosteric binding site. We then translate this information by synthesising the assets, then test them for bioactivities using various assay methods available from our collaborator's labs. Therefore, molecular modelling tools that we have a national license for, and available through the CHPC such as Maestro from Schrödinger is crucial in designing synthetically aware chemical matter in our research group. CHPC's HPC infrastructure has enabled us to find the synergy between in silico drug design and in vitro validation of the hypothesis derived by in silico methods. This is evident because some patents have been granted in various national phases such as RSA, China, Europe, Canada, and the USA. This then proves the impact of our work using the HPC tools offered by CHPC.
Principal Investigator: Dr Ndumiso Mhlongo
Institution Name: University of KwaZulu-Natal
Active Member Count: 1
Allocation Start: 2023-05-17
Allocation End: 2023-11-21
Used Hours: 59825
Project Name: Biomolecular Modelling Research Unit
Project Shortname: HEAL1002
Discipline Name: Health Sciences
This research group is based at the University of KwaZulu-Natal, Howard College Campus, under the School of Laboratory Medicine and Medical Sciences, Department of Medical Biochemistry. This group performs simulations of biomolecules, such as proteins and small molecules, implicated in infectious diseases particularly Tuberculosis to understand underlying mechanisms of disease. Our simulations include the following:
1. Drug Discovery - Homology Modeling, Molecular Docking & Virtual Screening
2. Protein structure dynamics and energetics
3. Peptide-/Protein-surface interface
4. Electronic molecular structure determination
5. X-ray reflection data interpretation by simulation
These projects aid in the identification of potential substances/drugs or alternative medicine that can be explored to treat infectious diseases. They are also indispensable in the identification of alternative drug targets in biological systems in pursuit of alternative treatment measures.
These projects rely on knowledge of available structural information of the molecular entities implicated in a disease. Such information is strategically prepared and virtually transformed into dynamic systems that are representative of or a reflection of a real life system. CHPC provides delicate resources to conduct these computationally expensive simulations.
We have made progress in terms of simulations and now need to shift towards validation of generated data through laboratory based experiments.
Principal Investigator: Dr Henry Otunga
Institution Name: Maseno University, Kisumu, Kenya
Active Member Count: 5
Allocation Start: 2023-05-18
Allocation End: 2024-01-23
Used Hours: 92137
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 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, growing ultrathin films of hematite, and introducing impurity atoms. In this work, the structure and energetics of of Fe2O3 clusters 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 collaborations in future.
Our group is known as the Computational Materials Science Group, based at the Department of Physics, Maseno University, Kenya. We basically do research on materials for energy applications. Members of the group are:
Dr Henry Otunga (PI)
Dr Nicholas Ong'wen
Mr Richard Onyango
Mr Benjamin Omubandia
Mr Adonijah Anindo
Principal Investigator: Mr Steven James
Institution Name: University of the Witwatersrand
Active Member Count: 7
Allocation Start: 2023-05-18
Allocation End: 2023-11-16
Used Hours: 59311
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.
We rely on the CHPC's cluster to run large 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, and we are actively working on applying our methods to the open-world game of Minecraft, which has arisen as a grand challenge in AI.
Principal Investigator: Prof Francois Engelbrecht
Institution Name: University of the Witwatersrand
Active Member Count: 4
Allocation Start: 2023-05-19
Allocation End: 2023-06-05
Used Hours: 109856
Project Name: WITS Climate Modelling
Project Shortname: ERTH1200
Discipline Name: Earth Sciences
The GCI has launched the biggest climate change downscaling experiment ever undertaken on African soil, namely the downscaling of a large ensemble of CMIP6 global climate model projections over Africa.
The GCI has completed a convection-resolving set of attribution simulations of the Durban floods of April 2022. We expect that analysis of these simulations will reveal the role that climate change played in this devastating event.
Principal Investigator: Dr Elliot Menkah
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 5
Allocation Start: 2023-05-19
Allocation End: 2023-11-30
Used Hours: 336567
Project Name: Materials for Energy
Project Shortname: MATS1515
Discipline Name: Chemistry
The Menkah research group is part of the larger Computational Chemistry Research group at the Department of Chemistry, KNUST. Our focus is along two lines of computational chemistry research interest, development and application. We make use of the computing power provided to us by the CHPC to test newly implemented scientific concepts in the chemistry domain. The implementation we develop are used to aid our research which is also along two lines of interest. One looks into energy generation from harnessing hydrogen from chemicals like hydrazine and the other focuses on understanding the chemistry of certain bio-chemical systems such as proteins in the aqueous environment of the human body. In our studies leading to energy generation, we use computational chemistry methods and techniques from the concept of density functional theory to look forward ground-state-energy structures to inform on our scientific investigations. This leads us to use the software package called Quantum Espresso. On the studies of the proteins in water, we use methods from concepts known as molecular dynamics and this leads us to utilize the software package called GROMACS. We have gone into the development of a machine learning algorithms and pipelines that could be incorporated into electronic structure elucidation.
Principal Investigator: Mr Reshendren Naidoo
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2023-05-22
Allocation End: 2023-11-30
Used Hours: 56876
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 Giuseppe Pellicane
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2023-05-23
Allocation End: 2024-03-21
Used Hours: 340805
Project Name: Computational Study of Structure-Property Relationships in polymer blends relevant to OPV devices
Project Shortname: MATS0887
Discipline Name: Physics
Our focus has recently widened beyond computational studies of polymeric materials, relevant to organic photovoltaics/surface engineering, to study also cold atoms confined in bubble traps and on a surface. The latter have been observed in microgravity, and bubble inflation could drive 'model universe' experiments: that information may bring to a deeper understanding of our universe, which is often depicted by cosmologists as a swelling bubble. Our main investigator is both an associate professor at the University of Messina (Italy) and honorary associate professor at UKZN. Members include Mr Emmanuel Ayo-Ojo (PhD student), Prof. Tsige (Full Professor of Polymer Science at the University of Akron, US - the 2nd biggest department in US for research budget in the field of polymers) and Dr Workineh (postdoctoral researcher in Barcelona, Spain). Our expertise spans over a range of computational tools, including density functional theory, molecular dynamics, and Monte Carlo methods to study the thermodynamic and structural properties of complex fluids. We routinely share our scientific results by publishing them on international, scientific journals and presentations in international conferences/workshops. We are deeply indebted to CHPC for theoutstanding staff support we receive each time (Dr Anton Lopis), and for the generous allocation of computational resources, which is vital for our research activities.
Principal Investigator: Dr Caroline Kwawu
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 43
Allocation Start: 2023-05-23
Allocation End: 2023-11-30
Used Hours: 2497972
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: Prof Kevin Naidoo
Institution Name: University of Cape Town
Active Member Count: 12
Allocation Start: 2023-05-23
Allocation End: 2024-02-06
Used Hours: 107516
Project Name: Reaction Dynamics of Complex Systems
Project Shortname: CHEM0840
Discipline Name: Chemistry
3. Press Release: Professor Kevin Naidoo has held the SARChI Scientific Computing research chair the award period 2007-2021. The chair was jointly established in a collaboration with UCT and the CHPC. Since then UCT has established a Research Chair in Scientific Computing that Prof Naidoo has been appointed to. Professor Naidoo's group develops cutting edge chemical, chemical biological and biological software packages that enables the discovery of Drugs and Diagnostics. Following the core development in the Scientific Computing Research Unit (SCRU) at UCT his group tests the packages and then applies the computer models using the CHPC's GPU and CPU clusters to urgent healthcare problems focused on cancer and respiratory diseases SCRU develops therapeutics and diagnostics for cancer and respiratory diseases. This has led to Professor Naidoo being the PI on a Phase 1 breast cancer diagnostic trial where the groups bioinformatics and machine learning methods have led to a potential breast cancer biomarker. Further the development of cancer and respiratory therapeutics are being experimentally tested. The combined high development of SCRU software and the power of the CHPC's compute environment has enabled Professor Naidoo to establish a world first translation compute to clinic platform
Principal Investigator: Prof Cornie van Sittert
Institution Name: North-West University
Active Member Count: 21
Allocation Start: 2023-05-23
Allocation End: 2023-11-30
Used Hours: 2165677
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 has been coal; at present, coal provides approximately 70% of South Africa's primary energy needs. However, electricity generated from coal combustion comes at a very high cost, namely air pollution and the influence of air pollution on human health. A possible solution would be to expand the use of affordable, clean, renewable energy sources. The most promising of these energy sources is hydrogen gas. However, hydrogen gas must be produced. Currently, the cleanest production method for hydrogen gas is water electrolysis. Water electrolysis is the dissociation of water into oxygen and hydrogen by applying electricity over two electrodes or plates (typically made from an inert metal such as platinum) placed in the water. However, platinum is a rare and expensive metal, so it is not economically viable for long-term and large-scale hydrogen production. Hence, various attempts have been made to reduce or eliminate the platinum content while not compromising the process performance. To do this, the electrochemistry during water electrolysis on platinum must be understood, and the influence of reduction or elimination of the platinum content must be investigated at a fundamental level. This level of understanding is only possible with the use of computational chemistry. The resources needed for this type of investigation, namely high-performance cluster computers and different types of software, are of cardinal importance.
The Laboratory for Applied Molecular Modelling (LAMM) within the Chemical Resource Beneficiation Research Area (CRB) at the North-West University (NWU) focus on the research mentioned above. Although resources for the computational study are available at North-West University, they can not fully support the Laboratory of Applied Molecular Modelling (LAMM) research. So, without access to the CHPC resources, the research progress would be much slower.
Principal Investigator: Dr Holliness Nose
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 6
Allocation Start: 2023-05-24
Allocation End: 2023-11-30
Used Hours: 1280066
Project Name: Inorganic Computational Chemistry
Project Shortname: CHEM1003
Discipline Name: Chemistry
Dr. Holliness Nose is currently a Lecturer of Inorganic and Computational Chemistry at the Technical University of Kenya, School of Chemistry and Material Science, located in Nairobi, Kenya, and a thematic head of the Inorganic discipline. Dr. Nose obtained her BSc (Hons) degree in Chemistry from the University of Nairobi, MSc degree in Chemistry from the University of the Ryukyus in Okinawa, Japan, and PhD degree in Inorganic and Computational Chemistry from Wayne State University located in Michigan, United States of America. Her research area is in Quantum Chemical Modeling with main focus on the design of transition metal complexes, investigation of their coordination behavior and determination of their quantitative structure-activity and quantitative property-activity relationships leading to the development of useful materials for water purification, catalysts in various organic transformations and sustainable processes, drug leads for various diseases and environmental pollution remediation. Dr. Nose's research in modeling relies heavily on CHPC located in South Africa. The center provides her with computers and Gaussian software for her research works. A lot of computational work is ongoing in the various areas mentioned above and should yield several publications beginning 2024 and beyond. Dr. Nose has attracted research grants to fund her research activities. These include: National Research Fund-Kenya, The World Academy of Sciences, Kenya Education Network. She has published a number of research articles in the fields of Chemistry in a broad scope of journals; New Journal of Chemistry, ChemPlusChem journal, Physical Chemistry A, among others. In terms of mentorship, Dr. Nose is currently supervising undergraduates and postgraduates. Dr. Nose is currently a member of the following academic organizations: - Royal Society of Chemistry, Materials Research Society of Kenya, Women in Technical Education and Development-TUK Chapter, Organization for Women in Science for the Developing World, and Kenya Chemical Society.
Principal Investigator: Dr Nkululeko Emmanuel Damoyi
Institution Name: Mangosuthu University of Technology
Active Member Count: 1
Allocation Start: 2023-05-24
Allocation End: 2023-11-30
Used Hours: 64522
Project Name: Surface Reaction Mechanisms
Project Shortname: CHEM1105
Discipline Name: Chemistry
Dr Nkululeko Damoyi leads the Computational Modelling Research Team (CMRT) in the department of Chemistry at Mangosuthu University of Technology. The research team is involved in modelling both chemical and biological systems and has produced 9 research publications in the last 5 years. Technological advances continue to make it possible to do research in computational modelling which otherwise would be difficult or impossible to do in normal experimental laboratories. Present research within the group comprises modelling the conversion of naturally prevalent alkanes to more industrially valuable products through catalytic oxidative dehydrogenation mechanisms. One masters and two doctorate students have recently joined our group and are presently going through training in computational modelling. A variety of modelling software that includes Gaussian16 and Schrodinger are utilized to model chemical and biological systems using high-level Ab Initio, Density Functional Theory and molecular dynamics methods. Technical and resource support from the Centre for High Performance Computing (CHPC) has made it possible for our research group to conduct research and produce knowledge and publications efficiently.
Principal Investigator: Prof Edet Archibong
Institution Name: University of Namibia
Active Member Count: 6
Allocation Start: 2023-05-25
Allocation End: 2023-11-30
Used Hours: 29365
Project Name: (1) Computational Study of Semiconductor Clusters. (2) Computational Study of Bio-active Molecules Extracted from Plants
Project Shortname: CHEM0969
Discipline Name: Chemistry
Our Computational Chemistry Group at the University of Namibia (UNAM) actively uses the Lengau Supercomputer of the HPC in South Africa to study the interactions of large molecules. As of this period, we are studying the inhibition of enzymes associated with breast and esophargeal cancers by molecules isolated from plants and sea weeds. We hope that the results of these studies will shed light on the mechanism of action through which these cytotoxic compounds prevent the proliferation of malignant cells.
Principal Investigator: Dr Winfred Mulwa
Institution Name: Egerton University, Egerton, Kenya
Active Member Count: 12
Allocation Start: 2023-05-25
Allocation End: 2023-11-30
Used Hours: 125930
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. We are now working on what happens at the sink of the refrigerator (Thermoelectric properties)
Principal Investigator: Dr Benjamin Lamptey
Institution Name: University of Ghana
Active Member Count: 13
Allocation Start: 2023-05-29
Allocation End: 2023-11-30
Used Hours: 1088
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) and students from the University of Ghana, Legon, Kwame Nkrumah University of Science and Technology (KNUST), Centre for Scientific and Industrial Research in Ghana, among others.
The different activities done included testing an atmospheric model (Weather Research and Forecasting, WRF) domain for use in operational weather prediction in the Ghana Meteorological Agency;
Principal Investigator: Prof Thulani Makhalanyane
Institution Name: Stellenbosch University
Active Member Count: 19
Allocation Start: 2023-05-29
Allocation End: 2023-11-29
Used Hours: 157753
Project Name: Metagenomics of extreme environments
Project Shortname: CBBI1023
Discipline Name: Bioinformatics
The microbiome@UP research group based at the University of Pretoria is dedicated to exploring
microbiomes. The research conducted in the group is focused on understanding the interaction of microbial communities and the roles they play in their natural environments. This includes studying how wastewater treatment plants may contribute towards the dissemination of antibiotic resistant bacteria as well as antibiotic resistance genes. Antimicrobial resistance has been indicated to be a growing public health concern globally and threatens to limit viable clinical treatment options. Therefore, the overall goal of our work is to understand the extent in which wastewater treatment plants may contribute towards the release of these compounds to the environment. To do these, we need to use chpc facilities to explore microbiomes from these facilities and the environment.
Principal Investigator: Prof Serestina Viriri
Institution Name: University of KwaZulu-Natal
Active Member Count: 30
Allocation Start: 2023-05-30
Allocation End: 2024-02-14
Used Hours: 182371
Project Name: Deep Learning in Medical Image Analysis
Project Shortname: CSCI1229
Discipline Name: Computer Science
The research group: Machine Learning and Computer Vision research lab at the University of KwaZulu-Natal is using the CHPC platform to implement Machine Learning models mainly for Medical Image Analysis.
The CHPC is providing state-of-the-art High-Performance Computing which enables to conduct of current innovative research, especially in Artificial Intelligence. 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 a life-saving type of research through Medical Imaging Analysis. State-of-the-art publishable positive results achieved are Accurate Brain Tumor Segmentation, Improved Segmentation of Blood Vessels on Retinal Images, Covid-19 Detection from Chest Radiographs, 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: Mr Lawrence Pratt
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 0
Allocation Start: 2023-05-31
Allocation End: 2023-11-30
Used Hours: 5205
Project Name: Solar Cell Defect Detection (SCDD)
Project Shortname: CSIR1379
Discipline Name: Computer Science
This CSIR Energy Centre and Next Generation Enterprises are developing a machine learning tool for multi-class solar cell defect detection (SCDD) in electroluminescence (EL) images of PV modules using semantic segmentation. EL images of PV modules are like x-ray images for humans. This research focuses on training deep learning models for defect detection and quantification in EL images of solar PV cells from mono-crystalline and multi-crystalline silicon wafer-based modules. The tool can be used by PV module manufacturers, developers, owners, and operators will be able to analyse thousands of EL images to identify potential defects that are otherwise invisible to the naked eye. This research shows that multi-class semantic segmentation models can provide accurate defect detection and quantification in both high-quality lab-based EL images and lower-quality field-based EL images of PV modules. While most EL images are collected in factory and lab settings, advancements in imaging technology will lead to an increasing number of EL images taken in the field. Thus, effective methods for SCDD must be robust to various images taken in the labs and the real world, in the same way that deep-learning models for autonomous vehicles that navigate the city streets in some parts of the world today must be robust to real-world environments.
Principal Investigator: Prof Amir H Mohammadi
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2023-06-01
Allocation End: 2024-01-18
Used Hours: 1953239
Project Name: Development of a new catalyst for the production of green hydrogen
Project Shortname: MATS1552
Discipline Name: Material Science
The research is from the Chemical engineering department, UKZN. We are working on the novel development of the materials that can be used for the production of green hydrogen that will help SA government to achieve energy transition plan. We have already proposed several materials and still working on other ones. All our proposed materials are novel, and this can only be achieved using CHPC facilities to validate that the materials we have developed are theoretical possible in the laboratory. We are nearly finishing the project and planning to perform experimental work beyond PhD study.
Principal Investigator: Dr George Manyali
Institution Name: Masinde Muliro University of Science and Technology, Kakamega, Kenya
Active Member Count: 14
Allocation Start: 2023-06-01
Allocation End: 2024-03-06
Used Hours: 213128
Project Name: Ab Initio study of Thermoelectric Materials
Project Shortname: MATS0712
Discipline Name: Material Science
Computational and Theoretical
Physics group (CTheP) is housed in the School of Natural Sciences (SONAS),
Department of Physics, Masinde Muliro University of Science and Technology, Kenya, is at the forefront in promoting computational Materials Science as a bridge between Experimental and Theoretical Physics. The Research group led by Dr. George Manyali, the Senior Lecturer in Physics, Faculty of Science at the Kaimosi Friends University. The group consists of researchers, undergraduate and postgraduate students. Their current research focus is in the field of thermoelectric materials for recovering of waste heat losses by turning it into useful energy. CHPC is useful in simulating the electronic structure to characterize the behavior of unknown thermoelectric materials. Several MSc and PhD projects are ongoing and we shall have several publications coming out this year 2024. Without CHPC, very little would have been done on these projects that demands HPC resources.
Principal Investigator: Mr Randall Paton
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2023-06-02
Allocation End: 2024-01-30
Used Hours: 534096
Project Name: Compressible Gas Dynamics
Project Shortname: MECH0847
Discipline Name: Other
Gas dynamics as a field of study is involved with the high-speed flows associated with flight faster than the speed of sound. This area of work is rapidly evolving, especially with the rise of autonomous or remotely-piloted vehicles. The research of our group aims to make these systems more efficient while also considering how to make them more human. The integration of AI into our research is also accelerating research with fast turnaround for design development.
Principal Investigator: Dr Michelle Gordon
Institution Name: University of KwaZulu-Natal
Active Member Count: 6
Allocation Start: 2023-06-02
Allocation End: 2023-12-02
Used Hours: 32775
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 CHPC has greatly benefited our research programme overall, and to date, 6 PhD students have completed their degrees using resources from the CHPC.
Principal Investigator: Dr Matshawandile Tukulula
Institution Name: University of KwaZulu-Natal
Active Member Count: 9
Allocation Start: 2023-06-05
Allocation End: 2023-11-07
Used Hours: 75418
Project Name: Medicinal Chemistry and Computer-Aided Drug
Project Shortname: HEAL1346
Discipline Name: Chemistry
The Tukulula's Medicinal Chemistry Research Group (TMCRG), under the main of Natural Product Chemistry, at the University of KwaZulu Natal (UKZN) has eight postgraduate students and two postdoctoral researchers. We are working on identifying new medicaments for diabetes, HIV/AIDs, Malaria, and tuberculosis. We work on the interface of drug discovery that encompasses synthetic chemistry, pharmacology, and computational chemistry. Tuberculosis and HIV/AIDS are some of the most prevalent diseases in South Africa that infect and affect many people annually. Thus, there is a need for new medicaments for these diseases.
Small new chemical entities (NCEs) derived from bioactive natural heterocyclic scaffolds, such as quinolines, imidazoles, benzimidazole, and thiazoles, among others, are modified/derivatized within our group to improve their biological activities or their physicochemical properties. Chemically modifying or hybridizing some of these bioactive heterocyclic scaffolds with other bioactive scaffolds results in better or improved NCEs that show superior activities against the pathogens we are working on. The physicochemical properties are enhanced to develop compounds with excellent adsorption, distribution, metabolism, and excretion (ADME) properties using guidelines such as Lipinski's rule of five or Veber's rules. Computational chemistry plays a crucial role in predicting the likely ADME properties of compounds we design before their synthesis.
Computer-aided drug design (CADD) software is becoming more than just a complementary tool but essential for research. To this end, we have used CADD tools embedded in the Schrodinger and Gaussian Software provided by CHPC to design promising heterocyclic compounds that show excellent biological activities while showing no toxicity to normal cell lines. We have published 2 x papers this year that utilized CHPC infrastructure, and one more has just been accepted by ChemstrySelect. Furthermore, we graduated 2 x MSc students, and a PhD student is submitting her thesis later this month.
Principal Investigator: Dr Kevin Lobb
Institution Name: Rhodes University
Active Member Count: 30
Allocation Start: 2023-06-05
Allocation End: 2023-11-07
Used Hours: 629783
Project Name: Computational Mechanistic Chemistry and Drug Discovery
Project Shortname: CHEM0802
Discipline Name: Chemistry
This programme encompasses two areas of research. In mechanistic chemistry we try in this group to look at an overview of the system rather than concentrate on few reaction steps. In many mechanistic sequences effect of conformation is not taken into account in the generation of transition states, for example. Multiple redundant pathways are also often not explored and reported transformations may not be the best. In this project, we try to address these issues. Although simple transformations may be explored and be a part of the project, strategies for managing an overview of reaction sequences are the focus. In the drug discovery part of the research there is primary focus on chemical space and the generation of virtual libraries that explore some narrow region of chemical space. We do high throughput virtual screening on these virtual libraries and characterize these libraries in terms of chemical descriptors. Promising candidate ligands are subject to molecular dynamics. Peripheral to this is the generation of force field parameters, and (linking with focus area 1) is the exploration of enzyme mediated transformations using QM/MM techniques.
Principal Investigator: Dr Joseph Mutemi
Institution Name: University of Nairobi
Active Member Count: 6
Allocation Start: 2023-06-06
Allocation End: 2023-12-08
Used Hours: 36327
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 Prof. Joseph Mutemi, Senior Lecturer at the University of Nairobi, Department of Earth and Climate Sciences, Kenya, is focused in addressing key research questions in East Africa. During the reporting period, a draft manuscript was developed and is currently under review. Utilizing the CHPC resources, case studies were undertaken towards improvement of extreme rainfall forecasting in East Africa. One challenge identified was that operational models in both national and regional levels, are roughly at 10km spatial resolutions. At this scale, it was revealed that operational forecasts are highly biased over the highlands and inland water bodies yet these areas frequently experience extreme rainfall events. In this regard, we established that at convective permitting scales, at least 4km, local scale weather process were better represented. These results, focused on atmospheric circulation patterns related with extreme rainfall have been drafted as a manuscript which is currently under review at Frontiers in Climate Services for wider dissemination to the scientific community. It is expected that our results provides critical inputs towards improving operational weather services over East Africa, which is highly vulnerable to extreme weather.
Principal Investigator: Prof Yin-Zhe Ma
Institution Name: Stellenbosch University
Active Member Count: 9
Allocation Start: 2023-06-06
Allocation End: 2023-12-08
Used Hours: 601877
Project Name: Machine learning in 21-cm cosmology
Project Shortname: ASTR1323
Discipline Name: Astrophysics
CHPC is a wonderful server. It provides us a place to do large computation, such as simulation and MCMC. This broadens our study methods. It also has many software installed. For example, openmpi, cfitsion, anaconda and so on. This results in that we don't need to install them by ourselves. For an unprofessional person, some software may require l long time to install correctly.
Dr. Guo-Jian Wang is a Postdoc of our group at UKZN. He focuses on 21-cm data analysis and applications of machine learning methods in solving problems in cosmology and astrophysics. He is currently working on cosmological parameter estimations with machine learning methods using 21-cm observations. In his research, he needs to do many simulations to train network models, which should be conducted on professional CPU and GPU machines. Therefore, his research needs to use public resources like the CHPC. In his research, he simulated data using the CPU nodes on CHPC and trained network models using the GPU nodes. Based on the CHPC, he has finished two papers published to AAS journals, and there are another two papers under preparation.
Principal Investigator: Prof Shazrene Mohamed
Institution Name: South African Astronomical Observatory
Active Member Count: 5
Allocation Start: 2023-06-06
Allocation End: 2023-12-08
Used Hours: 73174
Project Name: 3D rad-hydro simulations of the outflows of evolved stars
Project Shortname: ASTR0880
Discipline Name: Astrophysics
Mass loss occurs at all phases during a star's life, however, its impact on the star and its environment is most profound in highly evolved systems where material can be lost via a powerful, dense stellar wind. Recent observations of the outflows of Asymptotic Giant Branch (AGB) stars, luminous, cool evolved giants, appear to show the presence of substructures like spirals, arcs, clumps as well as strong departures from spherical symmetry - e.g., equatorial and bipolar outflows. The main aim of this project is to understand the processes that give rise to these complex outflows and their impact on the final stages of stellar evolution. With the recent tremendous improvement in the sensitivity and resolution of observational facilities (e.g., ALMA), together with continuously upgraded computational capabilities, this goal is now within reach. The results of our project will have far reaching implications, not only for our understanding of the formation of AGB outflows, but also for related systems, e.g., X-ray binaries, planetary nebulae and the progenitors of Type Ia supernovae.
Principal Investigator: Prof Francois Engelbrecht
Institution Name: University of the Witwatersrand
Active Member Count: 4
Allocation Start: 2023-06-06
Allocation End: 2024-01-18
Used Hours: 3396098
Project Name: WITS Climate Modelling
Project Shortname: ERTH1200
Discipline Name: Earth Sciences
The Wits Global Change Institute has launched the biggest climate change experiments ever undertaken in the African continent, on the Lengau cluster of South Africa's Centre for High Performance Computing (CHPC). In the first experiment, a regional climate model is used to downscale 10 global climate models of the international CMIP6 experiment to 8 km resolution over southern Africa, for both high and low mitigation scenarios. In the second experiment, the regional model is applied at 4 km resolution over the southwest Indian Ocean, to downscale the same set of GCMs. These two experiments are expected to reveal new insights into the possible occurrence of regional climate change tipping points in southern Africa, and in terms of the potential impacts of climate change impacting on landfalling tropical cyclones in Madagascar and Mozambique.
Principal Investigator: Prof Phuti Ngoepe
Institution Name: University of Limpopo
Active Member Count: 15
Allocation Start: 2023-06-06
Allocation End: 2024-01-22
Used Hours: 5745596
Project Name: Computational Modelling of Materials: Mineral Processing
Project Shortname: MATS1404
Discipline Name: Material Science
The minerals cluster program at the University of Limpopo, focuses mainly on minerals simulations, which include surface studies, surface adsorptions, and reagent molecules design and modifications. The main minerals are base metal sulphides (BMSs): pyrite, pentlandite, chalcopyrite, sphalerite, galena and arsenopyrite, and platinum group minerals (PGMs): sperrylite, pallado-arsenide, geversite, cooperite, platinum/palladium tellurides, platarsite, and platinum/palladium bismuth. The collectors are organic compounds that are used to target and render the mineral of interests (concentrates) hydrophobic and promote their recoveries. This work is aimed at providing solutions to the mining industry, in particular, the mineral processing sector to guide on what are the best collector reagents to efficiently separate minerals such as platinum, palladium and base metal sulphides. The research also overlaps to design of depressants for gangue minerals to suppress them and allow the valuable minerals to float. Furthermore, the research is also on lithium ores in order to understand the recovery of lithium for use in energy storage such as batteries. The outcome of the research work will benefit the country at large since we have the largest reserves of platinum group minerals of about 70% and therefore the use of public resources such as the CHPC is helpful to institutions such as the University of Limpopo to provide solutions to the country.
This work is also complemented by collaborative work on microcalorimetry and microflotation experiments from UCT and BGRIMM, respectively. The comparative research between computational and microcalorimetry has demonstrated that both techniques can produce similar outcomes. In this research, we use different codes embedded in programs such MedeA and Materials studio. These packages perform simulations of materials at an electronic and atomic-scale and these require a large number of cores to execute such tasks, as such the CHPC is of crucial importance for our research. All in all, the development contributes extensively to human capacity/capital development.
Principal Investigator: Dr Nicholas Ongwen
Institution Name: Maseno University, Kisumu, Kenya
Active Member Count: 0
Allocation Start: 2023-06-06
Allocation End: 2023-12-05
Used Hours: 65407
Project Name: Mechanics and thermodynamics of advanced materials for the aerospace
Project Shortname: MATS1599
Discipline Name: Physics
The research programme "Mechanics and thermodynamics of advanced materials for the aerospace" is program in Maseno University, Kenya. Currently, the program also includes members from Masinde Muliro University of Science and Technology, and Kisii University also (both are in Kenya). The programme entails computational determination of mechanical and thermal properties of novel materials (using DFT) for the construction of airplane bodies. These materials should be lighter and stronger than the aluminium alloys that are currently being used for the same purpose. The work includes creation of large supercells of the compounds with the desired mechanical and thermal properties (but the compounds are relatively heavier than that of aluminium) in order to allow for alloying. Since large supercells are involved, HPC comes in handy in order to address the large computational power requirement. Moreover, the computations also involve thermal properties (phonons) which are also computationally expensive. Due to these, we really need the service of the CHPC so as to enable us carry out the computations successfully. Currently, the programme has done creation of the supercells, alloying the supercells with the desired elements, and structural optimization of the alloyed supercells.
Principal Investigator: Prof Thomas Scriba
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2023-06-07
Allocation End: 2023-11-07
Used Hours: 39176
Project Name: Tuberculosis vaccine and biomarker development
Project Shortname: HEAL1390
Discipline Name: Health Sciences
The research programme – Tuberculosis Vaccine and Biomarker Development – is one of the research programmes within SATVI (the South African Tuberculosis Vaccine Initiative), a world leading TB research entity located within the Faculty of Health Sciences at the University of Cape Town. The research entity performs cutting edge clinical and immunological research in TB pathogenesis, biomarker development and clinical vaccine development.
One of the major obstacles in tackling TB disease is the poor understanding of the various stages in which the disease progresses in the body, and of particular interest the "subclinical" disease stage in which the individual exhibits no clinical symptoms but has radiological abnormalities or microbiological evidence of active TB disease. A deeper understanding this disease stage would make it possible to identify individuals who are in fact at this stage of the disease, although clinically asymptomatic, and treat them before they advance to the active clinically symptomatic disease state. Moreover, as some those in this subclinical stage are now known to transmit the infection, their identification and treatment would limit onward transmission of the disease.
In light of this, this particular research project aims to use transcriptomic profiling to understand subclinical and the other stages of TB disease progression in the body, and ultimately develop a diagnostic tool that can be used to tease apart individuals with subclinical TB disease from healthy ones.
The analysis of such a dataset, which is terabytes of data, is infeasible on standard laptop and desktop computers owing to memory and computing power requirements. Upon obtaining the raw data, we rely on the computing power and resources provided by CHPC to the analysis.
We are currently on course in achieving the objectives of this research project. The results of the study shall be made available to the general public in published articles.
Principal Investigator: Dr Nikiwe Mhlanga
Institution Name: Mintek
Active Member Count: 12
Allocation Start: 2023-06-07
Allocation End: 2024-02-12
Used Hours: 343508
Project Name: Hydrogen Storage Materials and Catalysis
Project Shortname: MATS0799
Discipline Name: Material Science
Advanced Materials Division (AMD) houses several research and development groups; catalysis, nanotechnology (health, water purification, and sensors), and physical metallurgy. The nanotechnology platform develops diagnostic kits for diseases such as malaria, tuberculosis. The kits are in the form of field-based quantitative lateral flows and quantitative lab-based surface-enhanced Raman spectroscopy (SERS) biosensors. Understanding the precursor materials and their interaction with the analyte is of paramount importance. The HPC platform enables simulations/calculations of these systems (large systems) to gain insight into their chemistry and biology for the fabrication of better kits. Also, HPC enables the study and establishment of new memory-shaped alloys by the physical metallurgy group. Ultimately the properties inform the experimental development of the alloys envisioned for aerospace engines. The development of diagnostic kits is one of the key factors in the eradication of illnesses such as TB and malaria. And the end product is envisioned to benefit the clinical sector. The structures normally simulated for these projects are massive and require a detailed tighter computational setting to yield informative outputs. We do not have the capacity to run such calculations on our local computer hence the need for the HPC platform which we continue to benefit from.
Principal Investigator: Prof Francesco Petruccione
Institution Name: Stellenbosch University
Active Member Count: 7
Allocation Start: 2023-06-07
Allocation End: 2023-12-05
Used Hours: 15239
Project Name: Quantum techniques for simulation and machine learning
Project Shortname: PHYS1216
Discipline Name: Physics
The Quantum Computing Group at Stellenbosch University, in an innovative collaboration with the Centre for High Performance Computing (CHPC), is at the forefront of pioneering quantum algorithms and simulating open quantum systems. This partnership underscores a shared commitment to pushing the boundaries of computational science and maintaining South Africa's competitive edge on the global stage.
Who? The initiative is led by the Quantum Computing Group at Stellenbosch University, a team dedicated to exploring the vast potential of quantum computing. By partnering with the CHPC, the group leverages unparalleled computational resources to advance their research.
What? The focus of the work is twofold: prototyping quantum algorithms that could redefine computational methodologies, and running classical simulations of open quantum systems, a critical step in understanding quantum mechanics' complex phenomena.
Why? This research is vital not only for the theoretical advancements it promises but also for the practical applications it could enable, from secure communications to drug discovery. Utilizing public resources such as the CHPC ensures that South Africa remains at the cutting edge of quantum computing research, contributing significantly to global scientific progress.
How? The collaboration utilizes the CHPC's advanced computing facilities to conduct extensive simulations and algorithmic developments. This powerful computational backbone is crucial for handling the complex calculations required in quantum computing research, enabling the team to explore new frontiers in science.
Progress: The project is progressing robustly, with significant advancements already achieved. The promising results have attracted a growing number of postgraduate students eager to utilize the CHPC's facilities in their research, indicating a bright future for quantum computing in South Africa.
By harnessing the computational might of the CHPC, Stellenbosch University's Quantum Computing Group is not only contributing to the global knowledge base but also inspiring the next generation of scientists in South Africa. This initiative exemplifies the transformative potential of combining academic curiosity with high-performance computing resources.
Principal Investigator: Dr Didam Gwazah Adams Duniya
Institution Name: BIUST
Active Member Count: 1
Allocation Start: 2023-06-08
Allocation End: 2024-01-19
Used Hours: 522351
Project Name: Cosmological Probes of Gravity, Dark Energy, and Large Scale Structure
Project Shortname: ASTR1480
Discipline Name: Astrophysics
Dr Didam Duniya (Botswana International University of Science and Technology) and Dr Bishop Mongwane (University of Cape Town) have done an impressive research work, which investigates the imprint of beyond-Horndeski gravity in the cosmic magnification. The cosmic magnification is able to probe the geometry of large scale structure on cosmological scales, thereby providing another window for probing theories of the late-time accelerated expansion of the Universe. The research incorporated relativistic corrections in the angular power spectrum, which are often neglected in magnification studies in the literature. The results suggest that surveys at low redshifts (less than or equal to 0.5) will be able to measure directly the total relativistic signal in the total magnification angular power spectrum, without the need for multi-tracer analysis (to beat down cosmic variance). Similarly, for the magnification Doppler signal, at the given redshift; whereas, the other signals require multi-tracer analysis in order to be detected. Conversely, at high redshifts (greater than or equals to 3), surveys will be able to measure directly the integrated Sachs-Wolfe, the time-delay, and the (gravitational) potential signals, respectively (with the total relativistic and the Doppler signals, respectively, requiring multi-tracer analysis, at the given redshifts). This was not known before. The results also show that the beyond-Horndeski gravity acts to boost relativistic effects; consequently, the cosmic magnification. In turn, relativistic effects enhance the potential of the total magnification angular power spectrum to detect the imprint of beyond-Horndeski gravity.
Principal Investigator: Dr Joseph Simfukwe
Institution Name: Copperbelt University
Active Member Count: 3
Allocation Start: 2023-06-13
Allocation End: 2024-02-01
Used Hours: 44828
Project Name: Computational Materials Science Research Group CBU
Project Shortname: MATS1469
Discipline Name: Physics
Computer simulations based on quantum mechanical methods have become important in understanding various properties of matter at both atomic and molecular levels. Electronic structure calculations methods can accurately predict various physical properties of materials and also provide a detailed understanding of experimental results. The complex nature of experimental processes sometimes has made it difficult to fully understand the results, in such situations theoretical calculations play a complementary role in shading more light for a detailed understanding of the results.
Besides, setting up large laboratory equipment to carry out effective research for many Universities in Africa and other countries remains a very big challenge and hampers many young and old researchers to continue with research work. Thankfully, through the cluster resources offered by CHPC, both young and old researches are provided with an opportunity to continue building up their research skills even long after completing their studies and contribute effectively to knowledge and skills required towards meeting the needs of our society.
Computational Materials Science Research Group CBU based at the Copperbelt University (CBU) in Zambia headed by Dr. Joseph Simfukwe a PhD graduate from University of Pretoria (UP) has continued to carry out computational research work through the recruiting of MSc and PhD students. The group currently works in collaborations with Dr. Mapasha and Prof. Diale of UP and other partners within Africa and abroad. The research focus of the group is to investigate and study materials that can be used to harvest solar energy by converting into hydrogen through water splitting or directly into electricity through photovoltaic. The heavy reliance on fossils fuels for energy by the world has brought about a number of environmental draw back such as global warming and climate change. Photoelectrochemical (PEC) water splitting using suitable semiconductors to decompose water into hydrogen (H2) and oxygen is a promising route to solve both the production of clean H2 and storage for solar energy. Our research is mainly computational and employs the density functional theory approach as implanted in Quantum espresso simulation package. Therefore, we heavily depend on the higher performers computers from CHPC for our effective functional. The group has continued to contribute to the board of scientific knowledge through our publications. We have continued to study and investigate different materials that can efficiently be used in water splitting and other applications.
Principal Investigator: Dr Kiprono Kiptiemoi Korir
Institution Name: Moi University, Eldoret, Kenya
Active Member Count: 13
Allocation Start: 2023-06-13
Allocation End: 2024-01-30
Used Hours: 218013
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, opto-electronics, and ultra-hard industry. The properties of 2D materials often differ from their bulk counterparts due to the quantum effects and increased surface-to-volume ratio, high flexibility, high electron mobility. In the case of ZnS, its 2D layers may exhibit unique electronic, optical, and mechanical properties, making them interesting for various applications. As such, various strategies for enhancing the sensing capabilities of 2D ZnS material are explored, in particular, the use of dopants and defects is investigated using Density Functional Theory approach. 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, 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. For example, in our recent work, using ab initio Density Functional Theory calculations, we explored the potential doping of 2D ZnS with selected transition metal as an optimization route for photo-electrochemical water splitting. The selected transition metals dopants (Co, Mn, and Fe) were found to induce minimal lattice strain, thus can be easily be incorporate into ZnS at low formation energies. Defect stability in ZnS remains consistent at 1–2% dopant concentration under both sulfur-rich and zinc-rich conditions. In sulfur-rich conditions, Cu and Fe-doped ZnS were least sensitive to changes in dopant concentration while under zinc-rich conditions, Cu-doped ZnS is the least affected. This discovery is crucial for carrier-controlled processes like PEC water splitting, guiding practical applications of transition metal-doped ZnS.
Principal Investigator: Dr Ian Kaniu
Institution Name: University of Nairobi
Active Member Count: 6
Allocation Start: 2023-06-15
Allocation End: 2024-01-18
Used Hours: 20780
Project Name: UoN Computational Physics Research Group
Project Shortname: MATS1560
Discipline Name: Physics
The Computational Physics Research Group at the University of Nairobi employs advanced simulation techniques to study complex physical systems and molecular interactions. Using computational tools like Monte Carlo methods and molecular dynamics, they explore material properties and predict behaviors. With access to high-performance computing and artificial intelligence, they delve into fundamental physical principles, validating simulations and accelerating material characterization. Collaborating with the Center for High-Performance Computing, the group uncovers intricate molecular interactions, impacting industries such as spectroscopy, food safety, energy, materials science, and pharmaceuticals. Driven by a pursuit of scientific excellence, they push the boundaries of knowledge using high-performance computing, aiming to drive technological advancements and transformative innovations.
Principal Investigator: Prof Peter Teske
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2023-06-22
Allocation End: 2023-12-22
Used Hours: 242515
Project Name: Coevolution of mangroves and mangrove-associated crabs
Project Shortname: CBBI0979
Discipline Name: Bioinformatics
Centre for Ecological Genomics and Wildlife Conservation. We use genomic resources analysed using HPC to improve the management of commercially exploited and threatened marine organisms. Several projects are progressing well, which includes a study by Conny Serite on the diet of the critically endangered estuarine pipefish, and a study by Paula Coito on genetic structure between the only two populations of the critically endangered limpet Siphonaria compressa.
Principal Investigator: Dr Clement Agoni
Institution Name: University of KwaZulu-Natal
Active Member Count: 6
Allocation Start: 2023-06-26
Allocation End: 2024-01-04
Used Hours: 168724
Project Name: Structural Modelling and In-Silico Peptide Design Research
Project Shortname: HEAL1524
Discipline Name: Health Sciences
The structural modelling and In-Silico Peptide Design Research project is based in the College of Health Sciences at the University of KwaZulu Natal. The team explores drug-target interactions of novel small molecule inhibitors against diseases of global concern such as tuberculosis, malaria, cancer, and viral infections using molecular modelling techniques. The second aspect of the research involves the structural modelling of peptides toward the discovery of bioactive peptides from natural sources for therapeutic purposes, with a central question of whether structural modelling can accelerate the development of bioactive peptides. Resources from CHPC allow our group to perform computationally intensive processes such as Molecular Dynamics simulations and Machine Learning which hitherto would have been very expensive and time-consuming using local computers with limited capacities. So far, we are have successfully published the findings of some of the research investigations in the project in reputable journals even as we continue to explore the research domain.
Principal Investigator: Prof Pieter Rousseau
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2023-06-27
Allocation End: 2024-01-27
Used Hours: 180647
Project Name: University of Cape Town Applied Thermal-Fluid Research Unit
Project Shortname: MECH1279
Discipline Name: Computational Mechanics
Rising energy demand and the imminent threat of climate change are critical issues in society today. Thermofluid systems provide the backbone of almost all energy conversion processes for renewable and conventional power generation, as well as heating and cooling systems such as heat pumps and refrigeration cycles. The Applied Thermofluid Process Modelling Research Unit (ATProM) at the University of Cape Town specialise in modelling these systems to evaluate novel technologies, improve the efficiency and control of processes, and detect anomalies for condition monitoring purposes.
Fundamental models are built using detail Computational Fluid Dynamics (CFD) and integrated one-dimensional thermofluid networks. These are often combined with advanced optimization techniques and data-driven models that are derived via machine learning (ML) techniques. This unique combination of fundamental thermofluid principles and ML techniques enable the development of versatile and accurate numerical tools to address industry needs. However, applying these techniques often involve resource intensive computational procedures. Given this, the services and facilities provided by CHPC are invaluable in generating industry-scale research outputs.
The current focus of research is on supercritical CO2 (sCO2) Concentrated Solar Power (CSP) plants, biomass-fired boilers and combined cycle power plants, flexibility of fossil fired power plants, design and optimization of heat pump systems, and Physics Informed Neural Networks (PINN) applied to energy systems.
Principal Investigator: Dr Gebremedhn Gebreyesus Hagoss
Institution Name: University of Ghana
Active Member Count: 6
Allocation Start: 2023-06-27
Allocation End: 2024-02-01
Used Hours: 350276
Project Name: Atomistic simulations and condensed matter
Project Shortname: MATS1031
Discipline Name: Physics
The research group at the Department of Physics, University of Ghana, is dedicated to exploring the structural, electronic, magnetic, and optical properties of both 2D and bulk materials. Our investigations utilize advanced computational simulations based on density functional theory, extended Hubbard functionals (implemented in QUANTUM ESPRESSO), GW approximation of many-body perturbation theory (MBPT), and the Bethe-Salpeter equation (BSE). The execution of our computational work is made possible through the enhanced computing resources provided by the CHPC in South Africa.
Our workflow typically involves preparing input files on local laptops and workstations, submitting jobs to the CHPC cluster, and monitoring progress daily. Upon completion, results are downloaded for further analysis.
Key Research Areas:
Electronic, Magnetic, Structural, and Optical Properties of Transition-Metal Oxides: Our primary focus is on studying these properties using first-principle calculations. We rigorously compare computed results with experimental data.
Perovskite Materials for Energy Applications: We aim to establish an accurate description of the structural, electronic, and optical properties of low-temperature phase perovskite materials using extended density functional theory (DFT+U+V).
2D Materials Research: Primarily centered on transition metal dichalcogenides, we investigate compounds with the chemical formula MX2 (where M = Ti, Mo, Nb, W, Hf, Re, etc., and X = S, Se, and Te). Our focus includes monolayers, bilayers, and heterostructures of transition metal disulfides (TMS2) for potential applications as photo-catalysts for hydrogen evolution reactions. Additionally, we explore the excitonic properties of 2D HfS2 monolayers through lanthanide substitutional doping using GW and BSE.
Ruddlesden-Popper Perovskite Ruthenates: Our project centers on calculating the electron-phonon couplings of Sr4Ru3O10 using DFT, including the onsite Hubbard correction (DFT+U), and spin-orbit coupling.
These endeavors showcase the diversity and depth of our research, contributing valuable insights to the understanding of materials and their potential applications. The CHPC's computing resources play a vital role in facilitating our groundbreaking work.
Principal Investigator: Prof Zeno Apostolides
Institution Name: University of Pretoria
Active Member Count: 29
Allocation Start: 2023-06-27
Allocation End: 2023-12-27
Used Hours: 1926
Project Name: Receptomics
Project Shortname: CBBI0926
Discipline Name: Bioinformatics
We are the Complimentary and Alternative Medicines group in the Department of Biochemistry, Genetics and Microbiology at the University of Pretoria. Prof Zeno Apostolides is the principal investigator and supervises ten post-graduate students. The postgraduate students of Dr Rebamang Mosa and Dr Samkelo Malgas work on similar projects based on medicinal plants. Two papers have been published during 2023. This project aims to find the chemical compounds and enzyme targets of medicinal plants, herbs and spices that have ethnobotanical claims for use in treating diabetes. The chemical structures of the plant-based compounds are used as lead compounds from which to develop new drugs for diabetes. The reason for this project is that type 2 diabetes is a very important global disease. Diabetes affects about 12% of South Africans, especially elderly persons living on a low-cost, high-starch diet. We use computer models of alpha-amylase and alpha-glucosidase and test the binding of the new chemical structures in these models. We follow the paradigm that chemical structures with good binding in these computer models will probably be good drugs in the laboratory assays and in the clinic after detailed pre-clinical research. This project is progressing well; we have had three publications over the past four years. We have two new publications in the peer review process for 2023.
Principal Investigator: Mr Asad Jeewa
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2023-06-27
Allocation End: 2024-02-01
Used Hours: 28234
Project Name: Towards Real-World Reinforcement Learning
Project Shortname: CSCI1602
Discipline Name: Computer Science
The project was created to allow postgraduate researchers at the University of KwaZulu-Natal to perform cutting-edge reinforcement learning research. RL, which pertains to behaviour-learning or sequential decision-making, has the potential for the most significant impact compared to traditional machine learning methods and is already vital in tools such as ChatGPT and self-driving cars. However, there remain many open challenges that block more widespread adoption in the real-world and our focus is hence on learning policies and behaviour for real-world tasks or tasks that exhibit such characteristics such as the need for multi-agent coordination, balancing multiple objectives and partial observability. Further research is also undertaken in general deep learning on real-world datasets.
Significant compute power is required and this work is only possible through the use of the CHPC. The project is in the early stages with significant growth expected in 2024, welcoming a minimum of 4 new researchers.
Principal Investigator: Dr Ikechukwu Achilonu
Institution Name: University of the Witwatersrand
Active Member Count: 5
Allocation Start: 2023-06-29
Allocation End: 2024-01-10
Used Hours: 92244
Project Name: Computational approach to modelling druggable proteins of neglected tropical diseases parasites and ESKAPE pathogens
Project Shortname: CHEM0849
Discipline Name: Bioinformatics
Unlocking the Power of High-Performance Computing: A Gateway to Limitless Discovery
Johannesburg, 15th February 2024 – In our data-driven era, high-performance computing (HPC) emerges as a beacon of transformative potential, offering researchers, scientists, and innovators unprecedented capabilities across diverse fields. While the term may initially seem daunting to newcomers, its implications are nothing short of revolutionary. HPC involves utilizing advanced computing resources and techniques to solve complex problems and process vast amounts of data at remarkable speeds. At its core, HPC empowers researchers to tackle grand challenges, explore uncharted territories, and expand the boundaries of human knowledge.
Consider a world where scientists can simulate intricate biological systems, model climate patterns with precision, or optimize life-saving drug designs—all in a fraction of the time conventional methods would require. This is the promise of HPC—a promise that unlocks new frontiers in science, engineering, and beyond. Whether you're a biologist delving into the mysteries of the human genome, an environmental scientist grappling with climate intricacies, or a materials engineer crafting cutting-edge technologies, HPC opens a gateway to boundless discovery.
For those with limited experience in computational studies, HPC offers abundant opportunities. It provides access to a vast ecosystem of tools, resources, and expertise that can elevate research endeavors to new heights. By entering the world of HPC, individuals join a community of trailblazers leveraging its power to make groundbreaking discoveries and shape the future.
Whether embarking on the first steps into computational research or seeking to enhance existing skills, embracing HPC marks a leap into a realm of limitless potential. Though the journey may pose challenges, its rewards are boundless. Join us as we embark on a voyage of exploration, innovation, and discovery—powered by the boundless potential of high-performance computing.
Principal Investigator: Dr Lucy Kiruri
Institution Name: Kenyatta University, Nairobi, Kenya
Active Member Count: 6
Allocation Start: 2023-06-30
Allocation End: 2024-04-30
Used Hours: 20309
Project Name: KU Computational Chemistry Research Group
Project Shortname: CHEM1032
Discipline Name: Chemistry
CHEM1032: Kenyatta University Computational Chemistry Research Group
We have used the lengau clusters for more than 6+ years to carry out calculations both in molecular dynamics and quantum mechanics. This has helped my students and myself do sophisticated calculations using the state-of-art supercomputers and use better levels of model chemistry. We are grateful to CHPC.
Currently, there are only 4 members who are active. Our research interest in Molecular dynamics involves nanomedicine, malaria, Tuberculosis and COVID-19. We also use gaussian16 to carry out calculations of nanomaterials and catalysis.
Dorothy Nganga has not graduated yet and project is on derivatives of chitosan as a nanoparticle carrier for curcumin. She is using MD simulationsvto examine the structural stability and thermodynamic properties, and behavior of chitosan and curcumin in a neutral environment. The MD simulation has revealed strong binding affinities and significant intermolecular interactions (hydrogen bonding and van der waals interactions) between curcumin and the N,O- carboxymethyl chitosan. This indicates its great potential to be the preferred derivative of chitosan to be used in controlled drug release systems for hydrophobic bioactive compounds. Joseph Auka has completed her masters and he is in his final stages of defending his thesis. His research is on natural products compounds which shows high potency as inhibitors of against Protein Kinases A and B in Mycobacterium tuberculosis.
Currently, Lucy and Daniel are working on drug discovery for anti-malarial drug. Our research on malarial is motivated by the discovery of small molecules (natural products) whose activity was observed to be high in vitro and in vivo, however, the actual model and mechanisms of actions remains not well explored. We have employed computational approach to understand the mechanisms of action. Although our preliminary results are promising and helps to explore the underlying mechanisms, we are still exploring many other mechanisms of actions of the drug like molecules. All members are grateful to CHPC, SA for according us computing time.
Principal Investigator: Prof Andries Engelbrecht
Institution Name: Stellenbosch University
Active Member Count: 12
Allocation Start: 2023-06-30
Allocation End: 2024-03-21
Used Hours: 407678
Project Name: Computational Intelligence for Optimization
Project Shortname: CSCI0886
Discipline Name: Computer Science
The artificial intelligence research group in the departments of Computer Science and Industrial Engineering at Stellenbosch University continued with the development of nature-inspired algorithms to develop solutions to complex optimization problems and to develop more efficient approaches to develop predictive models. Empirical analysis of the performance of these stochastic algorithms is computationally demanding, relying heavily on the computational resources provided by the CHPC.
Principal Investigator: Prof Albertus Smit
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2023-07-03
Allocation End: 2024-01-17
Used Hours: 39035
Project Name: Extreme climatic events in the coastal zone
Project Shortname: ERTH1192
Discipline Name: Earth Sciences
In a ground-breaking scientific advancement, researchers have unveiled the world's first detailed analysis of deep ocean marine heatwave dynamics, employing the high-resolution INATL20 ocean model. With its impressive 0.05° and 0.04° longitude and latitude resolution across 46 depth levels, this model has provided unprecedented insights into the behaviour of thermal extremes in the deep ocean.
For the first time, this analysis has revealed the significant impact of deep ocean topography on the modulation of marine heatwaves and cold spells. It uncovers how underwater mountains and valleys play a critical role in shaping warm and cold thermal extremes. This finding marks a significant leap in our understanding of deep ocean dynamics.
A particularly intriguing discovery is the prolonged duration of these thermal extremes in the deep ocean compared to surface waters. This aspect of marine heatwaves has remained largely unexplored until now, and it presents new challenges and opportunities for marine scientists and oceanographers.
The INATL20 model's high-resolution data is pivotal in enhancing our understanding of the deep ocean, which remains one of the least explored on our planet. This analysis is not just a scientific triumph but also a crucial step towards better understanding the impacts of climate change on the deep ocean ecosystems.
Principal Investigator: Prof Krishna Bisetty
Institution Name: Durban University of Technology
Active Member Count: 9
Allocation Start: 2023-07-05
Allocation End: 2024-01-23
Used Hours: 7293
Project Name: Computational Modelling & Bioanalytical Chemistry
Project Shortname: CHEM0820
Discipline Name: Chemistry
The Computational Modeling and Bioanalytical Research Group at the Durban University of Technology is eternally grateful to the CHPC. The resources at the CHPC are pivotal to establishing synergies between the experimental and computational approaches used to design electrochemical biosensors.
Focusing on smart-engineered nanostructured electrode materials, electrode surfaces, and single particle characterization shows a new way of doing research that is solving problems and making biosensor technology better. Postgraduate students in chemistry are trained to effectively utilize computational resources in conjunction with experimental approaches. Electrochemical biosensors developed through this research could contribute to advancements in healthcare, environmental monitoring, and food safety.
Principal Investigator: Prof Fernando Albericio
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2023-07-06
Allocation End: 2024-01-10
Used Hours: 7927
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. We have been involved in photophysical studies of crystals. The other 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 Bettine van Vuuren
Institution Name: University of Johannesburg
Active Member Count: 6
Allocation Start: 2023-07-06
Allocation End: 2024-01-31
Used Hours: 38393
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.
Biodiversity is being lost at unprecedented rates. Factors such as climate change, habitat fragmentation, and environmental degradation (including alien species) are influencing the distribution and abundance of species, often in ways that are impossible to predict. As conservation geneticists, we are interested in exploring spatial and temporal genetic trends in a variety of organisms (plants, invertebrates, microorganisms) on sub-Antarctic islands, with a special focus on Marion Island.
Our aim is to investigate genetic patterns and structure in the context of environmental changes (e.g. climate change), with the intention of using our study species as proxies for monitoring global change and its impact on biodiversity as a whole.
To do this, we use multiple workflows to create next-generation sequencing (NGS) data. By using the CHPC cluster, we can perform phylogenomic, transcriptomic, and population genomic analyses on our NGS data. Since no other platforms can manage the size of the data indicated above, we would not be able to conduct our research without the CHPC facilities. We are pleased with our success thus far and are grateful to the CHPC for their assistance.
Principal Investigator: Dr Krishna Govender
Institution Name: University of Johannesburg
Active Member Count: 22
Allocation Start: 2023-07-07
Allocation End: 2024-01-18
Used Hours: 610168
Project Name: Computational approaches to design novel anticancer agents
Project Shortname: CHEM0792
Discipline Name: Chemistry
The Computational Chemistry and Molecular Modelling Group and the University of Johannesburg focuses primarily on drug design to target cancer treatment. With recent collaborations there is a large drive in the group to find local natural products that can be used to treat various cancers. Due to the various natural product sources in South Africa we wish to build a database of these products as well as computationally develop other possible candidates which will all be used as test cases on known cancer cell lines. It is expected that the database will be considerably large and as a result local resources will not sufficiency when it comes to testing the natural products within reasonable timeframes and as such CHPC resources will be imperative to ensure the success of this work.
Principal Investigator: Prof Juliet Pulliam
Institution Name: Stellenbosch University
Active Member Count: 10
Allocation Start: 2023-07-10
Allocation End: 2024-01-23
Used Hours: 60122
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 Gerard Tromp
Institution Name: Stellenbosch University
Active Member Count: 16
Allocation Start: 2023-07-10
Allocation End: 2024-01-25
Used Hours: 110044
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. SATBBI also has an important educational and training mandate. The CHPC is a vital resource for these activities.
Principal Investigator: Dr Vuyo Mavumengwana
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2023-07-10
Allocation End: 2024-01-23
Used Hours: 30251
Project Name: Microbial symbionts bioactive compounds and their virtual screening
Project Shortname: CBBI1434
Discipline Name: Bioinformatics
The Vuyo Lab is a group of 3 PhD and 2 masters students working towards earning the degrees. Further, the group also has 3 postdoctoral researchers who all incorporate in-silico work in their respective projects.
Principal Investigator: Dr Lawrence Borquaye
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 13
Allocation Start: 2023-07-12
Allocation End: 2024-01-09
Used Hours: 1125284
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: Dr Benjamin Victor Odari Ombwayo
Institution Name: Masinde Muliro University of Science and Technology, Kakamega, Kenya
Active Member Count: 9
Allocation Start: 2023-07-12
Allocation End: 2024-02-08
Used Hours: 87911
Project Name: Ab initio study of Solar Energy Materials
Project Shortname: MATS1426
Discipline Name: Material Science
Solar energy materials have been widely characterized experimentally using different techniques for a variety of properties such as structural, electrical, optical and defects. In search of suitable materials that can replace silicon in fabrication of efficient and stable solar cells, Inorganic–organic metal halide perovskite solar cells (PSC) are currently in the limelight of solar cell research due to their rapid growth in efficiency which has crossed 25% for laboratory scale devices but have stability and reliability issues. Our group, Computational and Theoretical Physics (CTheP) research group in Masinde Muliro University of Science and Technology, through the programme: Ab initio study of Solar Energy Materials, endeavor to investigate stability issues in perovskite solar cells and suggest remedies from a Density Functional Theory perspective. Our studies are on Triple Cation Mixed Halide perovskite materials of the form Cs0.5FA0.3MA0.2Pb(I0.2Br0.8)3 and are effectively calculated in a HPC environment due to the large number of atoms involved. We are investigating the intrinsic stability of the materials which constitute the band structure, defects, thermodynamic and phase stability. Knowledge gained will greatly help in adopting strategies to further improve the efficiency and stability of PSCs. We also study emerging materials for photovoltaics such as tetrachlorocobaltate hybrid perovskite salts, photocatalytic materials such as BaTiO3 for Piezo-Photocatalytic Degradation of Organic Pollutants in Wastewater, and mechanical properties of Al-Mg-Si alloys. So far, one of our articles that has e been published in the journal of Alloys (MDPI). These systems of 108 atoms each, would not have been possible to study without the support of CHPC, Capetown. We therefore, have acknowledged CHPC resources to MATS1426 programme in this article.
Principal Investigator: Prof Josua Meyer
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2023-07-13
Allocation End: 2024-01-31
Used Hours: 510647
Project Name: Fundamentals of forced and mixed convection in heat exchangers
Project Shortname: MECH1094
Discipline Name: Computational Mechanics
In April 2022, Professor Josua Meyer was appointed as a professor at Stellenbosch University in the Department of Mechanical and Mechatronic Engineering, having previously held the same position at the University of Pretoria. Throughout his tenure, he served as the Head of Mechanical and Aeronautical Engineering for 20 years and as the Chair of the School of Engineering for 17 years. The School of Engineering is recognized as one of the world's largest engineering schools, and Prof. Meyer led one of the largest heat transfer research groups globally.
Prof. Meyer holds an A-rating from the NRF, denoting his status as an esteemed scientist acknowledged by peers for exceptional international scholarship in their respective field. His recent research outputs have demonstrated high quality and significant impact. Currently, he is establishing a new research group with a primary focus on the thermal sciences, particularly in the area of heat exchangers. His work in this domain centers on fundamental investigations of internal forced convection and transitional flow regimes, with applications in thermal-solar, wind, and nuclear energy.
As part of his ongoing endeavors, Prof. Meyer is engaged in a program involving the generation of computational fluid dynamics (CFD) data. These data complement experimental measurements and facilitate the identification and quantification of several previously unrecognized flow phenomena. Specifically, the comparison of experimental and CFD data obtained from water flowing through a circular tube with different Reynolds numbers and heat fluxes has revealed four significant phenomena that were previously unidentified. These include the distribution of wall temperature in simultaneous hydrodynamic and thermal developing boundary layers, the presence of a tube recirculation region at the tube inlet, a non-linear fluid temperature gradient during flow development, and the need for a new definition of "fully developed flow."
In summary, Prof. Meyer's appointment at Stellenbosch University marks his transition from the University of Pretoria, where he held prestigious positions within the Department of Mechanical and Mechatronic Engineering. His influential research and leadership in the field of heat transfer have contributed to the growth and recognition of his research group. Through his investigations of thermal sciences, particularly heat exchangers, Prof. Meyer has uncovered significant flow phenomena that were previously unexplored.
Principal Investigator: Prof Ray Everson
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2023-07-14
Allocation End: 2024-01-31
Used Hours: 595628
Project Name: CO2 Capture in Circulating Fluidized Beds
Project Shortname: MECH0866
Discipline Name: Chemical Engineering
The Research Programme is focused on emissions abatement and sustainability with a broader focus on CO2 and SO2 capture and management. The current use of the CHPC resources has been on the modelling of SO2 capture in Flue Gas Desulphurization.
In spray-dry scrubbing, hot flue gas is contacted with a spray of an alkali slurry in order to remove SO2 from the gas stream. The advantage of this process is the generation of dry product, eliminating the need for slurry handling and reducing the overall water usage and waste-water production of the desulphurization process. In this work successive modelling of the three key phenomena occurring in spray-dry scrubbing, which entail Hydrodynamics modelling, Evaporation/Drying modelling and SO2 absorption modelling, including Chemical reaction modelling, is implemented in a computational fluid dynamics platform (Starccm+). The process itself is a mulitiscale, multiphase and multiphysics problem requiring high computing systems to solve the complex differential equations defining these phenomena, which has been made possible by the CHPC.
The work is part of the on-going efforts by the centre for Emissions Control at the North West University in assisting South Africa to meet both national and global environmental regulations with respect to CO2 and SO2 emissions.
Principal Investigator: Dr Caleb Kibet
Institution Name: International Centre of Insect Physiology and Ecology, Nairobi, Kenya
Active Member Count: 9
Allocation Start: 2023-07-17
Allocation End: 2024-01-17
Used Hours: 110426
Project Name: Insect Genomics
Project Shortname: CBBI1470
Discipline Name: Bioinformatics
The program explores transcriptional gene regulation of chemosensory genes in insect vectors, including tsetse and mosquitoes. This research entails analysing massive genomic data including, protein binding microarrays, ChIP-seq, and whole-genome sequences. In this research, we build machine learning models to scan whole genomes for potential binding sites, use multiple evidence lines to understand how olfaction is regulated. This information will allow us to design better vector management tools"
Principal Investigator: Dr Molemi Rauwane
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 6
Allocation Start: 2023-07-17
Allocation End: 2024-02-01
Used Hours: 14616
Project Name: Molecular Biology and Bioinformatics of plant-pathogen interactions
Project Shortname: CBBI1564
Discipline Name: Bioinformatics
The research group of Molecular Biology and Bioinformatics of Plant Pathogen interactions is led by Dr Molemi Rauwane from Nelson Mandela University, in collaboration with UNISA and the Agricultural Research Council.
The group focuses on the use of molecular biology techniques and bioinformatics tools to identify characterize and understand/unravel mechanisms of plants in response to biotic and abiotic stress. Our group focuses on understanding plant-pathogen interactions as well as plant-abiotic (heat and drought) stress in crops of economic importance such as wheat, beans, cassava, and sweet potatoes, among others. Other projects from different collaborators also work on understanding plant-pathogen interactions in vegetable crops such as tomato and okra.
These studies are done for breeding crops with resistance/tolerance to multiple stress caused by climate change. The crops can then be planted anytime without challenges of loosing them because of biotic or abiotic stress, or both stresses combined. This can go a long a way in alleviating poverty.
With the crops been exposed to different biotic and abiotic stress daily, understanding their response to these factors enable the development of improved varieties with resilience to biotic and abiotic stresses. CHPC platform helps in analysing the data generated from NGS system, so as to interpret the data that entails response of plants to biotic and abiotic stress. This plays a role in decisions made in terms of improving important varieties of crops of economic importance.
Two manuscripts will be submitted for publications in peer-reviewed journals in January.
Principal Investigator: Dr Madison Lasich
Institution Name: Mangosuthu University of Technology
Active Member Count: 8
Allocation Start: 2023-07-26
Allocation End: 2024-01-25
Used Hours: 311549
Project Name: Chem Thermo
Project Shortname: CHEM1028
Discipline Name: Chemical Engineering
The Chem Thermo project is led Dr Madison Lasich and includes her post-doctoral scholar Dr Victoria Adeleke and current Masters candidate Mr Themba Ngcobo. Recently the research group contributed to an international project together with MacEwan University in Canada which investigated the compatibility of template-monomer-crosslinkers-solvent for cortisol molecularly imprinted polymer receptors that can efficiently recognize and capture cortisol from biological fluids. High performance computing was instrumental for this study as it allowed for a multilayered approach combining density functional theory with classical atomistic simulations to study these materials at the molecular level, while also reducing the need for costly laboratory experiments. There is growing interest in the development of cortisol (a known stress hormone biomarker) molecularly imprinted polymers as molecular receptors for sensor development. This study was published in a leading international journal in chemical sciences,
Molecular Systems Design & Engineering.
Principal Investigator: Prof Jeanet Conradie
Institution Name: University of the Free State
Active Member Count: 8
Allocation Start: 2023-07-19
Allocation End: 2024-01-29
Used Hours: 2203090
Project Name: Computational chemistry of transition metal complexes
Project Shortname: CHEM0947
Discipline Name: Chemistry
The CHPC resources played a crucial role in facilitating our research group and collaborators to comprehend and illuminate experimental observations. Theoretical calculations were validated by comparing them with existing experimental results, enabling a comprehensive understanding and prediction of experimental behavior.
Our theoretical investigation into redox potential, focusing on the stability of molecules towards oxidation and/or reduction, finds practical applications in catalysis and as redox mediators in dye-sensitized solar cells. Similarly, the theoretical examination of UV-vis properties using TDDFT has implications as dyes in dye-sensitized solar cells. The exploration of liquid and liquid-mixture properties holds significant industrial relevance, spanning areas such as organic extraction, organic synthesis, polymer chemistry, oil extraction, separation processes, product formulation, and functional fluidics.
Furthermore, our adsorption studies of pollutants contribute to advancements in wastewater treatment strategies. Investigations into metal extraction from pyrite, with a focus on recovering gold from mine tailings, and from electric arc furnace dust (a fine powder waste resulting from the industrial melting of iron scraps and end-of-life iron-based products) revealed the specific metal products formed during the extraction process.
Principal Investigator: Dr Annerine Roos
Institution Name: University of Cape Town
Active Member Count: 11
Allocation Start: 2023-07-19
Allocation End: 2024-01-23
Used Hours: 11402
Project Name: DCHS and MRI studies
Project Shortname: HEAL1267
Discipline Name: Health Sciences
We are a group of neuroscientists and clinicians in the field of psychiatry who investigate brain correlates of psychiatric and neurological disorders. The Universities of Cape Town and Stellenbosch collaborate with international brain imaging groups in this work. The aim is to find out what goes wrong in the brains of people suffering from such disorders, to inform suitable interventions and treatment. We for instance, image young children using MRI and follow them over time with repeat scans, to determine how environmental influences such as prenatal substance exposure or maternal depression may impact neural development. Such projects are crucial to identify vulnerable groups and key periods for intervention to optimise development. Evidence shows the earlier interventions, the better the outcomes. We also investigate disorders in adults such as obsessive-compulsive-and-related disorders and Parkinson's disease, to gain a better understanding of underlying neural issues. CHPC enables us to analyse brain data that requires powerful technical resources. Brain data comes with very large files and programs need to have the computer capacity to process the data. If it was not for CHPC, it would have taken months to produce certain output on one's own computer; it takes less than a month to do the same work on CHPC that uses multiple computers at the same time. We upload the raw imaging data from the scanner onto CHPC's system, and subject it to programs that conduct specific steps to produce results. Results may include files on the size and thickness of brain regions, and the intactness of brain tracts interconnecting such regions. We are presenting and publishing numerous pieces of work using this output.
Principal Investigator: Dr Lonnie van Zyl
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2023-07-19
Allocation End: 2024-01-19
Used Hours: 10780
Project Name: Engineering bacterial pyruvate decarboxylase for increased thermostability
Project Shortname: CBBI1265
Discipline Name: Bioinformatics
From the 11th till the 14th of September 2023 IMBM researchers together with researchers from Stellenbosch University (Dept. Microbiology and Soil Science), University of Pretoria (CMEG) and several researchers from the USA (Kent State University and University of Texas Austin) travelled to Koringberg 118km North of Cape Town to sample termite mounds both in pristine renosterbos as well as the adjoining cultivated fields. This multi-disciplinary group aims to integrate our understanding of soil geology/chemistry and microbiology to determine how physicochemical and microbiological factors come together in termite mounds to make them potent carbon sinks. This could happen through the transport and sequestration of carbon in the form of oxalate produced by the surrounding plants, cut down and transported into the mound by termites, acted on by fungi and bacteria in the termite gut and soil, then leached into the soil by rain water. Ryan Byrd, an MSc student in IMBM has isolated bacteria from these samples and determined their ability to utilize oxalate as sole carbon source and sequenced their genomes to determine the genetic basis of their ability to do so. We've already identified genomes that encode the known frc genes involved with the precipitation of calcium carbonate (CaCO3) via the oxalate-carbonate pathway (OCP) and in CO2 being sequestered into soils as insoluble calcite. However, interestingly we have also isolated bacteria capable of utilizing oxalate as sole carbon source without these genes being present. This offers the opportunity to discover potentially novel mechanisms by which microorganisms play a role in this process.
Principal Investigator: Dr Emmanuel Dufourq
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 6
Allocation Start: 2023-07-25
Allocation End: 2024-02-28
Used Hours: 111444
Project Name: Machine Learning for Ecology
Project Shortname: CSCI1563
Discipline Name: Data Science
The Machine Learning for Ecology Research Group is part of the African Institute for Mathematical Sciences. The group focuses on research and scientific discoveries for conservation ecology using advancements in machine learning. By harnessing the capabilities of machine learning, we can process and interpret data from various sources, primarily from audio recorders.
The world has witnessed a distressing decline in biodiversity, brought about by various factors such as resource overexploitation, deforestation and climate change.
These challenges necessitate an abundance of information and more sophisticated solutions. While it is evident that the populations of threatened species are declining, significant conservation efforts have been implemented to counteract this trend. Researchers and rangers actively monitor these populations using various methods, including the use of microphones and cameras in the environment, and analysing the recorded media for evidence of species of interest. Passive acoustic monitoring (PAM) is a non-invasive approach for studying soundscapes. However, analysing thousands of hours of recordings poses a challenge in terms of manual processing.
To date, we have developed methodologies to assist with the monitoring of critically endangered primates in China and Madagascar, as well as vulnerable birds in Malawi. Our methodologies have led to new insights on animal behaviours to be discovered.
Using machine learning, and powerful graphical processing units provided by the CHPC, we are able to develop and execute models which assist with wildlife monitoring of species around the world.
Principal Investigator: Prof Rosemary Dorrington
Institution Name: Rhodes University
Active Member Count: 8
Allocation Start: 2023-07-26
Allocation End: 2024-02-01
Used Hours: 4409
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 Uljana Hesse
Institution Name: University of Western Cape
Active Member Count: 8
Allocation Start: 2023-07-26
Allocation End: 2024-02-16
Used Hours: 47508
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 focuses 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.
To date, we have generated a high quality assembly of the nuclear and chloroplast genomes of rooibos, finalised gene predictions using short and long rooibos transcriptome data as supporting evidence, and completed functional annotation of the rooibos genes. For long read DNA and RNA sequencing, we have established Oxford Nanopore (MinION) technologies at UWC and a computational pipeline for assembly, annotation and comparative transcriptomics analyses at CHPC. We are also finalising a Convolutional Neural Network algorithm trained to identify and classify transporter genes, which can be adapted for the analysis of any other protein family. All computational analyses, which require substantial computational power and prowess, are being conducted locally at CHPC. This proves that Medicinal Plant Genomics can be completed entirely in South Africa, strengthening the countries independence in the bioprospecting of its natural resources, including the native flora and fauna.
Principal Investigator: Dr John Mack
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2023-07-26
Allocation End: 2024-01-25
Used Hours: 13366
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, seven MSc and three 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 Pritika Ramharack
Institution Name: Medical Research Council
Active Member Count: 16
Allocation Start: 2023-07-27
Allocation End: 2024-02-01
Used Hours: 91411
Project Name: Phytomedicine in Metabolic disorders
Project Shortname: HEAL1387
Discipline Name: Health Sciences
The aim of my new Molecular modeling and Bio-computation research group within the Biomedical Research and Innovation Platform (BRIP), SAMRC, is to conduct predictive biological target identification, compound physio-chemical descriptions, molecular modeling, molecular docking and molecular dynamic simulations that are required for the enhancement of current therapeutic regimens in various metabolic disease conditions. These techniques may also be implemented in identifying and optimizing vaccine developments against SARS-CoV-2 variants amidst the Covid-19 pandemic. The group is currently still being established, with students currently being recruited for the 2021/2022 academic cycles. The work will focus on the use of the Schrodinger suite for the design and characterization of newly synthesized compounds and co-crystals, as well as the use of Glide for molecular docking. The use of the Amber suite will also be utilized to simulate a theoretical experimental environment that will be programmed using specialized chemical forcefields, thus allowing for molecular interactions and free-binding energy of the complexes to be analysed. This will provide critical information on the potential structural mechanisms of action of the compounds, as well as the structural dynamics of enzymes, with particular interest on mutational modifications. To perform these studies, the use of the CHPC will be critical in accessing the Schrondinger and Amber suites and to perform large scale molecular simulations. The successful use of the CHPC in my research is documented in various studies that are evidenced in 25 internationally peer-reviewed Journal articles (https://orcid.org/0000-0001-5850-6782?lang=en). My goal is to continue utilizing this platform to facilitate and expand computational chemistry capacity development within South Africa, focusing on previously disadvantaged universities. The collaborative work within the SAMRC, using CHPC, will also provide key genomic and proteomic insights on new and circulating SARS-CoV-2 variants detected in South Africa.
Principal Investigator: Prof Ozlem Tastan Bishop
Institution Name: Rhodes University
Active Member Count: 10
Allocation Start: 2023-07-28
Allocation End: 2024-02-15
Used Hours: 906562
Project Name: Structural Bioinformatics for Drug Discovery (2)
Project Shortname: CBBI1425
Discipline Name: Bioinformatics
The Research Unit in Bioinformatics (RUBi) graduated 4 PhD and 2 MSc students in the October graduation. All PhD students and 1 MSc student achieved their degrees with a great contribution from CHPC. Their projects were in the different aspects of drug discovery and drug metabolism.
Principal Investigator: Prof Mahmoud soliman
Institution Name: University of KwaZulu-Natal
Active Member Count: 35
Allocation Start: 2023-07-31
Allocation End: 2024-02-06
Used Hours: 915523
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 a 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 are employed in performing the molecular dynamic calculations and the corresponding post-molecular dynamic simulation analysis
Principal Investigator: Dr Marilize Le Roes-Hill
Institution Name: Cape Peninsula University of Technology
Active Member Count: 1
Allocation Start: 2023-08-01
Allocation End: 2024-02-01
Used Hours: 5197
Project Name: Actinobacterial genomics/metagenomics
Project Shortname: CBBI1347
Discipline Name: Other
The Applied Microbial and Health Biotechnology Institute (AMHBI) is a newly formed research institute based at the Cape Peninsula University of Technology. The institute aims to perform research that covers the full innovation chain - from fundamental to experimental to applied research, with the end goal being the development of new products. Certain components of our research also focus on biodiversity and how biodiscovery is driven by it. In order to understand what is happening within a specific environment, we often look at what we can culture from the environment (in order to access new products such as antibiotics and novel enzymes) but are typically guided by the total population structure as determined by metagenomics. As such, in order to analyse large data sets generated through next generation sequencing, we have made use of the resources of the Centre for High Performance Computing (CHPC) for the processing of the data. The outcome of the analyses has highlighted the great degree of bacterial diversity in South African environments; especially the great diversity of specific antibiotic-producing bacteria, the actinobacteria. With the worldwide increase in the number of drug- and multidrug-resistant pathogens, there is a continued need for the discovery of novel antibiotics. This study therefore contributes to our current knowledge base as to where we can potentially source these novel antimicrobial agents, while also focusing on the discovery of novel microorganisms often not cultivated during culture-based studies.
Principal Investigator: Dr Tshepo Khoza
Institution Name: 0 Other
Active Member Count: 1
Allocation Start: 2023-08-01
Allocation End: 2024-07-31
Used Hours: 29146
Project Name: IGEOSCIESOL2023
Project Shortname: INDY1606
Discipline Name: Earth Sciences
The Research Group is called Integrated Geoscience Solutions. We conduct geoscientific research in the fields of groundwater, geohazards, mineral and energy mapping, environmental characterization and climate change. We collaborate with other local and international research organizations in terms of technology sharing.
Our work contributes to the understanding of natural resources and provides input into their sustainable management. For example, we conduct regional groundwater mapping in order to understand the location and quality of groundwater resources. Given that South Africa is a water-scarce country, the knowledge of groundwater resources is critical to their management in the short and long term. Given the regional nature of the work, it relies on the using high computing resources of the HPC. The project is progressing very well and will be reported on in the next few months
Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 8
Allocation Start: 2023-08-02
Allocation End: 2024-02-02
Used Hours: 183151
Project Name: Computational and statistical methodologies for human and environmental health prediction
Project Shortname: CBBI0818
Discipline Name: Bioinformatics
Computational risk prediction and Artificial Intelligence (AI) for multi-omics-driven human health challenges are running from my research group and continue to support several African researchers and students via several African universities, H3African and DS-I African consortia. This research programme is fundamentally aiming:
1) to determine the environment and genomics variation that causes the human species to look different, having differences 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 humans.
These are addressed through the design of machine learnings, AI methodologies and statistical approaches to analyse DNA data of thousands of 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 make a huge number of data difficult to manage, store and 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 and the Cloud has critically increased our research portfolio to meet the international standard concerning the large-scale genomic era. This programme has already developed several genomic-based software tools that address African genetic variation challenges and provided advanced training around parallel programming concerning large-scale genomic data to African postgraduate students/researchers.
Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 7
Allocation Start: 2023-08-02
Allocation End: 2024-02-02
Used Hours: 22951
Project Name: African Multi-Omics Data Science
Project Shortname: CBBI1039
Discipline Name: Bioinformatics
Training in computational risk prediction and Artificial Intelligence for multi-omics-driven human health challenges is running from my research group as a joint appointment from the University of Kinshasa, DR Congo, and Northumbria University, Newcastle, UK. This research/training programme continues to support the training of several African students from several African universities and H3African and DS-I African consortia, and recently from the University of Kinshasa (D.R. Congo). This research training programme is fundamentally aiming:
1) to provide students with experience and training in computational cost tasks and large-scale data analysis
2) to determine the environment and genomics variation that cause the human species to look different, having differences 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 humans.
These are addressed through the design of machine learnings and AI methodologies and statistical approaches to analyse DNA data of thousands of 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.
Principal Investigator: Prof Yoshan Moodley
Institution Name: University of Venda
Active Member Count: 7
Allocation Start: 2023-08-02
Allocation End: 2024-02-02
Used Hours: 158202
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.
Principal Investigator: Prof Eric van Steen
Institution Name: University of Cape Town
Active Member Count: 7
Allocation Start: 2023-08-03
Allocation End: 2024-02-05
Used Hours: 671982
Project Name: Lateral interactions on surfaces
Project Shortname: CHEM0780
Discipline Name: Chemistry
The emission of CO2 is linked to global warming and associated with climate change, and the reduction of CO2 emissions is thus necessary to reduce its impact on society. The reduction of CO2 emission into the atmosphere is not straight forward for all sectors. For instance, the cement industry produces essential materials for growing economies (cement, concrete), but its production accounts for ca. 7% of the global CO2 emissions. It is expected that cement manufacture will expand in Africa, but new technologies are needed to curb the inevitable CO2 production associated with the production of cement. This can be achieved by converting CO2 produced in this industry with renewable hydrogen to liquid hydrocarbons. This has several advantages, viz. reduction of CO2 emission at the cement manufacturing site, being able to store renewable hydrogen readily and use the product as fuel for sectors which are difficult to decarbonize such as the aviation industry and the agricultural sector (thus replacing the use of fossil fuels in these sectors with fuels containing renewable hydrogen).
The hydrogenation of CO2 is a challenge, and can proceed via the indirect route in which CO2 is first converted into the more reactive CO or the direct route (https://care-o-sene.com/en/). In both cases the transformation of COx to hydrocarbons needs to proceed effectively requiring transition metal promoters. The role of the promoters is studied using first-principal calculations requiring HPC-resources provided by CHPC. These calculations make use of models to describe the catalytically active metal and the promoter; possible roles of the promoter in the reaction pathways are explored, so that improved catalysts can be developed.
Principal Investigator: Dr Jaco Badenhorst
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 5
Allocation Start: 2023-08-03
Allocation End: 2024-02-05
Used Hours: 2133
Project Name: Automatic transcription of broadcast data
Project Shortname: CSIR0978
Discipline Name: Other
The Voice Computing (VC) 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: Dr Fortunate Mokoena
Institution Name: North-West University
Active Member Count: 5
Allocation Start: 2023-08-04
Allocation End: 2024-02-04
Used Hours: 35711
Project Name: Protozoan parasites and cancer drug discovery
Project Shortname: CBBI1293
Discipline Name: Bioinformatics
Our work looks into discovering new compounds which can be developed further for the treatment of diseases mainly affecting the African continent. We use a combination of ligand design, structure based design and machine learning to come up with new compounds or previously unexplored chemical spaces to conduct molecular docking using different target proteins as receptors. Following which, we then conduct molecular dynamics simulations.
Principal Investigator: Prof Matt Hilton
Institution Name: University of the Witwatersrand
Active Member Count: 5
Allocation Start: 2023-08-04
Allocation End: 2024-02-23
Used Hours: 155036
Project Name: Cosmology and astrophysics from Sunyaev-Zel'dovich selected galaxy clusters
Project Shortname: ASTR1534
Discipline Name: Astrophysics
At the Wits Centre for Astrophysics, Prof. Matt Hilton and his research group are using CHPC to analyse data on galaxy clusters, the largest gravitationally bound structures found in the universe. In one project, CHPC is being used to analyse maps of the sky produced by the Atacama Cosmology Telescope (ACT), in order to measure the abundance of galaxy clusters over a 10 billion year span of cosmic history. CHPC is also being used to simulate the ACT cluster survey and measure cosmological parameters, such as the amount of dark matter and dark energy in the universe. In another project, CHPC is being used to process radio data from MeerKAT on clusters detected by ACT. The aim of this work is to determine the nature and evolution of the mysterious diffuse radio emission in galaxy clusters, which is produced when clusters collide. Such cluster mergers are the most energetic events in the universe since the Big Bang. High performance computing resources, such as those provided by CHPC, are crucial to allow the large datasets involved to be processed efficiently.
Principal Investigator: Dr Brigitte Glanzmann
Institution Name: Stellenbosch University
Active Member Count: 17
Allocation Start: 2023-08-07
Allocation End: 2024-02-21
Used Hours: 54679
Project Name: SAMRC Precision Medicine African Genomics Centre
Project Shortname: CBBI1195
Discipline Name: Bioinformatics
The South African Medical Research Council's Genomics Platfrom had quite humble beginnings where we sequenced the first 6 human genomes on the African continent. We not stand on the cusp of sequencing the 10 000th sample at the Genomics Platform and we have diversified from humans, to animals, plants, soil and microbes.
Principal Investigator: Prof Adrienne Edkins
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2023-08-07
Allocation End: 2024-02-07
Used Hours: 4682
Project Name: Molecular and Cellular Biology of the Eukaryotic Stress Response
Project Shortname: CBBI1405
Discipline Name: Health Sciences
The Biomedical Biotechnology Research Unit (BioBRU) is a biomedical research unit at the Department of
Biochemistry and Microbiology_Rhodes University. The research group is part of a larger collaborative research unit focused on understanding the structure and function of the cellular stress response. The current studies are focused on DnaK biology and substrates linked to drug
resistance in treating tuberculosis (TB). The computational part of the study involves molecular dynamic simulations
of Mtb proteins to examine if such mutations destabilize the protein and ligand docking screens to identify putative new therapeutic molecules that can be progressed into laboratory-based experiments.
Considering that this analysis is computationally resource-demanding, the CHPC platform is invaluable. We are happy
to report that we completed the runs and achieved this goal through CHPC.
Principal Investigator: Prof Markus Boettcher
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2023-08-07
Allocation End: 2024-02-15
Used Hours: 85911
Project Name: Modeling time-dependent emission from blazar jets
Project Shortname: ASTRO1535
Discipline Name: Astrophysics
Blazars are a peculiar type of active galactic nuclei, characterized by highly variable radiation across the electromagnetic spectrum - from radio waves to gamma-rays - that originates in a plasma jet ejected from a central super-massive black hole in the center of the galaxy. While there isa large body of work studying short-term, eruptive flux enhancements (flares) of blazars, their unpredictable long-term variability is currently poorly understood. North-West University Ph.D. student Hannes Thiersen has embarked on a project to study, through numerical simulations, the nature of the long-term variability of blazars. For this purpose, he uses a time-dependent blazar emission model and produces stochastic variations of selected input parameters. He then studies the resulting, simulated light curves in various electromagnetic frequency bands. A key result that has been obtained is that the observable variability patterns systematically deviate from the input-parameter variability patterns. Specifically, for parameter variations that exhibit strong variability on very short time-scales, this short-term variability is significantly suppressed in the observable flux light curves.
Principal Investigator: Dr Sphelele Sosibo
Institution Name: North-West University
Active Member Count: 8
Allocation Start: 2023-08-07
Allocation End: 2024-03-05
Used Hours: 2148
Project Name: Molecular Dynamics of target enzymes
Project Shortname: HEAL1414
Discipline Name: Chemistry
The Organic and Medicinal Research Group uses the CHPC to identify the interaction of plant based photochemical compounds against various protein disease targets.
The isolation of plant bioactive material is a naturally destructive process. Computational Chemistry allows for studying of chemical entities without the use of actual chemicals. This reduces the number of experiment that can be performed in in-vitro and in-vivo testing.
We are using the CHPC parallel computing facilities to scale some of the project we carry in personal computers. We have had success in publishing some of the work from CHPC.
There is currently a good perception of the CHPC services from the students and it is envisioned that most of the work will be published and result in graduations.
Principal Investigator: Prof Mwadham Kabanda
Institution Name: University of Venda
Active Member Count: 2
Allocation Start: 2023-08-08
Allocation End: 2024-02-08
Used Hours: 959969
Project Name: Reaction mechanism for atmospheric relevant molecules
Project Shortname: CHEM1161
Discipline Name: Chemistry
The research group lead by Prof MM Kabanda is currently is consisting of four PhD students, Masuku G.M, Sithuba T., Tshikhudo F. and Ratshikombo R. Currently, the students are still collecting data. The work involves study of interactions between selected corrosion inhibitors that are interacting with different metal surfaces. The outcome of the work is relevant towards environmental protection of metal materials that are used in different industrial applications.
The necessary ot utilising public resources sterms from the fact that the computational power needed for the calculations is significantly great and can only be fulfilled by the help of CHPC. However, the outcome of the results, once published, will be beneficial to the public also because they will provide important information on the protection of metal surfaces that are used in industrial applications. The project is going very well, results are coming slowly because of load shedding.
Principal Investigator: Dr Fabio Cinti
Institution Name: NITHEP
Active Member Count: 4
Allocation Start: 2023-08-08
Allocation End: 2024-02-29
Used Hours: 25482
Project Name: Quantum Monte Carlo for ultra-cold atoms
Project Shortname: PHYS0892
Discipline Name: Physics
The group led by Fabio Cinti, associate professor at University of Johannesburg, aims to study pattern formation of special structures like stripe phases, cluster crystals, quasicrystals and curved surfaces in a quantum regime. Newly developed numerical simulations demonstrate that bosons trapped in a narrow spherical shell can become supersolid: a crystal-like structure which supports frictionless particle flow. Bubble traps, confining ultracold atoms close to the surface of an ellipsoid, are currently the focus of considerable theoretical and experimental activity. Curvature is important in a variety of fields, from cosmology to biology, and being able to measure its effects on the properties of many-body quantum systems opens new and exciting avenues of investigation. Experiments so far have focused on weak interactions between the atoms; they have been performed in space to contrast the effects of gravity, which causes particles to collapse to the bottom of the bubble trap. In this work, strongly-interacting bosons are considered instead. Simulations show that a supersolid can arise in a spherical geometry for two different interactions: in particular, soft-core interactions lead to a homogeneous arrangement of clusters on the sphere, which for small radii takes the shape of a (semi)regular polyhedron; conversely, a dipolar interaction leads to the formation of a supersolid ribbon of clusters around the equator. Bringing curvature and supersolidity together for the first time, these results stimulate further studies of the influence of curved confinement on strongly-interacting many-body systems.
Principal Investigator: Dr Sunita Kruger
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2023-08-08
Allocation End: 2024-02-29
Used Hours: 275309
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 and fluid-structure interaction. Specifically heat transfer in naturally ventilated greenhouses, and the modelling of rock drills. 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 rooftop greenhouse. Smaller greenhouses containing a single and multi-spans have also been investigated. Currently, three dimensional models of greenhouses subject to buoyancy driven flow are being investigated, as well as the fluid-structure interaction to improve the efficiency of rock drills.
Principal Investigator: Dr ADEDAPO ADEYINKA
Institution Name: University of Johannesburg
Active Member Count: 17
Allocation Start: 2023-08-08
Allocation End: 2024-02-08
Used Hours: 1072526
Project Name: Computational Design of Molecules
Project Shortname: CHEM1221
Discipline Name: Chemistry
The Computational Design of Molecules Research group is based located within the Department of Chemical Sciences at the University of Johannesburg. We aim to design and simulate new or improved molecules, and nanomaterials for applications in Catalysis, Renewable energy, and nanotechnology. 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 various 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. We rely on computational resources from the Centre for High-Performance Computing to carry out our computational work efficiently to achieve our goals. To date, we have been able to computationally design various unique molecules that have demonstrated great potential as adsorbents for greenhouse gases as well as for application in electrocatalysis. Several articles have been published in top journals as output from the various projects under this research program.
Principal Investigator: Dr Saheed Sabiu
Institution Name: Durban University of Technology
Active Member Count: 26
Allocation Start: 2023-08-10
Allocation End: 2024-02-13
Used Hours: 668073
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: Dr Collins Obuah
Institution Name: University of Ghana
Active Member Count: 3
Allocation Start: 2023-08-10
Allocation End: 2024-02-08
Used Hours: 15531
Project Name: Bioinorganic Chemistry
Project Shortname: CHEM1351
Discipline Name: Chemistry
We the computational group at the University of Ghana, Department of chemistry are researching into the improvement of the compounds which are used in solar panels. Power is the backbone for every economy. The effective and clean production of power is the goal of every country. There are compounds which are used in solar panels to produce electricity. However, they need further improvement in their efficiency. Our research looks into modifying these compounds to improve the efficiency. We are using the CHPC facility to predict the efficiency of tetrazine base compounds that we have designed. So far we have been able to show that these compound are effective for their use are solar cell materials. Results from this work is been put as manuscript for publication soon.
Principal Investigator: Prof Koop Lammertsma
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2023-08-11
Allocation End: 2024-02-13
Used Hours: 177510
Project Name: ChiralCat
Project Shortname: CHEM1410
Discipline Name: Chemistry
The ChiralCat project is conducted at the University of Johannesburg under the direction of Prof. K. Lammertsma with Prof. A. Muller as co-supervisor and Dr. G. Dhimba as computational chemist and with PhD and MSc students performing experimental studies.
ChiralCat is about chiral-at-metal catalysis in which the chiral integrity of the transition metal catalysts is maintained during a chemical reaction. The rational design of such catalysts capable of effecting enantioselective chemical transformations is of paramount importance to satisfy the increasing industrial demand for chiral fine chemicals. ChiralCat is an innovative approach in asymmetric catalysis, requiring a detailed understanding to advance the field. So far, asymmetric catalysis is dominated by catalysts carrying expensive chiral ligands. Such conventional catalysts require exhaustive screening of the chiral ligand pool to obtain products with high enantiomeric excess. Not only is this a tedious and costly process, also the chiral ligands are often far more expensive than the transition metals. ChiralCat explores instead the use of abundantly available transition metals with readily available simple ligands to compose catalysts that are inherently chiral and that keep their chiral integrity during the catalytic reaction.
To provide these insights and assist experimentalist in synthesizing chiral-at-metal catalysts requires insight in the molecular behavior of the catalysts and their catalytic reactions. Computational chemistry is by far the best and most effective means to provide this insight, which may well simplify many industrial processes. Because of the available and indispensable compute power of CHPC we could make much progress in the first six months of this project showing the feasibility of asymmetric epoxidation of olefins with a simple molybdenum catalyst.
Principal Investigator: Dr Lynndle Square
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2023-08-11
Allocation End: 2024-03-07
Used Hours: 1023674
Project Name: Exploring poly(2,5)benzimidazole enhanced with carbon nanotubes for space applications
Project Shortname: MATS1088
Discipline Name: Physics
The work from this group considers materials for space applications in Low Earth Orbit in the Centre for Space Research at the North West University. To date, poly(2,5)benzimidazole composites are investigated using computational physics and experimental techniques for space application and radiation shielding consideration. 2023 publications thus far be found at https://pubs.aip.org/aip/apm/article/11/7/071103/2900822/ABPBI-MWCNT-for-proton-radiation-shielding-in-low and in the conference proceedings at https://ieeexplore.ieee.org/abstract/document/10231300. The computational methods used consider different scales, computational fluid dynamics to model the deposition process published recently in IEEE Transactions on Plasma Science ( Volume: 50, Issue: 12, December 2022), molecular dynamics, reactive molecular dynamics and density functional theory. All of which give vital information about the polymer and its composites. The work is complemented, guided and verified using various experimental techniques and national facilities, for example, iThemba labs Gauteng, for which different ion bombardments were investigated. The multiple studies explored under the supervision of the PI, Dr Square, in PhD, MSc, and BSc honours projects have, to date, shown encouraging results. The computational work uses the national license made available by the CHPC and its infrastructure for parallel computing.
Principal Investigator: Prof Mahmoud Ibrahim
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2023-08-14
Allocation End: 2024-02-12
Used Hours: 84007
Project Name: Computer-Aided Drug Discovery
Project Shortname: CHEM1607
Discipline Name: Chemistry
The current project is managed and directed by Mahmoud Ibrahim, from the School of Health Sciences. The project focuses on the discovery of potent hits for the treatment of viral infections. Several sub-groups with different research interests work together, including computational chemistry, quantum chemistry, and medicinal chemistry. Such a project has a global and local impact. Public resources are needed to accomplish the defined goals. The project's pipeline starts from target definition and validation and ends with large-scale molecular dynamics of the hit-target complex. CHPC offered the PI's group all the required computational resources to achieve the project's goals. The afforded facilities included CPU and GPU resources. In addition, CHPC offered technical support during the project's life-time.
Principal Investigator: Ms Tania Daniels
Institution Name: South African Weather Service
Active Member Count: 2
Allocation Start: 2023-08-14
Allocation End: 2024-02-12
Used Hours: 1021
Project Name: WAVE AND WATER LEVEL MODELLING
Project Shortname: ERTH1609
Discipline Name: Earth Sciences
This project feeds into a larger consortium project which is led by a team at CSIR, We as SAWS will be running models for climate change studies with a special focus on waves and water levels. The study is done for The National Ports Authority.
The study focuses on how water levels and waves could possibly change under various climate projects scenarios, thus how will the operations at the various ports be affected in the future.
The focus of the study is along the South African coastline, this component of the project will have a regional domain covering the local waters of South Africa.
This study will provide guidance to policy makers and also scientists as to how to prepare for possible changes along the South African coastline in the future. This will in turn inform decisions for future port and coastal infrastructure development and investment.
We will be using various climate change scenarios climate projections atmospherics and wave data to downscale the information using the Delft-3d WAVE and FLOW model configuration currently used at SAWS, the SAWS Wave and Storm Surge model to generate wave and water level output along the South African Coast. This data will then be used to be further downscaled into the various ports to provide even high-resolution information at the various ports.
Principal Investigator: Prof Thuto Mosuang
Institution Name: University of Limpopo
Active Member Count: 12
Allocation Start: 2023-08-14
Allocation End: 2024-04-23
Used Hours: 31245
Project Name: Computational studies of various ultra-hard materials
Project Shortname: MATS0875
Discipline Name: Material Science
The research group is based in the Department of Physics, University of Limpopo. The groups is made of one Associate Professor and three Senior Lecturers which are active computational research and training of postgraduate students. Three (3) doctoral students are still progressing well, with the intention to recruit two (2) masters and three (3) honours students. Computationally the research projects investigate various materials such as molybdenum disulphides, molybdenum diselenides, copper sulphides, copper selenides, gallium nitride, gallium arsenide, graphene oxide, boron nitride, gold, silver, nickel, and copper nanoparticles. The gold, silver, nickel, and copper nanoparticles are probed for possible toxicity/non-toxicity when ingested in human tissues. Molybdenum disulphides, molybdenum diselenides, and boron nitrides are investigated for possible chemical sensing. Specifically, electronic, structural, optical, 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 is useful on the structural, dynamical and thermodynamics properties. The exciting code is informative on the electronic, excited states and transport properties of these materials. Now lately, Materials Studio also through CHPC is being used to understand precious metal – protein molecules interactions. A journal article: Correlation of the electronic, elastic and thermo-electric properties of alpha copper sulphide and selenide (Computation 2023, 11(11), 233(1-12) https://dio.org/10.3390/computation11110233) has been published. Two SAIP2023 conference proceedings; Electronic, elastic and thermoelectric properties of hexagonal CuSe phase (Proceedings of SAIP 2023 ISBN: 978-0-7961-3774-6, pg 72) and Binding nature of fibrin molecules onto Au92 and Ag92 nanoparticles (Proceedings of SAIP 2023 ISBN: 978-0-7961-3774-6, pg 45) have also been produced. Another conference proceeding: Au- and Ag-nanoparticles interaction with fibrin protein molecules (MATEC Web of Conferences 388, 07009 (2023) https://doi.org/10.1051/matecconf/202338811002) has also been published.
Principal Investigator: Prof Rajshekhar Karpoormath
Institution Name: University of KwaZulu-Natal
Active Member Count: 0
Allocation Start: 2023-08-15
Allocation End: 2024-02-15
Used Hours: 112719
Project Name: Design of small novel organic compounds as potential drug candidates
Project Shortname: HEAL0835
Discipline Name: Health Sciences
Throughout the academic year 2023, our utilization of CHPC has been pivotal in the conception and execution of numerous projects, showcasing our commitment to cutting-edge research. Notably, we have contributed to the academic discourse by publishing 15 research articles, each explicitly acknowledging the indispensable role played by CHPC facilities in our investigations.
Our academic endeavours have been further marked by the successful graduation of two Master's students and three PhD candidates while concurrently hosting two postdoctoral researchers. This underscores our dedication to nurturing talent and fostering a dynamic research environment.
In our pursuit of advancing knowledge, we have harnessed computational tools across some of the 15 journals to design innovative molecules targeting malaria, cancer, and tuberculosis. Additionally, the application of Materials Studio has enhanced our ability to predict the properties of novel nanocomposite materials, expanding the scope of our research.
In tandem with our computational work, we have completed the synthesis phase of 10 research projects focused on antimalarial, anti-TB (DNA gyrase), and anti-cancer drug discovery. We are poised to initiate comprehensive computational studies on these projects as we progress, further integrating experimental and theoretical approaches.
Our commitment to knowledge dissemination is evident through our active participation in national conferences and the delivery of talks at international institutions. These engagements showcase our research and contribute to the global scientific dialogue. Again, we are happy to inform you that the University of KwaZulu Natal has awarded our SMCRG group as one of the top 30 research groups in UKZN 2023. As we reflect on the past year's accomplishments, we eagerly anticipate the continued growth and impact of our research initiatives.
Principal Investigator: Dr Rian Pierneef
Institution Name: University of Pretoria
Active Member Count: 28
Allocation Start: 2023-08-15
Allocation End: 2024-02-15
Used Hours: 105056
Project Name: Bioinformatic and Computational Biology analyses of organisms
Project Shortname: CBBI1124
Discipline Name: Bioinformatics
The CHPC research programme "Bioinformatic and Computational Biology analyses of organism" is a collection of researchers and students with the Principal Investigator based at the University of Pretoria. This programme uses bioinformatics and computational biology applications to analyse and interpret high-throughput next-generation sequencing data from a diverse range of environments and organisms. The programme is further focused on the development of human capapcity and training of students. The increase in production of large and complex biological data sets requires increased training and skills development to keep up. The CHPC allows this reseacrh programme the ability to train and mentor students and researchers in the field of bioinformatics and computational biology. In essence, the CHPC has become our teaching black board. Thank you CHPC!
Principal Investigator: Prof Oleg Reva
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2023-08-16
Allocation End: 2024-02-16
Used Hours: 6355
Project Name: Modeling the cytotoxicity of new anti-cancer antibiotics by molecular docking
Project Shortname: CBBI1037
Discipline Name: Bioinformatics
The research conducted on the international project titled "Target Identification and Efficacy Enhancement of Proven MDR Overcoming Piper spp Derived Compounds Towards Candidate Drug Development Against WHO Priority 1 (Critical) MDR Pathogens: P. aeruginosa, E.coli, K. pneumoniae, and M. tuberculosis" was facilitated by the use of CHPC (Centre for High Performance Computing) resources. This project, funded by BRICS, leveraged CHPC's software tools to simulate the molecular interactions between newly discovered natural compounds and the target molecules found in pathogenic bacteria. Additionally, the analysis of whole genome sequences, generated by Nanopore sequencers, was accelerated using GPUs provided at CHPC. The findings from this study are slated for publication in peer-reviewed scientific journals.
Principal Investigator: Mr Jean Pitot
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2023-08-17
Allocation End: 2024-02-16
Used Hours: 15523
Project Name: SAFFIRE Programme
Project Shortname: MECH1121
Discipline Name: Computational Mechanics
The University of KwaZulu-Natal's Aerospace Systems Research Institute (ASRI) 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, ASRI 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 realisation 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 2024 has seen the intake of numerous new postgraduate and undergraduate students. In total, 19 postgraduate students are currently involved in ASRI's cutting-edge projects.
Principal Investigator: Dr Thokozani Justin Kunene
Institution Name: University of Johannesburg
Active Member Count: 1
Allocation Start: 2023-08-17
Allocation End: 2024-02-29
Used Hours: 30705
Project Name: TurboMagFluids
Project Shortname: MECH1573
Discipline Name: Applied and Computational Mathematics
Our research group is comprised of postgraduate students with a keen interest in numerical studies. The students are from the University of Johannesburg's Mechanical & Industrial Engineering department. We have recently collaborated on research on numerical simulations with the Geology and Applied Mathematics departments. The group is called TurboMagFluids. It aims to provide valuable and practical knowledge that will influence design parameters for rotary groups of machines and flow behaviour. The influence of fluid behaviour on performances is our crucial area of research, phenomenally so. It also includes niche areas of Fluid-Structure-Interactions (FSI), Magnetohydrodynamics flows (MHD), Rheology, Multiphase flows and Nanofluids where any machine parts are affected by these segments of fluid mechanics. The computing ability to numerically solve problems in our field of research is made possible with CHPC through its cyber infrastructures. Our research progresses suitably because of the computing power that CHPC provides.
Principal Investigator: Prof Liliana Mammino
Institution Name: University of Venda
Active Member Count: 4
Allocation Start: 2023-08-18
Allocation End: 2023-09-06
Used Hours: 5060
Project Name: computational study of biologically active molecules of natural origin
Project Shortname: CHEM0959
Discipline Name: Chemistry
WHO WE ARE
A professor and postgraduate students at the University of Venda.
THE NATURE OF OUR RESEARCH
We study biologically active molecules of natural origin computationally.
Biologically active molecules are molecules that can cause some effects in the organism. We study molecules whose effects can help in the treatment or prevention of diseases.
We choose molecules of natural origin because their effects are already known from traditional medicine; therefore, they are ideal for the development of more powerful drugs.
WHY IT IS INTERESTING TO STUDY MOLECULES COMPUTATIONALLY
The biological activity of a substance depends on the properties of its molecules. Computational studies enable us to know the properties of a molecule. Knowing them helps understand how they relate to the molecule's activity.
For instance, we can study a certain number of molecules having anticancer activity and compare their properties. Then we can study how each of them can attach itself into a certain area (active site) of a protein that is important for a cancer to grow, and block its function; we can compare the ways and strength with which each molecule interacts with that protein and know which ones are more effective.
HOW MOLECULES ARE STUDIED COMPUTATIONALLY
The calculation of the properties of molecules is very demanding in terms of computer power. Performing calculations on normal computers would require enormous amounts of time, and the most demanding ones would not manage to complete. Using the CHPC enables us to obtain results in a reasonable time, and to perform also the most demanding ones; it is therefore essential for us to conduct our research effectively.
HOW THE PROJECT IS PROGRESSING
We are currently studying molecules with antimalarial, anticancer and antioxidant properties. We have already published some of our results, and we are in the process of obtaining new ones.
Principal Investigator: Dr Shama Khan
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2023-08-18
Allocation End: 2024-02-16
Used Hours: 4553
Project Name: Bioinformatics and Drug Discovery
Project Shortname: CBBI1612
Discipline Name: Bioinformatics
My research group is based at Chris Hani Baragwanath Hospital, Soweto, Gauteng with Vaccines and Infectious Diseases Analytics (VIDA) research unit. We are working on bacterial infections specifically on ESKAPE pathogens leading to neonatal sepsis. We are using to CHPC to analyze the protein drug interaction networks.
Principal Investigator: Dr Adeola Rotimi
Institution Name: Agricultural Research Council
Active Member Count: 0
Allocation Start: 2023-08-18
Allocation End: 2024-02-16
Used Hours: 4577
Project Name: Genomic data Analysis
Project Shortname: CBBI1611
Discipline Name: Bioinformatics
The mandate of the ARC's Biotechnology Platform (BTP) is to develop and implement high-throughput resources and technologies required for applications in genomics, metagenomics, next generation sequencing-based diagnostics, quantitative genetics, genomics assisted selection in breeding, plant phenomics and bioinformatics to participants in the agricultural sector – from small smallholder and commercial producers, to seed companies, food processing facilities and universities working in these and associated fields. Established to conduct both research and provide services, the BTP is an environment in which highly skilled researchers and postgraduate students can be hosted and trained to undertake world-class research paralleled with the provision of genomics and bioinformatics services to agriculture and other sectors.
Hence, with the help of CHPC service for Bioinformatics Data analysis ARC-BTP reports to the following outcomes:
Enhanced resilience of Agriculture
A skilled and capable Agriculture Sector
Building Genomics and Bioinformatics capacity
Principal Investigator: Prof George Amolo
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 15
Allocation Start: 2023-08-18
Allocation End: 2024-03-07
Used Hours: 1291810
Project Name: Properties of Materials for Green Energy Harnessing
Project Shortname: MATS862
Discipline Name: Material Science
MATS862 is largely a Kenyan group based at the Technical University of Kenya (TU-K), Nairobi. In TU-K we have the PI, early career PhDs (2 male and 2 female) and postgraduate students (3 female and 3 male).
While other members are based in Kenya, 2 early PhD careers who are also collaborators are based in Central Africa.
Our work involves simulations that support experimental work in the areas of energy materials, hard materials, properties of materials in the core of the earth. In situations where experimental work does not exist, carefully performed simulation predictions can be used as useful guide for decision support in the development of new materials. In the last 2 years, our work has embraced Artificial Intelligence (AI) in the form of Machine Learning (ML).
Our country lacks capacity in critical areas such as energy harvesting, energy materials and technology development at large which would reduce dependence on products and services from other continents as well as create local employment. Postgraduate students and early PhD staff who form the largest members are part of the next generation of researchers, which guarantees continuity.
To perform simulations, details of the structure of the materials must be known and provided as an input to the computer code being used. The simulations are then run and the output data collected subjected to analysis as well as interpretation. Some calculations can run for weeks or are large making it necessary that the compute nodes are in a data centre that functions 24/7, with sufficient storage and computing power thus the need for the CHPC.
MATS862 continues to make good progress and is now attracting attachees supported by the Kenya Education Network (KENET) as well as postdoctoral students from within the African continent.
Principal Investigator: Mr Ernest Opoku
Institution Name: Nesvard Institute of Molecular Sciences, Ghana
Active Member Count: 13
Allocation Start: 2023-08-21
Allocation End: 2024-02-21
Used Hours: 245240
Project Name: Molecular Quantum Chemistry
Project Shortname: CHEM1352
Discipline Name: Chemistry
Nesvard Institute of Molecular Sciences is an African-focused private nonprofit research and educational institute in Ghana founded in 2019 and incorporated in 2021 under the companies Act, 2019 (Act 992). The liability of its members is limited by guarantee. Our broader objective is to propagate a new paradigm in molecular science education and research to complement the African development project.
Our vision is to advance molecular sciences in Africa through free and open world class education, training, advocacy, research, and collaboration to prepare the next generation of native African molecular scientists to solve African problems.
We aim to provide fundamental requisite skills that are less common to obtain from traditional educational institutions in Africa to complement further education. We collaborate with laboratory researchers in industry, nonprofit, government, or academic laboratories across Africa and beyond.
And even more than that, our goal has been to teach, mentor and collaborate with younger, but also more experienced native African scientists, on how to set up and perform good scientific research, write good scientific articles, and give them a springboard for further education in rewarding molecular sciences disciplines in more prestigious institutions.
Research works at Nesvard Institute of Molecular Sciences focus on wide area of molecular sciences. We employ techniques of basic and advanced theoretical and computational chemistry and molecular modeling such as (but not limited to) elementary and advanced Hartree-Fock theory, electron correlation methods, density functional theory (DFT), models and concepts of chemistry, linear algebra, symmetry, and group theory, classical and statistical thermodynamics to study molecular properties and associated features.
Through CHPC generous computational time and resources, multiple research projects are completed with several currenting ongoing.
Principal Investigator: Prof Monde Ntwasa
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2023-08-21
Allocation End: 2024-02-21
Used Hours: 1681
Project Name: Anti-Cancer Drug Discovery
Project Shortname: HEAL1237
Discipline Name: Health Sciences
UNISA Biotechnology Department Develops Promising Anti-Cancer Compounds with CHPC Support
The Biotechnology Department at the University of South Africa (UNISA), particularly its Anticancer Research Group, is making significant strides in the development of innovative anti-cancer compounds. This groundbreaking research aims to combat the increasing prevalence of cancer, a disease that continues to affect millions worldwide.
Cancer remains one of the leading causes of mortality globally, necessitating the development of more effective treatments. The research conducted by our team focuses on creating compounds that can potentially offer new therapeutic options for cancer patients. By leveraging advanced computational techniques, we aim to identify and optimize compounds that can inhibit cancer growth more effectively than existing treatments.
Our research heavily relies on the computational resources provided by the Centre for High-Performance Computing (CHPC). The development of anti-cancer compounds involves complex molecular simulations and data analyses, which require substantial computational power. CHPC's high-speed computing capabilities enable us to perform these simulations more efficiently and accurately, accelerating the pace of our discoveries.
The project is progressing exceptionally well. Our team has identified several lead compounds that have shown promising results in preliminary tests. These compounds are now undergoing further evaluation in wet lab settings to confirm their efficacy and safety. This phase of testing is crucial as it will determine the potential of these compounds to move forward into clinical development.
The support from CHPC has been instrumental in our research, allowing us to harness cutting-edge technology to address one of the most pressing health challenges of our time. The successful development of new anti-cancer treatments not only holds the promise of saving lives but also underscores the importance of continued investment in high-performance computing for scientific research.
Principal Investigator: Prof Lyudmila Moskaleva
Institution Name: University of the Free State
Active Member Count: 13
Allocation Start: 2023-08-18
Allocation End: 2024-03-06
Used Hours: 409485
Project Name: Understanding surface reactivity of solids using DFT simulations
Project Shortname: CHEM1294
Discipline Name: Chemistry
The group of Prof Moskaleva at the University of the Free State investigates 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, can be used successfully to achieve a mechanistic understanding of reactivity at the microscopic level, which is required to optimize functional materials (such as catalysts, electrocatalysts, semiconductors, optoelectronic materials) with respect to their target properties. We are thankful to the CHPC for providing state-of-the-art computational facilities which enable us to use computational chemistry software and run challenging computations of molecular and crystalline systems.
We would like to highlight three of our successful subprojects. One of them is a computational study on the chemistry of nanoporous gold, a versatile material possessing interesting mechanical, optical, and catalytic properties. Recently, we contributed to a comprehensive review on the topic (Wittstock et al. Chem. Rev., 2023, 123, 6716-6792, DOI: 10.1021/acs.chemrev.2c00751). Our study is focused on the remarkable low-temperature catalytic activity of np-Au and its high selectivity toward partial oxidation reactions. CO and methanol oxidation have been studied as a model. A dynamic behavior of the catalytic surface (including the diffusion and restructuring processes) has been studied with the help of ab initio molecular dynamics simulations. The calculations are very computationally expensive and possible only through the use of HPC resources.
In another subproject funded by NRF, we investigate the hydrocarbon combustion chemical reactions using density functional theory (DFT) and high-level ab initio quantum chemistry methods. The objectives of this study are to determine valuable information such as geometric, thermodynamic, and kinetic properties of some of the important elementary combustion reactions. The outcomes of this study have been recently published, Kandpal et al., Phys. Chem. Chem. Phys. (2023) 25, 27302–27320, and further research is underway.
In a third subproject, computationally investigated a series of luminescent binuclear Au-Au complexes featuring N-substituted PNP ligands. By employing time-dependent density functional theory (TDDFT), we computed the absorption and emission spectra of these complexes. Our calculations provided valuable insights for interpreting the experimental results, particularly highlighting the phosphorescent nature of the emission and explaining the differences in emission wavelengths observed among complexes with varying counterions.
Principal Investigator: Dr Moses Okpeku
Institution Name: University of KwaZulu-Natal
Active Member Count: 8
Allocation Start: 2023-08-21
Allocation End: 2024-02-21
Used Hours: 27527
Project Name: Genomics and Bioinformatics Group Westville Campus
Project Shortname: CBBI1185
Discipline Name: Bioinformatics
The Genomics and Bioinformatics Group is based in the Discipline of Genetics, University of KwaZulu-Natal, Westville.
The Group is working on creating Malaria vaccine using molecular genetic approach.
Malaria is a serious infectious disease endemic to most parts of Africa, Asia, and South America, it is a vector-borne disease responsible for the death of thousands annually. Efforts of the South African Government have resulted in the rollback of the disease from 6 of the 9 provinces of South Africa and the disease is still endemic in 3 major provinces in South Africa. Current approaches for malaria treatment have evolved into drug resistance in both parasite and host. An effective way of eradicating infectious disease is vaccination, however, available synthetic vaccines are ineffective, We are working on a genetic-based vaccine. The process of vaccine development that is both time and cost-effective is to develop model proteins and simulate the reaction of the protein in humans using predictive tools. These predictive tools are either too expensive for the group to purchase or not available to small groups like ours. We depend HEAVILY on the CHPC for access to these tools which are very paramount to the success of our research.
Principal Investigator: Prof Scott Hazelhurst
Institution Name: University of the Witwatersrand
Active Member Count: 6
Allocation Start: 2023-05-22
Allocation End: 2024-01-23
Used Hours: 3663
Project Name: Bioinformatics and Experimental Algorithms (BEAT)
Project Shortname: CBBI0930
Discipline Name: Bioinformatics
Molecular dynamics
A key part of our work is understanding how mutations in key pharmacogenes affect the functioning of the genes, which are responsible of the way in which important drugs are metabolised. Understanding the impact of these variations found in African populations is important for building a database informing drug safety and efficacy in African populations.
One strand of work has been directly to model how mutations affect the dynamic stability of important genes. A second
proposes including a machine learning model to predict how missense variants would potentially impact the interaction between enzymes and their ligands.
Principal Investigator: Dr Marilize Everts
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2023-08-21
Allocation End: 2024-05-17
Used Hours: 43514
Project Name: Fundamentals of single-phase and multi-phase flow
Project Shortname: MECH1574
Discipline Name: Applied and Computational Mathematics
Accurate design information and correlations are key to optimise the heat exchangers. Extensive research has been done on single-phase flow through tubes heated with a constant heat flux, but gaps in literature exist when it comes to tubes with a constant surface temperature along the length or non-circular channels. Therefore, the purpose of this project is to numerically investigate the heat transfer characteristics of flow through single tubes with different cross-sections and exposed to different boundary conditions.
The research is conducted by postgraduate (Honours and Masters) students and academics at the University of Pretoria. Ansys Fluent is used and the numerical simulations are performed on the CHPC.
The project is progressing well and it is expected to produce two journal papers by the end of 2024. One conference paper will be presented in June.
Principal Investigator: Dr Thishana Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2023-08-25
Allocation End: 2024-05-09
Used Hours: 154311
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) currently, uses computational chemistry as a tool in the field of Green Chemistry to compare the chemical reactivity properties of bioactive molecules for drug delivery. Conceptual DFT which is often referred to as 'computational nutraceutics' is a concept used to predict the molecular structure, spectroscopy, and chemical reactivity of nutraceuticals (food or part of a food that provides medical/health benefits, including the prevention/treatment of diseases) 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.
Principal Investigator: Dr Njabulo Siyakatshana
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 23
Allocation Start: 2023-08-25
Allocation End: 2024-02-22
Used Hours: 253990
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 have been instrumental in informing climate reporting to the UNFCCC, as well as applications for climate adaptation in climate-change impacted industries such as agriculture and logistics as well as for policy-making
Principal Investigator: Prof Robinson Musembi
Institution Name: University of Nairobi
Active Member Count: 11
Allocation Start: 2023-08-28
Allocation End: 2024-03-07
Used Hours: 198923
Project Name: CMCG-UoN
Project Shortname: MATS1321
Discipline Name: Material Science
The Monolith Research group is the computational materials research group based at the Department of Physics University of Nairobi. The group is led by Prof Robinson Musembi as the PI and currently, 5 PhD students and 2 continuing master of science students. In 2023, 4 master's students graduated. Most of the work being done by the group members is mainly to study semiconductor materials. Semiconductors are materials which are to be used in making devices like solar cells, light emitting diodes (light emitting diodes produce light when an electrical current passes through them, they light like a bulb but the only difference is that they are solid material), gas sensors (gas sensors are materials which can sense the presence of gas and they are used in places like industries to detect flammable or harmful gases or give alert on gas leak), etc. Semiconductors are one of the most useful materials used in consumer electronic industries since the main useful components are manufactured using these materials. Apart from semiconductor materials, the group also works on drug discovery methods. Some of the work being done on drug discovery is on prion diseases, also known as transmissible spongiform encephalopathies (TSEs), which are a family of rare progressive neurodegenerative disorders that affect both humans and animals.
The CHPC compute facility is an important equipment to the research group without which our research group wouldn't have been able to do the work the group has been able to accomplish so far. The research group currently is using software installed at the facility including Quantum Espresso, GROMMACS, and Python. Other software of interest to the group are LAMMPS and ORCA, this will enable the research group members to tackle different kinds of problems using different types of software.
Principal Investigator: Dr Samuel Atarah
Institution Name: University of Ghana
Active Member Count: 2
Allocation Start: 2023-08-28
Allocation End: 2024-04-22
Used Hours: 122907
Project Name: Ab initio studies of electronic and magnetic properties of selected elements
Project Shortname: MATS1162
Discipline Name: Physics
We are part of the Condensed Matter Physics group in the Department of Physics at the University of Ghana. Our current research effort is to study material with semiconductor properties; focusing on their observed electrical properties energy band gaps, phonon dispersion properties and physical stability . Research in active material such as semiconductors is important because of their applications in science and technology.
A typical process involves setting up a basic unit cell or super structure of the known (experimental) structure; making a self consistent quantum mechanical calculation of its minimum total energy. The minimum total energy hold a lot of information on the properties of the solid material and enables detailed computational charaterization of such. These computations have often benefited the use of the CHPC. The suitability of double perovskite material for photovoltaic applications was the focus of our work during the period. Phonon dispersion studies on double perovskites require massive computing resources and the the support of the CHPC computing facility remains invaluable to our work.
Principal Investigator: Prof Malik Maaza
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2023-08-28
Allocation End: 2024-04-18
Used Hours: 385017
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.
Principal Investigator: Prof Mpho Sithole
Institution Name: Sefaku Makgatho Health Sciences University
Active Member Count: 10
Allocation Start: 2023-08-29
Allocation End: 2024-02-29
Used Hours: 7411
Project Name: Computational modeling of titanium based alloys
Project Shortname: MATS1228
Discipline Name: Physics
The material modeling research group is based at Sefako Makgatho Health Sciences University. The research focus areas are: Titanium and Titanium alloys; Shape memory alloys; Permanent magnets, and the interfaces of materials. The alloys are important for biomedical applications. The permanent magnets are used in recent technologies. The properties of the materials are calculated by employing the first principle method. Therefore, the CHPC facilities are used for calculating large data. A number of students have shown an interest in this research field, so far, we have registered 2 Hons, 6 MSc and 1 PhD students. The group is collaborating with two departments at CSIR Pretoria.
Principal Investigator: Ms Larysha Rothmann
Institution Name: 0 Other
Active Member Count: 1
Allocation Start: 2023-08-30
Allocation End: 2024-02-28
Used Hours: 55022
Project Name: CenGen
Project Shortname: CBBI1615
Discipline Name: Bioinformatics
CenGen (Central Genetics) is a plant and pathogen R&D lab in Worcester, that services the agricultural plant breeding industry and supports collaborative crop and plant research projects. CenGen has partnered DIPLOMICS, a distributed OMICS research infrastructure programme, to take on the de novo sequencing and assembly of the indigenous and environmentally significant "Spekboom" or Portulacaria afra plant species.
This is a challenging assembly since we have no established genomic resources of a closely related reference species. Also, the ploidy (multiple copies of the genome) and highly repetitive nature of plant DNA further complicates the "piecing together of the puzzle pieces" i.e. the strings of DNA that come off a sequencing machine in the form of many, many text files. To give you an idea – the raw DNA sequence data for one genome can add up to 1TB.
However, we can tackle these challenges due to the rapidly improving technology at our disposal – the first being Oxford Nanopore Technology long reads, which have become accessible through their affordability – and make it possible to generate "strings of DNA" that are longer than we've ever been able to sequence, at a remarkably accurate standard. The second is that we can work with this scale data through the national initiative of the CHPC (Centre for High Performance Computing), which we've come to depend on for the computing power to run our analysis. In addition, it has provided the platform and environmental set-up that enables us to establish an automated pipeline, for increased scale, reproducibility, and efficiency for any future assemblies.
To date, we have generated a high-quality draft genome assembly and developed our pipeline. We have also benchmarked the effect of assembly polishing with high-quality short reads such as MGI and Illumina. We plan to refine these methods and our assembly in the coming months and add additional data to "fill in the gaps". This would be the first genomic resource of its kind for an important South African plant – laying the genomic foundation for further work on this species biodiversity, environmentally significant genetics, and genome structure.
Principal Investigator: Dr Ndanduleni Lethole
Institution Name: University of Fort Hare
Active Member Count: 4
Allocation Start: 2023-08-31
Allocation End: 2024-02-29
Used Hours: 264511
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, situated within the Department of Physics at the University of Fort Hare, was established in February 2020 and consists of the Principal Investigator and three MSc students. Currently, the group relies solely on the Centre of High Performance Computing (CHPC) facility for access to the Material Studio modeling and simulation environment. The group's objective is to expand to a minimum of five students by 2024 and obtain a license for the Vienna ab initio simulation package.
The group is currently engaged in two research projects: (1) Computer simulation studies on M-Pt (M: Mn, Fe, Co, and Ni) alloys for potential applications in advanced performance permanent magnets, ultra-high-density magnetic data storage, and biomedical applications; (2) Exploration of new Calcium-ion (Ca), Magnesium-ion (Mg), and Zinc-ion (Zn) Battery Cathode Materials. The first project is particularly significant due to the increasing data storage density of magnetic disk drives, which is anticipated to be limited by the "super-paramagnetic limit" in the near future. Overcoming this limit requires the development of new magnetic storage materials that are energetically, electronically, magnetically, mechanically, and dynamically stable. The second project is crucial as Multivalent (MV) battery chemistries offer greater potential for future battery storage applications. Multivalent ion insertion/extraction involves double/triple electron transfer per ion in the intercalation reaction, resulting in higher specific energy density and volumetric power compared to monovalent ions.
Thanks to the advanced simulation packages and ample computing resources available at the CHPC, the group can investigate various properties of crystal structures by theoretically calculating the forces acting on the nuclei. These simulations are essential for advancing our understanding of materials and their potential applications in various fields. Simulations are set up on the local computer using the BIOVIA Materials Studio modeling and simulation environment and submitted to the CHPC computing resources using the CASTEP code.
Principal Investigator: Prof Craig Law
Institution Name: University of the Witwatersrand
Active Member Count: 4
Allocation Start: 2023-08-31
Allocation End: 2024-02-29
Used Hours: 11660
Project Name: Aerothermodynamics with vortices, vorticity and shear
Project Shortname: MECH1532
Discipline Name: Other
The Aerothermodynamics research programme at the University of the Wtiwatersrand is headed by Prof. Craig Law. He and his team investigate the flow of fluids. This can include topics as diverse as understanding why an owl is so efficient in flight or an investigation of the shape of a Hydrogen-Oxygen combustor nozzle for a rocket engine. Recent work on understand the flow field of a rocket aerospike engine nozzle has explored fluid injection at the wall
which can change the direction of the jet exiting the nozzle. We are using rocket engine combustors and nozzles to learn how to better model the combustion of hydrogen accurately and in the process learning to build better rocket engines. The lessons learned hear can be used to investigate how best to use hydrogen combustion in future power, industial and aerospace applications. This knowledge will be critical as we seek alternatives to fossil fuels and need to better understand the viability of hydrogen as a means to store energy.
The use of numerical models allows for a fairly cost effective and safe means to explore the effect of combustor and nozzle geometries on the flow fields. This can reduce the overall number of experiements required to demonstrate a concept and allows for these experiments to be done without the risk of building a rocket engine and test cell. The flow fields that are being investigated are typically constantly changing with time and require a lot of computing resources to model successfully. The CHPC is an invaluable partner in providing the computational support that makes the numerical aspects of these investigations possible.
Principal Investigator: Prof Catharine Esterhuysen
Institution Name: Stellenbosch University
Active Member Count: 12
Allocation Start: 2023-09-01
Allocation End: 2024-03-12
Used Hours: 35299
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 major focus area is the uptake of molecules by porous compounds, since the manner in which such species interact has an influence on their behaviour. Calculations performed using the CHPC's computational facility have allowed us to explain the role that intermolecular interactions play in the 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 beneficiation of CO2.
Principal Investigator: Dr Samuel Egieyeh
Institution Name: University of Western Cape
Active Member Count: 8
Allocation Start: 2023-09-04
Allocation End: 2024-03-04
Used Hours: 34788
Project Name: Computational (Cheminformatic and Bioinformatic) Drug Discovery, Design and Development for Infectious Diseases
Project Shortname: CBBI1212
Discipline Name: Health Sciences
Our research focuses on computational drug discovery and design, analysis and interpretation of chemical and bioactivity data using Cheminformatics, Bioinformatics, Machine Learning and Biostatistics techniques in conjunction with relevant in-vitro bioassays in order to discover, design and develop novel drug candidates, especially from natural products, for infectious diseases.
Principal Investigator: Dr Hezekiel Kumalo
Institution Name: University of KwaZulu-Natal
Active Member Count: 21
Allocation Start: 2023-09-04
Allocation End: 2024-03-05
Used Hours: 15881
Project Name: Molecular modeling and computer aided drug design
Project Shortname: HEAL1009
Discipline Name: Health Sciences
Our research group, situated at the UKZN Durban Medical School campus and closely affiliated with the University of KwaZulu-Natal in South Africa, is deeply immersed in the intricate realm of biological systems within the domain of drug design. Employing computational and molecular modelling as our guiding compass, we embark on a journey of scientific inquiry with a primary mission: to meticulously design and thoroughly investigate targets with profound biological and therapeutic implications. Our endeavours delve into the complexities of chemical and biochemical reactivity, focusing on key aspects such as the transition state, environmental influences on reactions, catalysis origins, and kinetic isotope effects. Within the realm of enzymatic responses, our research explores mechanistic pathways, transition states, and the development of enzyme inhibitors. Additionally, we scrutinise the intricacies of evolved targets' binding and catalytic properties. Central to our methodology is advanced computational techniques, including Quantum Mechanics/Molecular Mechanics (QM/MM) MD simulations, Quantitative Structure-Activity Relationship (QSAR) analyses, and bioinformatics tools. These methodologies deepen our understanding of molecular interactions, dynamic behaviours, and binding free energy calculations. Beyond academia, our efforts extend to nurturing pharmaceutical scientists with specialised skills, preparing them to navigate seamlessly through the pharmaceutical industry and academia, thereby bolstering the local pharmaceutical landscape. Despite fiscal challenges often faced by emerging research groups, our partnership with the Centre for High-Performance Computing (HPC) propels our progress, providing invaluable resources to formulate and scrutinise hypotheses and elucidate complex experimental data rapidly. Our research group is committed to pursuing scientific enlightenment, training future pharmaceutical scientists, and advancing South Africa's pharmaceutical industry. While specific project progress details remain undisclosed, our unwavering dedication to these objectives underscores our academic commitment and work's significance in driving scientific understanding and innovation.
Principal Investigator: Prof Mahmoud Ibrahim
Institution Name: University of KwaZulu-Natal
Active Member Count: 14
Allocation Start: 2023-09-04
Allocation End: 2024-03-05
Used Hours: 917476
Project Name: Computer-Aided Drug Discovery
Project Shortname: CHEM1607
Discipline Name: Chemistry
The current project is managed and directed by Mahmoud Ibrahim, from the School of Health Sciences. The project focuses on the discovery of potent hits for the treatment of viral infections. Several sub-groups with different research interests work together, including computational chemistry, quantum chemistry, and medicinal chemistry. Such a project has a global and local impact. Public resources are needed to accomplish the defined goals. The project's pipeline starts from target definition and validation and ends with large-scale molecular dynamics of the hit-target complex. CHPC offered the PI's group all the required computational resources to achieve the project's goals. The afforded facilities included CPU and GPU resources. In addition, CHPC offered technical support during the project's life-time.
Principal Investigator: Prof Liliana Mammino
Institution Name: University of Venda
Active Member Count: 4
Allocation Start: 2023-09-05
Allocation End: 2024-03-06
Used Hours: 190323
Project Name: computational study of biologically active molecules of natural origin
Project Shortname: CHEM0959
Discipline Name: Chemistry
WHO WE ARE
A professor and postgraduate students at the University of Venda.
THE NATURE OF OUR RESEARCH
We use computational methods to study biologically active molecules of natural origin, selecting molecules that were isolated from plants used in traditional medicine, for the treatment or prevention of diseases.
We choose these molecules because their effects are already known from traditional medicine; therefore, they are ideal for the development of more powerful drugs.
WHY IT IS INTERESTING TO STUDY MOLECULES COMPUTATIONALLY
The biological activity of a substance depends on the properties of its molecules. Computational studies enable us to know the properties of a molecule. Knowing them enables better understanding of the molecule's activity.
For instance, we can study a certain number of molecules having anticancer activity and compare their properties. Then we can study how each of them can attach itself into a certain area (active site) of a protein that is important for a cancer to grow, and block the function of that protein. We can also compare the ways and strength with which each molecule interacts with that protein and know which ones are more effective.
HOW MOLECULES ARE STUDIED COMPUTATIONALLY
The calculation of the properties of molecules is very demanding in terms of computer power. Performing calculations on normal computers would require enormous amounts of time, and the most demanding ones would not manage to complete. Using the CHPC enables us to obtain results in a reasonable time, and to perform also the most demanding ones. Using the CHPC is therefore essential for us to conduct our research effectively.
HOW THE PROJECT IS PROGRESSING
We are currently studying molecules with antimalarial, anticancer and antioxidant properties. We have published some recent results, and we are in the process of obtaining new ones.
Principal Investigator: Prof Zander Myburg
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2023-09-05
Allocation End: 2024-03-27
Used Hours: 6047
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. The group has successfully used systems genetics approaches in interspecific hybrid populations of Eucalyptus grandis x E. urophylla to map key genomic regions affecting gene expression and metabolic profiles associated with growth and wood chemistry traits. Over the past five years, the FMG Programme has successfully used single nucleotide polymorphism (SNP) chip technology to genotype thousands of Eucalyptus and pine trees. These SNP chips 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, the FMG Programme has obtained funding from the US-Dept of Energy to sequence the genomes of over 2000 E. grandis trees to study woody biomass formation, carbon drawdown and genotype by environment interactions. This capacity is already being extended to genera such as Acacia, Macadamia and pine. The programme has strong collaborations with the Bioinformatics and Computational Biology Centre at the University of Pretoria (Prof Fourie Joubert) where they have access to a few servers and a cluster. They are also collaborating with Prof Jill Wegrzyn at the University of Connecticut, and have access to the cluster at UConn. Emerging work in the Programme will rely on high-throughput processing of DNA sequence data and applying machine learning towards genomic prediction of breeding values in trees.
Principal Investigator: Prof Charalampos (Haris) Skokos
Institution Name: University of Cape Town
Active Member Count: 10
Allocation Start: 2023-09-05
Allocation End: 2024-03-05
Used Hours: 185485
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 Patricia Swart
Institution Name: 0 Other
Active Member Count: 7
Allocation Start: 2023-09-05
Allocation End: 2024-03-05
Used Hours: 38250
Project Name: DIPLOMICS_CLARITY
Project Shortname: CBBI1617
Discipline Name: Bioinformatics
CLARITY is a bioinformatics marketplace made possible by DIPLMICS, a research infrastructure program funded by the Department of Science and Innovation. CLARITY emphasizes the skills and value of bioinformaticians by providing access to expert bioinformatic consultants in genomics, proteomics and metabolomics, who can guide project design, conduct data analysis on large data and interpret the results. The team determines the project's bioinformatics requirements and develops a solution package/ The CHPC provides the computational resources needed to analyse these large-omic datasets. Currently, CLARITY are analysing human whole genome sequencing data to explore the benefits of Oxford Nanopore long-read sequencing. The results of this analysis will likely positively impact the genomics landscape in South Africa. In addition, CLARITY are assisting several South African researchers in understanding and interpreting their data and has provided part-time job opportunities to four local bioinformaticians. This will lead to degrees, publications and career-development.
Principal Investigator: Dr James Sifuna
Institution Name: The Catholic University of Eastern Africa, Nairobi, Kenya
Active Member Count: 8
Allocation Start: 2023-09-05
Allocation End: 2024-03-21
Used Hours: 450823
Project Name: Ab initio study on novel materials for novel functionalities.
Project Shortname: MATS1424
Discipline Name: Material Science
The Theoretical Condensed Matter Group at the Catholic University of Eastern Africa comprises two leaders and a few students who share common interests in material discovery. Currently, I lead the group, and our rapport with each member has been excellent.
Recently, we had the pleasure of hosting a team from CHPC in Nairobi, and the experience of sharing ideas with them was fantastic.
Our research group is highly focused on exploring novel materials as alternatives to traditional fossil fuels, including solar, wind, and hydroelectric power. We utilize Density Functional Theory (DFT) implemented in SIESTA and Quantum ESPRESSO codes for our calculations.
CHPC plays a crucial role by providing computing facilities that surpass what we have at our university. Given our focus on studying large systems, which require significant CPU hours to converge, CHPC's support is invaluable.
Currently, we have achieved nearly half of our set objectives, and we are grateful to CHPC and its technical team for their assistance.
Regarding conference presentations or other outputs, tWe have a paper accepted and I will definitely share with you once out next week. Now, regarding conferences, we will be hosting an East-African School on DFT that is fully funded. See link https://siesta-project.org/siesta/events/EA_School_DFT-2024/
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 14
Allocation Start: 2023-09-05
Allocation End: 2024-03-21
Used Hours: 4317291
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 Dr. Raji (UNISA, South Africa) and the group of Dr. Brice Malonda (Marien Ngouabi University, DRC). 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) to investigate these materials. We aim to modify the pristine properties of selected solids through defect engineering, materials heterostructures, alloying and interface engineering.
The last two decades have witnessed efforts at discovering materials with novel properties for specific applications such as in electronic and magnetic devices. The discovery of new materials are sometimes accompanied by previously unknown physical, chemical or electronic processes which necessitate the use of advanced theoretical approaches. One of the aims of our research therefore, is to discover novel materials via computational methods and to exploit the unique properties of these materials for potential technological applications. Ultimately, our research is theory-led discovery of novel materials underpinned by DFT and similar first-principles method. The numerical implementation of the latter is computational intensive, requiring several computational hours, large data storage and memory requirements, beyond the capacity of ordinary table-top computers. Therefore, 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 10 postgraduate students of various nationalities working in various aspects of the project.
This research has enabled collaboration between South Africa based academic researchers and colleagues in Congo, Germany, Mexico and Italy. The scope of the project will guarantee regular postgraduate students training who are able to undertake cutting-edge research and contribute to scientific development of South Africa and the rest of Africa continent. Also, the research aim to continuously produce high-impact research publications.
Principal Investigator: Dr Leigh Johnson
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2023-09-05
Allocation End: 2024-03-05
Used Hours: 35861
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 impact of different HIV programmes on trends in HIV incidence.
Principal Investigator: Mr Adebayo Azeez Adeniyi
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2023-09-06
Allocation End: 2024-03-06
Used Hours: 99938
Project Name: Drug Discovery Research Using Quantum and Molecular Dynamic Simulation
Project Shortname: CHEM0958
Discipline Name: Chemistry
The CHPC stands as an integral component of our research, providing indispensable facilities that render our work more feasible. The availability of CHPC resources significantly influences the progress of our research, and its utilization has proven instrumental in achieving impactful results and enhancing overall productivity.
Since the submission of the last report in September 2023, we have published three additional articles. The CHPC facilities have empowered us to broaden our research scope, encompassing machine learning, deep neural networks, vaccine development, photochemistry, and polymer chemistry. This expansion complements our existing focus on drug development and the electrochemical properties of small molecules.
Our reliance on CHPC resources extends to various packages for Bioinformatics, Quantum computing, and Molecular Dynamic Simulation. The diverse range of tools available has facilitated our exploration into epitopes-based vaccine development, polymer chemistry, photochemistry for photoactive compound applications, and molecular electrochemistry. The decision to diversify our research focus stems from a recognition of societal needs and global challenges.
Theoretical modeling is a cornerstone of our research methodology, offering rational insights into identified problems and aiding in the design of experimental solutions. The CHPC plays a pivotal role in supporting our research group, and we regularly utilize software such as Gaussian, Orca, Games, and Newchem. Additionally, molecular dynamics packages like Gromacs, Amber, and Lammps contribute to our simulations. Quantum packages have been applied to study the chemical and spectroscopic properties of small molecules, allowing us to reproduce experimental results.
It is evident that the progress and achievements of our research are intricately tied to the invaluable support provided by CHPC. Without the resources and assistance from CHPC, much of our research output would not have been possible.
Principal Investigator: Dr Ruben Cloete
Institution Name: University of Western Cape
Active Member Count: 9
Allocation Start: 2023-09-06
Allocation End: 2024-03-05
Used Hours: 493261
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 possibly 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 improved 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 protein structures is key. Therefore, large scale computing resources are required to run large protein systems. Currently, we received SAMRC funding to computationally investigate SARS-CoV2 coronavirus protein targets to identify drugs and purchase the compounds to test them experimentally.
Principal Investigator: Dr Edwin Mapasha
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2023-09-06
Allocation End: 2024-04-04
Used Hours: 666286
Project Name: Studies of defects in two dimensional materials such as graphene and tin disulphide for technological applications.
Project Shortname: MATS1429
Discipline Name: Physics
Institution: University of Pretoria
Research group: Theoretical and computational solid state research group
Project title: Studies of defects in two dimensional materials such as graphene and tin disulphide for technological applications.
Semiconducting silicon has been one of the primary materials used in the microelectronic industry for the past several decades. The silicon-based technology is nearing the limits of its use since current technologies require vastly scaled down devices. Because of this, there is a search for new, novel materials mainly two-dimensional materials that can meet this demand. Some of such two dimensional material are graphane and tin disulphide. The peculiar properties of graphane and tin disulphide include high quality Crystalinity, large surface area, high charge carrier mobilities and wide energy band gap to mention few. These unique properties ignited a large interest as a potential alternative to silicon and a candidate for various new technological applications. Some of the applications include the use of graphane for micro electronic devices, hydrogen storage (fuel cells) and as a lithium-ion battery anode. The aim of this project is to use the density functional theory methods implemented in the Quantum Espresso Package to optimize the electronic performance of graphane and SnS2 in order to facilitate its viable use in microelectronic applications. To efficiently produce reliable results we heavily rely on the higher performance computers.
Principal Investigator: Prof Sophie von der Heyden
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2023-09-06
Allocation End: 2024-03-06
Used Hours: 5786
Project Name: Marine genomics and conservation
Project Shortname: CBBI1038
Discipline Name: Bioinformatics
Our research utilises genomic data to inform marine conservation specifically in fisheries management. We have been conducting research on various genomic metrics in commercially important fish species such as Hake and Anchovy. For example, we look at variables such as genetic diversity, population structure and population size. We also hope to identify which environmental variables are driving genetic differences between populations and whether there are signs of adaptation to specific environmental conditions along the coastline. The genetic data generated from this work will be used in climate change modelling to look at how future environmental conditions will affect species diversity, and their distribution.
Principal Investigator: Dr Ofentse Pooe
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2023-09-06
Allocation End: 2024-03-06
Used Hours: 21771
Project Name: Computational and biochemical Characterisation of recombinant protein interactions using bioinformatics approaches
Project Shortname: CBBI0983
Discipline Name: Chemistry
Our current research interests are broadly focused on identifying and validating the interactions between small molecules and various target proteins using bioinformatics and lab-based approaches. Specifically recently our studies have focused on identifying compounds that can be potentially be used to control Plasmodium falciparum. The continued development of drug resistance of have prompted the need for discovering new and effective antimalarial compounds with an alternative mode of action. In our studies we have focussed on identifying inhibitors of selected Heat shock proteins (PfHsp90 and PfHsp70). Hsps facilitate protein folding and is a promising antimalarial drug target. Our studies have allowed us to investigate the abilities of selected compounds to bind target proteins by molecular docking and dynamics simulations. The support CHPC has granted us the platform to validate some of our drug discovery findings using computational approaches. We are now able to run molecular dynamics and virtual screening experiments much quicker. Our turnover and student training has also increased significantly. We intend on now training hons students, in order to build capacity within our students.
Principal Investigator: Dr Marc Henrion
Institution Name: Malawi Liverpool Wellcome, Blantyre
Active Member Count: 13
Allocation Start: 2023-09-07
Allocation End: 2024-03-07
Used Hours: 11555
Project Name: Malawi - Liverpool - Wellcome Clinical Research Programme
Project Shortname: CBBI1513
Discipline Name: Health Sciences
Malawi Liverpool Wellcome Programme (MLW), a clinical and epidemiological research institution based in Blantyre, Malawi, has recently been set-up to use the high performance computing resources built by the CHPC team. Prior to the CHPC system, MLW did not have access to similar computational resources.
MLW is currently making use of the CHPC system for several research projects:
1. To align RNA-seq reads for a tuberculosis drug-discovery project,
2. To perform multiple imputation of missing data in a large observational study among ART patients (the RHICCA study),
3. To evaluate different data impuation methods in the context of clustered, longitudinal count data.
The CHPC resources provides crucial infrastructure to run computationally demanding aspects of the public health research done by MLW. The aim of our research is to conduct excellent science to benefit health and to train the next generation of researchers. The CHPC systems allows us to do better science and the training required to use such resources also develops the skillsets of our researchers.
The CHPC team are also working with the Government of Malawi to deploy a smaller HPC system in Malawi and we hope that through the use of the CHPC resource, our researchers will be ready to use the Malawi system once fully set-up.
Principal Investigator: Dr Trisha Salagaram
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2023-09-07
Allocation End: 2024-03-21
Used Hours: 46844
Project Name: Computational studies of Transition Metal Dichalcogenides and Two-dimensional Materials
Project Shortname: MATS1264
Discipline Name: Physics
Researchers from the Department of Physics at the University of Cape Town and Hydrogen South Africa (HySA hosted by Northwest University and the Council for Scientific and Industrial Research) have modelled the interaction between various gas molecules and a pristine hafnium disulfide (HfS2) monolayer. Using density functional theory (DFT) simulations, conducted with the Quantum Espresso software package, the researchers studied the adsorption behavior of both toxic and non-toxic gases on the surface of HfS2.
This research is important as it sheds light on the potential applications of HfS2 in gas sensing, which is vital for addressing environmental and safety challenges. By understanding the adsorption mechanisms of different gas molecules, scientists can engineer HfS2-based materials for enhanced performance in various industrial processes.
Through the analysis of adsorption energies and other metrics, the team found that gases such as H2 and CH4 exhibited a weak, physically adsorbed state on the HfS2 monolayer, while others like CO, CO2, H2O, NH3, and SO2 did not. Their results thus far indicate that further investigations into the impact of impurities on gas adsorption in HfS2 are required to provide information on how the actual monolayer may perform in a gas sensing device.
The project is progressing steadily, with initial findings showing promise in understanding the adsorption behavior of various gas molecules on HfS2. The computational resources provided by the CHPC (Center for High-Performance Computing) have been instrumental in facilitating this research, enabling calculations and simulations to be carried out efficiently. Further studies are necessary to pave the way for the development of advanced materials with tailored properties.
For more information on this research, please contact Dr Trisha Salagaram (Department of Physics, University of Cape Town) via email at trisha.salagaram@uct.ac.za.
Principal Investigator: Dr Shane Murray
Institution Name: 0 Other
Active Member Count: 7
Allocation Start: 2023-09-11
Allocation End: 2024-03-11
Used Hours: 235180
Project Name: DIPLOMICS 1KSA
Project Shortname: CBBI1622
Discipline Name: Bioinformatics
DIPLOMICS stands for Distributed Platform in OMICS and is a research infrastructure program funded by the Department of Science and Innovation. We are in the pilot phase of one of our high-impact, high visibility projects – 1KSA: Decoding South Africa's Biodiversity – which will be used to sequence the genomes of over 1000 South African species and facilitate method development and training in genomics. 1KSA is a national project, generating whole genome sequencing data with Oxford Nanopore Technology at several genomic service labs in South Africa. These data need to be managed, analyzed and stored. The CHPC provides the computational power needed to assemble these sequencing data into draft genomes which can then be used as a resource for future research. DIPLOMICS are thankful to the staff at CHPC for their willingness to help and commitment to making this project a success. The genome assemblies and nextflow pipeline will be highlighted at the 1KSA launch on the 19th of March, 2024, at Intaka Island, Cape Town.
Principal Investigator: Dr Johannes Pretorius
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2023-09-11
Allocation End: 2024-03-31
Used Hours: 69227
Project Name: Thermo-fluid simulation of natural and forced draft heat rejection systems
Project Shortname: MECH1510
Discipline Name: Computational Mechanics
We are part of the Solar Thermal Energy Research Group (STERG) under the Department of Mechanical and Mechatronic Engineering at Stellenbosch University. We are currently investigating two research topics: The performance of natural draft direct dry cooling systems, and the performance of forced draft cooling systems for supercritical carbon-dioxide (sCO2) applications. We do this by one-dimensional (1D) calculation and three-dimensional (3D) Computational Fluid Dynamics (CFD) simulations.
The natural draft direct dry cooling system is a unique system, typically used as part of power generation applications, that aims to combine the advantages of two traditional cooling methods to achieve a more cost-effective solution. Our research should establish how competitive this system is compared to current alternatives, and potentially improve power generation efficiency while maintaining water conservation. To evaluate the performance of the system, the equations for fluid flow and heat transfer are solved at millions of points across the geometry of the system (consisting of a large dry cooling tower) – which is where we need the computing resources of the CHPC. To date we have successfully modelled the steady and unsteady plant performance with 1D calculations under no-wind conditions, as well as simulated steady state performance for no-wind and windy conditions using co-simulation. The co-simulation involves modelling the steam-side using a 1D Python program, while the airflow through the system is modelled using CFD. We are currently co-simulating the unsteady (start-up) performance of the system, which is our final objective for the study.
Power cycles which utilize supercritical CO2 have the potential to produce power at high efficiencies and utilize turbomachinery at a fraction of the scale of steam-cycle equipment. Our research aims to establish efficient forced draft dry-cooling systems employed in the heat rejection components of these cycles. Again, the equations of fluid flow and heat transfer are solved at millions of points across the system geometry, requiring the CHPC's resources. We simulate a complete 8-bladed fan, while modelling the heat exchanger as a porous zone. The flow of supercritical CO2 inside the tubes of the heat exchanger is modelled using a 1D Python program, while the flow over the outside of the heat exchanger tubes is modelled using CFD. To date we have successfully completed a sensitivity study on the configuration of the fan and heat exchanger for cold-flow conditions. Next, we will introduce heat into the simulation by coupling the sCO2-side Python code to the air-side CFD program.
Principal Investigator: Prof Mario Santos
Institution Name: University of Western Cape
Active Member Count: 22
Allocation Start: 2023-09-12
Allocation End: 2024-03-12
Used Hours: 845066
Project Name: Cosmology with Radio Telescopes
Project Shortname: ASTR0945
Discipline Name: Astrophysics
An array of 350 radio telescopes in the Karoo desert of South Africa is getting closer to detecting "cosmic dawn" — the era after the Big Bang when stars first ignited and galaxies began to bloom.
In a paper accepted for publication in The Astrophysical Journal, the Hydrogen Epoch of Reionization Array (HERA) team reports that it has doubled the sensitivity of the array, which was already the most sensitive radio telescope in the world dedicated to exploring this unique period in the history of the universe.
While they have yet to actually detect radio emissions from the end of the cosmic Dark Ages, their results do provide clues to the composition of stars and galaxies in the early universe. In particular, their data suggest that early galaxies contained very few elements besides hydrogen and helium, unlike our galaxies today.
Principal Investigator: Prof Gert Kruger
Institution Name: University of KwaZulu-Natal
Active Member Count: 16
Allocation Start: 2023-09-14
Allocation End: 2024-04-16
Used Hours: 239215
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: Dr Maya Makatini
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2023-09-14
Allocation End: 2024-04-16
Used Hours: 66116
Project Name: Wound healing and Antimicrobial peptides
Project Shortname: CHEM1406
Discipline Name: Chemistry
As the Peptide synthesis group at Wits University, we have benefited immensely from the academic facilities provided by the CHPC. We can describe our experience with the CHPC as follows:
The facilities provided by the CHPC help visualize and process data in a manner that any scientist could easily interpret. The programs provided by the CHPC reduce the cost and time associated with conducting extensive experimental trials. Working with highly skilled CHPC staff members makes using computational software to interpret and visualize data a very easy task, even for those who do not have prior knowledge of computers and the various software provided by the CHPC. The CHPC has revolutionized the scientific world through state-of-the-art technology and infrastructure. Peptide synthesis for pharmaceutical purposes is a challenging task, therefore, the use of CHPC resources has helped us to limit our synthesis to peptides that are proposed to have pharmaceutical properties by various software provided by the CHPC.
Principal Investigator: Dr Anna Bosman
Institution Name: University of Pretoria
Active Member Count: 25
Allocation Start: 2023-09-14
Allocation End: 2024-03-27
Used Hours: 361775
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 led 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: loss 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 image analysis and segmentation; (2) evolution of network architectures; (3) automated software testing; (4) biologically plausible machine learning. Studying loss landscapes of neural networks deepens our general understanding of the fundamental principles of neural networks, and enables progress in fundamental artificial intelligence. Deep learning applications allow us to apply modern artificial intelligence techniques in the South African context, as well as to explore novel algorithmic ideas in this field. 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. The research program yields annual publications in highly ranked international journals and conferences. This indicates that the research program is productive, and successfully delivers academic outputs. Thus, the usage of CHPC helps us strengthen machine learning and artificial intelligence research in South Africa.
Principal Investigator: Prof Ignacy Cukrowski
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2023-09-14
Allocation End: 2024-03-14
Used Hours: 119234
Project Name: Understanding chemistry from QM study of molecular systems
Project Shortname: CHEM0897
Discipline Name: Chemistry
A chemical bond is a central concept in chemistry. Not being a QM-defined property, the nature and kinds of chemical bonds are subject of endless and often fruitless debates.
Our aim is to challenge long-standing and textbook strengthened orthodox concepts on how the universe of chemistry works. We continuously explore the power and applicability of a unique concept of bonding (without classical chemical bonds) developed by research group lead by Prof Cukrowski in the Department of Chemistry, University of Pretoria; it is called a molecular-wide and electron density-based (MOWED) concept of bonding. In our approach, we reject chemical bonding as a physical process taking place between just two atoms but rather explore chemical bonding as electron density sharing among all atoms of a molecular system. Each atom and atom-pair contributions as localized and delocalized electron density (ED) contribution to the total ED are quantified to reveal major players in the all-atom chemical bonding. To this effect, we make an extensive use of computational resources provided by the Centre for High Performance Computing (CHPC) in Cape Town as well as our own codes.
Principal Investigator: Dr Jennifer Veitch
Institution Name: SAEON
Active Member Count: 13
Allocation Start: 2023-09-15
Allocation End: 2024-03-15
Used Hours: 29311
Project Name: SAEON Coastal and Regional Ocean Modelling Programme
Project Shortname: ERTH1103
Discipline Name: Earth Sciences
The overarching vision of SOMISANA is a sustained and transformed critical mass of internationally recognized South African numerical ocean modelling experts who provide accurate information about the changing state of the ocean for enhanced impact. In order to facilitate this vision, the mission statement of SOMISANA is to develop an ocean modelling hub and platform that promotes the inclusive development of local expertise and that produces and provides state-of-the-art ocean information, tools and research that is visible and accessible to all. The key aspects of the mission statement are captured in four broad strategic objectives: 1) The development of a recognized ocean modelling platform, 2) Capacity Development, 3) Research Excellence and 4) To enhance visibility and accessibility. A number of strategic actions are identified for each key objective.
Principal Investigator: Dr Adam Skelton
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2023-09-15
Allocation End: 2024-04-16
Used Hours: 106443
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 Soraya Bardien
Institution Name: Stellenbosch University
Active Member Count: 5
Allocation Start: 2023-09-17
Allocation End: 2024-04-17
Used Hours: 6588
Project Name: Parkinson's disease Research Group
Project Shortname: HEAL1381
Discipline Name: Health Sciences
The Parkinson's disease Research Group is based at Stellenbosch University. It is the only research group in the country focussing on the genetic causes of Parkinson's disease. This is a multidisciplinary team comprising geneticists, neurologists, laboratory scientists, bioinformaticists and research nurses. Parkinson's disease is a complex and currently incurable neurological condition that has been understudied on the African continent.
One of the main aims of our group is to identify the genetic causes of Parkinson's disease in South African individuals. For this, we have recruited 689 individuals with this disorder as well as their affected and unaffected family members. We currently have a biobank comprising almost 2,000 DNA samples for our research projects. We collaborate with a large international consortium known as the Global Parkinson's Genetics Program (GP2; https://gp2.org/) whose goal is to understand the genetic factors implicated in Parkinson's disease, on a global scale. GP2 has generated masses of sequencing data on the South African study participants, and we need the CHPC resources to systematically analyse this data to find the underlying genetic causes. We have PhD and MSc students analysing this data as part of their postgraduate degrees.
We recently obtained the genetic data and so the students are in the early stages of this analysis. Working with the international consortium means we have access to high-level expertise and knowledge. However, the CHPC is a valuable part of our research since South African students must learn how to analyse genetic data from South Africans in South Africa.
The significance of this work is that if we find the genetic cause in a South African individual with Parkinson's disease, this will improve the clinical management of their disease. Also, we can offer presymptomatic genetic testing to their at-risk family members. Furthermore, these families can enlist in clinical trials targeted at their specific genetic defect i.e. personalized medicine.
Principal Investigator: Prof Thirumala Govender
Institution Name: University of KwaZulu-Natal
Active Member Count: 7
Allocation Start: 2023-09-18
Allocation End: 2024-04-18
Used Hours: 245869
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 and sepsis. Antibiotic resistance is considered a global crisis currently, affects the development of human society, and has high-cost implications for 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 allow our group to integrate molecular modelling with our research 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 Gerhard Venter
Institution Name: University of Cape Town
Active Member Count: 8
Allocation Start: 2023-09-18
Allocation End: 2024-04-04
Used Hours: 378126
Project Name: Simulation of Ionic Liquids
Project Shortname: CHEM0791
Discipline Name: Chemistry
Gerhard Venter's research group uses quantum chemistry, classical molecular dynamics computer simulation and machine learning methods to study and predict the properties ionic liquids and electrolytes. Ionic liquids are molten salts consisting of organic or inorganic ions that have low melting points such that they are liquids at ambient temperature. Green and sustainable chemistry calls for solvents that minimize harmful waste products and environmental hazards and ionic liquids are important candidates that can fulfil this role.
A better understanding of the physical and chemical properties of ionic liquids can lead to improved rational design of new, environmentally friendly liquids with applications as electrolytes in next-generation batteries and as energetic materials. Computer simulations not only provide first-principles characterization of ionic liquids and solutes, but also form the basis of models that aim to use machine learning for the prediction of thermodynamic properties.
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 Eno Ebenso
Institution Name: North-West University
Active Member Count: 6
Allocation Start: 2023-09-19
Allocation End: 2024-04-23
Used Hours: 316140
Project Name: Theoretical Investigations of Corrosion Inhibition Activities of Organic Compounds
Project Shortname: CHEM1176
Discipline Name: Chemistry
Our research group, the Materials Science Innovation and Modelling (MaSIM) Research Focus area at the North-West University in collaboration with our affiliate teams at University of Johannesburg and Obafemi Awolowo University, Nigeria has developed series of new formulations that could reduce the rate of metal corrosion in various corrosive environments over a period of time. This research has led to the introduction of new materials that could be used to protect metals against rapid acid attacks with potential applications in oil and gas industries. Screening a large set of potential chemicals and reducing the set to a manageable size that could be experimented in the laboratory requires the use of CHPC resources to generate molecular properties that could guide in pre-experimental screening.
Principal Investigator: Dr Geoff Nitschke
Institution Name: University of Cape Town
Active Member Count: 29
Allocation Start: 2023-09-19
Allocation End: 2024-03-19
Used Hours: 415973
Project Name: Evolving Complexity
Project Shortname: CSCI1142
Discipline Name: Computer Science
This research aims to use collective and swarm robotics platforms as a means to test and evaluate new evolutionary machine learning methods for the purpose of designing adaptable and autonomous robotic systems that can be deployed across a range of environments to autonomously solve various tasks. These simulations rely on high-performance computing architectures since potentially hundreds of robots must be simulated concurrently, while also simulating the task-performance impact of multiple behaviours. Current simulated collective and swarm robotic tasks are surrogates for various real-world tasks including: toxic waste collection, environmental monitoring, search and rescue and collective construction.
Principal Investigator: Mr Mogesh Naidoo
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 4
Allocation Start: 2023-09-19
Allocation End: 2024-03-19
Used Hours: 151514
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 still 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 Sarah Roffe
Institution Name: Agricultural Research Council
Active Member Count: 9
Allocation Start: 2023-09-19
Allocation End: 2024-03-19
Used Hours: 476244
Project Name: ARC-NRE Agrometeorology
Project Shortname: ERTH1556
Discipline Name: Earth Sciences
The Agrometeorology division of the Agricultural Research Council represents a research group focused on weather and climate in relation to agricultural activities. One aspect of the group's activities is to investigate how climate change could impact agricultural activities, focusing on smallholder to large-scale commercial farming activities. To understand the future effects of climate change for consideration in agricultural decision-making, Global Climate Models (GCM) can provide us with climate change projections, which represent potential future climate scenarios. However, GCMs have very coarse spatial resolutions (around 100 x 100 km or more), which are not appropriate to apply for decision-making in agriculture. Therefore, to appropriately guide agricultural decision-making across South Africa, the Agrometeorology division has begun dynamically downscaling GCM outputs from selected models contributing to the sixth phase of the Coupled Model Intercomparison Project (CMIP6). For this task, we are utilising the Weather Research and Forecasting (WRF) model to downscale GCM outputs to an 8 x 8 km spatial resolution for a range of future scenarios (i.e., SSP1-2.6, SSP2-4.5, and SSP5-8.5). To undertake this massive task, the division relies very heavily on the computing resources offered by the Centre for High Performance Computing (CHPC) Lengau Cluster; without these resources, this dynamic downscaling task would not be possible. To date, we have progressed substantially with this task. Although we still quite far from being complete, we anticipate that our activities will be complete by roughly mid-2024.
Principal Investigator: Dr Malebogo Ngoepe
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2023-09-19
Allocation End: 2024-05-31
Used Hours: 1160075
Project Name: PROTEA
Project Shortname: MECH1194
Discipline Name: Computational Mechanics
We work on computational models in biofluid contexts for surgical interventional planning. Most of our models use CFD as a base and are often coupled to other techniques. Our CFD simulations are computationally expensive, requiring the use of HPC.
Principal Investigator: Prof Gerhard Venter
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2023-09-19
Allocation End: 2024-03-31
Used Hours: 818593
Project Name: Finite Element Analysis and Numerical Design Optimization
Project Shortname: MECH0883
Discipline Name: Computational Mechanics
Both projects are in a stage where it is a bit premature to make a press-release in my opinion. We should hopefully have results by the end of the next reporting period that would make more sense to write into a press release.
We are the MOD research group that stand for Materials, Optimization and Design. The MEng student is co-supervised from the thermo-fluid size and the PhD student from the material science side.
The ultimate goal of the MEng study is to optimize the front bumper of an EV truck to reduce drag. For the PhD student we aim to better understand the alloying process in the laser melt pool when performing laser power-bed fusion using powders from different materials.
Both these projects make use of commercial software (ANSYS and StarCCM+) and requires long runtimes that would not be possible to complete were it not for the computing resources of the CHPC.
Both projects are progressing according to plan and both students plan to graduate the end of 2024. Significant results will hopefully be available by the end of the year.
Principal Investigator: Prof Paulette Bloomer
Institution Name: University of Pretoria
Active Member Count: 9
Allocation Start: 2023-09-20
Allocation End: 2024-03-20
Used Hours: 82899
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 several projects (Wildebeest, red roman, Cape buffalo and different birds including falcons and Houbara) that make use of the CHPC resources, with additional projects in the pipeline.
Principal Investigator: Prof Sheena Kumari
Institution Name: Durban University of Technology
Active Member Count: 7
Allocation Start: 2023-09-20
Allocation End: 2024-03-20
Used Hours: 59991
Project Name: Wastewater Treatment, Emerging Pathogens & Pollutants in Water, Risk Assessment, Wastewater Based Epidemiology
Project Shortname: CBBI1627
Discipline Name: Bioinformatics
The research group focuses on Water and wastewater pathogen surveillance, antibiotic resistance, annamox, and microplastics research are critical due to their significant impact on public health and the environment. These areas of study aim to understand, monitor, and mitigate the risks associated with pathogens, pollutants, and emerging contaminants in water systems. Water and wastewater pathogen surveillance is essential for identifying and tracking harmful microorganisms such as bacteria, viruses, and protozoa that can cause waterborne diseases like cholera, typhoid fever, and dysentery. Monitoring these pathogens helps to ensure the safety of drinking water and prevents outbreaks of waterborne illnesses. Antibiotic resistance has become a global health concern as bacteria develop resistance to commonly used antibiotics. Research in this area focuses on understanding the mechanisms of resistance, identifying antibiotic-resistant genes, and developing strategies to combat the spread of resistance in water environments. This work is crucial for preserving the effectiveness of antibiotics for treating infections in both humans and animals.Annamox (Anaerobic Ammonium Oxidation) is a biological process that removes ammonia from wastewater without the need for oxygen, making it an energy-efficient and environmentally friendly method of wastewater treatment. Research in this area aims to optimize annamox processes for wastewater treatment plants, reducing energy consumption and minimizing the environmental impact of wastewater discharge. Microplastics, tiny plastic particles less than 5 millimeters in size, have become pervasive pollutants in aquatic environments, posing risks to marine life and human health. Research on microplastics focuses on understanding their sources, distribution, and impacts on ecosystems. This research informs strategies for mitigating microplastic pollution, their association with pathogens and developing effective waste management practices.
Utilization of bioinformatics tools and CHPC (Center for High-Performance Computing) services in these research areas enables efficient analysis of large datasets, genomic sequencing, and modeling of complex biological processes. These computational tools facilitate data processing, interpretation, and visualization, accelerating scientific discoveries and informing evidence-based decision-making in water management and environmental protection.
Overall, the progress of research groups in these areas is marked by paper drafts for publications, knowledge transfer to students, results being presented at conferences and students working toward graduation. Through interdisciplinary collaborations and the use of advanced computational resources like CHPC, researchers continue to make significant strides in addressing pressing challenges related to water and wastewater management.
Principal Investigator: Prof Graham Jackson
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2023-09-20
Allocation End: 2024-04-09
Used Hours: 85116
Project Name: Insect neuropeptides
Project Shortname: CHEM1101
Discipline Name: Chemistry
Insect flight is under hormonal control. The hormone binds to a receptor which initiates the release of energy. Using experimental and computational techniques we have investigated the binding of these hormones to their receptor and then designed novel compounds that would block the receptor binding site. Since each insect species has unique receptors, by blocking the receptor we are trying to develop species specific insecticides. To date we have worked on the malaria mosquito, the fruit fly and the desert locust. We have now mapped the binding site of the yellow fever mosquito. This mosquito is responsible for the spread of yellow fever but also dengue fever and, more recently the zika virus. Using the computer power of the CHPC we are now screening large databases of compounds, looking for antagonists. So far, we have identified three compounds that are potential receptor blockers. These compounds now need to be tested in vivo.
Principal Investigator: Dr Nangamso Nyangiwe
Institution Name: Tshwane University of Technology
Active Member Count: 4
Allocation Start: 2023-09-20
Allocation End: 2024-06-06
Used Hours: 179698
Project Name: Application of density functional theory in engineered nanoparticles
Project Shortname: MATS1427
Discipline Name: Material Science
The research group led by Dr Nangamso Nyangiwe at the Department of Physics at Tshwane University of Technology is conducting pioneering work in the application of density functional theory (DFT) to engineered nanoparticles and energy materials. This research focuses on using DFT to model and predict the electronic, structural, and chemical properties of engineered nanoparticles and energy materials. By employing DFT, the team can simulate interactions at the atomic level, providing insights into the behaviour and potential applications of these materials in various fields such as catalysis, drug delivery, and energy storage. The work is crucial for several reasons such as innovation in nanotechnology that focuses on understanding the fundamental properties of nanoparticles can lead to the development of new materials with enhanced performance for industrial and medical applications. It is crucial for efficiency and cost-effectiveness, computational methods like DFT reduce the need for extensive experimental trials, saving time and resources and lastly environmental Impact, by predicting the properties and behaviours of nanoparticles, researchers can design more efficient and environmentally friendly materials, contributing to sustainable technological advancement. Given the above potential benefits, the research justifies the use of public resources to drive innovation and address global challenges.
The research utilizes the capabilities of the Centre for High-Performance Computing (CHPC) at the Tshwane University of Technology. The process involves, model construction, building atomic-level models of nanoparticles. DFT simulations, running DFT calculations to analyse electronic structures, surface energies, and reaction mechanisms. Data Analysis, interpreting the results to predict material properties and guide experimental efforts.
The CHPC's computational power is essential for handling the complex and resource intensive DFT calculations, enabling the team to conduct high-fidelity simulations that would be otherwise impractical.
The project is making significant strides, the group recently added two MSc students who are also utilizing CHPC resources. The two MSc students are busy with their review papers. Dr NN Nyangiwe will be attending an international conference in Singapore later this year to present results obtained using CHPC resources.
Principal Investigator: Dr Xolani H Makhoba
Institution Name: University of South Africa
Active Member Count: 2
Allocation Start: 2023-09-20
Allocation End: 2024-03-20
Used Hours: 56045
Project Name: Drug development of COVID-19 alternative treatment using in silico analysis
Project Shortname: CBBI1629
Discipline Name: Bioinformatics
I am currently based at the University of South Africa, and I am establishing a bioinformatics research group to use the resources available at CHPC. From Honours to the PhD level. I believe that we will achieve a lot in this period with drug development and discovery.
Principal Investigator: Prof Tjaart Krüger
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2023-09-20
Allocation End: 2024-02-25
Used Hours: 218851
Project Name: A DFT study of bio-inspired organic solar cells
Project Shortname: MATS1498
Discipline Name: Material Science
A new approach to study aggregation types in conjugated polymers.
Conjugated polymers have found broad application in light-emitting diodes and organic solar cells and several breakthroughs in both technologies have been obtained in the past ten years. A deep understanding of the underlying photophysical parameters of these systems can push the technologies even further. One of the crucial parameters lacking understanding is how aggregates are formed in such devices.
Prof. Tjaart Krüger from the University of Pretoria has teamed up with Dr Newayemedhin Tegegne from Addis Ababa University to shed more light on aggregate formation in organic polymers. Dr Tegegne's team synthesised their own polymers and performed detailed experimental and computational studies. The experimental results served as an important reference for the computations. Their unique combination of three computational methods is a new but powerful approach to determining the aggregation types in polymers and serves as a platform for investigating numerous other types of polymers. In particular, they showed that their type of polymers are mainly H-aggregates, a formation that is key to producing high-performance solar-cell devices.
Due to the complexity of the organic polymer systems, the authors relied on a powerful computer cluster to execute the necessary calculations and are therefore grateful for the availability and capabilities of the CHPC to enable this work.
Principal Investigator: Dr Frederick Malan
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2023-09-22
Allocation End: 2024-05-07
Used Hours: 41703
Project Name: Proton-Responsive Metal Complexes as Catalysts for Sustainable Hydrogen Production and Storage
Project Shortname: CHEM1358
Discipline Name: Chemistry
The research of the Malan Inorganic Chemistry Research group, led by Dr Frederick Malan (University of Pretoria), revolves around the design, economic synthesis, and characterization of new transition metal compounds with a purpose. The catalytic activity associated with these compounds is evaluated mainly from a homogeneous catalysis point of view. Additional electrochemistry, computational chemistry, and single crystal X-ray diffraction studies aid in the understanding of the working of these catalysts. The aim of investigation of the role of proton-responsive ligands in carbon dioxide and nitrogen fixation processes is to efficiently make use of these cheap building blocks as an entry point to fuel and other fine chemicals, as well as to curb the effect of greenhouse gas pollution. Catalysts reduce the activation energy by which a reaction takes place, and therefore the calculation and prediction thereof (via the CHPC) is important in this research. To date, promising results have been obtained with two PhD projects and several honours projects, with more results (especially from a computational point of view) which includes geometry optimization, reaction outcome prediction using reaction energetics, as well as frontier orbital and electrochemical insights obtained. Currently, QM methods including DFT studies using mainly B3LYP coupled with 6-311G* and def2tzvpp basis sets are typically employed. More results from current and future students are pending.
Principal Investigator: Prof Edith Antunes
Institution Name: University of Western Cape
Active Member Count: 3
Allocation Start: 2023-09-22
Allocation End: 2024-04-30
Used Hours: 42934
Project Name: Elucidation of secondary metabolites from marine organisms, nanomaterials and porphyrinoid macrocycles.
Project Shortname: CHEM1172
Discipline Name: Chemistry
We are group with diverse interests in marine biodiscovery and in the synthesis and characterisation of large macrocycles and nanomaterials. Although the fields are diverse, our main interest is to identify, characterise and understand these molecules thoroughly in order to use these compounds in targeted anti-cancer studies. The chemical space these molecules occupy is extremely important to explore. The main intended use for the nanomaterials is as delivery and imaging agents.
Our group therefore consists of natural products chemists and inorganic/physical chemists from Chemistry and Pharmaceutical Chemistry.
A detailed understanding of the molecules/materials is needed in order to understand the processes that may take place in the molecule's intended usage. This can only be done by obtaining the experimental evidence and corroborating it with detailed computational studies. These computational studies would not be possible without CHPC as our department/unit does not have these facilities.
Principal Investigator: Prof Nelishia Pillay
Institution Name: University of Pretoria
Active Member Count: 9
Allocation Start: 2023-09-22
Allocation End: 2024-04-08
Used Hours: 1498322
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 and optimization 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, crop modelling and streamflow prediction and industry, e.g. logistics, scheduling and classification problems, as well as innovation in industry, e.g. routing, packing, recommender systems. 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: Prof Daniel Joubert
Institution Name: University of the Witwatersrand
Active Member Count: 19
Allocation Start: 2023-09-22
Allocation End: 2024-03-28
Used Hours: 928726
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 and co-researchers at other institutions 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 Nithaya Chetty
Institution Name: University of Pretoria
Active Member Count: 7
Allocation Start: 2023-09-26
Allocation End: 2024-07-03
Used Hours: 1481271
Project Name: Advanced Computational Resources for members of ASESMA
Project Shortname: MATS1050
Discipline Name: Material Science
This research program is dedicated to the members of African School for Electronic Structure Methods and Applications (ASESMA). ASESMA is a network of scientists in Africa who are building up research in computational materials science. The main focus of this group of researchers is the use of first-principles methods for calculations of electronic structure of materials.
Within this research program, each individual proposal is dedicated to solve the problems in physics, chemistry and materials science that have impact on science, technology and society. Currently, various projects on two dimensional (2D) materials such as transition metal dichalcogenides (TMD), transition metal oxides (TMO), aluminene and bilayer silica are on going. They are good candidates for several applications such as in lithium or sodium batteries, electronic devices, solar cells, etc. In order to improve or expand their applications, one can engineer their properties via different ways such as doping or creating defects. Carrying such study theoretically need the use of what is called supercell in order to imitate the experimental samples. These investigations can only be achieved using large supercomputer such as CHPC. Our results are promising for industrial applications.
Principal Investigator: Dr Babatunde J. Abiodun
Institution Name: University of Cape Town
Active Member Count: 37
Allocation Start: 2023-09-26
Allocation End: 2024-04-05
Used Hours: 850492
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 variability (that usually induce weather and climate extremes like droughts, extreme rainfall, heatwaves, and pollution episodes), the impacts of climate change at regional scale, and how to mitigate climate change impacts in the future.
We evaluated the capability of the Model for Prediction Across Scales (MPAS) in simulating the West African monsoon systems (WAMs) and heat waves. The results reveal that the model provides remarkable simulations of these atmospheric phenomena, although there are still notable biases in the simulation. We assessed how simulations from the Coupled Model Intercomparison Project Phase 6 (CMIP6) represent the climatological annual migration of three WAMS components: the West African Heat Low (WAHL), the West African Heat Band (WAHB), and the West African Rain Band (WARB). Our findings indicate close linkages between WAHL, WAHB, and WARB, and demonstrate that the models capture the climatological annual dynamics of all three features to some extent. However, we observed that in most of the analyzed models, the WAHL is too weak, and the WAHB and WARB are located too far south. Insights from these study can be valuable for investigating the future state of the WAMS. Additionally, model development for the region should prioritize improving the simulation of these features, specifically focusing on the intensity of the WAHL and the accurate placement of the WAHB and WARB.
Principal Investigator: Dr Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 14
Allocation Start: 2023-09-28
Allocation End: 2024-05-23
Used Hours: 781008
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 Center for Augmented Intelligence and Data Science (CAIDS) of the University of South Africa (UNISA) and is being led by Dr. Abdulrafiu Raji. The study focus is on computational studies of two- and three-dimensional (2D) crystals, surfaces, nanocrystals, organic semiconductors for potential applications in spintronics and catalysis. Other applications being envisaged are ultrathin refrigeration and air-conditioning systems, and any nanoarchitecture where cooling may be needed. The research aims to induce novel electronic and magnetic interactions in nanostructured materials which could be exploited for practical applications. For example, 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. This motivates our interest in computational studies of relevant bulk crystals, surfaces and material heterostructure not only for their magnetocaloric effect, but also for other potential applications such as in water purification, thermoelectricity and superconductivity.
Because of plethora of candidate materials that we are investigating and since experimental synthesis of such materials are prohibitive in time and human resources, large-scale computational studies is a better alternative. Indeed, 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 an ordinary desktop computer. The softwares have been made available on the CHPC platform. The CHPC administrators also maintain the softwares and provide different kinds of technical supports to students involved in the projects. Thus, the availability of high-performance computing (HPC) facility is absolutely necessary. The project currently have postgraduate students working on its several aspects.
Principal Investigator: Prof Abram Madiehe
Institution Name: University of Western Cape
Active Member Count: 5
Allocation Start: 2023-09-28
Allocation End: 2024-03-28
Used Hours: 1209579
Project Name: Nanobiotechnology
Project Shortname: CBBI1572
Discipline Name: Bioinformatics
The Nanobiotechnology Research Group at the University of the Western Cape performs research on the development of point-of-care diagnostics for both infectious disease, such as HIV, TB, SARS-Cov-2 and ebola; and non-communicable diseases, such as type 2 diabetes, and therapeutics for cancer and obesity. The students have used the HPC to select aptamers against their biomarker proteins. All students have been successful in obtaining aptamers, which they subsequently used in the experiments. One publication and 2 graduations have been achieved by the programme, thanks to our access to the HPC infrastructure.
Principal Investigator: Dr Mpho Ngoepe
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 1
Allocation Start: 2023-09-29
Allocation End: 2024-05-02
Used Hours: 87901
Project Name: DSI-Mandela Nanomedicine
Project Shortname: HEAL1547
Discipline Name: Health Sciences
The use on nanomaterials in medicine allows researchers to be able to targeted specific cells and thus reduce side effects that are associated with conventional drug delivery. In order to understand how the nanomaterials behavior, the use of various CHPC software help us to understand how these nanomaterials interact with targeted sites. Through simulations we are able to improve the design to ensure they have imrpoved therapeutic efficacy.
Principal Investigator: Prof Michelle Kuttel
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2023-10-02
Allocation End: 2024-04-25
Used Hours: 1595
Project Name: Molecular modelling of microbial polysaccharides and glycoconjugates
Project Shortname: CHEM1242
Discipline Name: Chemistry
The vaccine group at the University of Cape Town South Africa comprises Prof. Michelle Kuttel of the Department of Computer Science and Prof. Neil Ravenscroft of the Chemistry Department. Our primary research focus is on computational glycochemistry: using molecular modelling to predict the conformation and interactions of microbial surface carbohydrates that play key roles in infection, in order to inform the development of anti-microbial vaccines.Carbohydrate molecules are of particular scientific interest because they play key roles in microbial infection processes. However, they are challenging to model accurately because they are extremely structurally diverse and very flexible. Although the quality of current additive all-atom force fields for simulating carbohydrate molecules has been demonstrated in many applications, occasional anomalies reported for the behaviour of specific polysaccharides is a cause for concern. A more accurate polarizable "Drude" force field that simulates electronic polarization has been developed to address deficiencies in the current force fields. However, this model has not been tested across a wide variety of simulations. In this project, we are doing an extensive comparison of the additive and Drude polarizable CHARMM force fields for simulating carbohydrate molecules, using the NAMD simulation software. These complex simulations are only practicable if run on supercomputers, which is why access to the CHPC is so useful to our group.
Principal Investigator: Dr Vukosi Marivate
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2023-10-02
Allocation End: 2024-04-17
Used Hours: 2144
Project Name: Data Science for Social Impact
Project Shortname: CSCI1226
Discipline Name: Computer Science
We are the Data Science for Social Impact research group at the Computer Science Department, University of Pretoria. Assoc. Professor Vukosi Marivate, the ABSA UP Chair of Data Science, is the principal investigator.
Our general areas of work straddle Data Science for Society as well as Local Language Natural Language Processing. These two strands are complementary. Our work in Data Science and Society has allowed us to have a more nuanced approach to understanding the systematic challenges that face being able to do excellent science with local languages. Through Data Science for Society, we have to understand how when one carries through Data Science research, we situate how the users are part of the process. We find that we need to adjust our research to take care of these challenges and innovate in ways we gather direct data or alternative data.
For us, Data Science for Society means being able to improve approaches/methods or scientific tools for DS while enhancing the ways decision-makers can use the insights that come from these tools. Local Language Natural Language Processing is focused on ways to develop new tools, new data and methodology to improve the state of African languages.
CHPC continues to provide access to high-performance computing resources, including powerful servers, clusters, and specialized hardware accelerators. These resources are essential for handling large datasets, running complex algorithms, and conducting computationally intensive tasks inherent in data science and NLP research.
Principal Investigator: Dr Thierry Hoareau
Institution Name: University of Pretoria
Active Member Count: 7
Allocation Start: 2023-10-03
Allocation End: 2024-04-03
Used Hours: 52851
Project Name: Reneco Conservation Genomics
Project Shortname: CBBI1504
Discipline Name: Environmental Sciences
Over the last six months, we have dedicated ourselves to several objectives of the research group, which is the identification of geographic origin of falcon individuals that are candidate for a release in the wild and a project on the optimisation of the analysis of genomic data based ONT platform. Wild falcons are being used in the UAE for falconry (prey hunting) during the hunting season (October to January every year). There is a programme put in place that helps collect falcons at the end of the season to prepare them for a release in the wild. We have been developing a bioinformatic pipeline that use raw reads generated from these falcons to assign them to their population of origin for a successful release. To do so, we filter and trim the raw reads, we map these reads to a peregrine reference genome, we then select the best genomic sites, which are finally used to compare the birds to data from reference populations. The access to the CHPC is critical for our main activities that include the training of postgraduate students from University of Pretoria (2 Honours student this year). This helps strengthen collaboration between institutions.
Principal Investigator: Dr Jaap Hoffmann
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2023-10-04
Allocation End: 2024-04-30
Used Hours: 100410
Project Name: Flow through porous media
Project Shortname: MECH1116
Discipline Name: Computational Mechanics
Decarbonization of the economy is important to reduce greenhouse gas emissions.
Decarbonation of the power generation can be done via various options, such as solar PV, wind, hydro (although South Africa has limited hydro resources) and concentrated solar power. Recent thinkin (SolarPACES 2023) is that the most economic solutions might be a combination of all these technologies (and including battery storage), where the mix will be determined by the local resources.
However, solar heat for industrial processes relies on a heat source, and the only source that can realistically replace fossil fuels are concentrated solar heat. Due to the diurnal nature of resource, thermal energy storage is required to keep industry running 24/7.
Research in rock bed thermal energy storage has been going on at Stellenbosch University for the last decade, and resulted in numerous post graduate qualifications, presentations at national and international conferences and journal articles. The current research relies on pore scale CFD simulations, validated by experimental work.
Principal Investigator: Dr Aniekan Ukpong
Institution Name: University of KwaZulu-Natal
Active Member Count: 0
Allocation Start: 2023-10-06
Allocation End: 2024-04-22
Used Hours: 223534
Project Name: Theoretical and Computational Condensed Matter and Materials Physics
Project Shortname: MATS0941
Discipline Name: Physics
In a breakthrough study, our work has delved into the intricate world of quantum criticality in 2D magnetism, unraveling the mysteries surrounding the Spin Glass Ordering Transition and the Formation of the Griffiths-McCoy Phase.
Quantum criticality, a phenomenon observed in quantum many-body systems undergoing continuous phase transitions at absolute zero temperature, has long fascinated scientists. This groundbreaking work highlights the paramount importance of understanding quantum criticality in deciphering the physical laws governing transitions between various quantum phases at zero temperature.
The insights gleaned from this research not only deepen our comprehension of quantum matter where phase transition is driven purely by quantum fluctuations but also pave the way for the development of innovative materials with tailored properties. Such advancements hold immense potential in revolutionizing fields like quantum computing and information processing.
Key aspects of the current work center around the critical behavior of quantum fluctuations at the spin glass ordering transition in 2D magnetic crystals and the formation of the Griffiths-McCoy phase. By shedding light on the intricate interplay of quantum fluctuations, disorder, and quantum criticality in spin systems, this study whose findings have been presented at the Stellenbosch-Hamburg Condensed Matter Symposium, marks a significant milestone in the realm of quantum physics – especially because permanent magnetic moments are not expected to exist in monolayer materials at zero temperature.
Principal Investigator: Prof Evans Adei
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 48
Allocation Start: 2023-10-09
Allocation End: 2024-04-09
Used Hours: 1659178
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 understanding and 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 urgent real-world problems and our contributions would not have been possible without the support of CHPC. Three of our postgraduate students at the Department of Chemistry KNUST Kumasi, Justice Archer, Philomina Essel, and Jemima Misszento graduated with M.Phil. (Chemistry) in March 2024. The lack of local funding to support research particularly, postgraduate studies has fortunately opened our 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. Consequently, we could say that CHPC is an extremely important ally in our research activities and priming the training of our students; the future African molecular/material scientists. The three to seven of these students who go on to graduate school abroad each year together with those locally trained may potentially provide us with an enriched blend of African-trained molecular/material academic researchers for our future development. Those who will decide to work abroad might even serve as bridges in future North-South collaborations. Certainly, our modest contribution from KNUST to the global understanding of molecular/material reaction mechanisms in the development of functional molecular/materials through our publications would not have been possible without the support of CHPC. The new final fourth-year undergraduate young researchers who joined us late last year are making steady progress in their research. Power outages were a little bit of a problem but CHPC communications concerning these outages have been excellent.
Principal Investigator: Prof Ray Everson
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2023-10-09
Allocation End: 2024-04-30
Used Hours: 1111431
Project Name: CO2 Capture in Circulating Fluidized Beds
Project Shortname: MECH0866
Discipline Name: Chemical Engineering
The Research Programme is a collaboration between NWU and VUT focused on emissions reduction and sustainability with a broader focus on CO2 and SO2 capture and management. The current use of the CHPC systems has been on modelling SO2 capture in Flue Gas Desulphurization. The work is part of the ongoing efforts by the Eskom Power Plant Engineering Institute (EPPEI) specialization centre for Emissions Control at the North West University in assisting Eskom to meet both national and global environmental regulations with respect to CO2 and SO2 emissions. In spray-dry scrubbing, hot flue gas is contacted with a spray of an alkali slurry in order to remove SO2 from the gas stream. The advantage of this process is the generation of dry product, eliminating the need for slurry handling and reducing the overall water usage and waste-water production of the desulphurization process. In this work, successive modelling of the three key phenomena occurring in spray-dry scrubbing, which entail Hydrodynamics modelling, Evaporation/Drying modelling and SO2 absorption modelling, including Chemical reaction modelling, is implemented in a computational fluid dynamics platform (Starccm+). The process itself is a multiscale, multiphase and multiphysics problem requiring high computing systems to solve the complex differential equations defining these phenomena, which has been made possible by the CHPC. The spray drying process has been successfully modelled using the CHPC and validated with experimental data; we are currently working at fine-tuning some data for publication and the ambition is to have this completed by the end of August. We are also busy with the next section of the project wherein the desulphurization model will be concluded, deployed on the CHPC and the results validated with experimental data.
Principal Investigator: Dr Adeniyi ogunlaja
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 7
Allocation Start: 2023-10-10
Allocation End: 2024-04-10
Used Hours: 5697
Project Name: Chemistry and Material Science
Project Shortname: MATS1070
Discipline Name: Chemistry
Dr Adeniyi Ogunlaja (Research group -Analytical/Inorganic) research at Nelson Mandela University crosses many themes including Bio-materials, Nanomaterials and Catalysis. Three research questions guided my research. The first one asks about the conditions and approaches that can be adopted for oil recovery, detection of organosulfur compounds in fuel oils and purification of fuels such as adsorptive-catalytic treatment of fuels (denitrogenation and desulfurization methods). The second question focuses on tackling global warming by turning carbon dioxide into fuel, what levels of CO2 can be converted to fuels? The third question looks into potential antimicrobial and anticancer properties of metal complexes and cocrystals. Generally, findings show that redox properties of both metals complexes and cocrystals offer unusual routes for new mechanisms for antimicrobial and anticancer therapy. In all projects, the understanding of catalysts and new drugs electronic properties is very important, hence the need for computation study. 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: Dr Phindile Khoza
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2023-10-10
Allocation End: 2024-04-30
Used Hours: 54508
Project Name: Macrocyclic Molecules and Nanomaterials for Solar Energy and Environmental Remediation
Project Shortname: MATS1481
Discipline Name: Chemistry
Our research group is from the University of KwaZulu Natal; I am collaborating with my colleagues from a university in Nigeria. Our focus is on the synthesis of materials – nano, and micro for applications in solar energy, cancer, and water treatment. There is a dire need to discover materials that will be applicable in different areas. Cancer, wastewater treatment, and solar energy research are all very important fields requiring attention to come up with novel materials that'd be efficient and effective. Computational modelling of organic and/or inorganic novel materials before going to the lab saves time and affords you the opportunity to develop compounds with superior properties; this is where CHPC comes in, giving us the opportunity of virtually 'seeing' and developing a compound. This is an ongoing project, and it started in 2022. We have published four articles (since we started) in peer-reviewed journals. The computational method used is a relaxed potential energy surface scan (PES) with selected dihedral angles constrained to 4 steps of 90 degrees, using the TD-DFT (up to 50 excited states for each scan) at the B3LYP/6-31G level.
Principal Investigator: Dr Anthony Pembere
Institution Name: Jaramogi Oginga Odinga University, Bondo, Kenya
Active Member Count: 2
Allocation Start: 2023-10-10
Allocation End: 2024-04-25
Used Hours: 190162
Project Name: Investigating electronic and photovoltaic properties of organic semiconductors
Project Shortname: CHEM1540
Discipline Name: Chemistry
Our research group is called computational material science. We are based at the Department of Physical Science, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Bondo – Kenya, and collaborate closely with colleagues at the Department of Pure and Applied Chemistry, University of Calabar. We use computational methods to probe the dynamics, kinetics, chemical bonding and reactivity of novel inorganic and organic materials for applications in catalysis, solar cells, adsorption and drug delivery. Being given access to the CHPC facilities has been of great benefit to us, since it has enabled us complete the work that previously had been impossible due to limited computational facilities.
Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2023-10-12
Allocation End: 2024-04-30
Used Hours: 171506
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 is continuously validated using test cases from literature.
Principal Investigator: Dr Francis Opoku
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 20
Allocation Start: 2023-10-11
Allocation End: 2024-05-02
Used Hours: 3143398
Project Name: High-Throughput theoretical design of two-dimensional materials as an ultrasensitive toxic gas sensor
Project Shortname: MATS1423
Discipline Name: Chemistry
The ever-increasing global demand for energy and concerns regarding the environment have necessitated the discovery of renewable and clean energy sources to replace non-renewable fossil fuels. Solar energy is a significant potential substitution for fossil fuels as a clean and renewable resource. By converting solar energy directly into electric energy with the photovoltaic effect, solar cells are promising products that can efficiently capture light energy from the sun. Using first−principles DFT calculations and taking into account the impact of in−plane biaxial strain, we thoroughly explore the optical, electronic, mechanical, transport, and photocatalytic properties of 2D van der Waals (vdW) heterostructures.
1. Al2OS/Ga2SSe vdWH has remarkably higher electrical conductivity than corresponding monolayers in n − type doping region, responsible for large power factor and suitable Seebeck coefficient, making it promising for thermoelectric device applications.
2. The findings of the scavenger experiments and Electron spin resonance measurements proved that •OH and •O2− radicals played superior role in decomposition of sulfamethoxazole in water or wastewater.
3. The results show that using La-doped ZrO2/g-C3N4 nanocomposites for eosin yellow photocatalytic degradation yields an 87% efficiency with a rate constant of 11.301 × 10−3 min−1 within 210 min.
4. The phonon spectra, interlayer distance, binding energies and ab initio molecular dynamics calculations show the kinetic, mechanical, and thermal stability of GeC/g-C3N4 vdWH after hydrogenation at 300, 500 and 800 K and possesses anisotropic Poisson's ratio, Young's and bulk modulus, suggesting that it's a promising candidate for experimental fabrication.
Principal Investigator: Dr Kgothatso E Machaba
Institution Name: University of KwaZulu-Natal
Active Member Count: 1
Allocation Start: 2023-10-16
Allocation End: 2024-04-15
Used Hours: 28740
Project Name: Dr. Machaba's Bioinfo Group
Project Shortname: HEAL1634
Discipline Name: Health Sciences
The "Computational Group" at University of KwaZulu-Natal led by Dr. Kgothatso E Machaba focuses on using computational methods to study biological systems, with research interests including protein structure prediction, drug discovery, and systems biology. The work being done by our research group contributes to addressing societal challenges, advancing scientific knowledge, improving quality of life, training future leaders and encourage the development of international collaboration. These benefits justify the use of public resources to support research endeavors that have the potential to create positive impacts at local, national, and global levels.
The research process involves formulating hypotheses, designing experiments or simulations, collecting and analysing data, and interpreting results to draw conclusions. In computational research, this often includes running complex simulations or calculations using high-performance computing systems. The CHPC plays a crucial role in enabling us by providing state-of-the-art HPC resources and support services. Hence, the CHPC's supercomputers, have massive computing power and storage capabilities. The CHPC optimizes the allocation of resources, ensuring efficient execution of research tasks.
Overall, the project is progressing well, with significant achievements and milestones reached. The team remains focused on achieving project objectives and addressing any challenges that arise. With continued support from the CHPC, dedication and collaboration, we are confident in the project's success.
Principal Investigator: Dr Mary-Jane Bopape
Institution Name: South African Weather Service
Active Member Count: 25
Allocation Start: 2023-10-17
Allocation End: 2023-10-31
Used Hours: 103414
Project Name: Very Short Range Forecasting
Project Shortname: ERTH1022
Discipline Name: Earth Sciences
The South African Weather Service researchers working in collaboration with the National Research Foundation- South African Environmental Observation Network (NRF- SAEON) to investigate the performance of the Conformal Cubic Atmospheric Model when simulating high impact weather events. The results showed that the CCAM did not advance the weather system as well as in the observations when it was forced with data from the global forecast system (GFS). Experiments were also conducted where the CCAM was also forced with the ERA5 reanalysis, in which case, the model showed moved the system in better agreement to the observations, This work suggests that the lag in the weather system is because of the forcing data and not because of CCAM. This is an important conclusion because it points us to the potential source of errors in the weather forecasts. Model simulations are critical component of the early warnings value chain, and it is important that forecasts are produced with skill. More work will continue with the CCAM forced with the ERA5 for future sensitivity studies.
Principal Investigator: Prof Simon Connell
Institution Name: University of Johannesburg
Active Member Count: 13
Allocation Start: 2023-10-17
Allocation End: 2024-05-07
Used Hours: 129940
Project Name: Modelling of Multiphase Flow in Process Equipment
Project Shortname: MECH0837
Discipline Name: Computational Mechanics
Simon Connell's research group at the University of Johannesburg is actively involved in several key research areas. Their primary focus includes Computational Fluid Dynamics (CFD) modeling of infectious diseases, the ATLAS project, Hydrocyclones, and High-PIPE Heat Exchangers (HPHE). In their infectious disease modeling work, they employ CFD techniques to gain valuable insights into disease dynamics, aiding in the understanding and management of such diseases.
The group actively contributes to the advancement of the ATLAS project, lending their expertise to its development. They also conduct research on Hydrocyclones, exploring their applications and functionality to improve performance. Additionally, they dedicate efforts to researching High-Performance Heat Exchangers, aiming to enhance efficiency and overall performance.
Simon Connell and his team's research endeavors make significant contributions to infectious disease modeling, the ATLAS project, Hydrocyclones, and heat pipe heat exchange. Their commitment to addressing real-world challenges and driving innovation in these critical areas is evident in their work. The CHPC has provided all necessary computational resources to ensure the success of this project
Principal Investigator: Dr Salerwe Mosebi
Institution Name: University of South Africa
Active Member Count: 5
Allocation Start: 2023-10-18
Allocation End: 2024-04-18
Used Hours: 92915
Project Name: Centre for Metal-based Drug Discovery
Project Shortname: CHEM1013
Discipline Name: Health Sciences
Our research programme focuses on mechanisms of bacterial and viral pathogenesis and antiviral drug discovery, as well as the development of novel diagnostic tools for animal and human diseases. Here we use cell biology, genetics, structural biology, molecular or in-silico modelling and drug discovery techniques to investigate and understand the molecular properties of HIV integration, viral-host factor relationships in viral pathogenesis, and replication of retroviruses (e.g., HIV-1). The research is also looking at various cancer drug targets (Estrogen receptor alpha-36) and the potential inhibitors thereof. Here, the group relies heavily on the high computing tools provided by the CHPC as we are able to screen millions of compounds in-silico to identify potential chemical scaffolds that enable us to rationally select and synthesize prospective compounds for biological screening. Molecular dynamic simulations through CHPC tools are also utilized to help predict the binding affinity between drug candidates and their targets – a feat that assist us to identify molecules with the highest potential for therapeutic efficacy. Not only does this reduce the cost of our drug discovery research but it also allows us to expedite the screening process – a strategy that is used by Big Pharma.
We also conduct high-throughput screening (HTS) of chemical compound libraries (from commercial sources), natural products extracts (plant, marine and microbial) from Sub-Saharan Africa to identify new and characterize new antivirals and anticancer compounds. Accordingly, novel biological assays that enable us to identify ''hit" or lead compounds are developed in-house and adapted for HTS platform. Secondary follow-up assays (e.g., cytotoxicity and cell-based assays) are also conducted in-house for further compound characterization. Additionally, the research conducted is also aimed at identifying and characterizing disease-relevant target pathways and proteins as well as the synthesis of novel chemical scaffolds as potential inhibitors of identified and validated targets (e.g., SARS-CoV-2 Nucleocapsid and Spike proteins).
Furthermore, through industry collaborations, our group is working on the development of rapid, specific, and selective diagnostic assays for zoonotic diseases (e.g., Rift valley fever virus, Brucellosis) as well as communicable and non-communicable diseases like COVID-19, HIV, TB, malaria and cancer.
Principal Investigator: Dr Gavin Gouws
Institution Name: SAIAB
Active Member Count: 3
Allocation Start: 2023-10-18
Allocation End: 2024-04-18
Used Hours: 2326
Project Name: RADseq studies of aquatic biodiversity
Project Shortname: CBBI1274
Discipline Name: Other
The PI and his team of students and collaborators, mostly involving the National Research Foundation - South African Institute for Aquatic Biodiversity (NRF-SAIAB), employ a variety of genetic tools to understand the evolution and ecology of marine and freshwater fishes and 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 biodiversity conservation and fisheries management.
Over the last year, we have conducted studies to investigate the genetic structure and patterns of population connectivity in a commercially-exploited and previously-overharvested marine fish (the slinger, Chrysoblephus puniceus). In particular, this research assessed the connectivity between Marine Protected Areas and unprotected areas along the east coast of South Africa, to determine whether these form an efficient network to protect stocks of this species, and to investigate spill-over and resource provision from conservation areas to those areas where fishing is allowed. Additionally, we examined patterns of relatedness in juvenile fishes and attempted to determine likely parental populations to identify areas which seed both MPAs and unprotected areas. This information is important for the management of the fishery dependent on this species and provides a template for the study of other linefishes. This study was the focus of the PhD of Samantha Ockhuis, who graduated in April 2024.
Additional studies concerned the invasion pathways of freshwater crayfish and the movement patterns of freshwater crabs in and among river systems.
This research is yet to be published, but draft manuscripts are being prepared.
Principal Investigator: Prof Nosipho Moloto
Institution Name: University of the Witwatersrand
Active Member Count: 9
Allocation Start: 2023-10-19
Allocation End: 2024-04-23
Used Hours: 312542
Project Name: Wits Quantum Dots
Project Shortname: MATS1284
Discipline Name: Material Science
Pioneering Computational Approaches in Renewable Energy Research at the University of the Witwatersrand
The University of the Witwatersrand's groundbreaking research group, "Nanomaterials for Water, Energy,
Biomedical, and Sensor Applications" (NanoWEBS), is at the forefront of scientific efforts to address the energy crises in South Africa. NanoWEBS, based in the School of Chemistry within the Faculty of Science, specializes in cutting-edge research related to renewable energy technologies. Specifically, our work centres on modeling quantum dots and nanomaterials for various energy applications. These materials exhibit remarkable potential in transforming how we harness and utilize energy, from enhancing solar cells to developing catalysts for green hydrogen production. The importance of this work cannot be overstated. South Africa faces critical challenges in energy sustainability, and we are committed to pioneering innovative solutions. Renewable energy, particularly in the form of advanced materials, holds immense promise for achieving a sustainable future in this sector.
Our research team comprises both experimentalists and computational experts. While experimentalists focus on the synthesis and characterization of nanomaterials, computational specialists employ advanced models to explain our experimental findings. These computational simulations provide valuable insights into the properties and behaviours of nanomaterials, aiding our quest to unlock their full potential. As our research progresses, we anticipate an increasing need for computational resources. This is where the Centre for High-Performance Computing (CHPC) facilities play a pivotal role. They provide the
computational power required for in-depth analyses and simulations, helping us gain a deeper understanding of these transformative materials. Our project is going to a promising start, with a clear trajectory toward further breakthroughs. The impact of our research extends to renewable energy, water resources, biomedical applications, and sensor technologies, offering real-world solutions to the challenges facing South Africa.
Principal Investigator: Dr Marina du Toit
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2023-10-23
Allocation End: 2024-04-30
Used Hours: 38024
Project Name: Nuclear safety of PAR, new nuclear fuel development and hydrogen internal combustion
Project Shortname: MECH1507
Discipline Name: Computational Mechanics
Scientists in the energy field are focused on discovering alternative energy sources to replace fossil fuels. Future energy sources must meet certain criteria including suitability for transportation fuel, ease of conversion into other forms of energy, high utilization efficiency, safety throughout the fuel lifecycle, environmental friendliness, and affordability. Hydrogen energy is considered one of the most promising future energy carriers as it satisfies many desirable characteristics. However, the use of hydrogen energy remains a safety concern. During a hypothetical case of a severe accident in a nuclear power plant, hydrogen refueling station, or any other hydrogen infrastructure, a large amount of hydrogen can be released in the facility (confined or enclosed environment). Due to the wide range of the flammable concentration (4-75 vol.% hydrogen in air at STP), the hydrogen-air mixture can pose a significant danger of deflagration or explosion. In order to mitigate an accidental hydrogen release, dispersion, and explosion, the air ventilation systems or/and PAR can be considered for use. Air ventilation systems are generally installed where hydrogen infrastructure is present. PAR's operation is based on the principle of exothermic reaction of H2/O2 on platinum (Pt) catalyst. Computational Fluid Dynamics (CFD) is the numerical approach used to solve challenging problems related to fluid mechanics, heat transfer, chemical reactions, etc. The advent of CFD has been a significant advancement in studying the progress of chemical processes using the principles of similitude theory and modelling of chemical reactions, as well as heat and mass transfer.
Principal Investigator: Mr David Ngobeni
Institution Name: Council for Geoscience
Active Member Count: 16
Allocation Start: 2023-10-25
Allocation End: 2024-04-30
Used Hours: 139356
Project Name: Application of high performance computing at the Council for Geoscience
Project Shortname: ERTH1227
Discipline Name: Earth Sciences
The Council for Geoscience (CGS) was established under the Geoscience Act (Act No. 100 of 1993), as amended in 2010. The organisation is listed as a schedule 3A public entity in terms of the Public Finance Management Act (No. 1 of 1999). The principal act mandated the Council for Geoscience to generate, curate and publish world-class geoscience knowledge products and to render geoscience-related services to the South African public and industry. The mandate for the CGS includes basic geoscience research into the nature and origin of rocks, ores, minerals, formations, the history and evolution of life and the formation of the earth with a view to understanding the geological processes of the past and present and to compile and publish such research findings nationally and internationally to contribute to the understanding of the earth, its evolution and its resources. For the CGS to fulfil its mandate and advance the geoscience field in South Africa and beyond, it adopted modern software packages, among other approaches, that require high computing power, which a normal laptop or desktop cannot provide. For this reason, the CGS sought access to the Centre for High Performance Computing (CHPC) for the purpose of expanding its computing resources. The CHPC research programme entails running high-performance computer programs for geophysical modelling, seismological data processing, geological modelling, and any other packages that are currently not suitable for desktop computing. This program covers research in the many scientific operations of the CGS, including infrastructure and land use, water and environment, and minerals and energy.
Principal Investigator: Dr Phillip Nyawere
Institution Name: Kabarak University, Nakuru, Kenya
Active Member Count: 14
Allocation Start: 2023-10-25
Allocation End: 2024-05-09
Used Hours: 127750
Project Name: Barium Floride and Perovskites
Project Shortname: MATS0996
Discipline Name: Physics
MAT0996: BaF2 and Perovskites is a Physics computational group based in Kenya with PI based in Kabarak University. Our research group is interested in training postgraduate students in materials research. We are collaborating with Kisii University also based in Kenya to offer supervision in Physics to students taking computational research. Our research work involves use of computer codes such as fortran language to simulate properties of materials. These studies could as well be done in the laboratory but at elavated costs in terms of time and resources. We use high speed and high capacity computers to enable the calculations to run thorugh.These calculations require huge memories and high speed computers and cannot run successfully in PCs and laptops.
This work runs through mathematical numerical analysis that mimics the actual behaviour of materials at atomistic levels. This requires knowledge of the science and computer programing languages. We therefore need trained graduate students and CHPC staff that guides the job submissions. This collaborations enables successful completion of our tasks on time. This has indeed helped our students to accomplish their research within stipulated timelines.
So far we have managed to graduate a total of seven students with more students expected to graduate this year.
Principal Investigator: Prof Ponnadurai Ramasami
Institution Name: University of Mauritius
Active Member Count: 4
Allocation Start: 2023-10-25
Allocation End: 2024-05-07
Used Hours: 20932
Project Name: Computational Chemistry Methods to Study Structural and Spectroscopic Parameters
Project Shortname: CHEM1290
Discipline Name: Chemistry
Prof Ponnadurai Ramasami is the leader of the Computational Chemistry Group in the Department of Chemistry, Faculty of Science of the University of Mauritius. He also holds a UNESCO Chair in Computational Chemistry. The research group focuses on the use of computational methods to solve chemistry and interdisciplinary problems.
During the past 6 months, we used Gaussian and ORCA software to elucidate reaction mechanism for atmospheric reactions. We are also studying products that are expected to be present in the atmosphere at molecular level. We are currently working on one manuscript related to the reaction of hydrofluoroolefins and their contribution to ozone depletion and another manuscript on the reaction of dimethyl sulfide with halogens.
The URL of the website of his research group is https://sites.uom.ac.mu/ccuom/
Principal Investigator: Prof Sybrand van der Spuy
Institution Name: Stellenbosch University
Active Member Count: 7
Allocation Start: 2023-10-25
Allocation End: 2024-04-30
Used Hours: 1005690
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 five 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 and a number of theses, journal papers and conference publications have stemmed form this work.
Principal Investigator: Prof MJ Booysen
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2023-10-26
Allocation End: 2024-05-17
Used Hours: 407706
Project Name: Media Lab
Project Shortname: MECH1637
Discipline Name: Electrical Engineering
Electric water heating, commonly implemented in most domestic houses for hot water in South Africa, is one of the largest energy consumers in a our households, contributing to roughly between 40%-45% of the electricity bill.
We are a research group dedicated to fully characterizing these heating devices, located in the Media lab at Stellenbosch University. Our research goal is to develop intelligent models that are inexpensive to execute for geyser control strategies. These control strategies have the ultimate goal of reducing the load on the grid and the the money spent on the consumer's electricity bill.
The work that is done on the CHPC is to help characterize everything we need to know about the internal thermodynamic characteristics relating to these devices, so that we have an informed idea about what we want to control and how we can control it using different mathematical models.
The process is simple.
We take a very commonly-used geyser in SA, the 150L tak with a heating power of 3kW and we create a physical 3D model using CAD software.
Following this, we can import this 3D construction into Simulation software to very accurately see what the temperatures are in the tank, thus we know what the energy capacity is as time progresses under different operational conditions. These include heating from the coil, water draw, cooling down, etc.
The CHPC has given us the acceleration that we need in our project to fully understand and to characterize these devices for multiple use cases. We have successfully generated data that can be used by anyone once it is published.
The next steps include publishing the results from the simulations in a Data in Brief article followed by a more in-depth Article where these simulations are discussed in more detail.
Principal Investigator: Prof Regina Maphanga
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 12
Allocation Start: 2023-10-26
Allocation End: 2024-05-09
Used Hours: 1139426
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 Quentin Santana
Institution Name: Agricultural Research Council
Active Member Count: 2
Allocation Start: 2023-10-27
Allocation End: 2024-04-26
Used Hours: 2045
Project Name: Plant Pathogenomics
Project Shortname: CBBI1638
Discipline Name: Bioinformatics
Plant pathogenomics is a multidisciplinary field that combines genomics, molecular biology, and plant pathology to study the genetic makeup of plant pathogens, such as fungi, bacteria, and viruses, and their interactions with host plants. By analyzing the genomes of both the pathogens and their host plants, plant pathogenomics aims to understand the molecular mechanisms underlying plant diseases, identify potential targets for disease control, and develop strategies for breeding resistant crops. This knowledge can help mitigate the impact of plant diseases on agriculture and food security.
Principal Investigator: Dr Quinn Reynolds
Institution Name: Mintek
Active Member Count: 6
Allocation Start: 2023-10-30
Allocation End: 2024-05-30
Used Hours: 627885
Project Name: Computational Modelling of Furnace Phenomena
Project Shortname: MINTEK776
Discipline Name: Applied and Computational Mathematics
Here's what you do to make steel. You take iron ore, which is just rock containing iron oxides. You heat it up. And while it's hot you react it with carbon, which is just coal or metallurgical coke. This simple, cheap process makes metallic iron with a little bit of carbon in it – steel – which is a construction material of such astonishing versatility that it's fuelled humanity's technological development ever since its discovery more than two thousand years ago.
But there's a problem.
Reacting carbon with the oxygen in raw ore to make steel and many of the other critical commodities that our modern industrialised societies depend on produces carbon dioxide. A lot of carbon dioxide. In fact, it is estimated that steel production and other pyrometallurgical smelting processes currently generate nearly 10% of the world's CO2 emissions. Reducing or eliminating this industry's carbon footprint is one of the greatest challenges of our time, but it can be done. New smelting processes using clean reductants like hydrogen are being rapidly developed and fast-tracked into industry as we speak – and because time is not on our side when it comes to addressing the climate crisis, we need to leverage any and every tool available to study these processes and understand them well enough that they'll actually work when we turn them on. By developing and deploying advanced computational and numerical modelling techniques Mintek are able to perform detailed research and development on novel pyrometallurgical processes in silico, before a single brick is laid.
It's all hands on deck when it comes to the daunting task of decarbonising our metal production industries, and with access to resources like the Centre for High Performance Computing, Mintek is helping to turn that challenge into reality.
Principal Investigator: Prof Eric K. K. Abavare
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 7
Allocation Start: 2023-10-30
Allocation End: 2024-04-29
Used Hours: 834589
Project Name: Atomic and Electronic structures of semiconductor interface systems
Project Shortname: MATS1159
Discipline Name: Physics
26TH APRIL 2024
PRESS RELEASE, CHPC SOUTH AFRRICA
The Frontier Science Group (FSG) of the Department of Physics, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana is proud to be associated with the Centre for High Performance Computing (CHPC) in South Africa. The group's interest is on the investigation of atomistic and electronic properties of light materials using quantum mechanical approaches based on first principles calculations in the framework of density functional theory (DFT).
The group research basically focuses on the study of surfaces and interface, magnetic materials, optoelectronic and nanomaterials. 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 growths 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, for the magnetic materials, we concentrate on doping of the -phen materials; that is the doping of the single layer of group IV materials. We are also involved in greenhouse gases detection.
The cubic 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 involve 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 forward the frontiers of this area for mankind in our quest for the pursuit of scientific achievement and better human life through technology.
Principal Investigator: Prof Rotimi Sadiku
Institution Name: Tshwane University of Technology
Active Member Count: 11
Allocation Start: 2023-10-30
Allocation End: 2024-04-29
Used Hours: 768805
Project Name: NANOCOMPOSITE FOR ENERGY STORAGE
Project Shortname: MATS1376
Discipline Name: Material Science
Who: Prof. E.R. Sadiku and his esteemed research team at Tshwane University of Technology have achieved groundbreaking advancements in the realm of energy storage technology.
What: Their research endeavors encompass a wide range of investigations, including the development of electrode materials for advanced battery systems and the exploration of innovative drug delivery strategies using nanocomposites. Through computational simulations and ab-initio analyses, they have uncovered promising avenues for enhancing energy storage efficiency and combating virus infections.
In Brief: Prof. E.R. Sadiku and his team have made remarkable strides in the fields of energy storage and pharmaceutical sciences. Their multidisciplinary approach, coupled with state-of-the-art computational techniques, holds immense potential for addressing global challenges and improving human well-being.
Principal Investigator: Dr Thobani G. Gambu
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2023-10-31
Allocation End: 2024-05-02
Used Hours: 273826
Project Name: BET/Catalysis: Catalysis on responsive substrates - towards dynamic catalytic theory
Project Shortname: MATS1516
Discipline Name: Chemical Engineering
The utilization of carbon dioxide with green hydrogen to form clean fuels or chemicals is of paramount importance. The primary objective of this project is to generate new systems for the conversion of this greenhouse gas.
My new group at the University of Cape Towns, Catalysis Institute, aims to utilize dynamic electric fields and light eradiation to improve catalytic performance of ferroelectric based catalyst materials for this reaction. The CHPC resources are key in (i) identifying candidate catalyst systems with required properties and (ii) generating energetic data for microkinetic modelling necessary for the study of the catalytic performance under dynamic conditions. These models will enable us to gain insight into how these systems behave. Such insights will aid our primary goal of developing practical systems for these reactions under dynamic conditions.
Thus far, the project has focused on establishing a baseline by studying MoC and Cu based systems for the same application under static conditions. The work on MoC has provided key insights into the role and function of the catalyst.
The latter work will form part of a poster presentation at the International Congress on Catalysis (ICC), in July 2024, in France.
Since the last report, the project has also managed to raise funding for and recruit an MSc student whose work will focus on understanding the copper based catalyst for carbon dioxide conversion to methanol.
Principal Investigator: Prof Mwadham Kabanda
Institution Name: University of Venda
Active Member Count: 2
Allocation Start: 2023-10-31
Allocation End: 2024-04-01
Used Hours: 1540431
Project Name: Reaction mechanism for atmospheric relevant molecules
Project Shortname: CHEM1161
Discipline Name: Chemistry
The research group is under Prof Mwombeki Kabanda as the principal investigator. He is attached to the University of Venda in the department of Chemistry. There are 4 MSc and PhD students (which are Mr Masuku MG, Mr Nyembe S, Mr Ratshikombo R and Ms Tshikhudo F) working under Prof Kabanda's group (all of them submit their jobs through the principal investigator account, which is controlled and managed by Prof Kabanda). The work is associated with investigation of molecules with potential application in the corrosion inhibition processes and atmospheric processes. There is great concern in terms of finding corrosion inhibitors that have potential to inhibit or slow down the corrosion process worldwide, as it has destructive effects on structural materials. Our research group tackles this issue by studying the ability of selected corrosion inhibitors to interact with mild steel surface. In the other research related to the environment, we are investigating the ability of certain metal chelator molecules to trap certain metal cations from the seawater and be able to selectively separate them. The work is being done because the simulation of the interactions between metal surfaces and inhibitor molecules or that between metal chelator molecules and the cations are better obtained only through computational approaches. These approaches allows one to obtain the energies that are used as criteria to identify the stability of the species under investigation. CHPC therefore allows us to be able to receive the necessary computational resources that we would other wise be not able to reach. The calculations are performed by using the Gaussian program (version C) and Material studio, which are both available within CHPC. The computational resources provided allows for calculation of different types of geometries. The energies of the structures are then obtained from the output of the geometries. The project is progressing well, we have already obtained significant results and we hope to soon publish some of our results.
Principal Investigator: Prof Hasani Chauke
Institution Name: University of Limpopo
Active Member Count: 16
Allocation Start: 2023-10-31
Allocation End: 2024-05-02
Used Hours: 386990
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. Professor Hasani Chauke is the primary investigator under the minerals, metal and alloy development programme. The area of specialization is on mineral processing and metal alloy development using first-principles, molecular dynamics and machine learning techniques, which employ various academic and commercial software with different types of interfaces. The user interfaces are linked to local servers and also benefit from the Centre for High Performance Computing (CHPC). Most of the work carried out are projects at Honours (Hons), Masters (MSc) and Doctoral (PhD) studies. The programme continues to receive enormous support from the CHPC, particularly to run large-scale calculations at a more reasonable time. The programme supports about seven (07) postgraduate students at honours, masters, doctoral levels and two (02) post-doctoral fellows and one (1) senior researcher.
Principal Investigator: Prof Craig McGregor
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2023-11-01
Allocation End: 2024-05-01
Used Hours: 17391
Project Name: Solar thermal CFD
Project Shortname: MECH1640
Discipline Name: Chemical Engineering
The Solar Thermal Energy Research Group (STERG) is housed in the Department of Mechanical and Mechatronic Engineering at Stellenbosch University and is affiliated with the Centre for Renewable and Sustainable Energy Studies (CRSES), the national academic hub for renewable and sustainable energy.
The work is a PhD study based on an evacuated tube collector with a compound parabolic concentrator. Evacuated tube collectors are a unique solar thermal collector system with various domestic and industrial heating applications. The collector comprises a series of u-tubes; each u-tube forms a T-junction with the inlet and outlet headers, at its inlet and outlet, respectively. The effects of various inlet geometries have been investigated before, however, there remains a gap in the study of inlet effects on developing flow in smooth tubes. The study is being conducted to establish a better understanding of the fluid flow and heat transfer characteristics within the collector. This will provide insights into the effects of inlet geometries on the performance of various mechanical systems like solar thermal collectors and heat exchangers which are core systems in industrial processes.
The study includes an optical investigation of the collector which will be conducted using one of the radiation models available on ANSYS Fluent. Radiation models on ANSYS Fluent are computationally intensive hence the need for the CHPC resources. Additionally, to achieve accuracy with our results, the numerical model of the collector which incorporates results obtained from the radiation model will make use of a very fine mesh. To determine the right sized mesh, a mesh independence study is necessary. Finally, validation of methods is a very critical step in numerical research. The CHPC will contribute greatly towards efficiently achieving these key milestones of the study.
The project is progressing well. The radiation is currently being modelled using the Discrete Ordinates method in ANSYS Fluent. Once the parameters have been appropriately defined, the CHPC will be used to run the simulations.
Principal Investigator: Prof Marlo Moller
Institution Name: Stellenbosch University
Active Member Count: 11
Allocation Start: 2023-11-06
Allocation End: 2024-05-06
Used Hours: 126503
Project Name: Tuberculosis Host Genetics
Project Shortname: HEAL1360
Discipline Name: Health Sciences
Although approximately 25% of the world's population is infected with Mycobacterium tuberculosis, the vast majority will never develop any clinical tuberculosis (TB). Inter-individual variation in the immune response plays a major role in determining different clinical outcomes in infected persons. The Tuberculosis Host Genetics group based at Stellenbosch University aim to identify these unknown host genetic factors influencing immunity. Our investigations of the genetic contribution of the human host to individual and population susceptibility to tuberculosis span the full continuum of TB susceptibility, ranging from those extremely susceptible to disease to those seemingly resistant to infection. We have focused on TB genome-wide associations studies, host genes and strain interactions, the role of sex and ancestry in disease, TB "resisters", tuberculous meningitis and primary immunodeficiencies (PIDD) presenting with an increased TB susceptibility. Our experience in the genetic diagnosis of PIDD has allowed us to expand to the diagnosis of other rare genetic diseases by using the pipelines initially developed for PIDD. We also take the work to the cellular level by studying the function of the TB susceptibility genes discovered, with a specific interest in autophagy. Our insights into the latest genetic analyses available have allowed the work on genetic susceptibility to TB to benefit from population genetic analyses and next generation sequencing. Our work leverages the complex ancestry of South Africans, especially the unique genes from KhoeSan ancestry, to find novel genes and pathways involved in TB resistance or susceptibility, as shown by our admixture mapping. We are currently supervising a ground-breaking project on the sequencing and de novo assembly of an admixed South African genome and establishing recombination maps to African groups. Our chief strength is on putting a uniquely African emphasis on the current highly computational field of genetics as it impacts on human disease, while exploring the downstream functional effects. The findings of our work could in future contribute to the development of host-directed therapies. Moreover, we are contributing to diagnosing rare diseases, including primary immunodeficiencies, in a developing country.
Principal Investigator: Dr Ryno Laubscher
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2023-11-06
Allocation End: 2024-05-31
Used Hours: 139514
Project Name: CFD Programme for R Laubscher
Project Shortname: MECH1466
Discipline Name: Computational Mechanics
Significant milestones in simulation work were accomplished, pushing the boundaries of innovation in energy and healthcare. Researchers have successfully completed projects on gas turbine hydrogen combustion modelling, turbulent air flow modelling through boiler grates, and Fluid-Structure Interaction (FSI) modelling of aortic stenosis.
The FSI modelling project focuses on valvular diseases prevalent in sub-Saharan Africa, aiming to improve understanding and treatment of these conditions. The simulations employed industry-leading software, including ANSYS Fluent and Siemens Star CCM+.
These achievements demonstrate the CHPC's capabilities in driving cutting-edge research and development.
Principal Investigator: Prof Joanna Dames
Institution Name: Rhodes University
Active Member Count: 6
Allocation Start: 2023-11-07
Allocation End: 2024-04-09
Used Hours: 3567
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. This research in ongoing.
Principal Investigator: Prof Mark Tame
Institution Name: Stellenbosch University
Active Member Count: 5
Allocation Start: 2023-11-07
Allocation End: 2024-04-09
Used Hours: 16217
Project Name: Quantum simulation
Project Shortname: MATS1555
Discipline Name: Physics
The group at Stellenbosch consists of Prof. Mark Tame and his postgraduate students. We are working on simulating a variety of quantum systems on the classical computers available at the CHPC – from simulating small molecules using quantum chemical methods to simulating large systems of interacting atoms using quantum trajectories methods. The work we do is essential in the development of quantum algorithms that may eventually be run on quantum computers, as well as the realization of quantum systems for sensing and imaging purposes that have the potential to provide an enhancement in measurement precision. We make use of various software available on the CHPC – Gaussian, Schrodinger and Python – and hardware in the form of multiple computational processor units with very large RAM capacity, as well as graphics processor units. The projects are at an early stage, but they are coming along, with some initial positive results expected to be published in international journals soon.
Principal Investigator: Dr Kevin Lobb
Institution Name: Rhodes University
Active Member Count: 24
Allocation Start: 2023-11-07
Allocation End: 2024-04-09
Used Hours: 803233
Project Name: Computational Mechanistic Chemistry and Drug Discovery
Project Shortname: CHEM0802
Discipline Name: Chemistry
The Computational Mechanistic Chemistry and Drug Discovery Group at Rhodes University is led by Prof Kevin Lobb and Dr Tendamudzimu Tshiwawa. We explore several aspects of mechanistic chemistry and particularly enjoy working at a large scale in terms of chemoinformatics treatment of this kind of work. Further we look at target based virtual screening in the search for new active agents against disease and we have worked with a range of diseases including Malaria, COVID-19, TB, HIV and many more. In this research we look at virtual screening using molecular docking and other techniques, and take this through to a range of molecular dynamics including molecular mechanics based techniques but also quantum-mechanics/molecular mechanics multiscale techniques which are highly accurate in describing the active site of the enzyme target. For this work we do calculations, and these are heavily dependent on the high performance computing provided by the CHPC. Calculations are feasible at the CHPC in our work that would not be feasible on a desktop computer.
Principal Investigator: Prof Matthew Adeleke
Institution Name: University of KwaZulu-Natal
Active Member Count: 8
Allocation Start: 2023-11-08
Allocation End: 2024-05-08
Used Hours: 18972
Project Name: Computational and Evolutionary Genomics
Project Shortname: CBBI1231
Discipline Name: Bioinformatics
The Computational and Evolutionary Genomics group based in the Discipline of Genetics at the University of KwaZulu-Natal. The first focus of our work on parasite genetics and interaction with host, parasite molecular diagnostics and computational identification of vaccine candidate targets. Secondly, we employ metagenomics to quantify the abundance and diversity of microbiome in animals with a view to improving animal health and reduce methane emission to address climate change being impacted from animal agriculture. CHPC is required to handle large dataset being generated from the studies and to make use of the computational resources available in CHPC.
Principal Investigator: Dr Matshawandile Tukulula
Institution Name: University of KwaZulu-Natal
Active Member Count: 8
Allocation Start: 2023-11-08
Allocation End: 2024-04-10
Used Hours: 21236
Project Name: Medicinal Chemistry and Computer-Aided Drug
Project Shortname: HEAL1346
Discipline Name: Chemistry
Our research group is working in the field of Medicinal chemistry with the aim of discovering new inhibitors for HIV and TB. To date we have identified a number of potential inhibitors, some of which show excellent in vitro activities. We are currently working on various manuscripts on this aspect, and we hope to publish more on our endeavors.
Principal Investigator: Prof Ozlem Tastan Bishop
Institution Name: Rhodes University
Active Member Count: 12
Allocation Start: 2023-11-10
Allocation End: 2023-11-17
Used Hours: 201136
Project Name: Structural Bioinformatics for Drug Discovery refresh
Project Shortname: CBBI1436
Discipline Name: Bioinformatics
The Research Unit in Bioinformatics (RUBi) graduated 4 PhD and 2 MSc students in the October graduation. All PhD students and 1 MSc student achieved their degrees with a great contribution from CHPC. Their projects were in the different aspects of drug discovery and drug metabolism.
Principal Investigator: Prof Obodo Kingsley
Institution Name: North-West University
Active Member Count: 18
Allocation Start: 2023-11-10
Allocation End: 2024-06-13
Used Hours: 1026083
Project Name: Ab initio modelling of liquid organic hydrogen carriers catalyts and 2D materials
Project Shortname: MATS1366
Discipline Name: Physics
The research program "MATS1366: Ab initio modeling of liquid organic hydrogen carriers' catalyst and 2D materials" is conducted at the HySA infrastructure center of competence at North-West University, South Africa and currently the research leader is at Center for Space Research at the North-West University, Potchefstroom. Led by Kingsley Obodo the principal investigator, this program includes other researchers such as Asres, Georgies Alene, Hailouf Houssam, Okonkwo, Ifeanyichukwu, etc. The students in the program utilize the CHPC facility for their master's and doctorate research work, making significant progress in their field. Notably, the research group work includes the development of a dehydrogenation catalyst, an ab initio study of structural and electronic properties of Pt/Pd-based alloys, and research on hydrogenation of furfural-to-furfuryl alcohol over La-based inorganic perovskites.
This research program leverages density functional theory, implemented through software packages like CASTEP, Quantum Espresso, GPAW, and VASP, to carry out complex calculations. Additionally, the research group is working on other projects, including catalyst development for liquid organic hydrogen carriers (LOHCs) dehydrogenation and catalysts for water electrolysis, a process that breaks down water into hydrogen and oxygen. The team's innovative research is currently under review and pending publication, contributing to advancements in the field of battery, water splitting and catalyst development.
Principal Investigator: Prof Hadley Clayton
Institution Name: University of South Africa
Active Member Count: 5
Allocation Start: 2023-11-13
Allocation End: 2024-07-04
Used Hours: 52561
Project Name: Bioorganometallic Chemistry of Transition Metals
Project Shortname: CHEM1288
Discipline Name: Chemistry
The Organometallic Research Group led by Prof. Clayton is based at the Florida Science Campus at the University of South Africa. In this research group computer applications are used to investigate the bioorganometallic chemistry of transition metal complexes and their derivatives. This includes density functional methods which are applied to investigate chemical and physical properties of new transition metal complexes synthesized and molecular docking software which is used to study metal complex-protein interactions.
Our research focuses on the interaction between metal ions and biomolecules, aiming to uncover how these interactions influence biological activity. This research aims to unlock new insights into the fundamental processes of pharmaceutical-biomolecule interactions which has implications for medicine and drug discovery.
The research contributes to the development of structure-activity theories which guides the development of new drugs with potential for the treatment of cancer, rheumatoid arthritis, diabetes and malaria.
The complexity of these transition metal based pharmaceuticals requires detailed computational modelling to predict and understand the electronic properties of the metal-biomolecule interactions. The CSIR high-performance cluster provides the necessary computational power to model these systems at high levels of theory.
We have recently reported our finding on the potential use of zinc metal complexes as SARS-CoV-2 viral entry and replication inhibitors. The CHPC resources are used by two PhD students and one postdoctoral fellow in the group.
Principal Investigator: Dr Nicolette Chang
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 17
Allocation Start: 2023-11-14
Allocation End: 2024-05-17
Used Hours: 312467
Project Name: Southern Ocean Carbon - Climate Observatory SOCCO
Project Shortname: ERTH0834
Discipline Name: Earth Sciences
The Southern Ocean Carbon-Climate Observatory, based at the CSIR (SOCCO), is a research group that studies atmosphere-ocean carbon and heat in the Southern Ocean (SO). Globally, the SO plays a critical role in atmosphere-ocean carbon and heat exchange, transport, and storage and thus is a large source of uncertainty in both contemporary and end of the century climate projections, while the response of the SO carbon-climate system under different emission and mitigation scenarios is unknown. SOCCO observes and studies the mechanisms of fine-scale processes of the SO, which is poorly sampled at both spatial and temporal scales, in order to constrain these uncertainties and improve confidence in projections of climate risk by Earth System Models (ESM's). The complexity and size of these models depend on the use of NICIS-CHPC computational resources both for the simulation of ocean-ice-biogeochemistry experiments as well as the analysis of the large output data. Data from SOCCO's observational programme as well as from satellites require use of NICIS-CHPC to create new data products for climate interrogation and monitoring, for example, a machine-learning based carbon dioxide product. Additionally, SOCCO is expanding its capacity in model development and thus the efficient use of high performance computing, through model benchmarking studies. SOCCO is invested in human capital development, and NICIS-CHPC supports the training of interns and the theses of several postgraduate students enrolled at universities across South Africa.
Principal Investigator: Other Christo Venter
Institution Name: North-West University
Active Member Count: 7
Allocation Start: 2023-11-14
Allocation End: 2024-05-23
Used Hours: 48318
Project Name: Astrophysical Calculations and Data Analysis
Project Shortname: ASTR1245
Discipline Name: Astrophysics
Who? Several astrophysicists from the North-West University, along with international collaborators.
What? We are studying pulsars via complex numerical models and multi-wavelength data fitting.
Why? Pulsars have been an enigma since their discovery in 1967. Much progress has been made over the past decades, with the latest breakthroughs coming from the Fermi Large Area Telescope and ground-based Cherenkov telescopes that detected pulsars in the GeV to TeV energy range. We will continue to use the latest high-energy data to constrain our cutting-edge models and thus improve our understanding of pulsars. Broadly speaking, this contributes to highly skilled graduates who can make an impact in industry as well as communicate basic science to the public.
How? We are running large parallel codes on the CHPC in order to compute and fit models to data.
How is the project progressing? The progress has been steady and several publications are in view.
Principal Investigator: Prof Ozlem Tastan Bishop
Institution Name: Rhodes University
Active Member Count: 10
Allocation Start: 2023-11-15
Allocation End: 2024-05-15
Used Hours: 3379514
Project Name: Structural Bioinformatics for Drug Discovery refresh
Project Shortname: CBBI1436
Discipline Name: Bioinformatics
The Research Unit in Bioinformatics (RUBi) graduated 4 PhD and 2 MSc students in the October graduation. All PhD students and 1 MSc student achieved their degrees with a great contribution from CHPC. Their projects were in the different aspects of drug discovery and drug metabolism.
Principal Investigator: Prof RAGUPATHI RAJA KANNAN RENGASAMY
Institution Name: North-West University
Active Member Count: 1
Allocation Start: 2023-11-16
Allocation End: 2024-05-16
Used Hours: 10496
Project Name: Marine Drug Discovery
Project Shortname: HEAL1559
Discipline Name: Bioinformatics
Unlocking Nature's Pharmacy: Dr. Rengasamy's Research Group Dives into Marine Drug Discovery
North West University's Dr. Rengasamy and his dedicated team are making waves in the world of science with their groundbreaking research on Marine Drug Discovery. Delving into the depths of our oceans, they are uncovering potential life-saving compounds derived from marine organisms.
But why this focus on marine life? The answer lies in the vast biodiversity of our oceans, which remain largely unexplored. These underwater ecosystems harbor a treasure trove of unique organisms, each with the potential to produce compounds that could revolutionize medicine.
This research isn't just about scientific curiosity—it's about addressing pressing global health challenges. With antibiotic resistance on the rise and diseases like cancer continuing to devastate lives, novel therapeutic agents are urgently needed. Dr. Rengasamy's work offers hope for new treatments and cures.
So, how does it all work? Through a meticulous process of isolation and testing, Dr. Rengasamy's team extracts compounds from marine organisms and evaluates their potential medicinal properties. This process relies heavily on the advanced computational resources provided by the Centre for High-Performance Computing (CHPC), enabling the team to analyze vast amounts of data and accelerate their discoveries.
As for the project's progress, it's moving full steam ahead. Initial findings have been promising, with several compounds showing exciting potential for further development. While there's still much work to be done, Dr. Rengasamy and his team are committed to pushing the boundaries of scientific knowledge and bringing new hope to patients around the world.
Principal Investigator: Dr Zipporah Muthui
Institution Name: Chuka University, Chuka, Kenya
Active Member Count: 10
Allocation Start: 2023-11-17
Allocation End: 2024-06-06
Used Hours: 9605
Project Name: Electronic Structure and Magnetic Properties of Heusler Compounds
Project Shortname: MATS1112
Discipline Name: Physics
The MATS1112 group is composed of physics graduate students Bonface, Gabriel and Jane. Currently, Bonface and Gabriel have successfully completed their MSc graduated on 24th November, 2023. Jane has successfully defended her PhD proposal and has commenced her computations. Their research focuses on manipulation of material properties at the atomic level to provide alternative, environment friendly, green energy sources. Bonface dealt with modifying sodium bismuth titanate for piezoelectric applications, while Gabriel dealt with modification of molybdenum disulphide monolayer for visible light applications. Jane is dealing with modifications of TiO2 and ZrO2 for solar active photocatalytic applications. The PI, Dr. Zipporah Muthui has been working on a spin-gapless Heusler system for spintronic applications. These jobs require HPC resources as they involve supercells that require sufficient computing resources. Without the HPC resources provided, all these work would not have been possible.
Principal Investigator: Ms Robyn Jacob
Institution Name: SA Sugercane Research Institute
Active Member Count: 1
Allocation Start: 2023-11-20
Allocation End: 2024-05-20
Used Hours: 4347
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 continue research comparing genes identified in two eldana-challenged sugarcane transcriptomes 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: Dr Michelle Gordon
Institution Name: University of KwaZulu-Natal
Active Member Count: 6
Allocation Start: 2023-11-21
Allocation End: 2024-05-21
Used Hours: 857326
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 CHPC has greatly benefited our research programme overall, and to date, 7 PhD students have completed their degrees using resources from the CHPC.
Principal Investigator: Dr Thankhoe Rantso
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2023-11-23
Allocation End: 2024-05-23
Used Hours: 1558
Project Name: Advanced Protein Models
Project Shortname: HEAL1600
Discipline Name: Health Sciences
Our research group is led by Dr. Thankhoe Rants'o (PhD; Wits) and Dr. Gary Gabriels (PhD; UCT). Highly invested in proteomics work and in collaboration with international institutions, our group aims to uncover novel drug targets that drive cancer spreading (metastasis) and resistance to medicines.
This work is critical to not only identify potential new drug targets in the treatment of cancer but also, in the discovery of novel potent drugs. We perform molecular dynamics to find out how we can modulate the functions of proteins involved in drug resistance and metastasis. The CHPC platform has allowed us to study both the potential therapeutic and toxic effects of the molecules of interest. Our research and research group are constantly increasing.
Principal Investigator: Dr Nicholas Ongwen
Institution Name: Maseno University, Kisumu, Kenya
Active Member Count: 4
Allocation Start: 2023-11-23
Allocation End: 2024-06-06
Used Hours: 44401
Project Name: Mechanics and thermodynamics of advanced materials for the aerospace
Project Shortname: MATS1599
Discipline Name: Physics
The Mechanics and thermodynamics of advanced materials for the aerospace research group is a research group headed by Dr. Nicholas Ongwen from Maseno University (Kenya). The research group carries out research on mechanical and thermal properties of materials for use in the manufacture of airplane bodies such as frames and skins. The work aims at addressing the low hardness of aluminium by coming up with harder alloys that are also lighter than most of the alloys of aluminium. This can help the airspace industry to build lighter airplanes that can reduce the overall cost of travelling, since lighter bodies consume less fuel. Moreover, the new materials will help in reducing the overdependence on aluminium, which will then spare it for other uses. The work process includes structural optimization of input files, calculation of elastic constants using the thermo_pw code within the quantum espresso code, and the calculation of thermal properties using the thermo_pw code. These calculations (especially thermal) are usually highly computationally expensive, especially when the number of atoms is large, such as those in supercells. Moreover, some of my students also intend to employ hybrid functionals to calculate electronic properties of some of the alloys and thermoelectric materials. Since the hybrid functionals are equally very computationally expensive, the use of the CHPC in the computations becomes very helpful. Currently, the computations on the mechanics and thermodynamics of the materials for the aerospace is progressing on well. Mr. Pius Kipkorir (one of the master's students who has defended his thesis) intends to proceed to his PhD in the same area. Thermoelectrics is also being explored as a feasible area of research.
Principal Investigator: Dr Amin Saeidi
Institution Name: University of Limpopo
Active Member Count: 5
Allocation Start: 2023-11-23
Allocation End: 2024-06-30
Used Hours: 1219
Project Name: Designs and Codes from Finite groups
Project Shortname: CSCI1598
Discipline Name: Applied and Computational Mathematics
In our research project at the University of Limpopo's Department of Mathematics and Applied Mathematics, we are achieving significant strides in understanding the structures of linear codes and designs from finite groups.
This collaborative effort is leveraging the high-performance computing capabilities provided by the Centre for High-Performance Computing (CHPC). These computational resources have been fundamental in uncovering groundbreaking insights into the field of algebraic coding theory.
The team's research is not only academically significant but also holds promising implications in real life applications, such as information technology and communications.
The team heavily relies on CHPC resources to advance their work. Ongoing investigations into symplectic groups and the identification of invariant designs within these structures showcase the team's dependence on CHPC's computational prowess in furthering their understanding of mathematical concepts.
The team is led by Dr A Saeidi and his postgraduate students. We are also collaborating researchers from North-West University, namely Professor TT Seretlo and his postdoc student.
As the team continues their dedicated research efforts, their collaboration with CHPC remains instrumental in uncovering new dimensions of mathematical structures and exploring their potential real-world applications.
Principal Investigator: Dr Henry Martin
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 8
Allocation Start: 2023-11-24
Allocation End: 2024-06-13
Used Hours: 18763
Project Name: MCP
Project Shortname: PHYS1647
Discipline Name: Physics
Title: Groundbreaking Research at KNUST Tackles Real-World Challenges with Advanced Computing
The Mathematical and Computational Physics Research Group at Kwame Nkrumah University of Science and Technology (KNUST) is making significant strides in understanding and solving real-world challenges using cutting-edge digital techniques. This team of dedicated researchers focuses on applying advanced mathematical models and computational methods to a variety of pressing issues, from climate change to renewable energy and materials science. The core of the group's work involves creating digital twins—virtual models that accurately represent physical systems. These models help researchers study complex phenomena such as water systems, aerodynamics, and material properties under different conditions. By simulating these processes on computers, the team can predict behaviour, optimize performance, and develop innovative solutions without the need for costly and time-consuming physical experiments. One of the group's major projects is exploring the behaviour of materials and their interactions with atmospheric solutes at the atomic level. Understanding these interactions is crucial for developing stronger and more efficient materials for use in various industries, including aerospace and construction.
Another important project simulates the formation of planetesimals—tiny building blocks of planets. This research provides insights into the early stages of planet formation and helps answer fundamental questions about the origins of our solar system. This groundbreaking work is made possible by the high-performance computing (HPC) facilities provided by the Centre for High Performance Computing (CHPC). These powerful computers allow the research team to run complex simulations and process large amounts of data quickly and efficiently. The use of HPC resources enables the team to tackle problems that would be impossible to solve with standard computing tools.
Their work not only advances scientific knowledge but also has the potential to lead to practical applications that benefit society. By understanding and addressing some of the world's most pressing issues, the KNUST Mathematical and Computational Physics Research Group demonstrates the importance of supporting scientific research and investing in advanced computing resources.
Principal Investigator: Mr Lawrence Pratt
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 1
Allocation Start: 2023-11-27
Allocation End: 2024-05-31
Used Hours: 7203
Project Name: Solar Cell Defect Detection (SCDD)
Project Shortname: CSIR1379
Discipline Name: Computer Science
This CSIR Energy Centre and Next Generation Enterprises are developing a machine learning tool for multi-class solar cell defect detection (SCDD) in electroluminescence (EL) images of PV modules using semantic segmentation. EL images of PV modules are like x-ray images for humans. This research focuses on training deep learning models for defect detection and quantification in EL images of solar PV cells from mono-crystalline and multi-crystalline silicon wafer-based modules. The tool can be used by PV module manufacturers, developers, owners, and operators will be able to analyse thousands of EL images to identify potential defects that are otherwise invisible to the naked eye. This research shows that multi-class semantic segmentation models can provide accurate defect detection and quantification in both high-quality lab-based EL images and lower-quality field-based EL images of PV modules. While most EL images are collected in factory and lab settings, advancements in imaging technology will lead to an increasing number of EL images taken in the field. Thus, effective methods for SCDD must be robust to various images taken in the labs and the real world, in the same way that deep-learning models for autonomous vehicles that navigate the city streets in some parts of the world today must be robust to real-world environments.
Principal Investigator: Dr Michael Owen
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2023-11-27
Allocation End: 2024-05-31
Used Hours: 5873
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 and solar thermal energy systems.
Research continues with a focus on understanding and improving and understanding the performance of these technologies that contribute to more sustainable energy generation. 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. Similarly, solar thermal energy systems and related heat exchangers are an important technology for Southern Africa.
Principal Investigator: Prof Edet Archibong
Institution Name: University of Namibia
Active Member Count: 2
Allocation Start: 2023-11-27
Allocation End: 2024-06-20
Used Hours: 10053
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 present, our research at the Computational Chemistry Group of the University of Namibia in Windhoek involves computational study of bioactive compounds extracted from plants. Extracts of some plants species native to Namibia are known to possess medicinal properties. Our group make efforts to isolate, characterize and test the chemical compounds obtained from these medicinal plants for biological activity. The computational aspects of the research involve studying the structures and physicochemical properties of the isolated bioactive compounds. Our lab also carry out interaction studies to investigate the ability of these compounds to inhibit essential enzymes involved in diseases such as gonorrhea and various forms of cancer.
The bioactive molecules that our group study are large in size, containing tens of atoms, and as a result, computationally demanding. The studies often require significant computational resources (cpu time, memory and disk space) which we benefit from HPC resources as generously made available by the CHPC. Without the assistance of CHPC, it will be nearly impossible to conduct such important studies.
Principal Investigator: Dr Elliot Menkah
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 8
Allocation Start: 2023-11-27
Allocation End: 2024-06-18
Used Hours: 744452
Project Name: Materials for Energy
Project Shortname: MATS1515
Discipline Name: Chemistry
The Menkah research group is part of the larger Computational Chemistry Research group at the Department of Chemistry, KNUST. Our focus is along two lines of computational chemistry research interest, development and application. We make use of the computing power provided to us by the CHPC to test newly implemented scientific concepts in the chemistry domain as well as utilizing established concepts to unravel electronic structure elucidation.
Principal Investigator: Dr Winfred Mulwa
Institution Name: Egerton University, Egerton, Kenya
Active Member Count: 14
Allocation Start: 2023-11-27
Allocation End: 2024-06-11
Used Hours: 130006
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. We are now working on what happens at the sink of the refrigerator (Thermoelectric properties)
Principal Investigator: Dr Caroline Kwawu
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 41
Allocation Start: 2023-11-27
Allocation End: 2024-06-11
Used Hours: 1942284
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. The group has grown drastically to a number of about 40 due to the limitless available resources.
Principal Investigator: Dr Holliness Nose
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 6
Allocation Start: 2023-12-01
Allocation End: 2024-05-02
Used Hours: 2821468
Project Name: Inorganic Computational Chemistry
Project Shortname: CHEM1003
Discipline Name: Chemistry
Dr. Holliness Nose is currently a Lecturer of Inorganic and Computational Chemistry at the Technical University of Kenya, School of Chemistry and Material Science, located in Nairobi, Kenya, and a thematic head of the Inorganic discipline. Dr. Nose obtained her BSc (Hons) degree in Chemistry from the University of Nairobi, MSc degree in Chemistry from the University of the Ryukyus in Okinawa, Japan, and PhD degree in Inorganic and Computational Chemistry from Wayne State University located in Michigan, United States of America. Her research area is in Quantum Chemical Modeling with main focus on the design of transition metal complexes, investigation of their coordination behavior and determination of their quantitative structure-activity and quantitative property-activity relationships leading to the development of useful materials for water purification, catalysts in various organic transformations and sustainable processes, drug leads for various diseases and environmental pollution remediation. Dr. Nose's research in modeling relies heavily on CHPC located in South Africa. The center provides her with computers and Gaussian software for her research works. A lot of computational work is ongoing in the various areas mentioned above and should yield several publications beginning 2024 and beyond. Dr. Nose has attracted research grants to fund her research activities. These include: National Research Fund-Kenya, The World Academy of Sciences, Kenya Education Network. She has published a number of research articles in the fields of Chemistry in a broad scope of journals; New Journal of Chemistry, ChemPlusChem journal, Physical Chemistry A, among others. In terms of mentorship, Dr. Nose is currently supervising undergraduates and postgraduates. Dr. Nose is currently a member of the following academic organizations: - Royal Society of Chemistry, Materials Research Society of Kenya, Women in Technical Education and Development-TUK Chapter, Organization for Women in Science for the Developing World, and Kenya Chemical Society.
Principal Investigator: Prof Cornie van Sittert
Institution Name: North-West University
Active Member Count: 25
Allocation Start: 2023-11-30
Allocation End: 2024-07-23
Used Hours: 3565059
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 has been coal; at present, coal provides approximately 70% of South Africa's primary energy needs. However, electricity generated from coal combustion comes at a very high cost, namely air pollution and the influence of air pollution on human health. A possible solution would be to expand the use of affordable, clean, renewable energy sources. The most promising of these energy sources is hydrogen gas. However, hydrogen gas must be produced. Currently, the cleanest production method for hydrogen gas is water electrolysis. Water electrolysis is the dissociation of water into oxygen and hydrogen by applying electricity over two electrodes or plates (typically made from an inert metal such as platinum) placed in the water. However, platinum is a rare and expensive metal, so it is not economically viable for long-term and large-scale hydrogen production. Hence, various attempts have been made to reduce or eliminate the platinum content while not compromising the process performance. To do this, the electrochemistry during water electrolysis on platinum must be understood, and the influence of reduction or elimination of the platinum content must be investigated at a fundamental level. This level of understanding is only possible with the use of computational chemistry. The resources needed for this type of investigation, namely high-performance cluster computers and different types of software, are of cardinal importance.
The Laboratory for Applied Molecular Modelling (LAMM) within the Chemical Resource Beneficiation Research Area (CRB) at North-West University (NWU) focuses on the research mentioned above. Although computational study resources are available at North-West University, they can not fully support the LAMM's research. So, without access to the CHPC resources, research progress would be much slower.
Principal Investigator: Dr Thankhoe Rantso
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2023-12-05
Allocation End: 2024-05-23
Used Hours: 38130
Project Name: Advanced Protein Models
Project Shortname: HEAL1600
Discipline Name: Health Sciences
Our research group is led by Dr. Thankhoe Rants'o (PhD; Wits) and Dr. Gary Gabriels (PhD; UCT). Highly invested in proteomics work and in collaboration with international institutions, our group aims to uncover novel drug targets that drive cancer spreading (metastasis) and resistance to medicines.
This work is critical to not only identify potential new drug targets in the treatment of cancer but also, in the discovery of novel potent drugs. We perform molecular dynamics to find out how we can modulate the functions of proteins involved in drug resistance and metastasis. The CHPC platform has allowed us to study both the potential therapeutic and toxic effects of the molecules of interest. Our research and research group are constantly increasing.
Principal Investigator: Prof Thulani Makhalanyane
Institution Name: Stellenbosch University
Active Member Count: 26
Allocation Start: 2023-12-06
Allocation End: 2024-06-06
Used Hours: 265144
Project Name: Metagenomics of extreme environments
Project Shortname: CBBI1023
Discipline Name: Bioinformatics
The African Microbiome research group at Stellenbosch University aims to understand microbiomes, and their contribution in the environment. We use next generation tools to explore the and understand microbiomes in the human gut, terrestrial and aquatic environments, wit ha focus in Africa where microbiome studies have been carried out. Current projects include characterization of antibiotic-resistant bacteria and genes in African freshwater rivers Access to CHPC resources allows us to efficiently process these datasets Overall, both projects are progressing well and are expected to yield significant outputs.
Principal Investigator: Prof Zeno Apostolides
Institution Name: University of Pretoria
Active Member Count: 26
Allocation Start: 2023-12-06
Allocation End: 2024-06-06
Used Hours: 15411
Project Name: Receptomics
Project Shortname: CBBI0926
Discipline Name: Bioinformatics
The complimentary and alternative medicine group in the Department of Biochemistry, genetics and Microbiology, at the University of Pretoria, is led by Professor Zeno Apostolides and comprises eight post graduate students, at the Hons, MSc and PhD levels. Our work is focussed on developing new medicines for type 2 diabetes, based on biochemical compounds found in South African plants. We are interested in compounds that cannot be synthesised in the lab, but must be obtained from cultivated plants. This is to ensure the farmers get higher value for their crops. We use artificial intelligence to modify the plant derived compounds and predict their efficacy with computer models of enzymes important for treating diabetes. All the computer modelling work is done at the CHPC. Students on this project learn to use super computers and apply them to add value to ethnobotanical plants that can be cultivated in South Africa. Students with these scares skills are highly sought by industries worldwide.
The project is progressing well with students easily finding work in South Africa and overseas.
Principal Investigator: Prof Kenneth Ozoemena
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2023-12-11
Allocation End: 2024-06-11
Used Hours: 18417
Project Name: Materials Electrochemistry and Energy Technologies
Project Shortname: MATS1353
Discipline Name: Chemistry
We are the Ozoemena Research group at the University of the Witwatersrand (Wits). In the last 3 years, our research Focus on Materials Electrochemistry and Energy Technologies (MEETS) has been devoted to developing low-cost rechargeable zinc-air batteries (RZABs).
The key drivers for this RZABs are bifunctional electrocatalysts for oxygen reduction reaction (ORR) and oxygen evolution reaction (OER). To determine the best bifunctional electrocatalysts, we rely on the use of computational modelling (DFT) to understand their mechanisms for interaction with ORR and OER activities. We are happy to report that CHPC facility has made it possible for us to carry out DFT calculations that have allowed us to understand and synthesize appropriate bifunctional electrocatalysts for RZABs. One of our results is already being filed as a patent.
We hope to start technology demonstration this year which will pave way for large scale production of these electrocatalysts for the commercial development of RZABs in the country.
Principal Investigator: Prof Yin-Zhe Ma
Institution Name: Stellenbosch University
Active Member Count: 10
Allocation Start: 2023-12-11
Allocation End: 2024-06-07
Used Hours: 317797
Project Name: Machine learning in 21-cm cosmology
Project Shortname: ASTR1323
Discipline Name: Astrophysics
CHPC is a wonderful server. It provides us a place to do large computation, such as simulation and MCMC. This broadens our study methods. It also has many software installed. For example, openmpi, cfitsion, anaconda and so on. This results in that we don't need to install them by ourselves. For an unprofessional person, some software may require a long time to install correctly.
Dr. Guo-Jian Wang is a Postdoc of our group at Stellenbosch University. He focuses on 21-cm data analysis and applications of machine learning methods in solving problems in cosmology and astrophysics. He is currently working on cosmological parameter estimations with machine learning methods using 21-cm observations. In his research, he needs to do many simulations to train network models, which should be conducted on professional CPU and GPU machines. Therefore, his research needs to use public resources like the CHPC. In his research, he simulated data using the CPU nodes on CHPC and trained network models using the GPU nodes. Based on the CHPC, he has finished two papers published to AAS journals, and there are another two papers under preparation.
Principal Investigator: Dr Joseph Mutemi
Institution Name: University of Nairobi
Active Member Count: 6
Allocation Start: 2023-12-11
Allocation End: 2024-06-07
Used Hours: 51057
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 based at the University of Nairobi, Department of Earth and Climate Sciences, Kenya is focused on addressing key research questions in weather prediction and applications East Africa led by Prof. Joseph Mutemi. During the reporting period, two papers were published, one in Frontiers in Climate, https://doi.org/10.3389/fclim.2024.1311088, showing that the processes related with local weather modification due to the presence of inland lakes and mountains are better resolved in using two-kilometer resolution models, usually called 'convection permitting.' With better spatial details, convection permitting weather forecasts over the opportunity to enhanced the quality of weather forecasts, by providing locally relevant information that is necessary for supporting early warning to protect societies against weather hazards. The other paper on priorities of Africa weather and climate services published in nature communications is at https://www.nature.com/articles/s41467-024-46742-6. Our results, only possible through the Lengau cluster, presents benchmark case to promote the update of high resolution weather information as the basis for addressing region specific hydro-meteorological risk in East Africa.
Principal Investigator: Prof Albie van Dijk
Institution Name: University of the Free State
Active Member Count: 1
Allocation Start: 2023-12-11
Allocation End: 2024-06-10
Used Hours: 3653
Project Name: Investigations of restrictions to reassortment of rotavirus proteins and genome segments
Project Shortname: HEAL1649
Discipline Name: Health Sciences
Our research group is part of the Molecular Virology and Clinical Biochemistry laboratory in the Department of Microbiology and Biochemistry at the University of the Free State. Our research group is headed by Professor Albie van Dijk and currently consists of three PhD students. Current commercially available rotavirus vaccines are more than 90% effective in developed economies, such as the United States and Europe. In developing countries in Africa and Asia, the rotavirus vaccines have been shown to be between 40 and 60% effective. One of the reasons for this may be that the rotaviruses contained in the vaccines do no provide adequate protection against regional rotaviruses. This necessitates the future development of next-generations rotavirus vaccines. Our main focus is to investigate the determinants of how rotaviruses exchange genes, known as genome reassortment, as well as improving the safety of rotavirus vaccines by investigating the molecular determinants of rotavirus disease. Firstly, our work includes exchanging and improving the fit on virus particles of the outer spike protein of rotavirus, known as the VP4. This will allow us to develop future vaccines that contain rotaviruses that are regionally derived. Secondly, previous work done in our research group has shown that two amino acids in rotavirus NSP4 may influence reassortment. This may be important to prevent reassortment in next-generation rotavirus vaccines. Thirdly, we are investigating how we can remove the function of rotavirus proteins NSP1, NSP4, and NSP6, which is known as attenuation. The aim is to allow future development of vaccines that have no possibility of causing disease. Current use of the cluster involves molecular dynamics simulation of interacting rotavirus proteins. This models how proteins interact with their immediate environment to get an accurate picture of how proteins are behaving during interaction. Since this is computationally intensive, use of the cluster is essential to allow fast processing of data.
Principal Investigator: Dr Clement Agoni
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2023-12-12
Allocation End: 2024-06-12
Used Hours: 187835
Project Name: Structural Modelling and In-Silico Peptide Design Research
Project Shortname: HEAL1524
Discipline Name: Health Sciences
The structural modelling and In-Silico Peptide Design Research project is based in the College of Health Sciences at the University of KwaZulu Natal. The team explores drug-target interactions of novel small molecule inhibitors against diseases of global concern such as tuberculosis, malaria, cancer, and viral infections using molecular modelling techniques. The second aspect of the research involves the structural modelling of peptides toward the discovery of bioactive peptides from natural sources for therapeutic purposes, with a central question of whether structural modelling can accelerate the development of bioactive peptides. Resources from CHPC allow our group to perform computationally intensive processes such as Molecular Dynamics simulations and Machine Learning which hitherto would have been very expensive and time-consuming using local computers with limited capacities. So far we are have successfully published the finding of some of the research investigations in the project in reputable journals even as we continue to explore the research domain
Principal Investigator: Dr Sarah Roffe
Institution Name: Agricultural Research Council
Active Member Count: 10
Allocation Start: 2023-12-14
Allocation End: 2024-06-19
Used Hours: 2276507
Project Name: ARC-NRE Agrometeorology
Project Shortname: ERTH1556
Discipline Name: Earth Sciences
Researchers part of the Agriculture Research Council Agrometeorology Division are working towards improving our understanding of the climatic risks faced by the southern African agricultural sector. This is important to facilitate a prospering agricultural industry that is resilient to anthropogenically-induced climate change impacts that are occurring over southern Africa. Towards this goal, the Agromet researchers have been working on producing high-resolution climate projections by dynamically downscaling the coarse-resolution CMIP6 climate model projections using the Weather Research and Forecasting (WRF) model on the CHPC Lengau cluster. The WRF modelling process is extremely computationally expensive, thus without the CHPC resources, our work would not be possible. Ultimately, the product of our work will be a high-resolution climate projections dataset that can be applied by anyone who is interested in understanding future climate changes over southern Africa. Towards producing this dataset, we are almost halfway, and thus anticipate that our dataset will be ready towards the end of this year.
Principal Investigator: Dr DOROTHY NYAMAI
Institution Name: 0 Other
Active Member Count: 4
Allocation Start: 2023-12-20
Allocation End: 2024-06-19
Used Hours: 145894
Project Name: JKUAT BIOINFORMATICS GROUP
Project Shortname: CBBI1651
Discipline Name: Bioinformatics
JKUAT BIOINFORMATICS GROUP hosted in JKUAT, Kenya. We conduct research to explore drug compounds for treatment of various diseases, including malaria and cancer. We also conduct genome wide studies to identify mutations signatures to understand the underlying mechanisms of progression of diseases such as cancer. Malaria and cancer are prevalent diseases in Africa and this research will provide strategies for reducing mortality and increasing patient survival. For drug, discovery we screen thousands of natural compounds against known drug targets using CHPC results as personal computers have less computational power. In addition we validate these molecules through molecular dynamic simulations, which require use of a high performance cluster. CHPC enables us to conduct these calculations within a short period. In addition, the genome wide analysis study, involves variant calling in the entire genome which is time consuming when conducted using personal computers. Therefore, the CHPC is valuable in handling this computer intensive analysis. Currently we have a manuscript in the last stages of submission, whereas in the other studies we are still performing analysis.
Principal Investigator: Dr Hamilton Ganesan
Institution Name: Inqaba Biotec
Active Member Count: 2
Allocation Start: 2023-07-16
Allocation End: 2024-01-16
Used Hours: 31948
Project Name: General Analysis
Project Shortname: CBBI0843
Discipline Name: Bioinformatics
We at inqaba biotec, a private biotechnology company based in Pretoria, Muckleneuk with subsidiaries in East and West Africa and multiple sattelite offices across Africa, have been in the business of producing Next Generation Sequencing data for our wide client base for over twenty years. Throughout this time in operation, we have seen a significant increase accessibility to Next Generation Sequencing technologies thus fuelling the need for DNA to be sequenced at ever increasing speed.
Concomitant with the the rapid advancement in the speed of DNA sequencing technologies is the production of increasingly large data sets. This two-fold increase has had an impact on our operations because naturally, our digital storage capacity and compute resources has now become crucial with many of our clients requiring data storage and data analysis in some form or another.
Therefor, the compute resources made available at the CHPC has provided invaluable infrastructure in order for my company, inqaba biotec, to function optimally. In many cases, larger data sets such as human genome sequences need to be analyzed and due to its sheer size, requires considerable compute resources. Without access to the CHPC compute resources, the delivery time on many these projects would be extended to an unreasonable and unecceptably long period.
In the realm of personalized medicine, driven primarily by genomic data, the need to quickly transfer and analyze data has a direct impact on speed of diagnosis and understanding of a clinical case. This alone is a solid case in point to highlight the crucial service of High Performance Computing in our sphere.
Being a biotechnology company however, means we deal with sample types across a broad range including animal, plant, medical, veterinary & mining research to name a few. This of course means, our compute needs and software needs are broad too, leaving us even more indebted for a resource such as the CHPC.
I am truly thankful for the various staff that have a generally helpful and knowledge imparting attitude to its users, contributing to a thriving scientific environment in SA.