Press Releases

Principal Investigator: Dr Krishna Govender
Institution Name: University of Johannesburg
Active Member Count: 21
Allocation Start: 2024-01-05
Allocation End: 2024-07-16
Used Hours: 1489565
Project Name: Computational approaches to design novel anticancer agents
Project Shortname: CHEM0792
Discipline Name: Chemistry

There has been an estimated 20 million new cancer cases and 9.7 million deaths in 2022. Despite the current chemotherapeutic treatments available to treat cancer these have various unwanted side effects. Within the Computational Chemistry and Molecular Modelling Group at the University of Johannesburg we focus on trying to find alternative approaches to treat cancer with the aid of computational methods. One of the key methods we employ is to try and find new drug candidates with minimal to no side effects in the treatment of cancer. The datasets we use in our studies are, in some cases, substantially large. As a result, we cannot run our simulations timelessly on local hardware. To speed up our drug discovery process we are highly reliant on the resources provided by the CHPC and we would not be able to achieve our goals (graduating students on time and high impact publications) within the research group without these resources.

Principal Investigator: Prof Amanda Rousseau
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2024-01-08
Allocation End: 2024-07-08
Used Hours: 5453
Project Name: Antifolates and antimalarial kinase inhibitors
Project Shortname: CHEM1402
Discipline Name: Chemistry

Prof A Rousseau in the School of Chemistry at the University of the Witwatersrand is working on the design and synthesis of compounds with antimalarial properties. Malaria is a disease that is prevalent in Africa and caused by parasites of the genus Plasmodium, with Plasmodium falciparum being responsible for the most malaria fatalities worldwide. Folate inhibitors, known as antifolates, and in particular inhibitors of the enzyme dihydrofolate reductase (DHFR), find application as treatments in a range of disease classes, including for the treatment of malaria. We are utilising molecular modelling as a tool to assist with the design of inhibitors by using crystal structures of both wild type and mutant forms of the enzyme DHFR present in the P. falciparum parasite (PfDHFR). Molecular modelling using Schrodinger software allows us to computationally assess the potential of compounds of interest to bind in the active site of the PfDHFR enzyme. This helps us to determine which compounds to synthesise, and, once the compounds have been assessed for biological activity in vitro, can be used to optimise the biological activity against the target. The time taken to complete the computational assessment (in silico screening of inhibitors) is greatly reduced through the use of the CHPC, as multiple jobs can be submitted at once. Furthermore, more complex dockings which allow for movement of the amino acids within the protein (flexible docking protocols) can be readily accomplished.

Principal Investigator: Prof Mahmoud Ibrahim
Institution Name: University of KwaZulu-Natal
Active Member Count: 15
Allocation Start: 2024-01-09
Allocation End: 2024-07-09
Used Hours: 1066090
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 Parvesh Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2024-01-09
Allocation End: 2024-07-09
Used Hours: 26223
Project Name: Molecular dynamics and docking studies of organic compounds
Project Shortname: CHEM0795
Discipline Name: Chemistry

I am working as an Associate Professor in the School of Chemistry at UKZN. We are using different computer-based technologies such as molecular docking, QSAR, QSPR, and pharmacophore modeling to predict novel chemical assemblies from the online databases. The identified lead molecules are synthesized in our organic laboratory and tested in vitro. All the computer simulations are performed on the CHPC cluster. The CHPC facility is an excellent platform that helps us as researchers in SA to run computer simulations and use the compiled data to substantiate our experimental results, which in turn enable us to publish our research in high-impact journals. Running these jobs on normal computers would have taken months to finish or would die in middle. With this supercomputing facility in our hand, we not only managed to run complex calculations but obtained constructive scientific explanations for our experimental results.

Principal Investigator: Prof Phuti Ngoepe
Institution Name: University of Limpopo
Active Member Count: 15
Allocation Start: 2024-01-09
Allocation End: 2024-07-09
Used Hours: 7216137
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 Robert Warmbier
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2024-01-10
Allocation End: 2024-07-10
Used Hours: 111912
Project Name: Study of defects and doping of the atomic and electronic structure of materials
Project Shortname: MATS1653
Discipline Name: Physics

The Computational Material Science Group led by Dr Robert Warmbier from the Wits School of Physics uses quantum mechanical tools to model basic properties of materials on an atomic level to better understand - and to improve - their behaviour. Many materials we use technologically comprise of crystals, in which atoms are well ordered in repetitive patterns. Given this structure, many of the materials properties can be understood easily using quantum mechanics-based simulations. In practice every material has little defects though, which change the materials properties. We investigate how exactly this happens, not only to minimise these effects, but also to improve ways how to use these defects to our advantage.
In our most recent work Dr Chani van Niekerk is investigating the effects of defects in the structure of carbon nanotubes. Nanotubes are of significant technological interest, as they are lightweight, extremely strong and have excellent electrical conductivity. They can be woven into fibres for use in fabrics, or used as single nanotubes in computer circuitry. The amazing properties of nanotubes are limited by the loose interaction between different tubes. Our team is investigating how the interaction of nanotubes can be improved to yield a better product. Simulating the interactions of thousands or tens of thousands atoms is computationally demanding and would take years or decades on a consumer PC. We rely on the high-performance computing support by the CHPC for our work and are grateful for their support.

Principal Investigator: Dr Henry Otunga
Institution Name: Maseno University, Kisumu, Kenya
Active Member Count: 5
Allocation Start: 2024-01-11
Allocation End: 2024-09-09
Used Hours: 73694
Project Name: Computational Study of Hematite Clusters
Project Shortname: MATS0888
Discipline Name: Material Science

Sunlight is the most abundant renewable energy resource and considered to be the ultimate solution to address the global energy problem: The Tetrawatt Challenge. However, the vision of solar energy providing a substantial fraction of global energy infrastructure is still far from being realized. The major challenge is to develop an efficient and cost-effective approach for storing solar energy that can be used on demand on a global scale. Splitting water photoelectrochemically is a promising way in which solar energy can be harvested and stored through photocurrent-driven chemical bond rearrangement leading to the formation of molecular hydrogen (2H2O→2H2+O2, E0=1.23 eV, Standard Hydrogen Electrode, SHE), which can be used directly as fuel or as an intermediate in the production of other fuels.

Hematite (alpha-Fe2O3) has emerged as a candidate photoanode material due to several favorable features: a band gap of about 2.0 eV (which allows for a large fraction of solar spectrum to be absorbed), excellent stability under aqueous environments, and abundance in nature. Converting energy from the Sun to electricity efficiently via photoelectrochemical splitting of water is based on photo-induced charge separation at an interface (semiconductor/water interface) and the mobility of photo-generated 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 efficiency. These limitations can be dealt with by nano-structuring hematite, by growing ultrathin films of hematite, and by introducing impurity atoms in hematite. In this work, the structure and energetics of various size clusters of Fe2O3 have been investigated using the plane-wave pseudo-potential approach to Density Functional Theory (DFT) and ab initio Molecular Dynamics (MD). These calculations require a significant amount of compute resources in terms of memory and cpu scaling. In this respect, I am grateful to the CHPC for granting me access to their supercomputing facilities and I hope for more collaboration in future.

This research group is known as The Computational Materials Science Research Group of Maseno University. The members of the research group are
1. Dr. Henry Odhiambo Otunga (PI)
2. Nicholas Ongwen
3. Richard Onyango
4. Benjamin Omubandia

Principal Investigator: Dr Njabulo Gumede
Institution Name: Walter Sisulu University
Active Member Count: 5
Allocation Start: 2024-01-12
Allocation End: 2024-07-24
Used Hours: 13727
Project Name: Computer-Aided drug design for cancer therapy
Project Shortname: CHEM1058
Discipline Name: Chemistry

The Computational and Medicinal Chemistry group is located in the Department of Chemical and Physical Sciences at Walter Sisulu University (WSU). This research group is currently headed by Dr N.J. Gumede who is an NRF-Y2 rated researcher with an H7 index from Google scholar. This is a relatively new research group at WSU. It is comprised of one Postdoctoral research fellow, 2 PhD, 1 MSc, and 1 Honours candidate. These students are working on various projects in drug discovery and development such as Prostate Cancer designing inhibitors targeting CYP17A1 enzyme and the antagonists targeting the Androgen Receptor. Another student is involved in the design of inhibitors targeting the SARS-CoV-2 virus focusing on the viral entry and replication. The use of HPC resources in this group is important for the design of synthetically aware compounds using a vast array of in silicon tools offered by Schrödinger. We then design synthetic routes using retro synthesis analysis. We are now also interested in performing transition state modelling and reaction based energetics enumeration for mechanistic studies, such as cross-coupling reactions. Once the compounds are synthesised and purified. We test them using in vitro assay for potency, physicochemical properties, toxicity studies, PK/PD studies both in vitro and in vivo. We are doing this work because it is our duty as academics to induct students into the new ways of knowing and also to train scientific literacy through research. This will enable us to help students to develop research skills that will enable them to address challenges through science that affects the society, for the public good. This research is funded by two NRF grants i.e. the Italy/NRF bilateral grant and the Competitive Programme for Rated Researchers.

Principal Investigator: Prof Yoshan Moodley
Institution Name: University of Venda
Active Member Count: 7
Allocation Start: 2024-01-15
Allocation End: 2024-07-15
Used Hours: 110591
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 Biological Sciences are unlocking the genetic secrets required to more effectively conserve the world's endangered wildlife species.

Our group is unique in the Republic since the capacity for carrying out such work on non-model animals at the whole genome level is still very limited. Our lab has become a centre of excellence, generating postgraduate students with the rare skills of understanding, manipulating and interpreting genome level data.

My group works with big data, namely, whole genomes at the population level. This requires the manipulation and analysis of massive amounts of data. The service of the CHPC is invaluable to the success of the group, especially if our larger memory requirements can be met. This year, there are two new students and several members will be making use of the server to carry out their projects.

The group appreciates the support of the CHPC, as our local university IT capacity and support is limited to non-existent. Thus, the CHPC allows us to carry out Honours, MSc and PhD research that would otherwise be impossible to do at the University of Venda.

Principal Investigator: Prof Bettine van Vuuren
Institution Name: University of Johannesburg
Active Member Count: 6
Allocation Start: 2024-01-15
Allocation End: 2024-07-15
Used Hours: 30109
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 Molemi Rauwane
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 6
Allocation Start: 2024-01-15
Allocation End: 2024-07-15
Used Hours: 2246
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.

More research has been added onto the group in collaboration with Malawi University of Technology. The project aims at identifying fungal and viral diseases affecting common beans in SAn growing regions (North West, Limpopo, Mpumalanga and Free State), using metagenomics and metabarcoding tools.

A transcriptome profiling manuscript (common bean-rust interactions), and a genome assembly of Penicillium expansum have been submitted to journals for review with the Canadian Journal of Microbiology and BMC Genomics. We are currently awaiting response from the editors. In addition, a conference poster has been presented at the International Congress of Plant Pathology, August 2023, in Lyon France.

Principal Investigator: Prof Gerard Tromp
Institution Name: Stellenbosch University
Active Member Count: 14
Allocation Start: 2024-01-15
Allocation End: 2024-07-15
Used Hours: 44110
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: Prof Scott Hazelhurst
Institution Name: University of the Witwatersrand
Active Member Count: 6
Allocation Start: 2024-01-15
Allocation End: 2024-07-15
Used Hours: 28511
Project Name: Bioinformatics and Experimental Algorithms (BEAT)
Project Shortname: CBBI0930
Discipline Name: Bioinformatics

Variation in key genes known as pharmacogenomic genes affect the body's metabolism of drugs, affecting both safety and efficacy of the drugs. The SBIMB has several active pharmacogenomics projects

In this reporting period, our main focus was the AGORA-TM project, investigating the impact of pharmacogenomic variation on the way the body responds to anti-malarial and anti-tuberculosis medicines.

PhD student Blessing Sitabule has catalogued key variations in some important genes that are implicated in drug response. He is now applying machine learning techniques to explore these candidate variants to understand which are most likely to be important. This work is extremely computationally intensive and requires the powerful computers of the CHPC.

Principal Investigator: Dr Cari van Schalkwyk
Institution Name: Stellenbosch University
Active Member Count: 10
Allocation Start: 2024-01-15
Allocation End: 2024-07-15
Used Hours: 15489
Project Name: South African Centre for Epidemiological Modelling and Analysis
Project Shortname: CBBI1106
Discipline Name: Other

The South African Centre for Epidemiological Modelling and Analysis (SACEMA) is an academic research centre within the Centre for Epidemic Response and Innovation (CERI), hosted at Stellenbosch University. We use computational approaches to address questions of public health relevance to South Africa and the African continent. We use the CHPC primarily to run stochastic simulations and for simulation-based validation of novel inference methods.

Principal Investigator: Dr Vuyo Mavumengwana
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2024-01-15
Allocation End: 2024-07-15
Used Hours: 16447
Project Name: Microbial symbionts bioactive compounds and their virtual screening
Project Shortname: CBBI1434
Discipline Name: Bioinformatics

The Vuyo Lab is at Stellenbosch University, Tygerberg Medical Campus, Biomedical Research Institute. It comprises 3 PhD and 4 master's students working towards their degrees. Additionally, the group has 3 postdoctoral researchers who all incorporate in-silico work into their projects. Our focus is drug discovery mainly in infectious diseases and cancer. We use the CHPC to accelerate drug discovery by processing big (multi-omics data) to discover new therapeutic agents and targets.

Principal Investigator: Prof Matt Hilton
Institution Name: University of the Witwatersrand
Active Member Count: 7
Allocation Start: 2024-01-15
Allocation End: 2024-07-18
Used Hours: 222505
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 Krishna Bisetty
Institution Name: Durban University of Technology
Active Member Count: 9
Allocation Start: 2024-01-16
Allocation End: 2024-07-24
Used Hours: 31890
Project Name: Computational Modelling & Bioanalytical Chemistry
Project Shortname: CHEM0820
Discipline Name: Chemistry

The "Computational Modelling and Bioanalytical Chemistry" research group at the Durban University of Technology (DUT) is making significant strides in the development of smart materials for sensors and biosensors, thanks to the support provided by the Centre for High-Performance Computing (CHPC). Led by Professor K. Bisetty, the group employs a synergistic blend of experimental and computational techniques to explore smart biodevice platforms within the field of biosensor technology. His research group uses a diverse range of sensors to selectively detect analytes in specific environments. These sensors play a crucial role in identifying the presence of target molecules. To create biosensors, the team incorporates nanostructured electrode materials into electroactive smart matrices. These materials enhance the sensor's performance and sensitivity. High-level computational tools are pivotal in their research. These include; model statistical behaviour to predict system properties such as adsorption of the adsorbate on the substrate material (Monte Carlo Simulations); the binding of molecules to specific active sites (Molecular docking) and quantum mechanical method for predicting electronic and spectroscopic behaviour of materials (DFT).

Principal Investigator: Dr Saheed Sabiu
Institution Name: Durban University of Technology
Active Member Count: 26
Allocation Start: 2024-01-17
Allocation End: 2024-07-17
Used Hours: 1092978
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 John Mack
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2024-01-18
Allocation End: 2024-08-07
Used Hours: 16252
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 Joseph Simfukwe
Institution Name: Copperbelt University
Active Member Count: 4
Allocation Start: 2024-01-18
Allocation End: 2024-08-29
Used Hours: 32550
Project Name: Computational Materials Science Research Group CBU
Project Shortname: MATS1469
Discipline Name: Physics

There is an urgent call world over to reduce the continuous emission of greenhouse gasses such as carbon dioxide (CO2) from burning fossil fuels (FFs). The reliance on fossil fuels to supply energy for human use and industrialization has led to the increase in the earth's surface temperature and negatively affecting human health and sustainability. Therefore, it is apparent, that clean, renewable, cheap and sustainable sources of energy must be found to replace the FFs while meeting the increasing energy demand. Renewable energy sources such as solar have the potential to meet the global energy demand sustainably. To harness energy from the Sun, we need an efficient and inexpensive route to convert solar energy into chemical energy such as hydrogen (H2) fuel or Photovoltaic, for example solar panels and energy storage batteries. Currently, Zambia is undergoing heavy load shedding due to the EL Nino which badly hit Zambia, Zimbabwe and Malawi, affecting their crops and hydro power production. Therefore, these Nations are now embarking on the use of solar as an alternative source energy which is user friendly.
In this project, our focus is to study different properties of materials that can be used in PEC water splitting and their applications in addressing various societal needs such as clean energy and its storage. The method of study involves the application of first-principles simulations based on state-of-the-art density functional theory (DFT). This is a computational study which heavily depends on computational resources from the CHPC clusters. 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. We greatly appreciate will the support we receive from CHPC for cluster resources.

Principal Investigator: Prof Pieter Rousseau
Institution Name: University of Cape Town
Active Member Count: 4
Allocation Start: 2024-01-19
Allocation End: 2024-07-19
Used Hours: 401140
Project Name: University of Cape Town Applied Thermal-Fluid Research Unit
Project Shortname: MECH1279
Discipline Name: Computational Mechanics

Rising energy demand, climate change and the energy transition 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 Didam Gwazah Adams Duniya
Institution Name: BIUST
Active Member Count: 1
Allocation Start: 2024-01-22
Allocation End: 2024-07-26
Used Hours: 124965
Project Name: Cosmological Probes of Gravity, Dark Energy, and Large Scale Structure
Project Shortname: ASTR1480
Discipline Name: Astrophysics

Dr Didam Duniya pubished a research paper on redshift space distortions, with respect to interacting dark energy (IDE). Redshift space distortions are distortions in the clustering of sources that arise owing to the peculiar velocities of the sources relative to the observer.

This research is very relevant to current and future cosmological surveys. For example, a key problem in cosmology is to correctly identify the imprint of IDE (and dark energy in general), in order to avoid bias in constraints on IDE. Dr Duniya's paper investigates the large-scale imprint of IDE in redshift space distortions, using Euclid-like photometric prescriptions. For the first time, the IDE dynamics have been incorporated in the galaxy (clustering and evolution) biases. Dr Duniya found that when IDE dynamics are not included in the galaxy biases, as is conventionally done, the results suggested that an IDE with a constant dark energy equation of state parameter will lead to an alternating, positive-negative effect in the redshift space distortions angular power spectrum. However, when IDE dynamics is incorporated in the galaxy biases, the apparent positive-negative alternating effect vanishes. This implies that neglecting IDE dynamics in the galaxy biases can lead to an incorrect identification of the IDE imprint in the distribution of galaxies. Moreover, the results showed that redshift space distortions hold the potential to constrain IDE on large scales, at redshifts z≤1.

Principal Investigator: Dr Sadhna Mathura
Institution Name: University of the Witwatersrand
Active Member Count: 5
Allocation Start: 2024-01-22
Allocation End: 2024-07-22
Used Hours: 25209
Project Name: Bioinorganic Chemistry Research Group (Wits)
Project Shortname: CHEM1633
Discipline Name: Chemistry

Bioinorganic research group (Wits) examines the function of metal ions in a biological context. This field has many themes. Our lab mainly focuses on therapeutic agents and drug discovery (e.g. anticancer drugs). A lot of this work depends on geometry and coordination. We use HPC to optimise metallodrug structures and to simulate characterisation information e.g. uv-vis. Publishable research will benefit the public (drug development).

Principal Investigator: Prof Fernando Albericio
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2024-01-22
Allocation End: 2024-07-23
Used Hours: 4436
Project Name: Peptide chemistry and Organic chemistry
Project Shortname: CHEM1102
Discipline Name: Chemistry

We at Peptide Science Laboratory located in School of Chemistry and Physics, UKZN Westville campus, are engaged in development of newer reagent and synthetic strategies for peptide chemistry.
During the methodology, most of the time it is challenging to understand the reaction via analytical tools as the reaction is either too fast or intermediates are difficult to isolate. In such cases, QM calculations help us to understand the challenges faced during the synthesis while carrying out the reaction. In such a case, CHPC provides an amazing supercomputer facility at high speed which eliminates the delay in research.
So far, we have been able to understand the computational tools to some extent which can be seen as part of paper publications. Thanks to CHPC.
Currently, we are involved in understanding the reaction intermediates for challenges in nucleotide synthesis.

Principal Investigator: Prof Eric van Steen
Institution Name: University of Cape Town
Active Member Count: 8
Allocation Start: 2024-01-24
Allocation End: 2024-08-22
Used Hours: 438167
Project Name: Lateral interactions on surfaces
Project Shortname: CHEM0780
Discipline Name: Chemistry

Computational chemistry allows us to visualize the working of catalysts at a molecular level, but these calculations are computationally intensive thus necessitating us to utilize amongst others the resources at the CHPC. The use of modern computational tools such as machine learning with genetic algorithms speed up these calculations, which allows us in the Catalysis Institute at UCT to explore a greater variety of systems. In our work, we are looking at accelerating the conversion of CO2 into aviation fuel via the reverse water gas shift reaction followed by the cobalt-catalysed Fischer-Tropsch synthesis. The latter will need to operate preferably at high conversion, which can be achieved using manganese/titanium as a promoter. The functioning of manganese and/or titanium is still not well-known and various proposals have been made. The advanced computational tools allow us to explore the possible working of these promoters over a wide range of different conditions.

Principal Investigator: Dr Madison Lasich
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2024-01-24
Allocation End: 2024-07-25
Used Hours: 246518
Project Name: Chem Thermo
Project Shortname: CHEM1028
Discipline Name: Chemical Engineering

The Thermodynamics, Materials and Separations Research Group at MUT works on the areas of materials behaviour and phase separation. This research is of interest not only from a theoretical point of view in terms of advancing the fundamental understanding of physical chemistry and chemical physics, but also in terms of applications in chemical engineering and materials science. Presently some of our work is focused on environmental remediation, specifically the removal of organic pollutants such as dyes and antibiotics. Other work has led to the conceptual design of a biogas cleaning system which has potential for integration into a solar reforming process. This research requires not only the software licences offered by the CHPC, but also high performance computing resources to perform density functional theory and atomistic molecular simulations. None of these computationally intensive techniques would be possible without the facilities provided by the CHPC. We are making progress in developing deeper understanding of the behaviour of polymers with organic pollutants, in addition to the application of multiscale modelling approaches to chemical engineering problems.

Principal Investigator: Dr Marilize Le Roes-Hill
Institution Name: Cape Peninsula University of Technology
Active Member Count: 1
Allocation Start: 2024-01-25
Allocation End: 2024-07-25
Used Hours: 74279
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 Caleb Kibet
Institution Name: International Centre of Insect Physiology and Ecology, Nairobi, Kenya
Active Member Count: 8
Allocation Start: 2024-01-25
Allocation End: 2024-07-25
Used Hours: 291163
Project Name: Insect Genomics
Project Shortname: CBBI1470
Discipline Name: Bioinformatics

The Insect Genomics Group at Pwani University, hosted at the International Center of Insect Physiology and Ecology, uses Genomics and Computational Biology to research insects for food and feed and those that cause diseases in humans and animals. In human genomics, we explore how endosymbionts can be used to block malaria transmission, and in animal research, we seek to understand transmission patterns of animal trypanosomiasis. The CHPC enables us to assemble and annotate huge genomic data.

Principal Investigator: Mr Asad Jeewa
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2024-01-26
Allocation End: 2024-08-13
Used Hours: 21377
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 as we look to grow our group of researchers.

Principal Investigator: Dr Kiprono Kiptiemoi Korir
Institution Name: Moi University, Eldoret, Kenya
Active Member Count: 13
Allocation Start: 2024-01-26
Allocation End: 2024-08-08
Used Hours: 903311
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 of doped 2D ZnS with light elements on the removal of heavy metals from waste water. Our results showed that Cl-doped 2D MoS2 was more effective for the removal of mercury, cadmium, and zinc metal ions because of their moderate adsorption energies. Furthermore, our analysis of projected density of states revealed that the Cl-doped 2D ZnS capability to remove of mercury, cadmium, and zinc metal ions in water can be attributed to the hybridization of the d- and p-state electrons of the HMs and Cl-doped 2D MoS2 material. Further, upon thermal treatment of mercury, cadmium, and zinc heavy metal ions adsorbed on Cl-doped 2D MoS2 became detached at 322 K, 371 K, and 316 K, respectively. Thus, rendering the modified material reusable upon thermal treatment.

Principal Investigator: Dr Gebremedhn Gebreyesus Hagoss
Institution Name: University of Ghana
Active Member Count: 5
Allocation Start: 2024-01-26
Allocation End: 2024-09-12
Used Hours: 1117692
Project Name: Atomistic simulations and condensed matter
Project Shortname: MATS1031
Discipline Name: Physics

My research group at the Department of Physics, University of Ghana, onducts cutting-edge simulations to investigate the structural, electronic, magnetic, and optical properties of 2D and bulk materials. Computational simulations of these properties are studied using density functional theory and extended Hubbard functionals as implemented in QUANTUM ESPRESSO, GW approximation of many-body perturbation theory (MBPT), and the Bethe-Salpeter equation (BSE). Our computational work would not be possible without the enhanced computing resources available at the CHPC in South Africa. Typically, we prepare the input files on our laptops and works stations and submit the job to the CHPC cluster. The jobs are monitored at least once a day. The results are downloaded when completed.

Our research focuses on four key areas:

1. Transition-metal oxides: We study the electronic, magnetic, structural, and optical properties of doped and undoped materials, comparing computed results with experimental data.

2. Perovskite materials for energy applications: We investigate the structural, electronic, dielectric, and vibrational properties of low-temperature phase perovskites using extended DFT (DFT+U and DFT+U+V) and search for lead-free double perovskites. In this project, we are also using HSE06 and GW+BSE approach for the electrical properties.

3. 2D materials research: We explore transition metal dichalcogenides (MX2) for photocatalytic hydrogen evolution reactions, focusing on monolayers, bilayers, and heterostructures of transition metal disulfides.

4. Ruddlesden-Popper perovskite ruthenates: We calculate electron-phonon couplings in Sr4Ru3O10 using DFT+U and spin-orbit coupling. In this project, we will start to use DMFT approach for a better understanding of the materials meta-magnetic properties.

Principal Investigator: Prof Rebecca Garland
Institution Name: University of Pretoria
Active Member Count: 9
Allocation Start: 2024-01-29
Allocation End: 2024-07-31
Used Hours: 60651
Project Name: Air quality and atmospheric composition
Project Shortname: ERTH1484
Discipline Name: Earth Sciences

Global assessments estimate large impacts from exposure to poor air quality in many countries in Africa. However, these estimates have large uncertainties due to lack of information, which often stems from the lack of ground-based measurements. This lack of data impacts not only the understanding and quantification of air pollution levels and impacts, but also impacts on the understanding of climate as many air pollutants impact climate as short-lived climate forcing pollutants (SCLPs; e.g. particulate matter, ozone). Multiple platforms and data streams are useful in understanding and quantifying the spatial and temporal heterogeneity in air quality and atmospheric composition. In African cities this is especially important, not only due to the large heterogeneity in urban areas, but also due to the high costs of regulatory-grade instruments, resulting in a sparse network. However, there are now more data streams available to cities that help to understand and quantify air quality. This group investigates the application of satellite, low-cost sensors and modelling individually and together, to improve the understanding of urban air quality as well as regional atmospheric composition. CHPC resources are necessary due to the large size of these datasets and the analyses required to integrate them.

Principal Investigator: Dr Chika Nnadozie
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2024-01-29
Allocation End: 2024-07-29
Used Hours: 15329
Project Name: Campylobacteroisis
Project Shortname: CBBI1446
Discipline Name: Bioinformatics

Press Release

Livestock Identified as Major Source of Bacterial Contamination in Bloukrans River, South Africa

The Bloukrans River, located near Grahamstown in the Eastern Cape province of South Africa, is a tributary of the Kowie River. In a recent study, livestock has been identified as the primary contributor to bacterial pollution in the Bloukrans River, located in South Africa. The mSourceTracker analysis revealed significant findings regarding the sources of bacterial microbes in the river, with livestock being the predominant contributor.

The analysis showed that animals contributed significantly to the bacterial microbes in the river. In contrast, the human gut contributed approximately 10% at all sites. However, the study found a significant proportion of bacteria from unknown sources, accounting for up to 74% at some sites.

As expected, one site, which is mainly used for recreational activities such as swimming and baptism, showed a lower contribution from animals but a consistent contribution from human sources. This pattern suggests that livestock grazing near the river is the main source of bacterial pollution, rather than effluents from nearby wastewater treatment plants.

This finding aligns with previous research indicating that livestock is a primary source of freshwater bacterial contamination. The high proportion of bacteria from unknown sources is likely due to various forms of waste, including solid, electronic, and construction waste, as well as toxic chemicals from improperly disposed wastewater and agricultural runoff. Incorporating metagenomic samples from extreme environments in source tracking analyses could reduce the proportion of unknown sources.

In South Africa, intervention measures targeting pollution sources are generally lacking. Identifying the primary sources of bacterial contamination in the Bloukrans River is crucial for prioritizing, measuring the impact of, and implementing targeted interventions to improve water quality.

Chika F Nnadozie
Institute For Water Research, Rhodes University, Grahamstown, Eastern Cape
11th July, 2024

Principal Investigator: Dr Olivier Sheik Amamuddy
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2024-01-29
Allocation End: 2024-07-29
Used Hours: 3573
Project Name: Structural Bioinformatics and research for tool development
Project Shortname: CBBI1658
Discipline Name: Bioinformatics

At Rhodes University (Department of Biochemistry, Microbiology and Bioinformatics), we are currently studying the dynamics of the human DDAH-1 protein, which is implicated in certain types of cancers, in order to find new ways of targeting it that will hopefully be more specific and less toxic than compounds that have been reported in the literature so far. For this process we're relying on the CHPC for investigating the protein's behaviour during molecular dynamics simulations, without which this type of research would not be possible. We are currently at the data generation stage, after which we'll proceed with the analyses.

Principal Investigator: Prof Jeanet Conradie
Institution Name: University of the Free State
Active Member Count: 7
Allocation Start: 2024-01-29
Allocation End: 2024-07-29
Used Hours: 1872948
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 Collins Obuah
Institution Name: University of Ghana
Active Member Count: 3
Allocation Start: 2024-01-29
Allocation End: 2024-07-29
Used Hours: 96981
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 by using DFT and TD-DFT methods. 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 has been published and others are still ongoing.

Principal Investigator: Dr Chris Oosthuizen
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2024-01-29
Allocation End: 2024-08-21
Used Hours: 2056
Project Name: Bayesian Integrated Population Modelling of Southern Elephant Seals
Project Shortname: CBBI1533
Discipline Name: Environmental Sciences

Our research group in the Centre for Statistics in Ecology, the Environment and Conservation (SEEC) at the University of Cape Town use Bayesian capture-recapture models to estimate how wild animal populations are changing over time. There is a lot of uncertainty involved in modelling wild animal population dynamics, as we often only have partial information about the processes in action. As a result, we often resort to analytical means to overcome the deficiencies of observational data.
For example, in our southern elephant seal and African penguin work, we use Bayesian capture-recapture models that account for the fact that we may not perfectly observe animal life histories from birth to death. Apart from calculating 'detection probabilities', which allows for animals to go unobserved even if alive, we use individual random effects to account for the unique variability of each individual in the population (i.e., individuals surviving and breeding at different rates). These models must estimate individual-level random effects, and significant computational intensity arises from the hierarchical structure of such models. High-performance computing, such as provided by the CHPC, allows us not only to fit such models, but also to perform simulations to verify whether our models are working as well as we think they are. It is important to make such assessments, as our work can have applied conservation use through the work of partners such as SANCCOB – the Southern African Foundation for the Conservation of Coastal Birds. We are currently starting to explore how African penguin survival varies across time and space, and this analysis is important to better understand the drivers of their population declines, and conservation needs.

Principal Investigator: Prof Koop Lammertsma
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2024-01-30
Allocation End: 2024-07-30
Used Hours: 267201
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 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 and now also on asymmetric hydrogenation of ketones with a simple ruthenium catalyst.

Principal Investigator: Dr Lawrence Borquaye
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 26
Allocation Start: 2024-01-30
Allocation End: 2024-07-30
Used Hours: 1199520
Project Name: Biomolecular Computations
Project Shortname: HEAL1382
Discipline Name: Chemistry

We are the Borquaye Research Group, located at the Department of Chemistry, Kwame Nkrumah University of Science and Technology, in Kumasi, Ghana. Our group investigates natural substances such as plant extracts, peptides, essential oils, and other small molecules for their potential health benefits. Using advanced computer modeling techniques, we explore how these substances interact with proteins both in our bodies and in the bodies of microbes, such as bacteria and parasites. Our overarching aim is to identify new compounds that could serve as potential medicines and to understand their mechanisms of action. To conduct our research, we utilize powerful computers accessible through the CHPC (Lengau). We have made significant progress and are currently finalizing our experiments for publication, including gaining insights into how certain natural substances target and affect proteins in both human cells and microbial organisms.

Principal Investigator: Prof Kevin Naidoo
Institution Name: University of Cape Town
Active Member Count: 13
Allocation Start: 2024-01-30
Allocation End: 2024-08-29
Used Hours: 380766
Project Name: Reaction Dynamics of Complex Systems
Project Shortname: CHEM0840
Discipline Name: Chemistry

As before: 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 Robyn van Zyl
Institution Name: University of the Witwatersrand
Active Member Count: 4
Allocation Start: 2024-01-30
Allocation End: 2024-07-30
Used Hours: 13969
Project Name: Targeting Protozoal Infections
Project Shortname: HEAL1398
Discipline Name: Health Sciences

Malaria remains a problem in South Africa with an increase in number of clinical cases and deaths over the past years. After the COVID-19 pandemic the number of malaria infections and deaths increased worldwide due to misdiagnosis and funds being redirected to manage COVID-19 infections. To compound the potential for increased infections and deaths in the future is the development of resistance by the Plasmodium falciparum malaria parasite to two of the drugs used in South Africa to prevent malaria infections. Namely, artemisinin and atovaquone.
There are three recommended options to prevent a malaria infection by the South African Department of Health, namely, atovaquone-proguanil, mefloquine and doxycycline. Atovaquone-proguanil is often preferred by the public as it only has to be used for one week after returning from a malaria area compared to four weeks for mefloquine. Atovaquone is a highly effective drug against sensitive strains with a favourable pharmacological and safety profile. As such a study is underway to investigate additional compounds that inhibit the atovaquone-mitocondrial target in both sensitive and resistant strains and retain a favourable safety profile. Preliminary results have lead to the further investigation into a novel set of compounds that have been designed following molecular modeling of over 2000 compounds using the CHPC Modeling software and resources.These promising findings may have generated lead molecules into the development of a new antimalarial drug.

Principal Investigator: Dr Melissa Nel
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2024-01-30
Allocation End: 2024-07-30
Used Hours: 17189
Project Name: Harnessing the diversity of African genomes to drive novel disease gene and pathway discovery for ALS Spectrum Disorders
Project Shortname: CBBI1659
Discipline Name: Health Sciences

The Neurogenomics Lab works with the UCT Neurology Research Group and the ALSAfrica Network to study the genetic basis of amyotrophic lateral sclerosis (ALS) and other inherited neuromuscular disorders (NMD) in African populations. We are passionate about African-led genomics research and local bioinformatics capacity building to drive the real-world implementation of genomic medicine in resource-limited settings. The Neurogenomics Lab seeks to partner with DNA sequencing service providers in South Africa to enable us to deliver cost-effective and rapid analysis of genomic data according to international best-practice guidelines. We aim to provide ALS/NMD patients access to genetic diagnoses, opportunities to contribute to scientific discoveries through their participation in global research and promote their equitable participation in therapy development and trials. We make use of CHPC resources to analyse raw genomic sequencing data.

Principal Investigator: Mr Randall Paton
Institution Name: University of the Witwatersrand
Active Member Count: 6
Allocation Start: 2024-01-30
Allocation End: 2024-07-30
Used Hours: 335364
Project Name: Compressible Gas Dynamics
Project Shortname: MECH0847
Discipline Name: Other

The compressible flow research group makes use of the CHPC to model flows which govern many of the benefits we enjoy of modern life. These systems require high resolution, both spatially and temporally, to describe the physics at play. The greater understanding of these fundamental flows that results will allow for application in fields ranging from personalised health care to sustainable air transport. The group is now expanding on the traditional paradigm of computational fluid dynamics by leveraging these results with machine learning to develop more efficient ways of modelling flows based on high-quality training data. This will allow the benefits of high-performance computing to be more widely spread for the betterment of all.

Principal Investigator: Mr Steven James
Institution Name: University of the Witwatersrand
Active Member Count: 9
Allocation Start: 2024-01-31
Allocation End: 2024-07-31
Used Hours: 26621
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 representations of their environment in a way that is similar to humans. For example, when planning, humans reason about the world using higher-order concepts, which allow us to ignore the unimportant details and construct long-term plans. The ability to plan far into the future is a key aspect of human intelligence and is something that must be achieved if we are to deploy robots in the real world.

Our approach relies on the robot being equipped with a set of skills, and then autonomously learning high-level concepts to support planning with those skills. Our work allows these robots to transfer these concepts to new unseen environments, which is an important step towards creating flexible robots capable of solving a variety of tasks. Ultimately, we envision our approach being used to create robots capable of operating in multiple environments, such as kitchens, hospitals and warehouses, reducing the need to develop costly, single-purpose robots.

Our approach relies on the CHPC's cluster to run numerous experiments with varying amounts of data to measure how efficiently we can construct these higher-order concepts. These results are further averaged over many trials to improve the statistical significance of our results and ensure that the outcome was not simply a fluke. We have currently reached a stage where the first phase of the project is complete - experiments in simulated environments have validated our approach. Our next step is to deploy our work on a real, physical robot to demonstrate its real-world applicability.

Principal Investigator: Prof Josua Meyer
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2024-01-31
Allocation End: 2024-07-31
Used Hours: 37003
Project Name: Fundamentals of forced and mixed convection in heat exchangers
Project Shortname: MECH1094
Discipline Name: Computational Mechanics

The research program focuses on using CFD simulations via ANSYS/Fluent to explore fundamental heat transfer phenomena in heat exchangers. Large meshes will be employed to study forced and mixed convection heat transfer under various boundary conditions. These simulations will be compared with experimental results (when available) and used to develop correlations for designing energy-efficient heat exchangers. The program, led by Prof. JP Meyer at Stellenbosch University, will include a growing group of postgraduate students and postdocs, each investigating different aspects of internal forced and mixed convection in heat exchangers.

Principal Investigator: Dr Pritika Ramharack
Institution Name: Medical Research Council
Active Member Count: 17
Allocation Start: 2024-02-01
Allocation End: 2024-08-01
Used Hours: 203901
Project Name: Phytomedicine in Metabolic disorders
Project Shortname: HEAL1387
Discipline Name: Health Sciences

The South African Medical Research Council (SAMRC) is proud to announce the establishment of the Cheminformatics Research Group within its Biomedical Research and Innovation Platform (BRIP). Led by Dr. Pritika Ramharack, this pioneering group aims to revolutionize the fields of therapeutic regimens through advanced computational techniques and the innovative merging of natural product chemistry with cheminformatics.

The primary objective of the Cheminformatics Research Group is to conduct cutting-edge research in predictive biological target identification, compound physio-chemical descriptions, molecular modeling, molecular docking, and molecular dynamic simulations. These efforts are directed toward enhancing current therapeutic approaches for various metabolic diseases.

Dr. Ramharack's team will employ the Amber suite to simulate theoretical experimental environments using specialized chemical force fields. This approach allows for in-depth analysis of molecular interactions and free-binding energy of complexes, providing critical insights into the structural mechanisms of action of compounds and the structural dynamics of enzymes, particularly focusing on mutational modifications.

A unique aspect of the group's research is the integration of natural product chemistry with cheminformatics. By combining these disciplines, the team aims to identify and optimize naturally derived compounds, enhancing their therapeutic potential through advanced computational methods.

The utilization of the Centre for High-Performance Computing (CHPC) will be integral to the group's research, enabling large-scale molecular simulations and access to the necessary computational resources. Dr. Ramharack's successful use of the CHPC in her previous studies is well-documented, with findings published in 35 internationally peer-reviewed journals.

The group is actively recruiting students for the 2025/2026 academic cycles. The initiative also aims to enhance computational chemistry capacity development within South Africa, with a particular focus on previously disadvantaged universities.

Through collaborative efforts within the SAMRC and the use of CHPC resources, the research group will provide critical insights into the mechanisms of action of various therapeutic compounds. Dr. Ramharack's vision is to continue utilizing this platform to drive innovation and excellence in computational chemistry and bio-computation research.

Principal Investigator: Dr Lelanie Smith
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2024-02-04
Allocation End: 2024-08-31
Used Hours: 478839
Project Name: Aeronautical Research
Project Shortname: MECH1118
Discipline Name: Other

Simulating Flight for the Grey-Headed Albatross: How CHPC Powers Cutting-Edge Research

At the University of Pretoria, our research group focuses on understanding the aerodynamic properties of the grey-headed albatross, a bird known for its incredible long-distance flights across the Southern Ocean. Our research aims to uncover how these majestic birds manage to glide effortlessly over vast distances with minimal energy expenditure, a feat that could have important implications for biomimetic engineering, conservation, and ecological studies.

Using advanced simulation techniques, we recreate the flight dynamics of the grey-headed albatross. However, such complex modeling requires immense computational power to simulate the bird's interactions with its environment in fine detail. This is where the CHPC (Centre for High-Performance Computing) plays a crucial role. The CHPC's powerful computational resources allow us to run detailed simulations that would be impossible to conduct on standard equipment. The simulations provide valuable insights into the aerodynamics of the bird, enabling us to visualize how it adapts its flight patterns to varying wind conditions and body dynamics.

This research is particularly important because it allows for non-invasive methods of studying endangered species, reducing the need for live experimentation while still capturing vital data. Moreover, by advancing our understanding of the albatross's flight mechanics, we can explore new designs in aviation and drone technology, offering sustainable solutions for the future.

Thanks to the CHPC's support, we have made significant progress in the simulations, and we are close to completing our first series of tests. These results will provide a foundation for future studies and potentially open up new avenues in both wildlife conservation and engineering.

Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 5
Allocation Start: 2024-02-05
Allocation End: 2024-08-05
Used Hours: 316560
Project Name: Computational and statistical methodologies for human and environmental health prediction
Project Shortname: CBBI0818
Discipline Name: Bioinformatics

The group focuses on bioinformatics, computational and Artificial Intelligence approaches, and tool development pertinent to genomic diversity with the objective of uncovering the role of genetic and environmental in determining the risk and susceptibility of communicable and non-communicable diseases, and drug responses. Members of the group are mainly from the University of Cape Town, and other African institutions within the Southern African regions. The PI is both affiliated at the University of Kinshasa, D..R. Congo, and Northumbria University Newcastle.
The group CBBI0818 and CBBI0818_2 have recently conducted an intensive analysis of human and microbial genome variation and developed and evaluated several approaches for multi-omics data integration for both the host and pathogen perspectives to facilitate the transformation of omics-driven clinical practice. The group has currently launched a major project to investigate for the next 3 years, a novel artificial intelligence approach for disease risk prediction and stratification. This project is a computational cost and demands long-term storage and critical resources for high-speed computer processes. The group will continue to benefit from valuable CHPC resources to implement this project. For example, with such CHPC resources and support, in the last three months, the group has finalised the development of JasMAP software, a joint ancestry and genetic association method, tailored to multi-way mixed ancestry populations to efficiently unravel gene underlying ethics differences in disease risk. Without such CHPC support and resources, the group will not be able to deliver such research. The CHPC resources have been a valuable, supportive and helpful fplatform to effective enhace my research group which is heavily relies on large-scale sequence datasets and complex and memory cost pipelines. CHPC enabled us to not substain our research but provide supports to young, early and middle-career researchers.

Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 9
Allocation Start: 2024-02-05
Allocation End: 2024-08-05
Used Hours: 15718
Project Name: African Multi-Omics Data Science
Project Shortname: CBBI1039
Discipline Name: Bioinformatics

The group focuses on research training on bioinformatics, computational and Artificial Intelligence approaches, and tool development pertinent to genomic diversity with the objective of uncovering the role of genetic and environmental in determining the risk and susceptibility of communicable and non-communicable diseases, and drug responses. Members of the group are mainly from the University of Cape Town, and other African institutions within the Southern African regions. The PI is both affiliated at the University of Kinshasa, D..R. Congo, and Northumbria University Newcastle.
The group CBBI1039 has recently conducted an intensive analysis of human and microbial genome variation and developed and evaluated several approaches for multi-omics data integration for both the host and pathogen perspectives to facilitate the transformation of omics-driven clinical practice. The group has currently launched a major project to investigate for the next 3 years, a novel artificial intelligence approach for disease risk prediction and stratification. This research training project is a computational cost and demands long-term storage and critical resources for high-speed computer processes. The group will continue to benefit from valuable CHPC resources to implement this project. For example, with such CHPC resources and support, in the last three months, the group has finalised the development of JasMAP software, a joint ancestry and genetic association method, tailored to multi-way mixed ancestry populations to efficiently unravel gene underlying ethics differences in disease risk. Without such CHPC support and resources, the group will not be able to deliver such research. The CHPC resources have been a valuable, supportive and helpful platform to effective enhance our training research which is heavily relies on large-scale sequence datasets and complex and memory cost pipelines. CHPC enabled us to not substain our training research but provide training and supports to young, early and middle-career researchers so that they can be empower capacity to handle large-scale data and atomate/paralise task through High-Performance computing.

Principal Investigator: Dr Uljana Hesse
Institution Name: University of Western Cape
Active Member Count: 7
Allocation Start: 2024-02-05
Allocation End: 2024-08-05
Used Hours: 43519
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 have developed a Convolutional Neural Network algorithm for the genome-wide identification and classification of plant transporter genes, which is now being adapted for the analysis of other protein family (Carbohydrate active enzymes and P450s). 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 Fortunate Mokoena
Institution Name: North-West University
Active Member Count: 5
Allocation Start: 2024-02-06
Allocation End: 2024-08-06
Used Hours: 10988
Project Name: Protozoan parasites and cancer drug discovery
Project Shortname: CBBI1293
Discipline Name: Bioinformatics

We work on designing small molecules that could be thought of as potential drugs or starting point for drug discovery. Our effort is target-based where we start out with a protein that we believe to be critical to disease development and find molecules that can disable its function. To monitor the interactions between the protein and compounds of interest, we then conduct molecular docking and dynamics simulations.

Principal Investigator: Dr Benjamin Victor Odari Ombwayo
Institution Name: Masinde Muliro University of Science and Technology, Kakamega, Kenya
Active Member Count: 9
Allocation Start: 2024-02-08
Allocation End: 2024-09-05
Used Hours: 629693
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 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 Adrienne Edkins
Institution Name: Rhodes University
Active Member Count: 1
Allocation Start: 2024-02-08
Allocation End: 2024-08-08
Used Hours: 57015
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 team comprises three monomeric research groups, each
independently managed but forming part of a larger collaborative research unit focused on understanding the
structure and function of the cellular stress response. The current study identifies DnaK substrates linked to drug
resistance in treating tuberculosis (TB). The computational part of the study involves molecular dynamic simulations
of wild and mutant versions of the identified proteins to examine if such mutations destabilize the protein.
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: Dr ADEDAPO ADEYINKA
Institution Name: University of Johannesburg
Active Member Count: 13
Allocation Start: 2024-02-09
Allocation End: 2024-08-13
Used Hours: 621252
Project Name: Computational Design of Molecules
Project Shortname: CHEM1221
Discipline Name: Chemistry

The Computational Design of Molecules research group is based at the Department of Chemical Sciences, University of Johannesburg. We aim to design new and improved molecules and materials for applications in catalysis, renewable energy, energy storage and drug discovery using computational chemistry techniques augmented with Machine Learning . Since the availability of energy is one of the main challenges of the African continent, being able to achieve our aims as a group will provide clean energy solutions for the continent. We use computational chemistry software to explore the properties of molecules which is responsible for their activity and then use the knowledge gained to design more efficient and improved materials.

Principal Investigator: Ms Larysha Rothmann
Institution Name: 0 Other
Active Member Count: 2
Allocation Start: 2024-02-09
Allocation End: 2024-08-09
Used Hours: 151387
Project Name: CenGen
Project Shortname: CBBI1615
Discipline Name: Bioinformatics

CenGen, a plant and pathogen R&D lab in Worcester, is pioneering research in agricultural plant breeding and collaborative crop studies. Partnering with DIPLOMICS, CenGen is tackling the complex task of de novo sequencing and assembly of indigenous plants, particularly Spekboom, an environmentally significant plant. This project is particularly challenging due to the absence of genomic resources from closely related species and the plant's highly repetitive DNA, complicating the assembly process.
The raw DNA data for a single Spekboom genome can reach up to 1TB. However, CenGen is equipped to meet these challenges with cutting-edge technology. Thanks to its affordability, they are utilizing Oxford Nanopore Technology, which enables the generation of exceptionally long and accurate DNA sequences. The Centre for High-Performance Computing (CHPC) also provides the necessary computational power to handle and analyze this vast data. This collaboration has enabled CenGen to establish an automated pipeline, enhancing future genome assemblies' scalability, reproducibility, and efficiency.
CenGen has successfully generated a high-quality draft genome assembly for Spekboom, draft genome assemblies for an additional six species and developed a robust pipeline for ongoing and future research. These plant genomic resources set the stage for further exploration of its biodiversity, genetics, and genome structure.
Beyond scientific research, CenGen is also dedicated to education. Through the Veldkos project, they engaged Grade 11 learners, who produced a high-quality draft genome assembly of Carissa macrocarpa, known as the Grootnoemnoem or Natal Plum. This initiative is nurturing the next generation of scientists.
CenGen's work highlights the vital role of CHPC resources in advancing research that benefits both science and society.

Principal Investigator: Dr Nikiwe Mhlanga
Institution Name: Mintek
Active Member Count: 12
Allocation Start: 2024-02-10
Allocation End: 2024-08-12
Used Hours: 1116153
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: Ms Tania Daniels
Institution Name: South African Weather Service
Active Member Count: 3
Allocation Start: 2024-02-12
Allocation End: 2024-09-12
Used Hours: 28889
Project Name: WAVE AND WATER LEVEL MODELLING
Project Shortname: ERTH1609
Discipline Name: Earth Sciences

The principal focus of this project is on regional-scale wave and water level projections. This project uses the SAWS SWaSS to study climate change scenarios. SWaSS will downscale CMIP6 wind and wave projections. The projection of water levels (and regional waves) with the proposed modelling system (SWaSS) is particularly advantageous, as SWaSS is currently South Africa's only operational, high-resolution, public-good storm surge and wave forecast system. Consequently, the model is likely to behave similarly to the system that currently provides short-term forecasts for South Africa, thereby minimising the disconnect between future scenarios and event forecasts. It is also a fully calibrated, validated, and peer-reviewed modelling system, although the forcing and boundary conditions will naturally vary in this particular configuration.

Given the computational demands of the model, the wave and water level downscaled projections (from 1961-2100) can only be performed on the CHPC. In preparation for these efforts, the Delft-3D model has been compiled on the CHPC with the assistance of CHPC personnel, and the atmospheric forcing data, as well as wave and flow boundary data, are being pre-processed. The next phase of the project will involve running the simulations by the Marine Research Unit of the South African Weather Service.

Principal Investigator: Prof Francois Engelbrecht
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2024-02-12
Allocation End: 2024-08-30
Used Hours: 6237318
Project Name: WITS Climate Modelling
Project Shortname: ERTH1200
Discipline Name: Earth Sciences

Using the computational resources of South Africa's CHPC Lengau cluster, the Wits Global Change Institute has completed the first climate change attribution-modelling simulations ever performed on African soil (Engelbrecht et al., 2024; Under Review). The simulations were undertaken at the km-scale, that is, at such high spatial resolution that atmospheric convection can be simulated. The specific case studies was the devastating Durban floods of April 2022, and the simulations indicate that climate change worsened the floods by a factor of 40%. This finding has direct relevance to Loss & Damage considerations in terms of the role of climate change in the Durban floods. The GCI is additionally using the Lengau cluster to undertake extensive ensembles of projections of future climate change over southern Africa (focus on regional tipping points) and the southwest Indian Ocean (focus on landfalling tropical cyclones).

Principal Investigator: Prof Clement Nyirenda
Institution Name: University of Western Cape
Active Member Count: 5
Allocation Start: 2024-02-13
Allocation End: 2024-09-16
Used Hours: 38761
Project Name: Computational Intelligence Algorithms for Smart Environments
Project Shortname: CSCI1631
Discipline Name: Computer Science

This project focuses on developing nature-inspired computational intelligence algorithms for applications in smart healthcare, smart energy, astronomy, and other fields. The team comprises Principal Investigator Clement Nyirenda and three MSc students from the University of the Western Cape: Ms. Liyakhanya Tabata, Mr. Lwando Maciti, and Mr. Mathew Kaiser.

Key areas of work include:
1. Optimized Unsupervised Domain Adaptation (UDA) Mechanisms: UDA is essential for effectively handling new, unlabeled data distributions and bridging gaps between source and target domains.
2. Unsupervised Galaxy Morphology and Classification: This aims to analyze extensive galaxy image datasets objectively, uncovering patterns and insights into cosmic structure and evolution without human bias.
These components are data and compute-intensive, necessitating the use of high-performance computing (HPC) resources. For UDA, we install necessary software and libraries, ensuring compatibility with frameworks like TensorFlow and PyTorch. Models are selected or designed for UDA, incorporating deep learning architectures or specialized algorithms. These models are implemented using parallel programming to utilize HPC's distributed computing capabilities, enabling efficient training across multiple nodes or GPUs. HPC resources are also used for extensive hyperparameter tuning. While the process is progressing well, it is still in the early stages.

Principal Investigator: Dr Rian Pierneef
Institution Name: University of Pretoria
Active Member Count: 33
Allocation Start: 2024-02-14
Allocation End: 2024-08-14
Used Hours: 253759
Project Name: Bioinformatic and Computational Biology analyses of organisms
Project Shortname: CBBI1124
Discipline Name: Bioinformatics

The Bioinformatic and Computational Biology analyses of organisms programme is an energetic group of researchers and students employing the most recent technological methods to understand the biological complexity surrounding us. The programme focusses on large scale data analyses within the biological cluster. As the production of biological data becomes cheaper the amount of data to analyze has rapidly increased. This necessitates the training of researchers and students in accepted bioinformatics and computational biology protocols to keep abreast of the ever increasing amounts of biological data produced. The CHPC is a critical ally and contributing partner in this programme providing members a computational environment to efficiently complete their research objectives.

Principal Investigator: Dr Ruben Cloete
Institution Name: University of Western Cape
Active Member Count: 11
Allocation Start: 2024-02-14
Allocation End: 2024-08-14
Used Hours: 884377
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 Romina Henriques
Institution Name: University of Pretoria
Active Member Count: 8
Allocation Start: 2024-02-14
Allocation End: 2024-08-14
Used Hours: 127714
Project Name: Marine Genomics
Project Shortname: CBBI1661
Discipline Name: Bioinformatics

The Marine Genomics Group at University of Pretoria uses molecular data (DNA/RNA) to understand how the interplay between oceanographic features, fisheries and climate change influence the evolution of Southern African marine fishes. We are a diverse group of postgraduate students, postdocs and PIs, all focused on generating knowledge on commercially exploited fishes in Southern Africa, to assist with conservation and management actions, that ensure the long-term persistence of these important species. We currently have several projects on-going, on Red Roman, blacktail, the kobs, pyjama sharks, among others. As we generate Whole Genomes sequences for all these species, the CHPC is crucially important for our jobs, and greatly help us in achieving our research goals.

Principal Investigator: Dr Stefan du Plessis
Institution Name: Stellenbosch University
Active Member Count: 14
Allocation Start: 2024-02-15
Allocation End: 2025-01-28
Used Hours: 46150
Project Name: Shared Roots
Project Shortname: HEAL0793
Discipline Name: Health Sciences

Understanding the SHARED ROOTS of Neuropsychiatric Disorders and Modifiable Risk Factors for Cardiovascular Disease.
Shared Roots is a collaborative research project undertaken by researchers from the departments of psychiatry, neurology and genetics at Stellenbosch University and researchers from the South African National Bioinformatics Institute (SANBI). It is a MRC Flagship funded study and the principal investigator on the study is the executive head of the department of psychiatry Professor Soraya Seedat. Dr Stéfan du Plessis is responsible for the neuroimaging component. Our study included participants with posttraumatic stress disorder (PTSD), schizophrenia or Parkinson's disease. It is known that individuals with mental illness as well as other common brain disorders have higher rates of heart disease and stroke than the general population. It is not clear why this is the case. Our study therefore aims to collect information about all the potential factors that can play a role, to better understand the increased risk and enable the development of treatment strategies. To achieve this goal we will combine state-of-the-art research techniques such as genetic evaluations and the latest neuroimaging techniques. This will be combined in analysis with information evaluating the brain disorders, general health and lifestyle factors.
For our neuroimaging component, we scanned over 600 participants using Magnetic Resonance Imaging (MRI). Here we investigate potential brain changes associated with increased metabolic risk. We proceeded to calculate precise measurements of around 70 known brain regions using the MRI scans, which will be compared between cases and healthy controls. Processing takes around 24 hours for each scan. To finish in a timely manner, we used the Centre for High Performance Computing Rosebank, Cape Town, Sun Intel Lengau cluster.

Principal Investigator: Dr Moses Okpeku
Institution Name: University of KwaZulu-Natal
Active Member Count: 8
Allocation Start: 2024-02-15
Allocation End: 2024-08-15
Used Hours: 47487
Project Name: Genomics and Bioinformatics Group Westville Campus
Project Shortname: CBBI1185
Discipline Name: Bioinformatics

The Genomics and Bioinformatics group at the University of KwaZulu-Natal has made impressive strides in its research, utilizing advanced high-performance computing (HPC) resources to tackle critical health issues. Focusing on immunoinformatics, malaria drug design, and the study of sea cucumbers, the team has optimized its data analysis processes, significantly improving efficiency and speed.
At the time of current reporting, two PhD students are nearing graduation, having developed innovative research that contributes to our understanding of disease prevention and treatment. Their work, alongside several manuscripts currently in preparation for publication, showcases the group's commitment to advancing scientific knowledge.
By leveraging the power of the CHPC's Lengau supercomputer, the researchers have enhanced their computational capabilities, allowing for more complex analyses and quicker results. This progress not only supports ongoing projects but also positions the group as a leader in bioinformatics research.

Principal Investigator: Prof Francesco Petruccione
Institution Name: Stellenbosch University
Active Member Count: 6
Allocation Start: 2024-02-15
Allocation End: 2024-08-15
Used Hours: 58095
Project Name: Quantum techniques for simulation and machine learning
Project Shortname: PHYS1216
Discipline Name: Physics

Pioneering Quantum Research with the CHPC

The Quantum Research Group at Stellenbosch University, led by Prof. Francesco Petruccione, is advancing the frontiers of quantum science and technology. Our interdisciplinary team explores quantum computing, quantum biology, and quantum communication, with a strong focus on addressing real-world challenges. A significant portion of our research leverages the computational power of the Centre for High-Performance Computing (CHPC), an invaluable resource enabling breakthroughs in these cutting-edge fields.

One of our group's core pursuits is the development of efficient algorithms for quantum devices, particularly in noisy environments. For instance, our recent work, published in Scientific Reports, investigates the effect of classical optimizers and algorithm depth on the performance of the Quantum Approximate Optimization Algorithm (QAOA). Another study uses advanced quantum circuit optimization to simulate open quantum systems, paving the way for more accurate models of quantum noise.

In quantum machine learning, we explore novel hybrid approaches combining classical and quantum systems. For example, our research demonstrates how quantum-enhanced support vector machines and convolutional neural networks can classify pulsar signals with unprecedented accuracy, showcasing the potential of quantum computing in astrophysical data analysis.

Quantum biology also features prominently in our work, including a groundbreaking study on isotope effects in migratory animals, published in BioEssays. This research proposes a quantum mechanism underlying the evolution of animal migration, offering new perspectives on quantum effects in biological systems.

The CHPC is critical to our success. Its advanced infrastructure allows us to model complex quantum systems, optimize algorithms, and train sophisticated machine learning models. These capabilities enable high-fidelity simulations that would be infeasible on conventional computing systems.

As we continue to explore the quantum realm, the CHPC remains an indispensable partner in pushing the boundaries of knowledge, helping us translate fundamental research into technologies with societal impact.

Principal Investigator: Dr Brigitte Glanzmann
Institution Name: Stellenbosch University
Active Member Count: 19
Allocation Start: 2024-02-16
Allocation End: 2024-08-16
Used Hours: 52799
Project Name: SAMRC Precision Medicine African Genomics Centre
Project Shortname: CBBI1195
Discipline Name: Bioinformatics

The South African Medical Research Council (SAMRC) has a Genomics Platform that is a key initiative focused on advancing genomic research in South Africa. This platform aims to support and enhance research in human genetics, molecular biology, and related fields by providing access to cutting-edge genomic technologies and resources.
Key Objectives of the SAMRC Genomics Platform:

Research Support: The platform provides advanced genomic tools and services to researchers across South Africa, facilitating high-quality research in various fields such as human health, infectious diseases, and cancer genomics.

Capacity Building: The platform is dedicated to building capacity within South Africa by training scientists, researchers, and healthcare professionals in genomic technologies and bioinformatics. This helps in developing local expertise and promotes the growth of the genomics field in the region.

Collaborative Research: The Genomics Platform fosters collaboration between national and international research institutions, promoting data sharing and joint projects that address critical health issues relevant to South Africa and the broader African continent.

Public Health Impact: By focusing on genomics, the platform aims to contribute to the understanding of the genetic basis of diseases prevalent in South Africa. This knowledge can inform public health strategies and interventions, ultimately leading to improved healthcare outcomes.

Innovation in Genomics: The platform encourages innovation in genomics by supporting the development of new technologies, methods, and approaches that can be applied to research and clinical practice.

Principal Investigator: Dr Emmanuel Dufourq
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 5
Allocation Start: 2024-02-16
Allocation End: 2024-09-30
Used Hours: 32854
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: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2024-02-17
Allocation End: 2024-08-31
Used Hours: 135534
Project Name: CFD modelling of falling-film bioreactors
Project Shortname: MECH1001
Discipline Name: Computational Mechanics

Falling-film bioreactors have many applications that include algae grown for animal feed or for use as biofuels as a sustainable alternative to fossil-based fuels. In addition, produced algae can also be used in the production of pharmaceuticals, nutraceuticals, cosmetics and in the aquaculture industry. A key limitation to the efficient production of algae in falling films is the absorption of carbon dioxide into the film layer, requiring enhancement techniques to increase production. This is typically done using structured surfaces. As a method of studying the performance of falling-film bioreactors, Computational Fluid Dynamics (CFD) incorporating the Volume of Fluid (VOF) method to capture the gas-liquid interface, is used to quantify film thickness, waviness, and the mass transfer of CO2 into the film. The research is carried out in the Department of Mechanical and Aeronautical Engineering at the University of Pretoria. The CFD work is coordinated by Prof Ken Craig while the experimental part of the research is led by Dr Bradley Bock. The focus of the work is to develop validated simulation techniques of falling films that can be used for the optimal design of falling-film applications. Initially, the CFD models are validated against experimental data from literature. As part of the collaboration, there is the development of experimental measurement techniques to estimate film thickness, gas absorption, etc., activities that are crucial in supporting the simulation effort. Because of the computationally resource-intensive nature of the VOF technique, the resources of the CHPC are critical to the success of this programme.

Principal Investigator: Dr Lonnie van Zyl
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2024-02-19
Allocation End: 2024-08-19
Used Hours: 8048
Project Name: Engineering bacterial pyruvate decarboxylase for increased thermostability
Project Shortname: CBBI1265
Discipline Name: Bioinformatics

Launching the 1KSA project marks a pivotal moment in genomic research, powered by an alliance of dedication and expertise. A profound thank you to Tim Newman, Shane Murray, Setshaba Taukobong, Anja le Grange and Patricia Swart of DIPLOMICS (Distributed Platform in Omics ; Renate Zipfel and Nicky Olivier from UPGL; Gwynneth Matcher from NRF – South African Institute for Aquatic Biodiversity; Renee Prins from CenGen; and Lonnie van Zyl from University of the Western Cape for their invaluable insights. Together, we're embarking on an ambitious quest to sequence 1000 South African genomes, unveiling the hidden stories within our unique biodiversity. This collaborative effort stands as a testament to what we can achieve when we unite in science and discovery.

Check out the website and a video of the launch at the link below.

https://www.1ksa.org.za

https://tinyurl.com/42r8upfr

Principal Investigator: Dr Adeola Rotimi
Institution Name: Agricultural Research Council
Active Member Count: 7
Allocation Start: 2024-02-19
Allocation End: 2024-08-19
Used Hours: 2756
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: Dr Marc Henrion
Institution Name: Malawi Liverpool Wellcome, Blantyre
Active Member Count: 16
Allocation Start: 2024-02-20
Allocation End: 2024-08-20
Used Hours: 26048
Project Name: Malawi - Liverpool - Wellcome Clinical Research Programme
Project Shortname: CBBI1513
Discipline Name: Health Sciences

Malawi Liverpool Wellcome Research 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 to align RNA-seq reads for a tuberculosis drug-discovery project, to perform multiple imputation of missing data in a large observational study among ART patients (the RHICCA study), to map urban plastic waste (to study associations with human health) and for simulations to identify optimal longitudinal data imputation methods.
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: Mr Charmy Twala
Institution Name: University of South Africa
Active Member Count: 5
Allocation Start: 2024-02-22
Allocation End: 2025-02-25
Used Hours: 39119
Project Name: Computational Modelling Group
Project Shortname: HEAL1666
Discipline Name: Health Sciences

The Computational Modelling Group is a research programme that focuses on computational drug discovery and development. It is managed within the University of South Africa (UNISA) and involves Structure-based virtual screening (of various chemical databases), docking, and molecular dynamic simulations targeting DNA and cell cycle proteins. We also employ extensive computational analysis on in silico protein modeling and structure assessment, Density Functional Theory (DFT) analysis, lead optimization, and ADMET calculations. This work ultimately produces preclinical drug candidates for multiple diseases that can be further tested using both in vitro and in vivo studies. Due to the extensive computational power needed of our research projects, we heavily rely on CHPC to execute our objectives. We also have collaborative partners within South Africa and abroad which has led to 4 publications so far, whilst others are still in the pipeline and under review in prestigious international journals.

Principal Investigator: Prof Mahmoud soliman
Institution Name: University of KwaZulu-Natal
Active Member Count: 18
Allocation Start: 2024-02-22
Allocation End: 2024-08-27
Used Hours: 747931
Project Name: Drug Design, development and modelling
Project Shortname: HEAL0790
Discipline Name: Health Sciences

The research scope of Molecular Bio-Computation and Drug Design Laboratory (http://soliman.ukzn.ac.za/) 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. In my research group (http://soliman.ukzn.ac.za/) we rely extensively on the computational support from CHPC for the last 13 years. With such amazing support from CHPC, the lab has successfully grown significantly and manged to publish more than 350 publications in high impact factor journal with more than 100 student graduations. The impact of CHPC on developing research and human capacity as evident from research publications and student graduations is commended and highly appreciated.

Principal Investigator: Mr Mokgerwa Monama
Institution Name: University of Limpopo
Active Member Count: 7
Allocation Start: 2024-02-22
Allocation End: 2024-08-22
Used Hours: 115035
Project Name: Application of Bioinformatics Towards Drug Discovery
Project Shortname: CBBI1665
Discipline Name: Bioinformatics

Drug resistance, which claims millions of lives every year, generally results from a genetic alteration(s) that produces a modified protein in one or more binding sites, consequently reducing the affinity of one or more drugs to that protein target. Our research group falls under the Biochemistry, Microbiology and Biotechnology (BMBT) Department at the University of Limpopo (UL). We are currently focused on doing in-silico research to identify molecular mechanisms of resistance of viral proteins under the scope of drug discovery. We also aim to identify novel therapeutics with reduced resistance potential in viral and bacterial proteins. To gain structural and functional insights into the protein targets and ligands used, the conducted research is highly dependent on HPC resources due to the high computational needs of Molecular Dynamic (MD) simulation calculations. We are currently testing some drugs with reported therapeutics against mutated targets to discern the drugs' potential robustness.

Principal Investigator: Mr Ernest Opoku
Institution Name: Nesvard Institute of Molecular Sciences, Ghana
Active Member Count: 13
Allocation Start: 2024-02-22
Allocation End: 2024-08-27
Used Hours: 136190
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 Tjaart Krüger
Institution Name: University of Pretoria
Active Member Count: 3
Allocation Start: 2024-02-23
Allocation End: 2024-09-18
Used Hours: 232654
Project Name: A DFT study of bio-inspired organic solar cells
Project Shortname: MATS1498
Discipline Name: Material Science

Resolving molecular packing in polymer solar cells

Adding charges to conjugated polymers transforms them into semiconductors with unique electrooptical properties that can be sensitively tuned, depending on the molecular packing. A pervasive limitation in device application is the presence of static disorder, which gives rise to spatial localisation of excitons and the formation of electronic traps, thereby significantly shortening the exciton lifetimes and charge diffusion lengths. On a molecular level, the subunit packing density and arrangement are crucial parameters determining the susceptibility of molecular excitons to structural disorder.

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 by investigating different computational methods to quantify subunit aggregation types in specific organic polymers. Their unique combination of computational methods is a powerful approach to determining the aggregation types in polymers and serves as a platform for investigating numerous other types of polymers. They showed that inserting a particular molecular subunit into the polymer backbone affected the planarity of the polymer due to reduced steric hindrance between the donor and the acceptor units. This reduced steric hindrance was further evidenced by the difference in oscillator strength of the first excited state transition, identified as an intramolecular charge transfer transition.
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 Patricia Swart
Institution Name: 0 Other
Active Member Count: 7
Allocation Start: 2024-02-26
Allocation End: 2024-08-26
Used Hours: 83258
Project Name: DIPLOMICS_CLARITY
Project Shortname: CBBI1617
Discipline Name: Bioinformatics

CLARITY is a bioinformatics platform made possible by DIPLOMICS. We aim to highlight the importance of bioinformatics in any Omics project by enabling access to bioinformatics skills and expertise.
CLARITY uses the CHPC as their platform of choice because it is accessible; extremely well supported and freely available to South African researchers. Therefore, we build bioinformatic workflows to be compatible with the CHPC and enable clients, through training, to use the CHPC, thereby setting them up with sustainable solutions to conduct their own data analysis in the future.

Principal Investigator: Prof Sophie von der Heyden
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2024-02-26
Allocation End: 2024-08-26
Used Hours: 2972
Project Name: Marine genomics and conservation
Project Shortname: CBBI1038
Discipline Name: Bioinformatics

We would be delighted to put this together at the end of the project, but are not currently at a stage to report on our work.

Principal Investigator: Dr Shane Murray
Institution Name: 0 Other
Active Member Count: 7
Allocation Start: 2024-02-26
Allocation End: 2024-08-26
Used Hours: 207025
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. In March 2024 we launched one of our high-impact, high visibility projects – 1KSA: Decoding South Africa's Biodiversity – which aims 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. Please visit the 1KSA website to view some of the species that have been assembled (https://www.1ksa.org.za/)

Principal Investigator: Prof Rajshekhar Karpoormath
Institution Name: University of KwaZulu-Natal
Active Member Count: 11
Allocation Start: 2024-02-26
Allocation End: 2024-08-29
Used Hours: 111236
Project Name: Design of small novel organic compounds as potential drug candidates
Project Shortname: HEAL0835
Discipline Name: Health Sciences

The Synthetic Medicinal Chemistry Research Group (SMCRG) at [institution name] is leading groundbreaking research to develop new treatments for diseases like cancer, tuberculosis, and malaria. These diseases continue to pose significant global health challenges, and the group is working to create new drugs that can effectively combat them. The research is vital because it has the potential to save countless lives and improve the quality of life for people worldwide.
To achieve this, the team uses advanced computational techniques to design and test new drug candidates. They rely heavily on the Centre for High-Performance Computing (CHPC) to run complex simulations and analyze large datasets. This powerful technology allows the group to quickly identify the most promising compounds, accelerating the drug development process.
The project is making excellent progress, with several potential drug candidates already identified. These findings have been shared in leading scientific journals, highlighting the importance of the work. However, the team has faced challenges, such as optimizing their computational models to ensure accuracy and efficiency.
Overall, the research conducted by SMCRG is a crucial investment in public health, utilizing cutting-edge technology to address some of the world's most pressing health issues.

Principal Investigator: Prof Craig Law
Institution Name: University of the Witwatersrand
Active Member Count: 6
Allocation Start: 2024-02-26
Allocation End: 2024-09-02
Used Hours: 110805
Project Name: Aerothermodynamics with vortices, vorticity and shear
Project Shortname: MECH1532
Discipline Name: Other

Prof. Craig Law's aerothermodynamics research programme investigates the dynamic behaviour of fluid flows with aerospace applications in mind. This includes topics such as understanding how to point the thrust of an aerospike engine by changing how the flow expands and interacts at the exit. The benefit of this work is in minimising the mass and moving parts required for more efficient rocket engines. We are using rocket engine combustors and nozzles to learn how to better model the combustion of hydrogen accurately. This knowledge will help improve the weight and efficiency of future rocket propulsion systems that will be necessary to ensure a sustainable future for space flight.

Work has also recently been completed on a way to reduce the drag of rockets by re-imagining the nose. This work has demonstrated the concept with some success and has produced a patent of the engineering concept. There are still some interesting questions around the flight dynamics of the drag reduction system to be investigated, but we are also exploring other ways to apply the concept.

The use of numerical models allows for a fairly cost effective and safe means to explore the concepts described here. This can reduce the overall number of experiments required to demonstrate a concept and allows for these experiments to be done without the risk and high cost 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: Dr Patricia Swart
Institution Name: 0 Other
Active Member Count: 2
Allocation Start: 2024-02-26
Allocation End: 2024-08-26
Used Hours: 1080
Project Name: CPGR Projects
Project Shortname: CBBI1369
Discipline Name: Bioinformatics

The Centre for Proteomic and Genomic Research (CPGR), Woodstock, Cape Town is a multi-omics facility supporting and enabling science in South Africa. Data produced by high-throughput sequencing machines are large and sometimes not readable by humans. Therefore, specific skills and infrastructure are required to transfer and handle the data in order to make use of the data and find the hidden biological meaning. To do this, researchers and bioinformaticians need data transfer, compute and storage resources such as those provided by SANReN, CHPC and DIRISA, respectively. Users of CPGR are encouraged to make use of the CHPC to perform data analysis and to allow a smooth, timely and secure data transfer process. Therefore, data can efficiently move from where they are generated to where they will be analyzed

Principal Investigator: Mr Jean Pitot
Institution Name: University of KwaZulu-Natal
Active Member Count: 8
Allocation Start: 2024-02-27
Allocation End: 2024-08-30
Used Hours: 112419
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: Prof George Amolo
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 15
Allocation Start: 2024-02-27
Allocation End: 2024-09-30
Used Hours: 1490800
Project Name: Properties of Materials for Green Energy Harnessing
Project Shortname: MATS862
Discipline Name: Material Science

The Materials Modeling Group (MMG) is at The Technical University of Kenya (TU-K), Nairobi. It has 4 full time faculty in TU-K and others within the country as well as collaborators in University of Bangui in the Central Africa Republic and Congo Brazzaville. At the TU-K we have 6 postgraduate students. The group is also involved with international collaborators - Renata Wentzcovitch - Columbia University New York and George Amulele - Case Western, Ohio.

MMG employs first principles ab initio calculations to answer fundamental question in Materials Science and Technology as well as related thematic areas. In the last 3 years the group has included AI in both materials science and emerging areas that benefit from these techniques. Some of the emerging areas that need the help of MMG are in Nutrition and Dietetics and Medical Physics.

The works being carried out support experimental findings with deeper insights from fundamental basis. Studies of similar systems to those in actual applications can also be done to provide decision support tools in production and characterization tests in materials science, drug design, among other fields.

The group uses existing fundamental theory codes to study matter. There are also now plans to develop new codes and thus be self reliant. Results obtained from these codes are processed to give images, graphs and data for interpretation. The CHPC provides 24/7 access to these codes to ensure that they running uninterrupted and with outcome in a reasonable time frame.

MMG continues to make very good progress and now fully moving towards high throughput computing with codes such as AIIDA.

Principal Investigator: Dr Njabulo Siyakatshana
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 18
Allocation Start: 2024-02-28
Allocation End: 2024-08-30
Used Hours: 2375226
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 efforts towards the development of the first Africa-based Earth System Model (ESM) is beginning to produce tangible outcomes. One of the recent advances are the developed seamless climate prediction outputs in support of climate tailored climate services research and development. The tailored climate services cover several time scales including weather forecasts, seasonal predictions and climate projections. While the underlying sciences behind climate services is well established, the impact of user-centric earth system model predictions in Africa is yet to the realized. The CSIR climate modelling research in collaboration with the Commonwealth Scientific and Industrial Research Organization (CSIRO) in Australia and South Africa's Centre for High Performance Computing (CHPC) is contributing to climate change adaptation through championing novel climate services that co-defined and co-developed with the respective users. This is in contribution to the World Meteorological organization (WMO) ground-breaking "Early warning systems for all" call by 2027. The CSIR-CHPC partnership continues to pave the way for in-depth understanding of the climate system from the Southern Hemisphere lens. Some of the addressed scientific questions include the understanding of the processes that underlies low frequency high impact weather events such KZN floods, droughts, and heatwaves as well as tropical cyclones. The understanding of how the characteristics of these extreme my change under climate change is critical for climate resilience of all sectors of development. These the use of the latest available modelling science is instrumental in informing the national climate reporting to the UNFCCC, as well climate change adaptation policy-making development and implementation.

Principal Investigator: Prof Mpho Sithole
Institution Name: Sefaku Makgatho Health Sciences University
Active Member Count: 13
Allocation Start: 2024-02-28
Allocation End: 2024-09-11
Used Hours: 20879
Project Name: Computational modeling of titanium based alloys
Project Shortname: MATS1228
Discipline Name: Physics

The research group is at Sefako Makgatho Health Sciences University. Research projects are based on Titanium alloys and Shape memory alloys for biomedical applications, and permanent magnets for electronic applications. Currently, 2 Hons, 6 MSc, and 3 PhD students are registered under this group. One MSc student graduated this year. The group is collaborating with researchers at CSIR, Pretoria. The group utilizes the CHPC facilities for calculations, using the CASTEP code with the DFT employed. This package is used to optimize the materials and calculate their properties such as structural, mechanical, electrical, and thermodynamic properties.

Principal Investigator: Dr Ndanduleni Lethole
Institution Name: University of Fort Hare
Active Member Count: 6
Allocation Start: 2024-02-28
Allocation End: 2024-10-09
Used Hours: 119386
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 and one Honours 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 is currently engaged in two major research projects: (1) Computer simulation studies on bimetallic M-N (M: Mn, Fe, Co, Ni and N: Pt, Ir) 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 modelling and simulation environment and submitted to the CHPC computing resources using the CASTEP code.

Principal Investigator: Dr Jaco Badenhorst
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 6
Allocation Start: 2024-02-28
Allocation End: 2024-09-23
Used Hours: 7032
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: Prof Charalampos (Haris) Skokos
Institution Name: University of Cape Town
Active Member Count: 10
Allocation Start: 2024-02-28
Allocation End: 2024-09-12
Used Hours: 211690
Project Name: Chaotic behavior of Hamiltonian systems
Project Shortname: CSCI1007
Discipline Name: Applied and Computational Mathematics

Using modern numerical techniques of Nonlinear Dynamics and Chaos Theory we investigate in a unified mathematical way the behavior of models describing the energy transport in disordered and granular media, as well as the properties of new elastic materials like graphene and molecules like the DNA. This research is performed by members of the 'Nonlinear Dynamics and Chaos Group' in the Department of Mathematics and Applied Mathematics at the University of Cape Town. The performed investigations constitute an innovative combination of Applied Mathematics, Chaos Theory, Hamiltonian Dynamics and Nonlinear Lattice Dynamics. Their outcomes will provide answers to some fundamental questions about the effect of chaos on the energy transport in disordered and granular media, and on the behavior of graphene and DNA. Some of the questions we try to address are: Does the presence of impurities and nonlinearities enhance or suppress the propagation of energy (e.g. heat) in solids, of light in crystals, and of vibrations in granular material? How does the ratio of the different base pairs in DNA chains affect their structural stability and the temperature at which the double-stranded DNA breaks to single-stranded DNA?

Principal Investigator: Prof Serestina Viriri
Institution Name: University of KwaZulu-Natal
Active Member Count: 30
Allocation Start: 2024-02-28
Allocation End: 2024-09-30
Used Hours: 67680
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 provides state-of-the-art High-Performance Computing, enabling 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: Dr George Manyali
Institution Name: Masinde Muliro University of Science and Technology, Kakamega, Kenya
Active Member Count: 13
Allocation Start: 2024-02-29
Allocation End: 2024-10-16
Used Hours: 277214
Project Name: Ab Initio study of Thermoelectric Materials
Project Shortname: MATS0712
Discipline Name: Material Science

The Computational and Theoretical Physics (CTheP) Group, based in the School of Natural Sciences (SONAS) within the Department of Physics at Masinde Muliro University of Science and Technology, Kenya, is a leader in advancing computational materials science, bridging experimental and theoretical physics. Led by Dr. George Manyali, Senior Lecturer in Physics at Kaimosi Friends University, the group includes a diverse team of researchers, undergraduate, and postgraduate students.

The group's primary research focus is on thermoelectric materials, aimed at recovering waste heat and converting it into usable energy. The Centre for High Performance Computing (CHPC) plays a crucial role by enabling the simulation of electronic structures, which is essential for characterizing the properties of novel thermoelectric materials. Several MSc and PhD projects are currently in progress, with numerous publications expected in 2025. Without access to CHPC's high-performance computing resources, the completion of these resource-intensive projects would have been highly challenging.

Principal Investigator: Prof Robinson Musembi
Institution Name: University of Nairobi
Active Member Count: 9
Allocation Start: 2024-02-29
Allocation End: 2024-11-27
Used Hours: 433785
Project Name: CMCG-UoN
Project Shortname: MATS1321
Discipline Name: Material Science

Monolith Research is the acronym for the Computational Group for Condensed Matter and Material Science of the Department of Physics at the University of Nairobi. The research conducted by the Monolith group is diverse, primarily involving materials for optoelectronic applications, with one member focusing on degenerative prion diseases. Currently, the research group comprises 10 members, of whom four have completed their research work at the master's level, and two more are expected to complete their doctorate in philosophy degrees and potentially graduate by the end of the year 2024. The majority of the members in this group are investigating materials for optoelectronic applications. Examples of optoelectronic materials include solar cells, photosensors, photodiodes, and photoactuators. These materials typically function by generating electrical current when illuminated with light of the appropriate wavelength, which can stimulate them to respond. Optoelectronic materials have numerous applications in everyday devices, with the primary application being in photovoltaics. Photovoltaic solar cells are devices that generate electricity under illumination, and numerous countries have adopted these devices as an alternative energy source. For photovoltaic devices to function effectively, a crucial component known as the absorber layer is essential for light absorption. Our research group primarily focuses on investigating materials that can serve as an absorber layer. The sole member conducting bioinformatic work is engaged in research concerning prion diseases, utilising biophysical techniques and computational methods to conduct the study. Prion diseases are invariably fatal neurodegenerative disorders that affect humans and animals such as cattle, sheep and rabbits. The majority of patients afflicted with prion diseases begin to exhibit symptoms in their late fifties. Symptoms include memory loss, difficulty speaking, and insecurity, leading to progressive dementia and eventual death within months or years. At present, there is no cure or treatment available. This class of neurodegenerative diseases results from a single, minute mutation in a protein that causes it to misfold and subsequently aggregate into amyloid plaques in the brain. Due to the rarity of protein aggregation as a molecular event, investigating the mechanism of this phenomenon necessitates a molecular approach rather than experimental methods. The methodologies employed in conducting all the work were computational methods, specifically density functional theory for materials for optoelectronic applications and molecular dynamics to study prion disease. The CHPC remains an important resource equipment to the research group, and we are grateful for its availability.

Principal Investigator: Dr Fabio Cinti
Institution Name: NITHEP
Active Member Count: 4
Allocation Start: 2024-03-01
Allocation End: 2024-08-31
Used Hours: 51591
Project Name: Quantum Monte Carlo for ultra-cold atoms
Project Shortname: PHYS0892
Discipline Name: Physics

Along other interesting research, the Condensed Matter Theory group, at the University of Johannesburg (Department of Physics) and the University of Florence (Department of Physics and Astronomy), investigate the properties of systems made of bosons. These particles can condensate in the same quantum state which, under specific circumstances, gives rise to a macroscopic quantum phenomena known as superfluidity (the ability to flow without friction among other interesting properties). Under even more specific situations, a system made of bosons can oddly manifest superfluidity and crystal order at the same time, the paradoxal supersolid state. A full theoretical treatment of this system requires large-scale simulations in state-of-the-art computational facilities such as the CHPC. The understanding and designing of (new) materials that manifest macroscopic quantum phenomena are major goals in Physics. The application of this knowledge could open the favourable possibility of engineering long-sought devises such as fault-tolerant quantum computers.

Principal Investigator: Prof Lyudmila Moskaleva
Institution Name: University of the Free State
Active Member Count: 12
Allocation Start: 2024-03-01
Allocation End: 2024-09-18
Used Hours: 1084896
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 published on the topic in a top-ranked journal ACS Catalysis (Eltayeb et al. ACS Catal., 2024, 14, 7901-7906). 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 under the influence of adsorbates) 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), high-level ab initio quantum chemistry methods and statistical theory. 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, 6716–6792, and presented at the 27th International Symposium on Gas Kinetics and Related Phenomena, in Leeds, UK, 2024.
In a third subproject, have been modelling the ligand exchange reaction between Ba- and Ra-Macropa derivatives for in silico evaluation of candidate ligands showing a preference for Ra-complex formation over Ba-complex formation. The purpose of this research is for designing Ra-complexes - which may show increased stability and improved effectiveness – e.g. for radiotherapeutic treatment of cancer.

Principal Investigator: Dr Thokozani Justin Kunene
Institution Name: University of Johannesburg
Active Member Count: 1
Allocation Start: 2024-03-01
Allocation End: 2024-10-01
Used Hours: 19562
Project Name: TurboMagFluids
Project Shortname: MECH1573
Discipline Name: Applied and Computational Mathematics

Our research team consisted of graduate students from the University of Johannesburg's Mechanical and Industrial Engineering Department who were passionate about numerical studies. We recently joined forces with the Geology and Applied Mathematics departments for research on numerical simulations. Known as TurboMagFluid, our group aims to generate practical and valuable insights that will impact the design parameters of rotary machine groups and flow behavior. A critical area of study is the effect of fluid behavior on performance. This research also encompasses specialized fields such as fluid-structure interactions (FSI), magnetohydrodynamic flows (MHD), Rheology, Multiphase flows, and nanofluids, which influence various machine components. The CHPC's cyber infrastructure enables us to numerically solve problems in our research domain. The computing power provided by the CHPC has significantly contributed to the advancement of our research.

Principal Investigator: Prof Rasheed Adeleke
Institution Name: North-West University
Active Member Count: 16
Allocation Start: 2024-03-02
Allocation End: 2024-09-02
Used Hours: 20699
Project Name: Environmental and Agricultural Microbiology
Project Shortname: CBBI1183
Discipline Name: Environmental Sciences

Our research group programme at the Unit for Environmental Sciences and Management, North-West University, Potchefstroom continues to advance the understanding of microbial communities across different environmental samples (including food, water, crops, soils) and agroecosystems in general. Our core interest is towards soil, plant and human health management. The group is 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. In addition, we are currently investigating microbial community diversity of irrigation water contaminated with diverse antibiotic resistant genes and bacteria. We seek to generate novel solutions that address critical global issues, including antibiotic resistance, 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 Liliana Mammino
Institution Name: University of Venda
Active Member Count: 4
Allocation Start: 2024-03-04
Allocation End: 2024-09-04
Used Hours: 56892
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: Dr Lynndle Square
Institution Name: North-West University
Active Member Count: 8
Allocation Start: 2024-03-04
Allocation End: 2024-09-26
Used Hours: 705517
Project Name: Exploring poly(2,5)benzimidazole enhanced with carbon nanotubes for space applications
Project Shortname: MATS1088
Discipline Name: Physics

Researchers at North-West University's Center for Space Research are exploring innovative ways to protect satellites and spacecraft from harmful space radiation. The team is investigating a new type of thin film coating that could be used as a shield against radiation in Low Earth Orbit (LEO), where satellites and other space assets are constantly exposed to high radiation levels.

This work is critical because radiation can damage sensitive equipment, reduce the lifespan of satellites, and even put astronauts at risk. As space exploration and satellite deployment expand, finding effective and lightweight radiation shielding solutions has become more critical than ever.

The researchers focus on a material enhanced with carbon nanotubes—tiny, tube-shaped structures that are incredibly strong and have unique electrical and thermal properties. These nanotubes are integrated into a polymer, which is then applied as a thin coating to surfaces. The goal is to develop a material that not only protects against radiation but is also durable, lightweight, and suitable for the extreme conditions of space. The group has started to expand their research to include other nano additives.

The team uses advanced computer simulations to model and optimise the material and its application process to achieve this. These simulations run on high-performance computing (HPC) systems provided by the Center for High-Performance Computing (CHPC), allowing researchers to predict how the material will perform in space. HPC resources are essential for this project, enabling the team to analyse complex processes and refine their designs before any physical testing takes place.

This groundbreaking research could lead to better protection for our satellites, space stations, and future space missions, ensuring that space technology continues to advance while keeping costs down and improving safety.

Principal Investigator: Dr Geoff Nitschke
Institution Name: University of Cape Town
Active Member Count: 25
Allocation Start: 2024-03-05
Allocation End: 2024-09-16
Used Hours: 566565
Project Name: Evolving Complexity
Project Shortname: CSCI1142
Discipline Name: Computer Science

Our latest research project in the Evolutionary Machine Learning Group (UCT) trains deep-learning classifiers in orthopedic pathology to evaluate the efficacy of state-of-the-art supervised deep-learning image classifiers, complemented by data augmentation and transfer-learning. These classifiers are comparatively evaluated on two (cervical spine and elbow) small, multi-label (with unbalanced data distribution) orthopedic radiographic (X-ray) data-sets, with the objective of detecting multiple pathologies with high accuracy. The goal of this work is demonstrate the efficacy of computational tools as automated prognostic and diagnostic tools to assist orthopedic practitioners.

Principal Investigator: Prof Thuto Mosuang
Institution Name: University of Limpopo
Active Member Count: 12
Allocation Start: 2024-03-06
Allocation End: 2024-10-16
Used Hours: 39750
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. One doctoral student: Dr Moshibudi Ramoshaba graduated with PhD in the recent UL autumn graduation ceremonies 2024. Title her doctoral thesis: 'Computational and experimental studies of copper sulphides and copper selenides for solar cells applications.' Two (2) 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.
Centre for High Performance Computing (CHPC) is highly indebted for all the valuable work produced. HPC/CHPC continues to support my research group on pursuing our research work.

Principal Investigator: Dr Sphelele Sosibo
Institution Name: North-West University
Active Member Count: 8
Allocation Start: 2024-03-07
Allocation End: 2024-08-07
Used Hours: 4428
Project Name: Molecular Dynamics of target enzymes
Project Shortname: HEAL1414
Discipline Name: Chemistry

Molecular dynamics of target proteins research group belongs to the North-West University's Materials Science Innovation and Modelling (MaSIM) entity.

The focus of our research group aims at using fast computing technologies 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 as a skill to achieve their project objectives such as graduations and publications. We have produced about six honours, 1 MSc and 1 PhD. Currently training 2 MSc and 1 Honours candidates.

Principal Investigator: Dr Wilhelm Johann van den Bergh
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2024-03-08
Allocation End: 2024-09-06
Used Hours: 5193
Project Name: CFD investigation into heat transfer
Project Shortname: MECH1672
Discipline Name: Computational Mechanics

The research group at the University of Pretoria is focused on heat transfer, either in pipe or external, with special attention being paid the to the interplay between natural and forced convection in pipes.
Internal mixed convection developing flow in the laminar regime is very attractive in maxmising heat transfer in very specific scenarios. The fact that high Prandl number fluids are more easily in a laminar flow region, where mixed convection is encountered, makes studies of this field highly interesting.
Due to the fact that experimental work is by nature limited, takes up a lot of space, and is very delicate, running computational simulations before validating with experimental work is a critical component of this research.
At present, the docotoral student involved in this project is progressing at a fair clip, and is exploring certain unique aspects of high Prandtl fluids.

Principal Investigator: Dr Trisha Salagaram
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2024-03-08
Allocation End: 2024-09-26
Used Hours: 14705
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 complex calculations 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 Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 14
Allocation Start: 2024-03-11
Allocation End: 2024-09-30
Used Hours: 3285626
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.

Principal Investigator: Mr David Ngobeni
Institution Name: Council for Geoscience
Active Member Count: 16
Allocation Start: 2024-03-11
Allocation End: 2024-09-30
Used Hours: 231405
Project Name: Application of high performance computing at the Council for Geoscience
Project Shortname: ERTH1227
Discipline Name: Earth Sciences

The primary mandate of the Council for Geoscience (CGS) according to the Geoscience Act is to develop and publish world-class geoscience knowledge products and to render geoscience-related services to the South African public and industry. For the CGS to fulfil this mandate and also to advance the geoscience field within South Africa and beyond, the CGS registered a research programme with the Center for High-Performance Computing and is titled "The application of high-performance computing at the Council for Geoscience". This programme was formulated to expand the currently available computing resources at the CGS and the programme involves running high computing packages for geophysical modelling, seismological data processing, geological modelling and any other packages which are currently not optimum for desktop computing. Research and development of the various geoscience fields (geophysics, geology, geochemistry, hydrogeology) are covered in this programme. Currently, the CGS is embarking on training scientists to get them up to speed in the utilisation of this new technology in their line of work. The ultimate intention of the CGS is to extract value from geoscientific data. These data will be used for predictive mineral mapping, water mapping, pollution characterizations, geohazards modelling and climate change studies.

Principal Investigator: Prof Catharine Esterhuysen
Institution Name: Stellenbosch University
Active Member Count: 7
Allocation Start: 2024-03-12
Allocation End: 2024-10-02
Used Hours: 39513
Project Name: Computational chemistry analysis of intermolecular interactions
Project Shortname: CHEM0789
Discipline Name: Chemistry

The Computational Supramolecular Chemistry group at Stellenbosch University studies the role of intermolecular interactions on the behaviour of a variety of materials. One of their focus areas is the sorption behaviour of porous materials through understanding the nature and origin of their interactions with the compounds being adsorbed. Of particular interest is the interaction of CO2 with porous frameworks, which is difficult to study experimentally, but can easily be probed through calculations performed using the CHPC's computational facility. For instance, computational methods can be used to directly follow the motion of individual gas molecules within the frameworks thus explaining sorption behaviour. We are therefore able to understand the mechanism of uptake of greenhouse gases such as CO2, and also investigate the activation of CO2 sequestrated within the porous framework to produce useful chemical products. We aim to utilise this this information to design materials with improved properties. The CHPC's facilities thus allow us to obtain a thorough understanding of the behaviour of materials that we would not otherwise be able to achieve.

Principal Investigator: Dr Eric Maluta
Institution Name: University of Venda
Active Member Count: 14
Allocation Start: 2024-03-12
Allocation End: 2025-04-16
Used Hours: 90609
Project Name: Energy Material Modeling in the Application of different Photovoltaic Technologies
Project Shortname: MATS0827
Discipline Name: Physics

The University of Venda, Green Technology Confucius Institute, Energy Material Modelling Group, works on understanding different properties of materials to enhance the efficiency of different Photovoltaics technologies. The group has worked on different semiconductors materials for improving the efficiency of 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 a solution to this situation if we can 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: Dr Johannes Pretorius
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2024-03-11
Allocation End: 2024-09-30
Used Hours: 543242
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 three research topics: The performance of natural draft direct dry cooling systems (NDDDCS), the performance of forced draft cooling systems for supercritical carbon-dioxide (sCO2) applications and the optimization of a heat exchanger for the NDDDCS. We do this by one-dimensional (1D) calculation, three-dimensional (3D) Computational Fluid Dynamics (CFD) simulations, or co-simulations where we link the 1D codes to the 3D CFD for simultaneous simulation.

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 and unsteady 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 have recently finished all of our simulations on this topic. In a related topic, we have simulated various configurations of a finned-tube heat exchanger using 3D CFD in order to optimize its design, specifically for its use in a NDDDCS. From these simulations, we have produced a reduced-order model. This study is nearing completion.

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. Our co-simulations are currently still underway.

Principal Investigator: Mr Adebayo Azeez Adeniyi
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2024-03-13
Allocation End: 2024-08-13
Used Hours: 194682
Project Name: Drug Discovery Research Using Quantum and Molecular Dynamic Simulation
Project Shortname: CHEM0958
Discipline Name: Chemistry

The CHPC has been an indispensable resource for our research, providing critical computational infrastructure that has significantly accelerated our progress. Its support has been instrumental in achieving impactful results and expanding the scope of our investigations.
Since our last report in March 2024, we have published two additional articles, demonstrating the continued productivity enabled by CHPC resources. Our research has evolved to encompass a broader spectrum, including machine learning, deep neural networks, vaccine development, photochemistry, and polymer chemistry, in addition to our core focus on drug discovery and the electrochemical properties of small molecules.
To support this expanded research agenda, we rely on a diverse suite of computational tools, including quantum chemistry packages (Gaussian, Orca, Games, NewChem), molecular dynamics software (Gromacs, Amber, Lammps), and bioinformatics tools (Schrodinger, Haddock, Autodock, Attract). These resources have been pivotal in our exploration of epitopes-based vaccine design, polymer chemistry, photochemistry, and molecular electrochemistry.
The integration of theoretical modeling into our research process, made possible by CHPC, provides essential insights and guides our experimental efforts. By combining computational simulations with experimental data, we have been able to address complex challenges and develop innovative solutions. The continued support of CHPC is essential to the ongoing success of our research program.

Principal Investigator: Prof Paulette Bloomer
Institution Name: University of Pretoria
Active Member Count: 7
Allocation Start: 2024-03-13
Allocation End: 2024-09-13
Used Hours: 162209
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, bryde's whale, cape grysbok and different birds including falcons and Houbara) that make use of the CHPC resources, with additional projects in the pipeline.

Principal Investigator: Prof Andries Engelbrecht
Institution Name: Stellenbosch University
Active Member Count: 13
Allocation Start: 2024-03-13
Allocation End: 2024-10-09
Used Hours: 495479
Project Name: Computational Intelligence for Optimization
Project Shortname: CSCI0886
Discipline Name: Computer Science

Nature-inspired computation refers to the development of mathematical models and algorithms based on simple behaviors observed in social organisms encountered in nature. Such organisms include ant colonies, bee colonies, and bird flocks, among others. Our research specifically focuses on the development of bird flocking behavior models and the application of these models to solve complex optimization problems. In addition, models of bee and ant foraging have been developed towards application to control multiple agents (e.g. simple stimulus-response robots) to perform object collection and sorting tasks.

Principal Investigator: Prof Ignacy Cukrowski
Institution Name: University of Pretoria
Active Member Count: 10
Allocation Start: 2024-03-14
Allocation End: 2024-10-31
Used Hours: 144952
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 James Sifuna
Institution Name: The Catholic University of Eastern Africa, Nairobi, Kenya
Active Member Count: 9
Allocation Start: 2024-03-14
Allocation End: 2024-12-12
Used Hours: 349630
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 comprised two leaders and a few students who shared common interests in material discovery. At the time, I led the group, and our rapport with each member was excellent.

We recently had the pleasure of hosting a team from CHPC in Nairobi, and the experience of sharing ideas with them was fantastic.

Our research group was highly focused on exploring novel materials as alternatives to traditional fossil fuels, including solar, wind, and hydroelectric power. We utilized Density Functional Theory (DFT) implemented in SIESTA and Quantum ESPRESSO codes for our calculations.

CHPC played a crucial role by providing computing facilities that surpassed what we had at our university. Given our focus on studying large systems, which required significant CPU hours to converge, CHPC's support was invaluable.

At that point, we had achieved nearly half of our set objectives, and we were grateful to CHPC and its technical team for their assistance.

Regarding conference presentations or other outputs, we had a paper accepted and were ready to share it once it was published the following week. As for conferences, we were set to host an East-African School on DFT, which was fully funded. See the link: East-African School on DFT 2024.

Principal Investigator: Dr Zibo Keolopile
Institution Name: University of Botswana
Active Member Count: 3
Allocation Start: 2024-03-14
Allocation End: 2024-10-08
Used Hours: 358913
Project Name: Physics
Project Shortname: MATS1303
Discipline Name: Physics

Our research group is based in the Department of Physics, University of Botswana. It is focused on electronic structure calculations of molecular systems. Mr Larona 's research is s focusing on the
neutral and anionic trimer and tetramers of Oxalic acid molecules. In this study, our aim was to explore the anionic state of the oxalic acid trimer, focusing on its structural, electronic, and energetic characteristics. Specifically, we will investigated the stability provided by complex hydrogen bond networks, the electron localization within the trimer, the influence of molecular symmetry on its properties and the Non-covalent interactions. Our study holds a key to understanding nature's intricate design mechanisms and blueprints. Our molecule of choice is interesting because it is a simplest dicarboxilic acid which can have various types of orientations of the monomer due to the internal rotations of the C-C bond and inversions of the hydrogen bond. There is a lack of critical theoretical data on the lowest energy structure of OA trimer in gas-phase and the salient features of the interactions between three monomers. There is also scarcity of theoretical data which can be useful for more complex clusters of different molecules. two journal papers are underway.

Mr Moitshepisi is currently studying Cryptophanes, Cryptands, Nanotubes, Fullerenes and Metal-Organic Frameworks as host molecules and analyse how structure and electronic properties influence their suitability for sensor applications. Secondly, he is working on Guest selection: Choose a wide range of guest molecules such as gaseous molecules (e.g., methane, carbon dioxide, nitrogen dioxide and ammonia), metal ions, transition metal complexes and small organic compounds. Thirdly, Binding affinity investigation: Calculate binding affinities and analyze the role of specific interactions in host-guest systems, considering factors such as van
der Waals forces, dipoles, hydrogen bonding and coordination bonds. Fourthly, Sensitivity to Environmental Factors: Assess how environmental factors such as temperature, pressure, and solvent effects affect the stability of the host-guest systems and lastly, Design Optimization: Propose modifications in the design of host molecules
to enhance sensor application. The journal paper is in progress.

These are big calculations which cannot be done on a small workstation and require the use of high performing computer clusters, therefore, a need for CHPC.

Principal Investigator: Dr Ofentse Pooe
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2024-03-14
Allocation End: 2024-09-14
Used Hours: 15006
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. Our research work aims to deliver potential antimalaria drugs (hybrids) with dual therapeutic action with enhanced efficacy.
The designed and synthesised selected drugs are essentially investigated against malarial glycolytic pathway proteins, specifically lactate dehydrogenase and hexokinase.
Due to the emerged resistant malaria strains and the efficiency of the RTS,S/AS01 vaccine which is approximately 32 % against severe malaria, thus drug treatment remains a most viable option to manage malaria.
Therefore, CHPC essentially assist us as a group to conduct in silico work (molecular docking and dynamics simulation) which is our vital first step in investigating possible interactions of the drugs against our target diseases.

Currently, we are working on designing a multi-epitope vaccine which could be possible used against malaria. Therefore, providing a better understanding of how this vaccine could behave when tested.

Principal Investigator: Prof Mario Santos
Institution Name: University of Western Cape
Active Member Count: 22
Allocation Start: 2024-03-14
Allocation End: 2024-10-18
Used Hours: 855780
Project Name: Cosmology with Radio Telescopes
Project Shortname: ASTR0945
Discipline Name: Astrophysics

The Centre for Radio Cosmology at the University of the Western Cape is leading the world effort in using the new generation of radio telescopes to probe the Universe, in particular with the neutral hydrogen (HI) intensity mapping technique. The main goal is the development of pipelines and technical know-how in order to conduct the required radio surveys and tackle the huge data volumes that will be provided by these telescopes and ultimately extract exquisite cosmological constraints. The centre focuses on the use of the MeerKAT telescope and the Hydrogen Epoch of Reionization Array (HERA), both set in South Africa. These instruments are also precursors to the Square Kilometre Array, which will be the largest telescope in the world. The CHPC has been instrumental in running cosmological simulations, processing the data from these facilities and comparing the models against observations. Measurements from HERA have provided the strongest limits so far on the HI signal from the Epoch of Reionization and results from MeerKAT have provided the first detections of the signal during the late stages of evolution of the Universe.

Principal Investigator: Dr Emma Rocke
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2024-03-14
Allocation End: 2024-10-18
Used Hours: 142321
Project Name: The Benguela Microbiome
Project Shortname: ERTH1620
Discipline Name: Earth Sciences

The marine microbial ecology group at UCT focuses on the marine microbial community dynamics and function in the Benguela upwelling system.
We are building a knowledge base to understand how these critical communities support the food web in this highly productive region. No such work has ever been done before. We are doing this by analysing cruise samples from along the coast that were taken in 2022 (mission microbiome project). We are making good progress and should have a publication ready for submission by early next year.

Principal Investigator: Mr Mogesh Naidoo
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 5
Allocation Start: 2024-03-14
Allocation End: 2024-09-30
Used Hours: 140665
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 Anna Bosman
Institution Name: University of Pretoria
Active Member Count: 28
Allocation Start: 2024-03-15
Allocation End: 2024-09-30
Used Hours: 335853
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: Dr Prinessa Chellan
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2024-03-15
Allocation End: 2024-08-20
Used Hours: 1156
Project Name: Chellan Research
Project Shortname: CHEM1624
Discipline Name: Chemistry

This research group focuses on the development of novel organometallic agents which may be used in the treatment of diseases such as cancer, malaria, or TB.
Recently, computational methods for the determination of drug targets have become increasingly important. One such method is molecular docking. Molecular docking involves the use of computational software to predict the interactions between a small molecule (ligand) and a target protein's binding site. This process involves two steps: First is the generation of poses whereby a ligand is docked into the binding site in a variety of conformations. The second step is the scoring of the poses, here each pose is given a score based on factors such as hydrogen bonding, hydrophobic interactions, and electrostatic interactions. These scores are used to predict how well a compound may bind.
The docking of compounds to the binding site requires both the protein and the ligand to be in their lowest energy conformation before docking may take place. This is typically done by use of DFT studies which not only generates the lowest energy conformation but also gives insights into the chemical reactivity of the synthesized molecules by means of HOMO-LUMO energies, electrostatic potentials, and atomic charges.
The data obtained during these types of studies by this research group has demonstrated stable molecules which have high affinity for the target proteins which has informed our choice to carry on developing these molecules.

Principal Investigator: Ms Nomcebo Motsa
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2024-03-18
Allocation End: 2024-10-15
Used Hours: 158369
Project Name: Catalytic Decomposition of Ammonia
Project Shortname: CHEM1623
Discipline Name: Chemical Engineering

The research group is CHEM1623, from the Chemical engineering department of the University of Pretoria. The research is about the computational design of catalysts for ammonia decomposition to produce hydrogen. This work contributes to two major goals that are important to South Africa. First; the project is in line with national development plan 2030, objective number 5 "environmental sustainability-an equitable transition to a low-carbon economy". It contributes to the replacement of fossil fuels, a major culprit of carbon emissions. The project mitigates climate change by producing clean hydrogen and providing a safe method of hydrogen storage and transportation. Successful hydrogen production would assist South Africa to manage the transition to a low carbon economy and to protect the environment.
Second; the project supports SDG 7 "affordable and clean energy". The project provides an efficient method to produce hydrogen. Since part of the objectives of the project is to design catalysts that will work at lower temperatures, affordable energy will be available for everyone. This goal also focuses on climate change mitigation which is the gist of the ammonia decomposition project.
The project also supports SDG 13: "Take urgent action to combat climate change and its impacts". As stated earlier, ammonia decomposition to hydrogen contributes to clean energy production, mitigating climate change. The wholistic approach of the project entails computational modelling of the various catalysts via material studios, and investigating their respective catalytic efficiency via density functional theory. The design and necessary calculations intrinsic to this project is strongly dependent on access to a high performance computer which fortunately CHPC provides via access to their clusters.
Currently, the first stage of the project has been attained as our result shows the potential of our catalyst attaining comparable results to conventional catalysts used. This shows the feasibility of our catalysts, and future works are aimed at further optimization of the catalysts.

Principal Investigator: Prof Giuseppe Pellicane
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2024-03-18
Allocation End: 2024-10-17
Used Hours: 492112
Project Name: Computational Study of Structure-Property Relationships in polymer blends relevant to OPV devices
Project Shortname: MATS0887
Discipline Name: Physics

Our focus is constantly widening beyond computational studies of polymeric materials, relevant to organic photovoltaics/surface engineering, on phases and phase transitions of the proximity to a Ruelle-Fisher instability, marking the transition to a collapsed state. The importance of the topic is related to its implication on electrostatic interactions, which govern the stability of matter and the fact that such stability does not depend on the mass ratio of the differently charged species. In fact, we have proof of that when we look at atoms with a large ratio of nucleon to electron mass, such as hydrogen or deuterium atoms.
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 the outstanding 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 Jennifer Veitch
Institution Name: SAEON
Active Member Count: 15
Allocation Start: 2024-03-19
Allocation End: 2024-09-20
Used Hours: 433842
Project Name: SAEON Coastal and Regional Ocean Modelling Programme
Project Shortname: ERTH1103
Discipline Name: Earth Sciences

The primary usage of the SAEON Coastal and regional ocean modelling programme has been to support the SOMISANA initiatve at SAEON. The vision of SOMISANA is to support the development of a critical mass of internationally recognized South African numerical ocean modellers who provide information about the changing state of the ocean for enhanced impact. To this end, the two main objectives are capacity development and the production of ocean models that describe a past, or future state of the ocean. Capacity Building is done through student supervision (some of whom make use of the CHPC) and modelling workshops that are run with the support and collaboration of the CHPC. The development phase of the operational forecast models that are disseminated on the SOMISANA website (https://somisana.ac.za/) requires a series of model tests that are done on the CHPC servers.

Principal Investigator: Dr Gerhard Venter
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2024-03-19
Allocation End: 2024-10-03
Used Hours: 222333
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 Daniel Joubert
Institution Name: University of the Witwatersrand
Active Member Count: 19
Allocation Start: 2024-03-19
Allocation End: 2024-09-30
Used Hours: 695777
Project Name: Energy Materials: Numerical explorations
Project Shortname: MATS0800
Discipline Name: Physics

Imagine designing a material atom by atom. Imagine analysing the properties of tomorrow's novel materials before they exist. Computational materials science plays an important role at every of level of the design and engineering of new materials. The rapid advances in computer processing power and memory has given virtual, fundamental, materials design a boost. The first problem faced in designing a virtual material, a material that has not yet been made, is to find the stable configurations in which the atoms in the mix will settle into. The designer must find the configuration of electrons and nuclei, the building blocks of atoms, which result from the interactions among a number of particles that, even for a small piece of material, exceeds the number of particles of sand on all the beaches in the world. This daunting task has a simple solution. Instead of finding the configuration of the real material, the problem is solved for a fictitious material where the constituent particles do not interact. All that is necessary is to find the particle density distribution of the fictitious material, which by design, is the same as that of the real material. A Noble prize was awarded for this idea to the chemists Walter Kohn and John Pople in 1998.

A group of postgraduate students at the University of the Witwatersrand use the computer power at the national Centre for High Performance Computing to conduct virtual experiments on existing and novel materials to examine their potential as energy harvesters. They examine the potential of a selection of materials that can be used as cheap components in solar cells, materials that can generate electricity from waste heat and materials that can be used to split water molecules to extract hydrogen for energy production.

Principal Investigator: Prof Andreas Lemmerer
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2024-03-23
Allocation End: 2024-09-26
Used Hours: 19976
Project Name: Calculations involving Agrochemicals
Project Shortname: CHEM1676
Discipline Name: Chemistry

The Jan Boeyens Structural Chemistry Group, School of Chemistry, Faculty of Science, Witwatersrand University. This group develops novel co-crystals, salts, and polymorphs of small organic molecules that are useful in pharmaceuticals, agriculture, and technological advancement. We also probe the structure, symmetry, and nature of bonds in molecular crystals for better understanding of materials.
We are currently looking at agrochemical ingredients to address the global problem of malaria vectors. The widespread resistance of mosquitoes against insecticides has decreased the efficacy of the available insecticides, threatens the substantial progress made in controlling malaria disease in the 21st century, and endangers public health. The study focuses on developing novel polymorphs (same molecular structure but different structural arrangement) of these current insecticides, as well as novel co-crystals and/or salts (addition of coformer to the insecticides) with better efficacy against malaria vectors. The development of a modified version of the existing insecticide will have no environmental impact, no cost, and no time implications of going through different processes before approval. The study involves both experimentally and computationally approaches to obtain holistic (all) information about the material under investigation. The use of CHPC resources provides complementary data to the experimental results. The research process involves the development of novel polymorphs, co-crystals, and/or salts of insecticides experimentally and the determination of the structures using x-ray diffraction and IR. Thereafter, investigate the stability of the material with DSC and TGA; this property is important in the formulation process. The molecular structure obtained from x-rays will be computationally optimized to the global minimum in the gas and solvent phases; this will then be compared with the experimental geometry of a known structure (insecticide) to establish the formation of a new compound. The calculation of the energy of interaction between the molecules provides insight into the stability of the material. The energy of each material will be compared with one another and with the result obtained from the DSC. Furthermore, the solubility and the lethality test will also be determined.
The project has progress as we have obtained more than 5 polymorphs of the insecticides before we ran out of chemicals (starting materials). In the process of investigation, we obtain a novel polymorph of thiourea derivative, which has multi-disciplinary applications.

Principal Investigator: Mr Francois Meyer
Institution Name: University of Cape Town
Active Member Count: 6
Allocation Start: 2024-03-25
Allocation End: 2024-09-30
Used Hours: 173111
Project Name: NLP for South African languages
Project Shortname: CSCI1674
Discipline Name: Computer Science

The Computational Linguistics Group at the University of Cape Town, led by PhD candidate and Lecturer Francois Meyer, is at the forefront of addressing the challenges faced by low-resource languages in the digital age. South Africa's languages, such as isiXhosa and isiZulu, often lack the vast amounts of annotated data that more commonly spoken languages benefit from. This scarcity of data makes it particularly challenging to develop effective computational tools for these languages.

Our current projects are focused on building advanced computational tools to better understand and process these languages. One project, for example, is developing "Baby Language Models" for isiXhosa, which are highly data-efficient and suitable for low-resource languages. Another project is tackling the challenge of automatically analysing the grammatical structure of Nguni languages. These tools not only enhance our understanding of these languages but also contribute to the global field of Natural Language Processing (NLP) by providing models and methods that could be adapted to other low-resource languages.

This work is of great importance because it helps to bridge the gap in language technology for underrepresented languages, ensuring they are not left behind in the digital age. The Computational Linguistics Group relies heavily on the high-performance computing resources provided by the CHPC. These resources enable the processing of vast amounts of linguistic data and the training of complex models, which would be impossible to achieve on standard computing platforms.
Our research has already shown promising results, and we are excited about the potential impact of these tools on both the academic community and the speakers of these languages. As our projects near completion, we look forward to sharing our findings and making our tools available for broader use.

Principal Investigator: Prof Mwadham Kabanda
Institution Name: University of Venda
Active Member Count: 3
Allocation Start: 2024-03-26
Allocation End: 2024-09-26
Used Hours: 305962
Project Name: Reaction mechanism for biological, environmental and 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 postgraduate students (MSc and PhD students) involved in the research; who are Mr Masuku MG, Mr Nyembe S, Mr Ratshikombo R, Mr Sithuba T 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 solving environmental problems such as corrosion, studying biological process such as antioxidant 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 otherwise 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. We have now published a total of 16 research article type, one book chapter and 1 PhD student has graduated from the research work. Some PhD students (e.g., Mr Sithuba) have submitted their works and we are waiting for the results.

Principal Investigator: Dr Gugu Kubheka
Institution Name: Nuclear Energy Cooperation of SA
Active Member Count: 2
Allocation Start: 2024-03-26
Allocation End: 2024-10-10
Used Hours: 98366
Project Name: Transition metal oxides for applications as energy materials in solar panels and batteries
Project Shortname: MATS1678
Discipline Name: Material Science

The Necsa Applied Chemistry Department, Fluorine Chemistry Section, uses VASP software, through CHPC resources for academic purposes. The work is intended for training PostDocs and Postgraduates who are undergoing experiential training in the Energy storage field, focusing especially on metal oxide and their fluorinated counterparts. Energy Storage is a current hot topic and a growing field. Modelling work in this area allows discovery of unknown phenomena, and makes it possible that those who may want to take this work further for any other reason, have a strong scientific basis to start from. South Africa has to participate in the field, and considering the 2050 goal of Net Zero through JET program and others, our scientists have to grasp the scientific concepts in various areas of energy storage. This is why Necsa decided to train students through a dual approach, mixing experience in industry and accelerating academic excellence. It is known that most research begins as a blue sky research, and there is no better way to do this than to involve Post Docs and Post Graduates to use our resources such as the software, operated through cluster at CHPC, to support their academic ambitions. CHPC provides ability to carry out high intensity calculations, with faster turn around times, allowing research progress and training outcomes to be evaluated within a set time frame since Post graduates and Post Docs have limited time to complete their tasks. This approach is bearing fruit, as the first Post Doc to be trained in this area is already showing capacity to simulate and publish results related to research on Energy Storage materials. Dr Gugu Kubheka, under the supervision of Dr Mpho Lekgoathi, is a beneficiary of such a unique training program, and is establishing a path for improved training of Post graduates using a dual approach of academic and industrial excellence. The power of CHPC clusters allow such a structured training program to be undertaken with ease, and empowers the growth of our Post Docs and Post Graduates.
The transition metal oxides investigated include Manganese and Tin so far. These are for applications in solar cells, supercapacitors and batteries. These are normally done as part of the broader Industry-Academic collaborations. In the few months of her work on the cluster at CHPC, Dr Kubheka has collected enough data for conference presentation, Peer reviewed paper draft submission, and a 2nd paper is being written, in collaboration with a TUT student to add value to their publication in the Energy Storage Field. The process involves using resources at Necsa to conceptualize a problem, prepare structures using MedeA platform, and then submit calculations to CHPC for large atom based structures. The results are downloaded and processed by students at Necsa, then interpretation of data takes place, conference and publication outputs are targets. The work is going well, with two peer reviewed papers expected.

Principal Investigator: Dr Edwin Mapasha
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2024-03-27
Allocation End: 2024-10-08
Used Hours: 1447974
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 Disulfide for Technological Applications

Silicon has been a cornerstone of the microelectronics industry for decades, but as technology pushes for smaller devices, its limitations become apparent. This has spurred the search for innovative materials, particularly two-dimensional materials like graphane and tin disulfide, that can meet evolving demands.

Graphane and tin disulfide exhibit exceptional properties, including high crystallinity, large surface area, high charge carrier mobility, and a wide energy bandgap. These characteristics have generated significant interest as potential alternatives to silicon and candidates for various advanced technological applications. Notable uses include graphane in microelectronic devices, hydrogen storage for fuel cells, and as an anode material in lithium-ion batteries.

The aim of this project is to utilize density functional theory (DFT) methods in the Quantum Espresso package to optimize the electrochemistry performance of graphane, SnS₂ monolayer, ZrS₂ monolayer and Borophene thereby enhancing their viability for energy storage applications. To produce reliable results efficiently, we rely heavily on high-performance computing resources.

Principal Investigator: Dr Vernon Visser
Institution Name: University of Cape Town
Active Member Count: 1
Allocation Start: 2024-03-28
Allocation End: 2024-10-14
Used Hours: 1814
Project Name: Visser Lab CHPC
Project Shortname: CBBI1675
Discipline Name: Environmental Sciences

Knowing where species occur, both in the present day and in the future, is critical for conserving biodiversity and understanding the benefits we get from nature. I am a researcher within SEEC (www.seec.uct.ac.za), a statistical ecology group at the University of Cape Town, and I use species distribution models to answer questions related to spatial patterns of biodiversity. In my most recent work using the CHPC, I modelled the distribution of ~2500 plant species in southern Africa to investigate how biodiversity might contribute to climate change adaptation and mitigation. This work is ongoing but will be submitted for publication in a scientific journal within the next month.

Principal Investigator: Dr Shama Khan
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2024-03-28
Allocation End: 2024-09-28
Used Hours: 9752
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: Prof Graham Jackson
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2024-03-29
Allocation End: 2024-10-23
Used Hours: 4307
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 Holliness Nose
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 7
Allocation Start: 2024-03-29
Allocation End: 2024-09-30
Used Hours: 2745244
Project Name: Inorganic Computational Chemistry
Project Shortname: CHEM1003
Discipline Name: Chemistry

Dr. Holliness Nose is currently a Lecturer of 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 Chemistry from Wayne State University located in Michigan, United States of America. Her research area is in Computational Chemistry 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 high speed computers as well as Gaussian and Gromacs 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, and 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 Nontokozo Msomi
Institution Name: University of KwaZulu-Natal
Active Member Count: 1
Allocation Start: 2024-04-02
Allocation End: 2024-10-01
Used Hours: 7380
Project Name: Metabolic Disease Research
Project Shortname: HEAL1677
Discipline Name: Chemistry

Biomedical Research Group at the University of KwaZulu-Natal (UKZN), currently affiliated with the Department of Biochemistry.

Research focus' on antidiabetic and anti-obesogenic leads to manage lifestyle diseases and overall human health. Research addresses, the use of medicinal plants as potential sources of novel bioactive compounds, the application of nutraceuticals, functional foods, nanoparticles and sugar substitutes in mitigating type 2 diabetes.

The rise of non-communicable diseases, especially diabetes and cancer, represents a significant global health burden. Developing cost-effective, sustainable, and safe therapeutic agents is crucial. This research integrates plant-based resources and nanotechnology, aiming to discover innovative treatments with fewer side effects.

The research relies heavily on computational modelling and molecular dynamics simulations to understand the interactions between the sample materials and biological targets like enzymes implicated in diabetes and cancer. The CHPC provides the computational power necessary to run these complex simulations, which are too demanding for standard lab computers. These simulations help predict the efficacy and stability of the sample materials before conducting in vitro and in vivo experiments, saving time and resources.

The projects are progressing well. Initial computational studies on their interaction with relevant biological targets have been done. Ongoing simulations are further refining our understanding of these interactions.

Principal Investigator: Dr Lawrence Borquaye
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 25
Allocation Start: 2024-04-02
Allocation End: 2024-10-02
Used Hours: 2984827
Project Name: Biomolecular Computations
Project Shortname: HEAL1382
Discipline Name: Chemistry

We are the Borquaye Research Group, based in the Department of Chemistry at Kwame Nkrumah University of Science and Technology (KNUST) in Kumasi, Ghana. Our research focuses on investigating natural substances, including plant extracts, peptides, essential oils, and other small molecules, to explore their potential health benefits. Utilizing advanced computer modeling techniques, we study how these substances interact with proteins in both human cells and microbial organisms, such as bacteria and parasites. In addition to small molecule-protein simulations, we have expanded our research to include protein-DNA interactions and peptide-membrane simulations, enabling us to gain a more comprehensive understanding of these molecular systems. Our overarching goal is to identify new compounds with potential medicinal applications and to uncover their mechanisms of action. We rely on powerful computational resources available through the CHPC (Lengau) to carry out this work. Currently, we are finalizing experiments for publication, including significant findings on how natural substances target and affect proteins, DNA, and membranes in human and microbial cells.

Principal Investigator: Prof Gerhard Venter
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2024-04-02
Allocation End: 2024-10-31
Used Hours: 797851
Project Name: Finite Element Analysis and Numerical Design Optimization
Project Shortname: MECH0883
Discipline Name: Computational Mechanics

The Materials, Optimization, and Design (MOD) research group at Stellenbosch University has made significant strides in three pioneering projects, thanks to the support of the Centre for High-Performance Computing (CHPC). The use of CHPC's vast computational power has been essential in performing large-scale computational fluid dynamics and discrete element simulations, accelerating research that would otherwise be impossible.

The first of these projects focuses on optimizing the shape of the front bumper of a commercial truck. By adjusting this relatively small component, the MOD team aims to reduce the vehicle's overall drag coefficient. A lower drag coefficient translates into improved fuel efficiency, which can have significant environmental and economic benefits. The computational simulations performed on CHPC systems have allowed the research team to precisely evaluate various design iterations and optimize performance.

The second project investigates the aerodynamic effects of active wings attached to the front fairing of motorcycles. With safety as the primary goal, the research explores how these wings can enhance handling and stability, especially at high speeds. The computational resources provided by CHPC have allowed the team to simulate real-world conditions and evaluate how these design changes can improve rider safety.

Lastly, the MOD group is also working on the in-situ alloying of metal powders during the laser bed fusion process, a method commonly used in additive manufacturing. By simulating the power distribution and alloying process, the team aims to better understand and optimize this critical manufacturing technique to produce higher quality metal parts.

None of these advances would have been possible without the high-performance capabilities of CHPC, which continues to empower groundbreaking research in multiple fields.

Principal Investigator: Prof Mark Tame
Institution Name: Stellenbosch University
Active Member Count: 5
Allocation Start: 2024-04-03
Allocation End: 2025-03-10
Used Hours: 78369
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 Thierry Hoareau
Institution Name: University of Pretoria
Active Member Count: 10
Allocation Start: 2024-04-03
Allocation End: 2024-10-03
Used Hours: 13719
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 and collaborate with University of Pretoria through postgraduate students mentoring. The programmes relies on the CHPC to analyse large genomic datasets more efficiently. The CHPC cluster has provided the computing resources needed to conduct the research efficiently and effectively.

Principal Investigator: Prof Thirumala Govender
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2024-04-03
Allocation End: 2024-10-03
Used Hours: 819685
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 Samuel Egieyeh
Institution Name: University of Western Cape
Active Member Count: 9
Allocation Start: 2024-04-03
Allocation End: 2024-10-03
Used Hours: 51149
Project Name: Computational (Cheminformatic and Bioinformatic) Drug Discovery, Design and Development for Infectious Diseases
Project Shortname: CBBI1212
Discipline Name: Bioinformatics

The Computational Pharmacology and Cheminformatics Research Group, is within the School of Pharmacy, University of the Western Cape, Cape Town. Our research focuses on the use of computational drug discovery and design, data analytics and artificial intelligence techniques in conjunction with relevant wet laboratory experiments to discover, design and develop new drug candidates for infectious diseases.

Principal Investigator: Dr Stephan Schmidt
Institution Name: University of Pretoria
Active Member Count: 1
Allocation Start: 2024-04-07
Allocation End: 2024-10-06
Used Hours: 75533
Project Name: A hybrid model-based condition monitoring approach for large axial fans
Project Shortname: MECH1663
Discipline Name: Computational Mechanics

The Centre of Asset Integrity Management (C-AIM) group at the University of Pretoria has a special interest in the use of hybrid models for asset integrity management. Hybrid models combine physics-driven and data-driven models to achieve better overall model performance by bridging the gap between physics-based models, that might not capture all of the physics, and insufficient experimental data. One such research project investigates using computational fluid dynamics simulations using ANSYS Fluent to predict the performance and stall point of mining ventilation axial fans. In collaboration with Air Blow Fans (Pty) Ltd, a full-scale large axial fan experimental test setup was developed to research cutting-edge condition monitoring approaches including temperature and vibration measurements, blade tip timing, and casing pressure measurements.

The use of the CHPC facilitates the research into the model complexity and settings required to numerically predict the fan's performance and to simulate the pressure sensor response at various operating conditions. The ability to accurately simulate the pressure signal will enable the development of a hybrid model-based performance prediction and stall detection methodology which utilizes only a single pressure sensor.

Principal Investigator: Dr Kevin Lobb
Institution Name: Rhodes University
Active Member Count: 25
Allocation Start: 2024-04-09
Allocation End: 2024-11-01
Used Hours: 508609
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: Dr Maya Makatini
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2024-04-09
Allocation End: 2024-10-09
Used Hours: 55004
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 Ikechukwu Achilonu
Institution Name: University of the Witwatersrand
Active Member Count: 4
Allocation Start: 2024-04-09
Allocation End: 2024-10-09
Used Hours: 27178
Project Name: Computational approach to modelling druggable proteins of neglected tropical diseases parasites and ESKAPE pathogens
Project Shortname: CHEM0849
Discipline Name: Bioinformatics

New Research Aims to Combat Deadly Pathogens and Neglected Diseases

The ESKAPE and Neglected Tropical Diseases (NTD) research group, part of the Protein Structure Function Research Unit at the University of the Witwatersrand in Johannesburg, is making significant strides in fighting infections that threaten global health. The team is focused on finding new treatments for bacteria and parasites that cause life-threatening diseases, with special attention to ESKAPE pathogens—bacteria responsible for many hospital-acquired infections—and parasites causing neglected tropical diseases like schistosomiasis and malaria.

Led by Prof Achilonu in the School of Molecular and Cell Biology, this project uses advanced computational tools to study the structure of proteins within these harmful organisms. By understanding the way these proteins function, the team is identifying weak points where drugs can effectively target and disable the pathogens. The goal is to discover and design inhibitors—molecules that can block these essential proteins, stopping the infections they cause.

This work is crucial because both ESKAPE pathogens and neglected tropical diseases pose a growing threat worldwide, especially in regions with limited access to healthcare. Many existing treatments are becoming less effective due to the rise of drug-resistant bacteria and parasites. Finding new drug candidates is vital to protect vulnerable populations and improve global health.

Thanks to the resources of the Centre for High Performance Computing (CHPC), the research group is able to run powerful simulations that predict how potential inhibitors will interact with the target proteins. This saves time and resources by narrowing down the best candidates for laboratory testing. The project has progressed significantly, and the team has already identified promising inhibitors for druggable proteins in both ESKAPE pathogens and parasites such as Schistosoma and Plasmodium. These discoveries offer new hope in the fight against deadly infections.

Principal Investigator: Prof Evans Adei
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 41
Allocation Start: 2024-04-09
Allocation End: 2024-10-09
Used Hours: 2283292
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. 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. A clear testimony to this is the fact that the lead authors of our modest three publications (doi.org/10.1007/s00894-024-06074-0; https://doi.org/10.1002/poc.4645, and https://doi.org/10.1007/s00214-024-03121-0.), this reporting period Akonor, Is-mail, and Oyetey are all undergraduates. The potential or aptitude for future Basic research work of these 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. 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.

Principal Investigator: Prof Nelishia Pillay
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2024-04-10
Allocation End: 2024-11-11
Used Hours: 678503
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 Soraya Bardien
Institution Name: Stellenbosch University
Active Member Count: 6
Allocation Start: 2024-04-10
Allocation End: 2024-10-10
Used Hours: 22583
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 obtained genetic data in the form of array data, and high-throughput sequencing data, and so the students are already well into these analyses. 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 causes in South African individuals 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: Dr Jaap Hoffmann
Institution Name: Stellenbosch University
Active Member Count: 2
Allocation Start: 2024-04-11
Allocation End: 2024-10-31
Used Hours: 186347
Project Name: Flow through porous media
Project Shortname: MECH1116
Discipline Name: Computational Mechanics

Stellenbosch University and the Universitè de Sherbrooke started collaboration in 2024. Prof. Hoffmann visited Sherbrooke during his sabbatical, and Prof. Amiri will visit Stellenbosch in February 2025. We have already submitted a journal paper to the International Journal of Thermofluids, that is currently under review. Both teams focus on pore scale simulation of flow and heat transfer in packed beds of crushed rocks.

Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 5
Allocation Start: 2024-04-12
Allocation End: 2024-10-31
Used Hours: 249227
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: Prof Phuti Ngoepe
Institution Name: University of Limpopo
Active Member Count: 16
Allocation Start: 2024-04-12
Allocation End: 2024-10-14
Used Hours: 6489822
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; platinum group minerals (PGMs): sperrylite, pallado-arsenide, geversite, cooperite, platinum/palladium tellurides, platarsite, and platinum/palladium bismuth and oxide minerals: spodumene, feldspar and hematite. The collectors are organic compounds that are used to target and render the mineral of interests (concentrates) hydrophobic and promote their recoveries. In this reporting period we have attended the South African Institute of Physics (SAIP) at the Rhodes University and gave oral and poster presentations by the researchers and the students (PhD, MSc and Honours). These were paramount in engaging with other researchers to communicate our research and share our insights. The outcome of the minerals research work will benefit the country at large in recovering sulphide minerals using these highly selective collectors. The use of public resources such as the CHPC was helpful to the University of Limpopo to perform these simulations.

Principal Investigator: Prof Rotimi Sadiku
Institution Name: Tshwane University of Technology
Active Member Count: 10
Allocation Start: 2024-04-12
Allocation End: 2025-01-22
Used Hours: 737650
Project Name: NANOCOMPOSITE FOR ENERGY STORAGE
Project Shortname: MATS1376
Discipline Name: Material Science

Who: Prof. E.R. Sadiku and his distinguished research team at Tshwane University of Technology are pioneering energy storage and pharmaceutical technology advancements.

What: Their research spans the development of advanced electrode materials for cutting-edge battery systems, now incorporating borophene-based materials for enhanced performance in metal-ion batteries. Additionally, the team is exploring innovative drug delivery mechanisms, utilizing nanocomposites such as PEGylated graphene oxide to improve targeted treatments. Through computational simulations and ab initio analyses, the team has identified promising strategies to boost energy storage efficiency and enhance drug delivery efficacy.

In Brief: Prof. E.R. Sadiku and his team continue to make significant advances in energy storage and pharmaceutical sciences. Their multidisciplinary approach and use of state-of-the-art computational techniques promise impactful contributions to global challenges, particularly in sustainable energy and healthcare.

Principal Investigator: Dr Anthony Pembere
Institution Name: Jaramogi Oginga Odinga University, Bondo, Kenya
Active Member Count: 2
Allocation Start: 2024-04-12
Allocation End: 2024-10-31
Used Hours: 207832
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 Adeniyi ogunlaja
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 5
Allocation Start: 2024-04-15
Allocation End: 2024-10-15
Used Hours: 24681
Project Name: Chemistry and Material Science
Project Shortname: MATS1070
Discipline Name: Chemistry

Adeniyi Ogunlaja research group at Nelson Mandela University, Chemistry Dept. focuses on Inorganic/material chemistry research. The group recently commenced a project on CO2 utilization. Carbon dioxide is often viewed as a waste product from various industrial processes and human activities. However, scientists are exploring ways to utilize CO2 as a raw material for creating valuable chemicals. By converting CO2 into useful products, we can help reduce greenhouse gas emissions and contribute to more sustainable practices in chemistry and industry. The research on hydrocarboxylation of Schiff bases with CO2 represents an exciting frontier in green chemistry. It not only seeks to create valuable chemical products but also aims to address pressing environmental challenges by turning a greenhouse gas into a resource. Understanding the properties and mechanisms of catalysts for CO₂ requires precise modelling of atomic-level interactions, reaction pathways, and electronic structures. Access to a high-performance computing cluster from the Center for High-Performance Computing (CHPC) offers unparalleled capabilities to accelerate this research. The CHPC cluster has provided platform for advanced simulations, such as density functional theory (DFT) and molecular dynamics (MD), which are essential for predicting catalyst behavior under various conditions.

Principal Investigator: Prof Edith Antunes
Institution Name: University of Western Cape
Active Member Count: 3
Allocation Start: 2024-04-15
Allocation End: 2024-10-15
Used Hours: 15945
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: Dr Lucy Kiruri
Institution Name: Kenyatta University, Nairobi, Kenya
Active Member Count: 8
Allocation Start: 2024-04-15
Allocation End: 2024-10-23
Used Hours: 51938
Project Name: KU Computational Chemistry Research Group
Project Shortname: CHEM1032
Discipline Name: Chemistry

CHEM1032: Kenyatta University Computational Chemistry Research Group

We have used the CHPC for more than 7 years to carry out calculations both in molecular dynamics (MD) simulations and quantum mechanics (QM). This has helped my students and myself do sophisticated calculations using the state-of-art supercomputers and use more advanced methods in our calculations. We are grateful to CHPC and the the republic of South Africa. Currently, there are only 3 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. My PhD student Ndung'u is doing DFT simulations, incorporating anharmonic corrections through Gener alized Vibrational Perturbation Theory (GVPT2), along with the B3LYP and B2PLYP functionals paired with advanced basis sets like N07D and SNSD using Gaussian16 program. He is in the process of submitting his thesis for examination and two of his publications are under review.
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, I am 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: Dr Marina du Toit
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2024-04-15
Allocation End: 2024-10-31
Used Hours: 66771
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 a 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: Dr Sarah Roffe
Institution Name: Agricultural Research Council
Active Member Count: 10
Allocation Start: 2024-04-16
Allocation End: 2024-10-15
Used Hours: 3154797
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 influences on agricultural activities. One aspect of the group's activities is to investigate how future climate changes 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 been working to 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, and although we have a long way to go, we are already starting to produce some really exciting results that we believe could be hugely beneficial for the South African agricultural industry.

Principal Investigator: Prof Malik Maaza
Institution Name: University of South Africa
Active Member Count: 4
Allocation Start: 2024-04-16
Allocation End: 2024-11-05
Used Hours: 743843
Project Name: Modelling of Functional Materials at the Nanoscale
Project Shortname: MATS1306
Discipline Name: Physics

Press release:
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: Dr Kgothatso E Machaba
Institution Name: University of KwaZulu-Natal
Active Member Count: 1
Allocation Start: 2024-04-16
Allocation End: 2024-10-16
Used Hours: 27546
Project Name: Dr. Machaba's Bioinfo Group
Project Shortname: HEAL1634
Discipline Name: Health Sciences

The "Computational Group" at the 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 encouraging 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 conclude. 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 Samuel Atarah
Institution Name: University of Ghana
Active Member Count: 2
Allocation Start: 2024-04-16
Allocation End: 2024-10-18
Used Hours: 32371
Project Name: Ab initio studies of electronic and magnetic properties of selected elements
Project Shortname: MATS1162
Discipline Name: Physics

In the Condensed Matter Physics group in the Department of Physics at the University of Ghana my team's current research focus is on perovskite material as candidates for photovoltaic apllications . We use first principle studies, principally using the Quantum Espresso suite, to calculate the electronic properties that may give indication of performance factors such as, stability, conductivity or ductility of the perovskites that may make them suitable for solar energy harvesting material.

A typical process involves setting up a basic unit or cell of the known (experimental) structure; making a self consistent quantum mechanical calculation of its minimum total energy, its bands structure, and density of states. Further investigations for structural properties such as unit cell dimensions, bulk and shear moduli are based on the ground state solutions to the self consistent calculations. Phonon dispersion characteristics of the perovskites are also determined from which the stability of the perovskites are studies. With the support of the CHPC computing power, the project is seeing real progress.

Principal Investigator: Prof Richard Betz
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 25
Allocation Start: 2024-04-16
Allocation End: 2024-10-15
Used Hours: 89450
Project Name: Artificial Photosynthesis
Project Shortname: CHEM0872
Discipline Name: Chemistry

Photosynthesis is the process that allows plants to turn carbondioxide and water (two things humans and animals exhale and excrete) back into oxygen and carbohydrates (two things that humans and animals inhale and consume) by means of sunlight. And while the chemical reaction equation is deceitfully simple -- photosynthesis is also among the last fundamental processes that has never been emulated by scientists in a laboratory.

This research project is aimed at finding just the right conditions that would allow humans to reproduce the key and core steps associated with natural photosynthesis in a laboratory setting. As this entails gathering lots of experimental data, DFT calculations can assist in scouting prospective future pathways scientists can think off to solve this question by either showing specific ideas to be of a promising nature or by giving new ideas how to proceed best. The resources offered by CHPC are ideal and crucial for this.

The benefits will lie in a better and more fundamental understanding about the intricate processes that guide biological systems from a more holistic chemical point of view, thus opening pathways for future applications in industry, medicine and biocatalysis.

Principal Investigator: Dr Aniekan Ukpong
Institution Name: University of KwaZulu-Natal
Active Member Count: 8
Allocation Start: 2024-04-16
Allocation End: 2024-10-18
Used Hours: 307951
Project Name: Theoretical and Computational Condensed Matter and Materials Physics
Project Shortname: MATS0941
Discipline Name: Physics

The Theoretical and Computational Condensed Matter and Materials Physics Group at the School of Chemistry and Physics, University of KwaZulu-Natal, is developing codes for Monte Carlo Renormalization Group (MCRG) studies of quantum phase transitions in spin systems. These codes are being adapted to implement Machine Learning Renormalization Group techniques for identifying quantum critical points from computed data. We have a strong focus on supporting early-career researchers and postgraduate students, particularly those enrolled at specialized research centers such as the African Institute of Mathematical Sciences (AIMS). Our current emphasis is on developing and implementing computational models to address the interactions in correlated electron systems. These systems are crucial to materials research across diverse areas of modern society, from high-temperature superconductivity to spin-based energy interconversion for sustainable energy applications. Scientific computing is central to our research, as it allows us to perform calculations that provide insights into the behavior of electrons in materials containing a vast number of atoms—calculations that cannot be done on regular laptops or desktop computers. By leveraging high-performance computing, we are expanding our research capabilities in emerging fields such as machine learning for energy materials, with the potential for extension to other multidisciplinary problem areas.

Principal Investigator: Prof Hasani Chauke
Institution Name: University of Limpopo
Active Member Count: 12
Allocation Start: 2024-04-16
Allocation End: 2024-10-29
Used Hours: 766210
Project Name: Computational Modelling of Minerals, Metals and Alloys
Project Shortname: MATS1047
Discipline Name: Material Science

Professor Hasani Chauke is the primary investigator in the metal and alloy development research niche. The research is conducted at the Materials Modelling Centre (MMC), University of Limpopo. The area of specialization encompasses energy storage, mineral processing and metal alloy development using multi-computational techniques, i.e. first-principles, molecular dynamics and machine learning techniques, which employ various academic, open-source and commercial software with both GUI and LUI interfaces. The user interfaces are linked to MMC servers and the Centre for High Performance Computing (CHPC). Various research projects are linked to postgraduate training at Honours, Masters and Doctoral studies. The programme continues to receive enormous support from the NRF, DSI, CSIR, Mintek, and the CHPC, particularly to run large-scale calculations at a more reasonable time. The programme supports about seven (07) postgraduate students at masters (03), doctoral levels (04) and two (02) post-doctoral fellows and one (1) Research scientist

Principal Investigator: Dr Adam Skelton
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2024-04-17
Allocation End: 2024-10-17
Used Hours: 70645
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 Gert Kruger
Institution Name: University of KwaZulu-Natal
Active Member Count: 21
Allocation Start: 2024-04-17
Allocation End: 2024-10-17
Used Hours: 820426
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 Salerwe Mosebi
Institution Name: University of South Africa
Active Member Count: 6
Allocation Start: 2024-04-19
Allocation End: 2024-10-22
Used Hours: 41819
Project Name: Centre for Metal-based Drug Discovery
Project Shortname: CHEM1013
Discipline Name: Health Sciences

Our research at Unisa continues to focus 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).
We have synthesized small libraries of compounds that were evaluated for their inhibitory activity against various HIV and cancer targets. The progress of our projects remains satisfactory.
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 through the use of nanotechnology & DNA-based technologies. Here, the focus is on the development of rapid diagnostic tests that can be used at point-of-care (POC) or near-patient settings which are based on either gold-nanoparticle or aptamer-based lateral flow platforms.

Principal Investigator: Dr Tawanda Zininga
Institution Name: Stellenbosch University
Active Member Count: 5
Allocation Start: 2024-04-22
Allocation End: 2024-10-22
Used Hours: 19287
Project Name: Investigation of the role of Plasmodium falciparum Hsp70-Hsp90 chaperone system
Project Shortname: HEAL1355
Discipline Name: Bioinformatics

The Zininga research group at Stellenbosch University focuses on stress biology to understand the potential of designing drugs to inhibit the ability of microorganisms to survive stress. We are using the malaria parasite, Plasmodium falciparum as the model organism which is responsible for over 500 000 deaths in 2021 which makes it an important target. Our research depends on the CHPC facilities to predict and optimise our drug discovery efforts. So far we have benefited a lot from these services to train students who are now finalising their work for graduation.

Principal Investigator: Dr Mpho Ngoepe
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 1
Allocation Start: 2024-04-23
Allocation End: 2024-10-23
Used Hours: 1723
Project Name: DSI-Mandela Nanomedicine
Project Shortname: HEAL1547
Discipline Name: Health Sciences

The DSI-Mandela Nanomedicine research group focuses on pharmaceutical compounds and nanotechnology for human health applications. The CHPC resources have been utilized for public engagement by assisting a Grade 9 win a silver medal at the 44th Eskom Expo International Science Fair (ISF) held on the 23 to 27 September 2024. This work highlights the benefits of advanced computing in helping to solve real-world problems as it allowed the student to showcase how her drug delivery system would be ideal in tackling head and neck carcinoma. For postgrad academic use, the CHPC resources have been utilized for the evaluation of how metallic nanoparticles can be stabilized by phytocompounds. This work is crucial in studying the interaction of nanomaterials with various receptors of biological interest

Principal Investigator: Dr Francis Opoku
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 13
Allocation Start: 2024-05-02
Allocation End: 2024-10-04
Used Hours: 2794746
Project Name: High-Throughput theoretical design of two-dimensional materials as an ultrasensitive toxic gas sensor
Project Shortname: MATS1423
Discipline Name: Chemistry

The research team's work on 2D heterostructures is crucial for the following reasons: the global energy crisis and environmental pollution. The research focuses on designing new materials that enhance stability, catalytic performance, and overall efficiency in capturing solar energy, which could significantly impact renewable energy technologies. A recent study on two-dimensional heterostructures for renewable energy and pollutant degradation was conducted by collaborating with research groups from several institutions in Ghana and South Africa.
Investing public resources in this type of research is justified by the broad societal benefits it promises. The work can potentially revolutionise how we approach energy production and pollution control, offering long-term environmental and economic benefits and sustainable technology.
The team uses high-performance computing (HPC) resources to simulate the behaviour of these materials before they are synthesized. The Center for High-Performance Computing (CHPC) plays a crucial role by providing the computational power to model electron behaviour and optimize material design.
The research team working on developing two-dimensional heterostructures for renewable energy and pollutant degradation is making significant strides in laboratory experiments and computational simulations. These heterostructures show great promise in photocatalytic water splitting, a critical process for hydrogen production as a clean fuel. Over the past several months, the project has achieved key milestones that demonstrate the viability and potential scalability of the technology for real-world applications, with more than 54 publications appearing in high-impact peer-reviewed journals.

Principal Investigator: Dr Phindile Khoza
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2024-04-24
Allocation End: 2025-03-20
Used Hours: 50929
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 Thishana Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2024-04-24
Allocation End: 2024-10-04
Used Hours: 2251
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 Sybrand van der Spuy
Institution Name: Stellenbosch University
Active Member Count: 8
Allocation Start: 2024-04-24
Allocation End: 2024-10-25
Used Hours: 674451
Project Name: CFD simulation of turbomachinery
Project Shortname: MECH1187
Discipline Name: Computational Mechanics

The turbomachinery research group at Stellenbosch University consists of five to seven postgraduate (master's and PhD) students that are all doing CFD simulations of rotating machinery. The work stretches from modelling the noise and performance of large diameter cooling fans (used by Eskom), to the performance of small centrifugal compressors (used in a solar Brayton cycle) to the development of rocket engine turbines (used by the ASRI group). The focus of the work is on supporting local technology and in all the cases, the simulations have been coupled to actual experimental evaluations.

The group has been making use of the CHPC for its 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, fan noise and blade tip leakage flow that have not previously been possible within our group. Mesh sizes of 20 million + are now common and the information gained from these simulations give researchers the ability to present their work next to researchers from much more famous entities like Cambridge and MIT.

The results achieved to date have been world class and a number of theses, journal papers and conference publications have stemmed form this work. The group is continuously trying to increase the complexity of its outputs and it is hoped that they will shortly be able to model 100 million + size meshes.

Principal Investigator: Prof Regina Maphanga
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 13
Allocation Start: 2024-04-25
Allocation End: 2025-01-23
Used Hours: 768810
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 Phillip Nyawere
Institution Name: Kabarak University, Nakuru, Kenya
Active Member Count: 14
Allocation Start: 2024-04-25
Allocation End: 2025-02-06
Used Hours: 365474
Project Name: Barium Floride and Perovskites
Project Shortname: MATS0996
Discipline Name: Physics

BaF2 and Perovskites is a non profit group and academically focused in training students in Kenyan Universities; Kabarak University and Kisii University. The PI of the group is a graduate of University of Eldoret with research background in ICTP, Trieste, Italy. This group does not have funding to assist its students in computer resources such as the one offered by CHPC. This kind computational provision has helped most of our students who would otherwise been unable to pay for computational hours. Our simulations mimic in atomic scales, the behavior of microparticles and macroparticle states. Even though we complement experimental studies, computational calculations Reduces Experimental Costs: Computational studies eliminate the need for expensive lab equipment, materials, and resources often required in experimental research. Simulations also save both time and physical resources, especially in studies involving rare or hazardous materials. Therefore for our poorly equiped institutions where sophisticated experimental instruments may be a challenge to acquire, simulation serves the purpose. We therefore in this group have trained graduates who are capable of teaching and carrying out simulations worth publication in referred journals. In particular we are using first principles studies using Quantum Espresso Code which is a free to use code but requires powerful computers to host it. We also use SIESTA which is also based on the same principle.
We have so far simulated BaF2 to undescore its potential application in battery electrolytes, perovskite such as carbide based for superconductivity applications, gadolinium compounds for enhanced superconductivity amongst many others.
Superconductivity is a crucial area of research because it promises reduced energy costs. Thermoelectric materials are also critical in the energy sector because they use waste heat to create much needed energy.

Principal Investigator: Dr Hezekiel Kumalo
Institution Name: University of KwaZulu-Natal
Active Member Count: 17
Allocation Start: 2024-04-25
Allocation End: 2024-10-30
Used Hours: 209335
Project Name: Molecular modeling and computer aided drug design
Project Shortname: HEAL1009
Discipline Name: Health Sciences

Our research group, based at the UKZN Durban Medical School campus and affiliated with the University of KwaZulu-Natal (UKZN) in South Africa, is dedicated to advancing the field of drug design through computational and molecular modeling of biological systems. Our work focuses on exploring the complexities of chemical and biochemical reactivity, particularly in the context of viral diseases like influenza. By investigating key aspects such as transition states, environmental influences on reactions, and the development of enzyme inhibitors, we aim to design and evaluate therapeutic targets with significant biological implications. This research is essential not only for enhancing our understanding of viral mechanisms but also for developing effective antiviral therapies that can address pressing public health challenges. The significance of our work justifies the use of public resources, as it aligns with broader goals of improving healthcare outcomes and fostering innovation within the pharmaceutical sector. We utilize advanced computational techniques, including Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations and Quantitative Structure-Activity Relationship (QSAR) analyses, to deepen our insights into molecular interactions and dynamic behaviors. Our collaboration with the Centre for High-Performance Computing (CHPC) is critical to our progress, as it provides the necessary computational resources to conduct high-resolution simulations and analyze complex data efficiently. Currently, the project is progressing well; we have achieved several key milestones, including successful initial simulations that have yielded promising results regarding enzyme mechanisms and potential drug targets. With ongoing refinements to our methodologies and the support of CHPC resources, we are poised to expand our investigations into new therapeutic areas, reinforcing our commitment to producing impactful research that contributes to both academic knowledge and practical applications in drug design.

Principal Investigator: Prof Tobi Louw
Institution Name: Stellenbosch University
Active Member Count: 6
Allocation Start: 2024-04-26
Allocation End: 2024-11-26
Used Hours: 69183
Project Name: SU Process monitoring, modelling and control
Project Shortname: CSCI1370
Discipline Name: Applied and Computational Mathematics

The properties of liquid mixtures are essential for the optimal design and efficient operation of many chemical processes, but the sheer number of different possible mixtures at various temperatures, pressures, and compositions, renders the measurement of all possible combinations infeasible. In this work, we extended a machine learning method "Probabilistic Matrix Completion" (PMF), to predict the properties of mixtures that have never been measured before. PMF was originally used to predict which movies Netflix users would like based on correlating their preferences to other users. In the same way, we could use known properties of measured mixtures to infer the properties of unmeasured mixtures. The CHPC was instrumental in running the algorithms required to complete this work.

Principal Investigator: Dr Olatunbosun Nubi
Institution Name: University of Limpopo
Active Member Count: 3
Allocation Start: 2024-04-26
Allocation End: 2025-03-06
Used Hours: 9510
Project Name: Computational-Modelling of Novel Solid-State Materials
Project Shortname: MATS1630
Discipline Name: Physics

The research group is made up of Nubi, Olatunbosun (the PI) from the University of Limpopo, and two researchers from the University of Lagos, Olopade Muteeu and Oyebola Olusola.
Our work is majorly to determine/predict the properties of materials and see how the materials can be beneficial to the community at large. We are working on opto-electronic material with a bias towards photovoltaic materials and radiation detection materials which will be of immense benefit to the research community.
The work depends on CHPC as most of the constituents of the compounds are large atoms and require high processing power devices to finish the computation in a reasonable time.
The project initially focused on the experimental aspect of the work. The computational part has since commenced and will resume immediately after access to the CHPC resources is restored.
The project has made significant progress and promises a successful completion, possibly in a year.

Principal Investigator: Prof Eric K. K. Abavare
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 7
Allocation Start: 2024-04-26
Allocation End: 2025-01-16
Used Hours: 1507730
Project Name: Atomic and Electronic structures of semiconductor interface systems
Project Shortname: MATS1159
Discipline Name: Physics

3RD DECEMBER, 2024

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 research 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 interest 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 environments. 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 push 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 Frederick Malan
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2024-04-29
Allocation End: 2025-01-28
Used Hours: 4442
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 Thobani G. Gambu
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2024-04-29
Allocation End: 2025-01-28
Used Hours: 494277
Project Name: BET/Catalysis: Catalysis on responsive substrates - towards dynamic catalytic theory
Project Shortname: MATS1516
Discipline Name: Chemical Engineering

I am a new senior lecturer within the Catalysis Institute, which falls under the Department of Chemical Engineering at the University of Cape Town. My research interest is the in dynamic catalysis. I one MSc student working full time on the project and hoping to recruit another in 2025. We currently make use of the density functional theory (DFT) - as implemented in the VASP code. The main approach is centered around calculating reaction energies which are later used in microkinetic modelling. However, we also use a variety of global optimization calculations to explore the configurational space of materials of interest. My main project is titled BET/Catalysis.

BET/Catalysis, can be thought of as a call or recognition of societies gamble on catalytic advances to combat many global challenges. More technically, we decided on this term for this project to highlight the departure of this project from traditional catalysis. We considered the application of Magnetic field (B), Electric (E) field or Temperature (T) gradients - BET - on catalysts to assist them in their function. Our work spans the theoretical and experimental spaces. With the CHPC's resources we hope to understand the materials at the atomistic scale. Experiments involve synthesis of predicted materials as well as performance testing - i.e., place these materials in a reactor and apply BET on them while observing their productivity and selectivity towards preferred products.

We plan to apply these concepts in the study of current challenges in catalysis and chemical engineering. These involve the conversion of carbon dioxide to liquid products (fuels and chemicals), selective conversion of methane to methanol. Both of these reactions are of great interest to society as a whole. At this stage, we are beginning to understand the properties of the materials of interest. We will continue to build on this understanding in the coming months and year

Our work on molybdenum carbide was recently presented at the International Congress on Catalysis (ICC) in Lyon, France. We also have two upcoming conference contributions, (i) oral presentation during the next Catalysis Society of South Africa (CATSA) conference and (ii) poster presentation by my MSc student at the next CHPC national meeting/conference. We have multiple publications under preparation.

Principal Investigator: Prof Eno Ebenso
Institution Name: North-West University
Active Member Count: 6
Allocation Start: 2024-04-30
Allocation End: 2024-11-05
Used Hours: 1386276
Project Name: Theoretical Investigations of Corrosion Inhibition Activities of Organic Compounds
Project Shortname: CHEM1176
Discipline Name: Chemistry

This press release focuses on the article titled "Theoretical Study of the Mutual Degradative Interaction Between Elemental Mercury and Polyhalogenated Biphenyls" recently published in Chemistry Africa. The research, which was fully conducted with CHPC resources focused on environmental remediation, which is a strong cardinal point in the UN SDGs. The paper provided scientific information on the prospective degradation of long known pollutants (polychlorinated biphenyls, PCBs and polybrominated biphenyls, PBBs) in the environment, aided by another harmful material, mercury (Hg). The research findings revealed that PCBs and PBBs degradation could be aided by Hg in the same environment, while Hg is also oxidized to a less harmful species. In other words, the remediation process is a sustainable one that involves two unwanted materials being removed from the environment via mutual interactions. Our results revealed the kinetics and mechanism of degradation of PCBs and PBBs in the presence of Hg.
This research was conducted by researchers from Obafemi Awolowo University, Nigeria and University of Johannesburg, South Africa.

Principal Investigator: Dr Mary-Jane Bopape
Institution Name: South African Weather Service
Active Member Count: 32
Allocation Start: 2024-04-30
Allocation End: 2024-05-14
Used Hours: 15844
Project Name: Very Short Range Forecasting
Project Shortname: ERTH1022
Discipline Name: Earth Sciences

A group of scientists lead by the South African Weather Service have concluded a project funded by the Water Research Commission to build local capacity to develop home grown weather and climate models. The project was based on the Conformal Cubic Atmospheric Model, and the team learned the insides of the model and got to understand the dynamical core, the cloud microphysics, turbulence and cumulus schemes applied in the CCAM. This is very important because it means South Africa is moving away from applying models as black boxes. This also means when biases are identified the South African team, would be able to get into the code to change it to improve on the simulations. The PhD students supported by the project will still continue with their studies.

Principal Investigator: Prof Iain Paterson
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2024-04-30
Allocation End: 2024-10-29
Used Hours: 27168
Project Name: Cryophytum crystallinum population genetics
Project Shortname: CBBI1682
Discipline Name: Bioinformatics

The Centre for Biological Control (CBC) is a highly productive research group in the Department of Zoology and Entomology at Rhodes University. Our group focuses on controlling invasive weeds and agricultural pests using the natural enemies of the problem species. Biological control is an environmentally-friendly approach to the conservation and restoration of biodiversity, offering a sustainable solution to invasive species management.

The CBC is working towards implementing more advanced genetic techniques to answer evolutionary questions, starting with the use of a RADseq protocol for a population-level analysis of the crystalline ice plant, Cryophytum crystallinum. This plant is native to southern and northern regions of Africa (where some populations occur as far south as South Africa), with invasive populations establishing in the USA and Mexico, among others. This project aims to use RADseq data to uncover the exact source/s of the invasive populations in North America so that a targeted search for biological control agents can be initiated.

The analysis of large genetic datasets, such as RADseq, is reliant upon access to an HPC to assemble millions of fragment reads, and generate summarised data that can be used in downstream analyses. The CHCP has proved to be an invaluable resource to our research group, and has allowed us to efficiently work through the necessary data analysis steps through the submission of computationally-demanding job scripts. The project has progressed well over the last six months, during which we have developed a streamlined set of job scripts to run through the RADseq analysis pipeline from start to end on a preliminary data set. Once we have piloted this work on the crystalline ice plant, we plan to apply these methods to other projects aimed at controlling invasive species both in South Africa and globally.

Principal Investigator: Prof Thomas Scriba
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2024-05-02
Allocation End: 2024-10-08
Used Hours: 4652
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 Abdulrafiu Raji
Institution Name: University of South Africa
Active Member Count: 13
Allocation Start: 2024-05-02
Allocation End: 2025-01-29
Used Hours: 2256933
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: Dr Xolani H Makhoba
Institution Name: University of South Africa
Active Member Count: 2
Allocation Start: 2024-05-06
Allocation End: 2024-11-06
Used Hours: 105547
Project Name: Drug development of COVID-19 alternative treatment using in silico analysis
Project Shortname: CBBI1629
Discipline Name: Bioinformatics

.My research group focuses on drug development using computational tools. In my group, I have postgraduate students such as Sesethu Godlo, who is a PhD student and a beneficiary of the CHPC tools program. I also have Tinotenda Navhaya, who is a final year Master's student, also utilizing CHPC tools. With these few mentioned students, we have made great progress in answering questions related to research activities, such as protein-protein interactions.

Principal Investigator: Dr Quentin Santana
Institution Name: Agricultural Research Council
Active Member Count: 4
Allocation Start: 2024-05-06
Allocation End: 2024-11-06
Used Hours: 54322
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 plants. Research at the ARC Biotechnology Platform is being performed to better understand this interaction. By analyzing the genomes of both the pathogens and their host plants, plant pathogenomics aims to understand the 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: Prof Marlo Moller
Institution Name: Stellenbosch University
Active Member Count: 16
Allocation Start: 2024-05-07
Allocation End: 2024-10-08
Used Hours: 248947
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: Prof Simon Connell
Institution Name: University of Johannesburg
Active Member Count: 14
Allocation Start: 2024-05-08
Allocation End: 2024-10-31
Used Hours: 584600
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 focuses on several key areas, including Computational Fluid Dynamics (CFD) modeling of infectious diseases, CFD applications in controlled farming systems related to the ATLAS project, Hydrocyclones, and High-Performance Heat Exchangers (HPHE). They utilize CFD techniques to gain insights into disease dynamics, which aids in the understanding and management of infectious diseases.

The group contributes to the ATLAS project, applying their expertise to its development, while also researching Hydrocyclones to improve their performance. Additionally, they aim to enhance the efficiency of heat pipe heat exchangers through their research.

Overall, Simon Connell and his team make significant contributions to these fields, demonstrating their commitment to addressing real-world challenges and driving innovation. The CHPC has provided the necessary computational resources to support their work.

Principal Investigator: Mr Lawrence Pratt
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 2
Allocation Start: 2024-05-13
Allocation End: 2024-11-30
Used Hours: 19008
Project Name: Solar Cell Defect Detection (SCDD)
Project Shortname: CSIR1379
Discipline Name: Computer Science

The CSR Energy Centre is researching computer vision models for defect detection and quantification in the electroluminescence images of solar PV modules. The CHPC provides the hardware necessary to train deep learning models on large datasets consisting of hand-labelled El images in which defects are identified by colour code. After sufficient training, the computer model can interpret, analyze, detect, and quantify 15 defects and 15 features common in solar PV modules. The computer model can quantify the extent of defects in a large batch of PV modules that would otherwise be nearly impossible to evaluate with the human eye. The work has resulted in several journal articles, conference papers, and one PhD in computer science from the University of the Witwatersrand. The work planned for the next financial year will focus on evaluating alternative deep-learning models, such as vision transformers, in an effort to improve the model's accuracy. In parallel, the CSIR is developing a web-based tool that could one day make this technology available to the public.

Principal Investigator: Prof Craig McGregor
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2024-05-13
Allocation End: 2024-11-30
Used Hours: 35367
Project Name: Solar thermal CFD
Project Shortname: MECH1640
Discipline Name: Chemical Engineering

The research group is called the Solar Thermal Energy Research Group (STERG). It is housed in the Department of Mechanical and Mechatronic Engineering at Stellenbosch University and 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 a wide range of domestic and industrial heating applications. The collector is made up of a series of u-tubes. The effects of u-bends have been investigated before, however, there remains a gap in the study of u-bends 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 u-bend 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 a 2D optical investigation of the collector which has been conducted using the DO radiation model in ANSYS Fluent. Additionally, mesh independence and discretisation studies were conducted with the use of the CHPC. Finally validation was done using existing experimental work. A 3D thermal model was subsequently setup and the results obtained from the radiation model were used as input parameters. For this model, a mesh independence study was also conducted. All of the simulations were run using the CHPC. It has been instrumental in saving time and making progress.

Principal Investigator: Dr Matshawandile Tukulula
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2024-05-13
Allocation End: 2024-10-15
Used Hours: 38692
Project Name: Medicinal Chemistry and Computer-Aided Drug
Project Shortname: HEAL1346
Discipline Name: Chemistry

The Tukulula Medicinal Chemistry Research Group (TMCRG) at the University of KwaZulu Natal (UKZN) is working on the interface of organic synthesis and biology. Our projects are geared towards the field of Medicinal chemistry with the aim of discovering new inhibitors for HIV and TB, among others. Infectious diseases such as this are a burden on a developing continent like Africa that plagued by inadequate healthcare infrastructure in some settings.
The CHPC infrastructure allows us to design, model and in silico characterize our potential compounds of interest prior to synthesis. This way we synthesize compounds that we are confident in, in terms of their drug-like properties. The CHPC is used by all the students in the group and projects thus far are progressing well, with a few anticipated research outputs in the near future.

Principal Investigator: Prof Neil Koorbanally
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2024-05-13
Allocation End: 2024-11-11
Used Hours: 9333
Project Name: Medicinal Chemistry Research Programme
Project Shortname: CHEM1683
Discipline Name: Chemistry

I head the Organic and Medicinal Chemistry Research Group at the University of KwaZulu-Natal. There are two postdocs and 4 PhD students currently working in the group. We work on synthesis of hybrid heterocyclic molecules, which contain the frameworks of two or more pharmacophores combined into one molecule. The idea is that by combining the pharmacophores, we will get enhanced activity, as the resultant molecules may interact more effectively with the binding sites of enzymes being targeted for a therapeutic effect. The work is being carried out to identify lead molecules that could be developed into antibiotics, antitubercular drugs, anticancer agents and antidiabetic drugs.
One way of identifying potential activity is by conducting molecular docking studies, which measures the interactions and energies of the synthesized compounds in active sites of various enzymes targeted to provide a desired effect, leading to therapeutic effects. Molecular docking allows one to identify bonding between different parts of the molecule and the amino acid residues of the protein (enzyme). The CHPC also makes studying the molecular dynamics of the molecules possible. Using this technique, we are able to determine the electron and charge distribution around the molecules, predicting sites of attack and attachment to the various amino acids in the enzymes.
The work is progressing well. We have synthesized several libraries of hybrid molecules. Some of the compounds synthesized have shown good antibacterial, antitubercular, anticancer and antidiabetic activity. The computational experiments carried out with the help of the CHPC will help us determine possible mechanisms for the activity.

Principal Investigator: Prof Ozlem Tastan Bishop
Institution Name: Rhodes University
Active Member Count: 20
Allocation Start: 2024-05-14
Allocation End: 2024-11-14
Used Hours: 1372013
Project Name: Structural Bioinformatics for Drug Discovery refresh
Project Shortname: CBBI1436
Discipline Name: Bioinformatics

The Research Unit in Bioinformatics (RUBi) graduated 2 PhD and 2 MSc students in the October graduation. All graduates 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 Matthew Adeleke
Institution Name: University of KwaZulu-Natal
Active Member Count: 16
Allocation Start: 2024-05-14
Allocation End: 2024-11-14
Used Hours: 67474
Project Name: Computational Genomics
Project Shortname: CBBI1231
Discipline Name: Bioinformatics

Our research group is analysing genomes to identify targets for diagnostic applications and therapeutic interventions. To this end we have identified workable therapeutic target against Babesiosis in cattle though still require experimental validation. This work depends on CHPC to analyse genomic sequences, perform molecular docking and molecular dynamics simulations.

Principal Investigator: Dr Justin Lashbrooke
Institution Name: Stellenbosch University
Active Member Count: 3
Allocation Start: 2024-05-14
Allocation End: 2024-11-12
Used Hours: 57322
Project Name: Fruit Functional Genomics
Project Shortname: CBBI1684
Discipline Name: Bioinformatics

The Fruit Functional Genomics Lab (https://www.fruitgenomicslab.com) is based at the Genetics Department at Stellenbosch University and led by Dr Justin Lashbrooke. The research conducted in the group is focused on understanding and characterising the genetics of fruit species, such as grapevine, so that this knowledge can be used to develop more sustainable cultivars for the future. In the research program currently being run using the CHPC facilities, a PhD student in the group, Mr Dylan Grobler, is endeavouring to trace the genetic variation present across 5 000 different grapevine cultivars. The rapid advancement in DNA sequencing technology has resulted in a tremendous amount of so called "whole genome" sequence data being generated, yet for the most part this data remains massively underutilised. We are therefore interrogating this data to create predictive models of how the variations in the grapevine's DNA can lead to traits that can help us create higher quality plants better suited for a changing climate. This process has required considerable computational resources, with the genetic data for each cultivar typically requiring 5 – 45 GB of storage space, and approximately 10 CPU-hours to accurately assay for genetic variation. Thus far, we have established the methodologies for our work and optimised our pipeline, successfully processing approximately 10% of our target of 5 000 cultivars. Thanks to these optimisations, we anticipate that processing the remaining cultivars will require significantly less time, and we hope to predict the impact of DNA variation on plant growth and performance in the near future.

Principal Investigator: Prof RAGUPATHI RAJA KANNAN RENGASAMY
Institution Name: North-West University
Active Member Count: 1
Allocation Start: 2024-05-16
Allocation End: 2024-10-16
Used Hours: 12871
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: Prof Zeno Apostolides
Institution Name: University of Pretoria
Active Member Count: 27
Allocation Start: 2024-05-17
Allocation End: 2024-11-17
Used Hours: 7490
Project Name: Receptomics
Project Shortname: CBBI0926
Discipline Name: Bioinformatics

Drug discovery is the main aim of the Complementary and Alternative Medicines (CAM) group, in the Department of Biochemistry, Genetics and Microbiology at the University of Pretoria is led by Prof Zeno Apostolides. This group house 5 – 10 MSc and PhD students every year. Diabetes was known to the ancient Egyptians and diagnosed with sweet tasting urine. Literature documents many plants with ethnobotanical for treating diabetes. Our projects begin with literature studies of the biochemical structures in the plants that claim antidiabetic effects. These biochemical structures are screened for good inhibition of several clinical targets for diabetes in enzyme models. This screening is done at the CHPC on the Schrodinger software suite of programs. Protein docking is used as a pre-screen and the best chemical structures are then screened with Molecular dynamics. The most promising compounds are screened in laboratory-based enzyme assays for high efficacy and high selectivity. Our results are published in high-impact peer-reviewed academic journals, for other scientists to build on. The next steps may involve toxicity test, glucose uptake with liver and adipose cell cultures. Over the previous two years we have identified several lead compounds may support ethnobotanical claims of black and green tea for type 2 diabetes.

Principal Investigator: Other Christo Venter
Institution Name: North-West University
Active Member Count: 8
Allocation Start: 2024-05-17
Allocation End: 2024-11-29
Used Hours: 20965
Project Name: Astrophysical Calculations and Data Analysis
Project Shortname: ASTR1245
Discipline Name: Astrophysics

Researchers at the Centre for Space Research are actively involved in modelling pulsar emissions.
Pulsars emit broadband emission and still deliver surprises, even 50 years after their discovery. An example is the 20 TeV pulsations seen recently from the Vela pulsar.
Our group is continuing to make progress on multiple modelling projects, the latest being the prediction of TeV pulsar visibility for next-generation Cherenkov Telescopes.

Principal Investigator: Dr Michael Owen
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2024-05-20
Allocation End: 2024-11-30
Used Hours: 4265
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 Ken Craig
Institution Name: University of Pretoria
Active Member Count: 4
Allocation Start: 2024-05-20
Allocation End: 2024-11-22
Used Hours: 165722
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 design of heat exchangers. Laminar flow conditions are attractive in terms of pressure drop or necessitated by small-scale channels as in electronics cooling or compact heat exchangers. When operating in the mixed convection regime, heat transfer enhancement is possible in laminar flow. 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 heat flux or constant surface temperature along the length of non-circular and circular channels. This research aims to fill the gaps in literature by investigating developing flow numerically, augmenting previous experimental research by Everts et al. The research performed in this programme is fundamental, in order to better understand the complexity of the heat transfer mechanisms in these regimes, thereby leading to improved correlations for use in the optimal design of heat exchangers.

Principal Investigator: Dr Nangamso Nyangiwe
Institution Name: Tshwane University of Technology
Active Member Count: 4
Allocation Start: 2024-05-21
Allocation End: 2024-11-26
Used Hours: 309378
Project Name: Application of density functional theory in engineered nanoparticles
Project Shortname: MATS1427
Discipline Name: Material Science

The project titled "Exploring Materials Properties of Ba₂TaBiO₆ for Photovoltaic Applications: Insights from Density Functional Theory Investigations" focuses on the theoretical study of the material Ba₂TaBiO₆. Using Density Functional Theory (DFT), the research aims to explore the electronic and optical properties of this material to assess its suitability for photovoltaic applications, particularly in solar cells.This work is important because the search for efficient, cost-effective, and environmentally friendly materials for solar energy conversion is a global priority. Ba₂TaBiO₆ is a novel material that shows promise due to its unique electronic structure. Investigating its properties through computational methods can lead to the development of new, more efficient photovoltaic materials. The use of public resources is justified by the potential impact of this research on renewable energy technology, which is critical for addressing climate change and reducing dependence on fossil fuels.The project utilizes Density Functional Theory (DFT) calculations to simulate and analyze the material's properties. This method relies heavily on computational resources, particularly high-performance computing (HPC) clusters, such as those provided by the Centre for High-Performance Computing (CHPC). The CHPC's computational power enables the project to perform complex calculations that are essential for accurately predicting the material's behavior at the atomic level.The project is currently progressing well, with initial DFT calculations completed and preliminary results showing promising properties of Ba₂TaBiO₆ for photovoltaic applications. Further simulations and analyses are ongoing to refine these findings and explore additional material characteristics. The use of CHPC resources has been instrumental in advancing the project efficiently.

Principal Investigator: Ms Nomcebo Motsa
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2024-05-23
Allocation End: 2024-12-11
Used Hours: 358777
Project Name: Catalytic Decomposition of Ammonia
Project Shortname: CHEM1623
Discipline Name: Chemical Engineering

The CHEM1623 research group, based in the Department of Chemical Engineering at the University of Pretoria, focuses on the computational design of catalysts for ammonia decomposition to produce hydrogen. The main objective is to address the global challenge of greenhouse gas emissions and climate change by developing clean energy solutions. This aligns with initiatives such as the United Nations Sustainable Development Goals, the African Union's Agenda 2063 (Aspiration 1, Goals 3 and 7), and South Africa's target of achieving net-zero emissions by 2030/2050.

Hydrogen has been identified as a clean energy fuel. However transportation and storage of hydrogen is very expensive. In this regard, Ammonia (NH₃) has been identified as an ideal medium for hydrogen as it is cheaper to transport and store. However, ammonia decomposition is slow and requires a catalyst to enhance the reaction and reduce energy input. Currently, industry relies on the expensive and scarce ruthenium (Ru) catalyst for this process.

Our research aims to reduce the amount of Ru used in ammonia decomposition through a method called "Ru thrifting." We are also investigating whether non-noble metals can fully replace Ru by screening various metals and analyzing their electronic structures using CHPC's Materials Studio software. Significant progress has been made in proving that Ru thrifting can reduce catalyst costs while maintaining performance comparable to pure Ru. Furthermore, some non-noble metals are showing promising results, suggesting that they may provide a cost-effective alternative for ammonia decomposition.

In conclusion, our research is advancing towards making ammonia decomposition a more efficient and economical process for hydrogen production, contributing to global efforts to reduce carbon emissions and transition to cleaner energy sources.

Principal Investigator: Dr Nicholas Ongwen
Institution Name: Maseno University, Kisumu, Kenya
Active Member Count: 5
Allocation Start: 2024-05-24
Allocation End: 2025-01-22
Used Hours: 108744
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, and also on materials for manufacture of microelectromechanical systems. 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, and also at discovering flexible substrates for manufacture of the microelectromechanical systems. This can help the airspace industry to build lighter airplanes that can reduce the overall cost of travelling, since lighter bodies consume less fuel, and also in the fabrication of microbolometer and bio-MEMS. 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 intends to proceed to his PhD in the same area, while Bill Ogega and Edwin Omollo are already exploring thermoelectric properties in their master's proposals.

Principal Investigator: Dr Kedibone Masenya
Institution Name: South African National Biodiversity Institute
Active Member Count: 1
Allocation Start: 2024-05-27
Allocation End: 2025-01-28
Used Hours: 4722
Project Name: Computational Biology
Project Shortname: CBBI1644
Discipline Name: Environmental Sciences

Kedibone Masenya is currently working as a scientist at South African National Biodiversity Institute. Masenya's research is focused on Microbiome
research, ie Metagenomics, Metabarcoding, Transcriptomics, Genomics and Mediation
analysis. Her Skills and Expertise include Next Generation Sequencing, Environmental Science, Microbial Diversity, Molecular Biology and Bionformatics. These omics tools are utilized to answer important question on food security, food science, and biodiversity. Utilizing the NICIS server has resulted in significant outputs and milestones

Principal Investigator: Dr Henry Martin
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 8
Allocation Start: 2024-05-28
Allocation End: 2025-01-15
Used Hours: 91877
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: Dr Michelle Gordon
Institution Name: University of KwaZulu-Natal
Active Member Count: 5
Allocation Start: 2024-05-29
Allocation End: 2024-11-29
Used Hours: 996595
Project Name: Structural Implications of Mutations in HIV-1
Project Shortname: CBBI0928
Discipline Name: Bioinformatics

Our research group is based at the Nelson R Mandela Medical School at the University of KwaZulu-Natal and focusses on the effects of mutations that cause antiretroviral drug resistance on the structure of HIV-1 proteins. The drugs that patients take as part of their treatment against HIV-1 can stop working because the virus is always changing (mutating). We are looking at
how these mutations also change the structure of the virus. To do this, we make a structural model of the affected viral protein using specialised software that uses a lot of computational power.
By using the CHPC, I am able to access their high powered server, as well as the software for performing the molecular modelling. With the information gained from this analysis, we can design new drugs that can work against these mutated viruses.

Principal Investigator: Dr Quinn Reynolds
Institution Name: Mintek
Active Member Count: 5
Allocation Start: 2024-05-29
Allocation End: 2024-11-30
Used Hours: 99022
Project Name: Computational Modelling of Furnace Phenomena
Project Shortname: MINTEK776
Discipline Name: Applied and Computational Mathematics

As we move forward into a new era of low-carbon industrial manufacturing, the means of producing metallurgical products from raw materials is evolving rapidly. Traditional methods of producing commodities such as steel and other alloys involve burning large quantities of coal for both thermal energy and the chemical reactions necessary to reduce raw ores to metal. Due to the impact of carbon dioxide emissions on climate change this is no longer a desirable process route, and alternative means of metallurgical production are needed.

Current areas of research and development include the use of hydrogen as an alternative fuel and chemical reducing agent, and the electrification of metallurgical furnace units. When taken in combination such concepts promise to reduce the carbon footprint of metallurgical smelting to close to zero in the future. Unfortunately, working examples of such processes are limited in industry - and operators are faced with a risky "chicken and egg" problem when it comes to investing heavily in new and potentially untested technologies.

Using advanced computational and numerical modelling techniques together with the high-performance computing facilities at CHPC, Mintek works to create high-fidelity simulations of the next generation of furnaces and pyrometallurgical processes. Such models can be used as virtual prototypes and numerical experiments, helping to demystify and de-risk the challenges involved in transitioning to clean metallurgical production, and encouraging our industry to take the leap forward into a better world.

Principal Investigator: Prof Ray Everson
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2024-05-30
Allocation End: 2024-11-30
Used Hours: 226969
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 Malebogo Ngoepe
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2024-05-30
Allocation End: 2025-01-31
Used Hours: 3221589
Project Name: PROTEA
Project Shortname: MECH1194
Discipline Name: Computational Mechanics

Our group focuses on computational and experimental mechanics in biological problems. These include congenital heart disease, thrombosis, new heart attack therapies and curly human scalp hair. Our work is beneficial for understanding the behaviour of biological materials, disease progression and new therapies or diagnostic tools. The resources provided by the CHPC have been important for our computational simulations and we have made steady progress over the years.

Principal Investigator: Dr Zipporah Muthui
Institution Name: Chuka University, Chuka, Kenya
Active Member Count: 8
Allocation Start: 2024-06-03
Allocation End: 2025-01-15
Used Hours: 80137
Project Name: Electronic Structure and Magnetic Properties of Heusler Compounds
Project Shortname: MATS1112
Discipline Name: Physics

The MATS1112 group has one PhD candidate, Jane and one researcher, Bonface. Jane has successfully defended her PhD proposal upto graduate school level and has made a great deal of progress with her computations. Their research focuses on manipulation of material properties at the atomic level to provide alternative, environment friendly, green energy sources. Bonface is currently dealing with the properties of double perovskites. Jane is dealing with modifications of TiO2 and ZrO2 for solar active photocatalytic applications. The PI, Dr. Zipporah Muthui has been supporting both these projects. These jobs require HPC resources as they involve supercells that require sufficient computing resources. Without the HPC resources provided, all this work would not have been possible.

Principal Investigator: Dr Winfred Mulwa
Institution Name: Egerton University, Egerton, Kenya
Active Member Count: 13
Allocation Start: 2024-06-03
Allocation End: 2025-01-22
Used Hours: 222012
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: Prof Obodo Kingsley
Institution Name: University of KwaZulu-Natal
Active Member Count: 22
Allocation Start: 2024-06-03
Allocation End: 2025-03-05
Used Hours: 1727785
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 modelling of liquid organic hydrogen carriers' catalyst and 2D materials" is conducted at the Centre 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, 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. The research program "MATS1366: Ab initio Modelling of Liquid Organic Hydrogen Carriers' Catalysts and 2D Materials" is conducted at the HySA Infrastructure Centre of Competence at North-West University (NWU), South Africa. The program is currently led by Kingsley Obodo, the principal investigator, who is based at the Centre for Space Research at NWU, Potchefstroom. The research team includes scholars such as Asres Georgies Alene, Hailouf Houssam, among others.
Students involved in the program utilize the Centre for High-Performance Computing (CHPC) facility for their master's and doctoral research, making substantial contributions to the field. Key research areas include developing dehydrogenation catalysts, performing ab initio studies on the structural and electronic properties of Pt/Pd-based alloys, and investigating the hydrogenation of furfural to furfuryl alcohol using La-based inorganic perovskites.
The program employs density functional theory (DFT) for computational modelling, utilizing advanced software packages such as CASTEP, Quantum Espresso, GPAW, and VASP. In addition to catalyst development for liquid organic hydrogen carriers (LOHC) dehydrogenation, the team is also researching catalysts for water electrolysis, a process that splits water into hydrogen and oxygen. Their groundbreaking work is currently under review for publication, contributing to advancements in battery technology, water splitting, and catalyst development.

Principal Investigator: Dr Elliot Menkah
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 15
Allocation Start: 2024-06-03
Allocation End: 2025-02-06
Used Hours: 647344
Project Name: Materials for Energy
Project Shortname: MATS1515
Discipline Name: Chemistry

The Menkah Research Group is a part of the broader Computational Chemistry Research Group in the Department of Chemistry at KNUST. Our work focuses on two key aspects of computational chemistry: development and application. Leveraging the computational resources provided by the CHPC, we test and validate newly implemented scientific concepts within the field of chemistry. Additionally, we actively promote the benefits of high-performance computing in advancing scientific research. We're currently studying hydrazine systems for it's role in hydrogen evolution owing to its higher hydrogen density, comparative, when compared to molecular hydrogen. On such systems, our work is looking into the investigations from a materials chemistry point of view using quantum mechanical methods. Also, our biophysics research looks into intrinsically disordered protein systems where we're investigating inhibition mechanisms that would disfavor the disordered behaviour. This behavior of proteins is connected to proliferation and cancer ailment. This study is looking at the interaction using classical molecular dynamics as of now.

Principal Investigator: Dr Thankhoe Rantso
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2024-06-04
Allocation End: 2024-12-03
Used Hours: 14555
Project Name: Advanced Protein Models
Project Shortname: HEAL1600
Discipline Name: Health Sciences

Our cancer pharmacology research group is led by Dr. Thankhoe Rants'o and Dr. Gary Gabriels. Highly invested in proteomics work and in collaboration with international institutions, our group aims to discover the biology behind cancer spreading (metastasis) and identify novel drug targets that drive it.
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 cancer metastasis. The CHPC platform has allowed us to study both the potential therapeutic and toxic effects of the molecules of interest.

Principal Investigator: Dr Ryno Laubscher
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2024-06-04
Allocation End: 2024-11-30
Used Hours: 220754
Project Name: CFD Programme for R Laubscher
Project Shortname: MECH1466
Discipline Name: Computational Mechanics

The Institute of Biomedical Engineering and the Department of Mechanical Engineering at Stellenbosch University are making significant strides in scientific research with the support of the Centre for High Performance Computing (CHPC). Our research groups, focused on biomedical modeling and thermofluid systems, are leveraging cutting-edge computational resources to push the boundaries of their respective fields.

Recently, our biomedical modeling team achieved a major milestone by successfully simulating steady-state and dynamic blood flow and structural deformations of the human aortic valve specifically for sub-Saharan Africa diseases such as valvular deformations. This pioneering work, published internationally, has important implications for medical research and the development of advanced cardiovascular treatments in Africa.

In the realm of thermofluid systems, our research includes investigating sustainable energy generation technologies. For example, exploring biomass boilers, studying new power generation cycles such as sCO2 and simulating hydrogen combustion in gas turbines. These studies are crucial for advancing renewable energy technologies and optimizing industrial processes. By comparing our simulation results with experimental data, we ensure the reliability and applicability of our findings.

The CHPC has been instrumental in our progress. High-performance computing allows us to perform complex simulations that would be otherwise impossible. For instance, we utilized CHPC resources to run simulations with grid sizes of around 20 million cells and to conduct AI-driven simulations of blood flow using advanced neural networks. These computationally intensive tasks require substantial processing power, which the CHPC provides.

Our research is vital for advancing scientific knowledge and developing practical applications that can benefit society. By understanding and optimizing complex systems, from the human heart to industrial turbines, we contribute to medical advancements and sustainable energy solutions. The support from the CHPC is not just beneficial but essential, allowing us to maximize our research potential and make meaningful contributions to our fields.

As we continue to progress, we look forward to further collaboration with the CHPC, ensuring that Stellenbosch University remains at the forefront of scientific innovation and research excellence.

Principal Investigator: Dr Joseph Mutemi
Institution Name: University of Nairobi
Active Member Count: 6
Allocation Start: 2024-06-06
Allocation End: 2025-01-21
Used Hours: 27334
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. In December 2024, a member of the research group Anthony Mwanthi successfully defended his PhD thesis. His research, focusing on the interactive processes between the land surface and the atmosphere not only set the stage for improving weather forecasts utilizing high resolution models to resolve localized extreme events, but also generated useful knowledge on the impact of human activities on the climate system through landuse changes. The results are critical inputs for both operational forecasting centres, as well as development of policies for proper management of land management and ecosystem services.

Principal Investigator: Prof Thulani Makhalanyane
Institution Name: Stellenbosch University
Active Member Count: 35
Allocation Start: 2024-06-10
Allocation End: 2024-12-10
Used Hours: 169539
Project Name: Metagenomics of extreme environments
Project Shortname: CBBI1023
Discipline Name: Bioinformatics

The African Microbiome research group at Stellenbosch University focuses on understanding microbial communities in various environments, using next-generation tools to study microbiomes in the human gut, terrestrial, and aquatic ecosystems, with an emphasis on African contexts. Current projects include the characterization of antimicrobial resistance in freshwater rivers in South Africa and Africa. We also have projects focused on understanding the role of gut microbiome in childhood development. Access to CHPC resources has been instrumental in efficiently processing these datasets and providing insights into these questions.

Principal Investigator: Prof Yin-Zhe Ma
Institution Name: Stellenbosch University
Active Member Count: 10
Allocation Start: 2024-06-11
Allocation End: 2025-01-14
Used Hours: 357423
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 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.

With the advancement of cosmological galaxy surveys, high-performance computing (HPC) has become indispensable for handling massive datasets. A recent research project successfully utilized HPC resources to conduct an extensive search for galaxy pairs, shedding light on large-scale cosmic structures. By harnessing the parallel processing capabilities of HPC nodes, researchers significantly improved computational efficiency, analyzing datasets with unprecedented speed and accuracy. This work contributes to the understanding of galaxy clustering, a fundamental aspect of cosmology. The research underscores the crucial role of high-performance computing in modern astrophysics, paving the way for future discoveries.

Principal Investigator: Dr Anand Krishnan
Institution Name: University of the Free State
Active Member Count: 1
Allocation Start: 2024-06-11
Allocation End: 2024-12-11
Used Hours: 1136
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

Group leader: Dr. Krishnan Anand, UFS.

Our group is Drug Discovery, and development lead by Dr. Krishnan Anand. Our team is working on cancer chemotherapy, PROTAC, antivirals, etc. Our team used the CHPC resources for completing the project works. It helped the student to complete their research work in-time. Moreover, the outcome of the research project will be giving more insights to the scientific community, researchers, students, and public. It will contribute to the society in the terms of achieving better medications in-future.

In the realm of PROTACs, we aim to design molecules that harness the cell's natural protein degradation machinery to eliminate specific disease-causing proteins. Our EGFR research is crucial, given its role in various cancers. My commitment to advancing pharmaceutical chemistry is reflected not only in my extensive publication record but also in the groundbreaking research conducted by my team members. Our efforts are driven by the ultimate goal of improving human health and quality of life through the discovery and development of novel pharmaceuticals. I am proud to be a part of UFS and the broader scientific community, where innovation and collaboration drive our shared pursuit of scientific excellence.

Principal Investigator: Prof Chris Vorster
Institution Name: North-West University
Active Member Count: 3
Allocation Start: 2024-06-11
Allocation End: 2025-01-22
Used Hours: 15275
Project Name: Nngwe
Project Shortname: CBBI1691
Discipline Name: Bioinformatics

Nngwe is a rare disease initiative supported by DIPLOMICS. Dr Chris Vorster and his team are coordinating resources to build one united infrastructure to help decreased the time to diagnoses. Fifteen human samples have been sequenced to date and have been used to smooth out the process as the project prepares to scale up in 2025

Principal Investigator: Dr Mary-Jane Bopape
Institution Name: South African Weather Service
Active Member Count: 27
Allocation Start: 2024-06-12
Allocation End: 2025-01-17
Used Hours: 1156070
Project Name: Very Short Range Forecasting
Project Shortname: ERTH1022
Discipline Name: Earth Sciences

Research by PhD students at the South African Weather Service and the Council for Scientific and Industrial Research (CSIR) indicates that the Conformal Cubic Atmospheric Model (CCAM) is able to simulate large scape tropical and midlatitude systems. For both systems the model is generally able to capture the occurrence, path, winds and temperature associated with the systems, but it misses the intensity. The location extent is also missed for some systems. This further highlights a need for local development or improvement of these systems to assist with early warning systems for the benefit of all.

Principal Investigator: Prof Matt Hilton
Institution Name: University of the Witwatersrand
Active Member Count: 8
Allocation Start: 2024-06-12
Allocation End: 2025-01-31
Used Hours: 353878
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 Clement Agoni
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2024-06-12
Allocation End: 2025-01-20
Used Hours: 44922
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 Caroline Kwawu
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 38
Allocation Start: 2024-06-12
Allocation End: 2025-02-27
Used Hours: 1656787
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. Over the years CHPC has been a backbone of research in the Kwawu group. We are actively trying to develop novel materials for solar energy storage. We have made great progress and this would not have been possible without the support and computer resources.

Principal Investigator: Dr Robert Warmbier
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2024-06-13
Allocation End: 2025-03-20
Used Hours: 245931
Project Name: Study of defects and doping of the atomic and electronic structure of materials
Project Shortname: MATS1653
Discipline Name: Physics

The Computational Material Science Group led by Dr Robert Warmbier from the Wits School of Physics uses quantum mechanical tools to model basic properties of materials on an atomic level to better understand - and to improve - their behaviour. Many materials we use technologically comprise of crystals, in which atoms are well ordered in repetitive patterns. Given this structure, many of the materials properties can be understood easily using quantum mechanics-based simulations. In practice every material has little defects though, which change the materials properties. We investigate how exactly this happens, not only to minimise these effects, but also to improve ways how to use these defects to our advantage.

In our lead project Dr Chani van Niekerk is investigating the effects of defects in the structure of carbon nanotubes. Nanotubes are of significant technological interest, as they are lightweight, extremely strong and have excellent electrical conductivity. They can be woven into fibres for use in fabrics, or used as single nanotubes in computer circuitry. The amazing properties of nanotubes are limited by the loose interaction between different tubes. Our team is investigating how the interaction of nanotubes can be improved to yield a better product.

In collaboration with the Novel Materials group of Dr Abhishek Pandy at Wits we investigate the magnetic and electronic behaviour of certain types of materials in the hopes to understand better how and why some of them exhibit super-conductivity. This effect lowers the electrical resistivity to zero, which is needed for example to build the strong magnets one finds in MRI machines.

Simulating the interactions of thousands or tens of thousands atoms is computationally demanding and would take years or decades on a consumer PC. We rely on the high-performance computing support by the CHPC for our work and are grateful for their support.

Principal Investigator: Dr Nikiwe Mhlanga
Institution Name: Mintek
Active Member Count: 13
Allocation Start: 2024-06-13
Allocation End: 2025-02-06
Used Hours: 1089318
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 Ponnadurai Ramasami
Institution Name: University of Mauritius
Active Member Count: 5
Allocation Start: 2024-06-14
Allocation End: 2025-01-22
Used Hours: 43851
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, 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 the manuscript related to the reaction of dimethyl sulfide with halogens 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.

We also published one manuscript on novel solar dyes whereby we have used CHPC for high level computations.

The URL of the website of his research group is https://sites.uom.ac.mu/ccuom/

Principal Investigator: Prof Peter Teske
Institution Name: University of Johannesburg
Active Member Count: 6
Allocation Start: 2024-06-14
Allocation End: 2024-12-14
Used Hours: 164771
Project Name: Coevolution of mangroves and mangrove-associated crabs
Project Shortname: CBBI0979
Discipline Name: Bioinformatics

Who?
Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg

What?
Analysis of DNA and RNA data from a large portion of animal genomes.

Why?
To improve the management of commercially exploited species, optimise conservation efforts aimed at saving endangered species from extinction, and understand evolutionary relationships in nature.

How?
Genomic data sets generated using massive parallel sequencing technology results can only be assembled by means of supercomputers. Using CHPC, we are able to assemble a huge number of short reads into a meaningful sequence that reflects their order in the animal genome.

Progress?
CHPC and the valuable expertise it has gathered in one place has allowed our small lab to punch well above its weight, and we are now on our way of becoming an international player in the field of genomics who are being noticed by much larger (and much better funded) international research groups. We are looking forward to publishing several high-impact studies during the next few months that we would not have been able to complete without CHPC.

Principal Investigator: Prof Hadley Clayton
Institution Name: University of South Africa
Active Member Count: 6
Allocation Start: 2024-06-14
Allocation End: 2024-12-17
Used Hours: 88137
Project Name: Bioorganometallic Chemistry of Transition Metals
Project Shortname: CHEM1288
Discipline Name: Chemistry

Clayton Organometallic Research Group at the University of South Africa. Our research combines advanced synthetic techniques with crystallographic analysis and computational studies, to investigate how the structural properties of metal complexes influence their protein binding affinity and biological activity. Computer applications such as Gaussian, ORCA and DMol3 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 findings on the potential use of zinc metal complexes as SARS-CoV-2 viral entry and replication inhibitors.

Principal Investigator: Prof Cornie van Sittert
Institution Name: North-West University
Active Member Count: 26
Allocation Start: 2024-06-14
Allocation End: 2025-01-22
Used Hours: 4699098
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 Holliness Nose
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 7
Allocation Start: 2024-06-18
Allocation End: 2025-01-16
Used Hours: 2458826
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 in due time. Dr. Nose has attracted research grants to fund her research activities. These include: National Research Fund-Kenya, The World Academy of Sciences, and 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 Nomampondo Magwa
Institution Name: University of South Africa
Active Member Count: 3
Allocation Start: 2024-06-18
Allocation End: 2024-12-17
Used Hours: 40817
Project Name: Atomistic evaluation of thiazoles and metal-oxide/cellulose nanocomposite for water treatment, OLEDs and energy storage.
Project Shortname: CHEM1693
Discipline Name: Chemistry

The research group is the Material Science research group. This project explores the fundamental properties of compounds selected for water purification, heavy metal remediation, energy storage and OLED devices. The use of CHPC resources is required to evaluate the suitability of the selected compounds for these purposes prior to being synthesized, reducing the cost, efficiency, effectiveness, robustness and providing a greener path for the experiment. So far, the progress made was the attendance of one local and one international conference by two delegates as well as the submission of two manuscripts.

Principal Investigator: Prof David Lokhat
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2024-06-19
Allocation End: 2024-12-19
Used Hours: 736849
Project Name: Carbon dioxide hydrogenation
Project Shortname: CHEM1384
Discipline Name: Chemical Engineering

Our research group is the Chair in Sustainable Engineering and Process Intensification at the University of KwaZulu-Natal, supported by African Rainbow Minerals. Our study involves the development materials that can be used as cost effective catalysts for CO2 utilization. CO2 is a major contributor to climate change. These materials have the potential to help the national government and major industrial CO2 producers mitigate against environmental pollution and the negative implications they are facing. The general public may make use of these materials in various domestic and industrial applications where CO2 can be used to produce energy and fuels. Before these materials can be synthesized and tested, they must be designed. The computational work carried out using the CHPC can be used to determine which materials are suitable for CO2 hydrogenation.

Principal Investigator: Dr Saheed Sabiu
Institution Name: Durban University of Technology
Active Member Count: 29
Allocation Start: 2024-06-19
Allocation End: 2025-06-25
Used Hours: 2158872
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 program has been leveraging on this with appreciable progress made to date.

Principal Investigator: Dr DOROTHY NYAMAI
Institution Name: 0 Other
Active Member Count: 2
Allocation Start: 2024-06-20
Allocation End: 2024-12-20
Used Hours: 46659
Project Name: JKUAT BIOINFORMATICS GROUP
Project Shortname: CBBI1651
Discipline Name: Bioinformatics

The JKUAT Bioinformatics group focuses on exploring the cause and treatment of economically important diseases affecting the African population. Most of these diseases are understudied in Africa due to limited resources. However, the CHPC play a key role in understanding the cause and coming up with novel strategies to develop therapies for these diseases. This cluster has been very beneficial as bioinformatics tries to reduce the cost if understanding diseases and developing effective treatments. We have an Msc student almost completing his studies and an article in press.

Principal Investigator: Prof Mahmoud Ibrahim
Institution Name: University of KwaZulu-Natal
Active Member Count: 16
Allocation Start: 2024-06-21
Allocation End: 2025-01-07
Used Hours: 2543818
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 and designing drug nanocarriers. 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. For drug delivery part, geometrical optimization and energy calculations are carried out. 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 Warren du Plessis
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2024-06-24
Allocation End: 2025-01-17
Used Hours: 21652
Project Name: Electronic Warfare (EW) Technologies
Project Shortname: MECH0989
Discipline Name: Electrical Engineering

Some initial experimentation of the use of the tool gprMax was conducted with a view to potentially using it more extensively in future.

Principal Investigator: Prof Nithaya Chetty
Institution Name: University of Pretoria
Active Member Count: 8
Allocation Start: 2024-06-24
Allocation End: 2025-01-21
Used Hours: 2037824
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 the African School for Electronic Structure Methods and Applications (ASESMA), a network of African scientists advancing research in computational materials science. The primary focus of ASESMA researchers is based on the electronic structure calculations of materials. Each proposal addresses specific challenges in physics, chemistry, and materials science with potential impacts on science, technology, and society. Current projects currently explore two-dimensional (2D) materials, perovskites and silicates, which are promising candidates for applications in lithium or sodium batteries, electronic devices, solar cells, and more. To enhance or expand their applications, the properties of these materials can be engineered through methods such as doping or defect creation. Theoretical studies of these systems require the use of supercells to simulate experimental samples accurately. Such computations demand access to high-performance supercomputers like those at the CHPC. Our findings show great promise for industrial applications.

Principal Investigator: Dr Thommas Musyoka
Institution Name: Kenyatta University, Nairobi, Kenya
Active Member Count: 5
Allocation Start: 2024-06-27
Allocation End: 2024-12-27
Used Hours: 35239
Project Name: Kenyatta University Bioinformatics and Genomics Research Group
Project Shortname: CBBI1650
Discipline Name: Bioinformatics

The Bioinformatics and Genomics Research Group at Kenyatta University (Nairobi, Kenya) is at the forefront of integrating genomics and bioinformatics in drug discovery. Their work encompasses a range of activities designed to harness genetic information and computational tools to identify and develop new therapeutic agents. It has two broad areas:
A) Drug Discovery
1. Target Identification and Validation:
o Genomic Data Analysis: Utilizing genomic sequencing data to identify genes and proteins involved in disease processes.
o Pathway Analysis: Studying biological pathways to pinpoint potential intervention points for drug development.
2. Compound Screening:
o Virtual Screening: Using bioinformatics tools to screen large libraries of chemical compounds against identified targets.
o Molecular Docking: Simulating the interaction between drug candidates and their targets to predict binding affinity and efficacy.
3. Lead Optimization:
o Structure-Based Drug Design: Employing 3D structures of target proteins to design and optimize drug candidates.
B) Genomics Research
1. Genome Sequencing and Annotation:
o High-Throughput Sequencing: Performing whole-genome and targeted sequencing to gather comprehensive genetic information.
o Bioinformatics Analysis: Analyzing sequencing data to identify genetic variants, gene expression patterns, and regulatory elements.
2. Functional Genomics:
o Gene Function Studies: Investigating the roles of specific genes in health and disease through functional genomics approaches.
3. Bioinformatics Tool Development:
o Pipeline Creation: Developing bioinformatics workflows for data analysis, from raw sequencing data to biological insights.
Impact and Applications of the Ongoing work
Disease-Specific Research: Focusing on diseases that are prevalent in the region, such as malaria, tuberculosis, HIV/AIDS, and non-communicable diseases such as cancer to understand their pathogenesis as well as find possible hit molecules for drug development.
The two domains are highly expensive in the usage of computational resources and that is why we need the CHPC resources. We are grateful for the help accorded.

Principal Investigator: Dr Nkululeko Emmanuel Damoyi
Institution Name: Mangosuthu University of Technology
Active Member Count: 3
Allocation Start: 2024-07-04
Allocation End: 2025-01-21
Used Hours: 260423
Project Name: Surface Reaction Mechanisms
Project Shortname: CHEM1105
Discipline Name: Chemistry

My name is Dr Nkululeko Damoyi and I teach Inorganic Chemistry in the department of Chemistry at Mangosuthu University of Technology (MUT). My present research is in Computational Chemistry (CC) and the modelling calculations are done through the Centre for High Performance Computing (CHPC) in Cape Town. Research is registered at CHPC under the name: Surface Reaction Mechanisms. Presently there are three members in the group conducting simulations and more postgraduate students will join during the course of the year 2025. I presently supervise some MUT Advanced Diploma students in small CC research projects although they use their laptops for calculations. Current research output is in a form of nine publications in peer-reviewed journals.

A large production of alkanes, for example LPG gas, from imported crude oil and mined natural gas and coal exists in South Africa through a variety of industrial processes. The alkanes are used as starting materials for many other industrial organic compounds, such as plastics. However, the production of some of these industrial organic compounds is too costly and there is a high commercial demand for catalytic methods and new catalysts that would bring down the costs of production. Computer technological advances make it possible to do research in CC in order to model chemical reactions and predict chemical reaction properties which are difficult or impossible to determine from normal laboratory experiments. Most of our present research involves utilising CC to predict the likely chemical reaction mechanisms that produce valuable organic compounds from alkanes with use of catalysts and also without catalysts. Through CHPC we are able to use internet to connect to their cluster computers in order to run the calculations and from the results be able to model the energetics of chemical reactions and predict reaction mechanisms.

Principal Investigator: Dr Krishna Govender
Institution Name: University of Johannesburg
Active Member Count: 20
Allocation Start: 2024-07-05
Allocation End: 2025-01-16
Used Hours: 1937943
Project Name: Computational approaches to design novel anticancer agents
Project Shortname: CHEM0792
Discipline Name: Chemistry

The goal of the E=c2m2 research group is to develop a drug database that be used for treatment of different cancers. We are in the process of creating a natural product database that will later be shared with other researchers for them to make use of for other diseases. The group also looks to develop tools that will make it easier for conventional experimental chemists to make use so that they can make predictions related to their experimental work prior to going into the laboratory. Most of the work we conduct entails making use of large datasets that could take months on a conventional desktop computer as a result we are heavily reliant on the CHPC resources to ensure that our simulations are carried out in short periods of time. The primary applications that are utilized within our group include Schrodinger, Material Studio, Quantum Espresso, Gaussian, ORCA, NWChem, AMBER and Python allowing for simulations using quantum mechanics (density functional theory), molecular mechanics, molecular dynamics and machine learning to name a few. The licensed software packages utilized in the group are also offered by the CHPC allowing us to save on licensing fees.

Principal Investigator: Dr Bryan Phuti Moloto
Institution Name: University of Limpopo
Active Member Count: 3
Allocation Start: 2024-07-05
Allocation End: 2025-01-03
Used Hours: 1118
Project Name: Corrosion Science and Quantum Chemical Studies (Using State-of-the-Art AMS / ADF)
Project Shortname: CHEM1696
Discipline Name: Chemistry

We are a small group at the University of Limpopo housed in the Department of Chemistry, with diverse skills set--ranging from organic synthesis to theoretical physical chemistry. We synthesize organic compounds (in some cases, we procure them) and analyze them using electrochemical methods and the State-of-the-Art Amsterdam Modeling Suite (Which the CPHC does not have the licence for) / Amsterdam Density Functional (Quantum Chemical Studies) and Gaussian16 for usage as possible corrosion inhibitors for mild steel/aluminium/zinc metals in different media. With this type of research niche, we aim to synthesis and test our compounds to be possible corrosion inhibitors to minimize the rate of corrosion in industries, etc.. Our experimental findings are then, with the assistance and reliability of the CHPC clusters, are then corroborated in terms of Density Functional Theory (DFT) methods (Without the allocation of the CHPC CPU hours, this part of our research would not have sufficed). The research is progressing positively and should be able to submit two research articles.

Principal Investigator: Dr Collins Obuah
Institution Name: University of Ghana
Active Member Count: 3
Allocation Start: 2024-07-08
Allocation End: 2025-01-22
Used Hours: 72041
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 and also studying the reaction mechanisms. 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. Furthermore, The study of reaction mechanisms is essential in chemical research, focusing on the detailed steps and intermediates involved in chemical reactions. Researchers aim to identify transient species, map out reaction pathways, measure reaction rates, and analyze energy changes. This understanding helps in designing efficient chemical processes, developing new synthetic methods, and improving catalysts. It is particularly important in fields like pharmaceuticals, materials science, and environmental chemistry, where knowing how and why reactions occur can lead to significant advancements and innovations.
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 has been published and others are still ongoing.

Principal Investigator: Prof Sekelwa Cosa
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2024-07-10
Allocation End: 2025-01-08
Used Hours: 546382
Project Name: Natural Products and Bacterial Pathogens’ Interaction Interruption Research Group
Project Shortname: CBBI1697
Discipline Name: Bioinformatics

This research group (NAPBI_RG) has interest and focus on the potential therapeutic strategies to mitigate bacterial infections via interrupting bacterial communication systems and interactions. This we do by exploring the natural products (medicinal plants/microbes/propolis and other) and their bioactive compounds to attenuate multidrug resistance. The interest is mainly provoked by the existing indigenous knowledge on traditional medicine. In addition, there is a global emerging problem of antibiotic resistance where high levels of tolerance and resistance in bacterial pathogens are prevalent even within the public sector in SA. This research contributes to the increasing knowledge and acknowledgement of traditional medicine and or indigenous knowledge systems, bacterial virulence and multidrug resistance. Some of the techniques employed in successful execution of this research includes the molecular modelling approach, combined with various in vitro, in situ and molecular techniques. The work involves bringing in collaboration expertise from various disciplines such as Bioinformatics, Biomedical, Microbiology, Plant Science and other. What this groups envisages, is the development of these alternative strategies and drug candidates that would possibly repress the expression of cell-to-cell communication regulated phenotypes, which may have great clinical impact in relation to combating MDR infections. As the Principal Investigator, I envision to broaden the research scope to explore proteomics in this area; while training and striving to make a significant positive impact to young upcoming researchers (students) and contributing to the institution and national research interests.

Principal Investigator: Prof Phuti Ngoepe
Institution Name: University of Limpopo
Active Member Count: 0
Allocation Start: 2024-07-12
Allocation End: 2025-02-04
Used Hours: 7929072
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; platinum group minerals (PGMs): sperrylite, pallado-arsenide, geversite, cooperite, platinum/palladium tellurides, platarsite, and platinum/palladium bismuth and oxide minerals: spodumene, feldspar and hematite. The collectors are organic compounds that are used to target and render the mineral of interests (concentrates) hydrophobic and promote their recoveries. In this reporting period we have attended the University of Limpopo faculty of science and agriculture research day (FSA-RD) at The Ranch Resort (17-20 September 2024) and gave oral and poster presentations by the students (PhD, MSc and Honours). Mr Mashishi K.L. won an MSc best presenter at the FSA-RD. These were paramount in engaging with other researchers to communicate our research and share our insights. The outcome of the minerals research work will benefit the country at large in recovering sulphide minerals using these highly selective collectors. The use of public resources such as the CHPC was helpful to the University of Limpopo to perform these simulations.

Principal Investigator: Dr Vuyo Mavumengwana
Institution Name: Stellenbosch University
Active Member Count: 4
Allocation Start: 2024-07-15
Allocation End: 2025-01-15
Used Hours: 1100
Project Name: Microbial symbionts bioactive compounds and their virtual screening
Project Shortname: CBBI1434
Discipline Name: Bioinformatics

The Vuyo Lab is located at Stellenbosch University, Tygerberg Medical Campus, within the Biomedical Research Institute. The lab consists of four PhD students and one master's student who are all working towards their degrees. Additionally, there are three postdoctoral researchers in the group, all of whom incorporate in-silico methods into their projects. Our primary focus is on drug discovery, specifically targeting infectious diseases and cancer. We utilize the CHPC to accelerate drug discovery by processing large multi-omics datasets to identify new therapeutic agents and targets.

Principal Investigator: Dr Molemi Rauwane
Institution Name: Nelson Mandela Metropolitan University
Active Member Count: 6
Allocation Start: 2024-07-15
Allocation End: 2025-01-15
Used Hours: 1395
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, Agricultural Research Council, University of Venda and Malawi University of Technology.
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 losing 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, 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.
More research has been added onto the group in collaboration with Malawi University of Technology. The project aims at identifying fungal and viral diseases affecting common beans in SAn growing regions (North-West, Limpopo, Mpumalanga and Free State), using metagenomics and metabarcoding tools.
We are currently responding to the reviewers comments for all the three manuscripts. In addition, I was invited as a speaker for the CHPC conference (Gqeberha, 01-04bDec, 2024) and presented the outcomes of the use of the CHPC tools for analysis of data for our projects.

Principal Investigator: Dr Thendo_duplicate Mafuna_duplicate
Institution Name: University of Johannesburg
Active Member Count: 6
Allocation Start: 2024-07-15
Allocation End: 2025-01-15
Used Hours: 3350
Project Name: UJ Bioinformatics and Computational Biology
Project Shortname: CBBI1595
Discipline Name: Bioinformatics

Dr. Thendo Mafuna is aLecturer and researcher specializing in bacterial genomics at the University of Johannesburg. His research group focuses on understanding the genetic and genomic aspects of bacterial populations, particularly those relevant to health and environmental applications. Dr. Mafuna's team is engaged in cutting-edge research to sequence, analyze, and interpret bacterial genomes. This work includes identifying bacterial species, understanding their genetic diversity, and elucidating the functional roles of bacterial genes in various environments. The research is crucial for several reasons: Public Health: Understanding bacterial genomics can lead to better diagnostics, treatments, and prevention strategies for bacterial infections. Agriculture: Insights into bacterial populations can improve livestock health and crop yields by managing bacterial pathogens and promoting beneficial bacteria. Environmental Sustainability: Studying bacterial genomes helps in bioremediation efforts and understanding the ecological roles of bacteria in different environments. The significance of this research justifies the use of public resources as it addresses critical issues in health, agriculture, and environmental management, ultimately benefiting society at large. The research involves several key steps: Sample Collection: Gathering bacterial samples from various sources such as clinical settings, agricultural fields, and natural environments. DNA Extraction: Isolating genetic material from these samples. Sequencing: Using high-throughput sequencing technologies to decode the bacterial genomes. This is where the Centre for High Performance Computing (CHPC) plays a vital role, providing the computational power needed for large-scale genomic analyses. Data Analysis: Employing bioinformatics tools to interpret the sequencing data, identify genetic variants, and understand gene functions. Application: Using the insights gained to develop practical solutions in health, agriculture, and environmental management. The project is making significant strides, with several milestones already achieved: Initial Sequencing Phases: Successful sequencing of multiple bacterial genomes. Data Analysis: Identification of key genetic markers and functional genes. Publication and Collaboration: The research group has published findings in reputable journals and is collaborating with other institutions to expand the scope and impact of the work. The support from the CHPC has been instrumental in handling the vast amount of data generated, ensuring that the project continues to progress efficiently and effectively.

Principal Investigator: Prof Joanna Dames
Institution Name: Rhodes University
Active Member Count: 6
Allocation Start: 2024-04-09
Allocation End: 2025-01-16
Used Hours: 8336
Project Name: Mycorrhizal Interactions
Project Shortname: CBBI0966
Discipline Name: Bioinformatics

he Mycorrhizal Research group is based at Rhodes University, Makhanda.

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 molecular sequencing provides an opportunity to unravel this biodiversity to better understand factors which impact the relationship between plants, soil microbes and mycorrhizal fungi. This research is ongoing.

Principal Investigator: Prof Jeanet Conradie
Institution Name: University of the Free State
Active Member Count: 8
Allocation Start: 2024-07-16
Allocation End: 2025-02-07
Used Hours: 2011833
Project Name: Computational chemistry of transition metal complexes
Project Shortname: CHEM0947
Discipline Name: Chemistry

The computational resources provided by CHPC were instrumental in advancing the research efforts of our group and our collaborators. These resources enabled us to analyze, interpret, and provide deeper insights into experimental observations, bridging the gap between theoretical predictions and empirical findings. By rigorously comparing our computational results with existing experimental data, we were able to validate our theoretical models, leading to a more thorough understanding of complex chemical behaviors. This synergy between computation and experimentation not only reinforced the reliability of our theoretical frameworks but also facilitated accurate predictions of experimental outcomes.
Our research delves into the fundamental aspects of redox potential, emphasizing the intrinsic stability of molecules when subjected to oxidation and/or reduction. Understanding these redox characteristics is crucial for their application in various scientific and technological domains, particularly in catalysis and as redox mediators in dye-sensitized solar cells (DSSCs). Theoretical modeling plays a vital role in optimizing the design of efficient redox-active compounds, contributing to advancements in energy conversion and storage technologies.
Similarly, our theoretical investigations into the UV-visible (UV-vis) absorption properties of molecules, conducted using Time-Dependent Density Functional Theory (TDDFT), have significant implications in the field of photovoltaics. By predicting and fine-tuning the optical properties of dyes, we aim to enhance their efficiency when employed in DSSCs, thereby improving overall solar energy harvesting performance.
Beyond energy-related applications, our research extends to the study of liquid-phase systems, including pure liquids and liquid mixtures. These investigations have far-reaching industrial relevance, influencing key processes such as organic extraction, organic synthesis, polymer chemistry, oil recovery, separation techniques, and the formulation of various functional fluids. By gaining a theoretical understanding of the physicochemical properties governing these systems, we contribute to the optimization of industrial practices, leading to improved efficiency, sustainability, and innovation across multiple sectors.

Principal Investigator: Dr Madison Lasich
Institution Name: University of KwaZulu-Natal
Active Member Count: 7
Allocation Start: 2024-07-18
Allocation End: 2025-01-30
Used Hours: 246546
Project Name: Chem Thermo
Project Shortname: CHEM1028
Discipline Name: Chemical Engineering

The Thermodynamics, Materials, and Separations Research Group at MUT focuses on phase separation and interactions between solids, liquids, and gases. This research is significant not only for advancing theoretical knowledge in physical chemistry and chemical physics but also for its applications in chemical engineering and environmental science. Currently, some of our efforts are directed toward environmental remediation, particularly the removal of organic pollutants from water. Recently published work has yielded insights into the rational design of molecularly imprinted polymers for biomedical applications. Our work relies heavily on the software licenses and high-performance computing resources provided by the CHPC to conduct density functional theory and atomistic molecular simulations. These computationally intensive methods would not be feasible without CHPC's facilities. We are making progress in understanding the interaction of polymers with pollutant molecules and applying multiscale modeling techniques to address challenges in chemical engineering.

Principal Investigator: Dr John Mack
Institution Name: Rhodes University
Active Member Count: 2
Allocation Start: 2024-07-18
Allocation End: 2025-02-12
Used Hours: 21179
Project Name: Rational design of phthalocyanine, porphyrin and BODIPY dyes
Project Shortname: CHEM0796
Discipline Name: Chemistry

The Institute for Nanotechnology Innovation (INI) at Rhodes University under director Prof. Tebello Nyokong carries out research related to the use of molecular dyes in biomedical applications, such as cancer treatment through photodynamic therapy, the use of antimicrobial photodynamic chemotherapy for treating hospital superbugs and as sensors for ions that are harmful to human health.

Other applications of interest include wastewater treatment and the development of optical limiters to protect human vision, such as in aviation safety in protecting pilots from the irresponsible use of laser pointers during runway approaches. It is important to understand trends in the electronic and optical properties that make the molecular dyes suitable for these particular applications. The resources of the Centre for High Performance computing help to facilitate this by making it possible to carry out molecular modelling calculations that can be used to predict how changes to the structures of the molecular dyes will modify their properties. The flexibility that CHPC provides where memory allocations are concerned is often vital.

The INI currently has three staff members, nineteen PhD, eight MSc and five 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 Cari van Schalkwyk
Institution Name: Stellenbosch University
Active Member Count: 11
Allocation Start: 2024-07-18
Allocation End: 2025-01-18
Used Hours: 27964
Project Name: South African Centre for Epidemiological Modelling and Analysis
Project Shortname: CBBI1106
Discipline Name: Other

The South African Centre for Epidemiological Modelling and Analysis (SACEMA) is an academic research centre within the Centre for Epidemic Response and Innovation (CERI), 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 Francois Engelbrecht
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2024-07-19
Allocation End: 2025-02-03
Used Hours: 6217987
Project Name: WITS Climate Modelling
Project Shortname: ERTH1200
Discipline Name: Earth Sciences

Making use of the allocation on the CHPC, the Wits Global Change Institute has made substantial progress with three major climate modelling experiments, each generating unique simulations on the Lengau cluster. Specifically: 1) We have generated the first ensemble of convective-permitting climate change simulations over the southwest Indian Ocean enabling the analysis of tropical cyclone landfall in Madagascar, Mozambique and Malawi. These high resolution simulations are the first of their kind to be generated over this region, using an African-based HPC facility. Previously we completed a reanalysis downscaling and present-day and future downscalings of two global climate models (GCMs). We have completed the present-day and future downscalings of another GCM and are currently downscaling a further two GCMs in this experiment. 2) We are generating projected climate change simulations over southern Africa, to analyse regional tipping points (Engelbrecht et al., 2024). We have completed the downscaling of one GCM, have made substantial progress in downscaling a further two GCMs, and ultimately plan to downscale a total of ten GCMs as part of this experiment. This is the biggest climate change modelling experiment ever undertaken in Africa, using an African-based HPC system. 3) We have generated simulations used in the first climate change attribution modelling experiment undertaken in Africa, for the devastating Durban floods of April 2022 (Engelbrecht et al., 2024; Under Review).

Principal Investigator: Prof Parvesh Singh
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2024-07-22
Allocation End: 2025-01-22
Used Hours: 4900
Project Name: Molecular dynamics and docking studies of organic compounds
Project Shortname: CHEM0795
Discipline Name: Chemistry

I am working as an Associate Professor in the School of Chemistry at UKZN. We are using different computer-based technologies (molecular docking, QSAR, molecular dynamcis and DFT) to predict novel chemical assemblies from the online databases. The identified lead molecules are synthesized in our organic laboratory and tested in vitro. All the computer simulations are performed on the CHPC cluster. The CHPC facility is an excellent platform that helps us as researchers in SA to run computer simulations and use the compiled data to substantiate our experimental results, which in turn enable us to publish our research in high-impact journals. Running these jobs on normal computers would have taken months to finish or would die in middle. With this supercomputing facility in our hand, we not only managed to run complex calculations but obtained constructive scientific explanations for our experimental results.

Principal Investigator: Prof Bettine van Vuuren
Institution Name: University of Johannesburg
Active Member Count: 4
Allocation Start: 2024-07-22
Allocation End: 2025-01-22
Used Hours: 103008
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.

We aim to investigate genetic patterns and structure in the context of environmental changes (e.g. climate change), to use 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: Prof Krishna Bisetty
Institution Name: Durban University of Technology
Active Member Count: 9
Allocation Start: 2024-07-22
Allocation End: 2025-01-22
Used Hours: 1223
Project Name: Computational Modelling & Bioanalytical Chemistry
Project Shortname: CHEM0820
Discipline Name: Chemistry

Durban University of Technology's Research Group Advances Smart Materials for Sensors and Biosensors

The "Computational Modelling and Bioanalytical Chemistry" research group at the Durban University of Technology (DUT) is making significant strides in the development of smart materials for sensors and biosensors, thanks to the support provided by the Centre for High-Performance Computing (CHPC).

Led by Professor K. Bisetty, the group employs a synergistic blend of experimental and computational techniques to explore smart biodevice platforms within the field of biosensor technology. The research group utilizes a diverse range of sensors to selectively detect analytes in specific environments, playing a crucial role in identifying the presence of target molecules.

To create biosensors, the team incorporates nanostructured electrode materials into electroactive smart matrices. These materials significantly enhance the sensor's performance and sensitivity. High-level computational tools are pivotal in their research, including:

Monte Carlo Simulations: Modeling statistical behavior to predict system properties such as adsorption of the adsorbate on the substrate material.
Molecular Docking: Analyzing the binding of molecules to specific active sites.
Density Functional Theory (DFT): Predicting electronic and spectroscopic behavior of materials.

Professor Bisetty commented, "Our research is at the forefront of developing innovative biosensor technologies that have the potential to revolutionize various fields, from healthcare to environmental monitoring. The support from CHPC has been instrumental in advancing our work."

The advancements made by the DUT research group underscore the importance of interdisciplinary collaboration and the integration of cutting-edge computational tools in scientific research. These developments hold promise for the future of smart materials and their applications in biosensor technology.

Principal Investigator: Prof Koop Lammertsma
Institution Name: University of Johannesburg
Active Member Count: 3
Allocation Start: 2024-07-23
Allocation End: 2025-01-23
Used Hours: 232294
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 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 two years of this project showing the feasibility of asymmetric epoxidation of olefins with a simple molybdenum catalyst and now also on asymmetric hydrogenation of ketones with a very simple ruthenium catalyst.

Principal Investigator: Dr Pritika Ramharack
Institution Name: Medical Research Council
Active Member Count: 14
Allocation Start: 2024-07-23
Allocation End: 2025-01-23
Used Hours: 321210
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.

Principal Investigator: Dr Sadhna Mathura
Institution Name: University of the Witwatersrand
Active Member Count: 4
Allocation Start: 2024-07-23
Allocation End: 2025-01-23
Used Hours: 51790
Project Name: Bioinorganic Chemistry Research Group (Wits)
Project Shortname: CHEM1633
Discipline Name: Chemistry

Bioinorganic research group (Wits) examines the function of metal ions in a biological context. This field has many themes. Our lab mainly focuses on therapeutic agents and drug discovery (e.g. anticancer drugs). A lot of this work depends on geometry and coordination. We use HPC to optimise metallodrug structures and to simulate characterisation information e.g. uv-vis. Publishable research will benefit the public (drug development).

Principal Investigator: Prof Phuti Ngoepe
Institution Name: University of Limpopo
Active Member Count: 26
Allocation Start: 2024-07-23
Allocation End: 2025-03-05
Used Hours: 5870888
Project Name: Computational Modelling of Materials: Energy Storage
Project Shortname: MATS0856
Discipline Name: Material Science

The Energy Storage Cluster (MATS0856 Project) 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 the development of solid electrolyte materials using multi-scale simulation approaches. The were progressive results from both DFT and molecular dynamics simulations. On the side of cathode materials, we have moved to a better space in terms of translating most our work in the lab for synthesis. There were new developments from Synchrotron Analysis which were carried out in the United Kingdom. These paved way for cycling tests of our cathode materials that will later be incorporated as battery components to be tested.
In this reporting period we successfully attended the Centre for High Performance Computing (CHPC) national conference at Boardwalk International Convention Centre, Gqeberha, 01-04 December 2024 to share, communicate and engage with other researchers on our research through poster presentations by the students (PhD, MSc and Honours). Furthermore, get updates on latest developments on computing resources for high performance computing. There was also attendance of the RAPDASA conference at the Boardwalk International Convention Centre, Gqeberha where members of the research group presented research papers.

Principal Investigator: Dr André Storm
Institution Name: University of the Witwatersrand
Active Member Count: 2
Allocation Start: 2024-07-24
Allocation End: 2025-01-31
Used Hours: 119823
Project Name: Pulverised coal research
Project Shortname: MECH1550
Discipline Name: Computational Mechanics

This research is completed by the University of the Witwatersrand, Mechanical, Industrial and Aeronautical Engineering, MECH1550: Pulverised coal research. Two undergraduate students used the CHPC in 2024 to do their research projects under my supervision. Both of them passed (one by distinction) and have graduated. - Powder Screw conveyor simulations were conducted by these students using DEM in Star CCM+. The main objective was to calibrate the simulation by also using an experimental model since certain variables in the simulation can't be measured accurately beforehand. Therefore, these variables need to be changed manually in an iterative process until the simulation is calibrated according to the output parameters: mass flow and angle of repose. The students were able to calibrate the simulation for a certain level within the bunker. However, it was discovered that these variables are changing as the bunker is being emptied and the level is reduced and re-calibration is required. Therefore, this project needs to be further investigated in 2025 by other Undergraduate students and a Masters student. - The grinding of coal in a ball and tube mill is being simulated by using the DEM in Star CCM+ by the other Masters student. The goal is to use DEM modelling as a design tool to develop a small scale ball and tube mill and comparing the results afterwards. It is envisaged that this student will graduate middle next year.

It is envisaged that in 2025 the CHPC will be used in the following ways: - Screw conveyor project to continue with two undergraduate students and a Masters student - Coal grinding by means of a ball and tube mill by a Masters student - Coal combustion and Heat transfer in a Package boiler by the principle investigator.

Principal Investigator: Prof Jonathan Peter
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2024-07-24
Allocation End: 2025-02-05
Used Hours: 15042
Project Name: UCT Allergy
Project Shortname: HEAL1699
Discipline Name: Health Sciences

Uncovering the Genetics Behind a Dangerous Drug Reaction in South Africans

Researchers from the University of Cape Town's Allergy and Immunology Unit, in collaboration with partners across South Africa and the United States, have made important strides in understanding a rare but serious side effect of common blood pressure medication. Their study explored why some people experience severe swelling—known as angioedema—after taking angiotensin-converting enzyme inhibitors (ACEIs), widely prescribed to treat high blood pressure and heart disease.

This swelling, especially of the face, tongue, and throat, can be life-threatening and disproportionately affects people of African ancestry. Yet until now, no large-scale genetic studies on this condition had been conducted in African populations. This groundbreaking study examined the genomes of over 700 South Africans, comparing those who had experienced angioedema while on ACEIs with those who had not.

Using the powerful computing resources of South Africa's Centre for High Performance Computing, the team conducted what is known as a genome-wide association study (GWAS). This approach scans the entire genome for tiny differences in DNA that might influence a person's risk. The study identified several genetic markers near key genes that could help explain the higher risk of angioedema among people of African descent.

While more research is needed to confirm these findings, this is a crucial step toward developing safer, more personalized medicine. It also highlights the importance of including African populations in genetic research, ensuring that the benefits of precision medicine reach everyone.

The project is progressing well, with further studies planned to better understand how these genetic factors work and to extend the research to other regions of Africa. This research not only improves drug safety but also contributes to global efforts to close gaps in health equity.

Principal Investigator: Dr Ruben Cloete
Institution Name: University of Western Cape
Active Member Count: 9
Allocation Start: 2024-07-24
Allocation End: 2025-01-24
Used Hours: 330725
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 and database development. 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. Recently his group is involved in building a comprehensive 3D structural database for the Ebola virus proteome that will be completed this year and hosted on the CHPC cloud infrastructure. Therefore, large scale computing resources are required to run large protein systems on the CHPC and access to the cloud infrastructure.

Principal Investigator: Prof Scott Hazelhurst
Institution Name: University of the Witwatersrand
Active Member Count: 6
Allocation Start: 2024-07-24
Allocation End: 2025-01-24
Used Hours: 51117
Project Name: Bioinformatics and Experimental Algorithms (BEAT)
Project Shortname: CBBI0930
Discipline Name: Bioinformatics

Project 1: Many computing jobs require multiple computer systems to fulfil the computational requirement systems of the jobs: parallel computing. Parallel computing is a difficult problem. Daniel Ohene-Kwofie a PhD student in the School of Electrical & Information Engineering at Wits. He investigates novel computer architectures to make parallel computing more efficient.

Project 2: Drug safety and efficacy is significantly affected by genomic diversity. This is particulary an issue in Africa because of the genomic diversity of Africa, and the fact that many drugs are not designed with African populations in mind. Blessing Sitabule is a PhD student at the Sydney Brenner Insitute for Molecular Bioscience at Wits. He has indentfied variants in key genes responsibe for metabolising drugs for hypertension and malaria. These genes produce proteins that interact with the drugs and the variants in the genomic sequence may affect the shape of the proteins and so how the body reacts to the drugs. Blessing uses computationally expensive modelling algorithms to determine how these variants found in African populations change how the proteins and drug interact.

Project 3: The gut microbiome of any animal has an important role in that animal's health. Almost nothing is known about the lion gut microbiome, especially those in the wild Wits MSc student Carl Belger has DNA samples from the bacteria and viruses in the gut of 20 lions. Ten of these have been sequenced using new DNA sequencing technology called Oxford Nanopore -- these data produced requires preprocessing using the GPUs such as those at the CHPC. GPUs are very powerful co-processors that can accelerate many processing tasks.

Principal Investigator: Dr Marilize Le Roes-Hill
Institution Name: Cape Peninsula University of Technology
Active Member Count: 2
Allocation Start: 2024-07-24
Allocation End: 2025-01-24
Used Hours: 2830
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 Lara Donaldson
Institution Name: 0 Other
Active Member Count: 3
Allocation Start: 2024-07-24
Allocation End: 2025-01-22
Used Hours: 2878
Project Name: Sorghum microbiome
Project Shortname: CBBI1700
Discipline Name: Environmental Sciences

The ICGEB is running a collaborative sorghum microbiome project with research groups accross the continent and in the process training scientists from the developing world, mainly Africa and including researchers from South African HDIs. We are trying to identify beneficial microbromes in the rhizosphere that can be used for sustainable agriculture solutions. To do this we are sequencing the microbiomes and using the HPC for data analysis. This is crucial for our work. The project is ongoing and progressing well. We expect to be able to have our first publication this year.

Principal Investigator: Dr Nicolette Chang
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 18
Allocation Start: 2024-07-26
Allocation End: 2025-02-14
Used Hours: 997297
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.

Principal Investigator: Dr Olivier Sheik Amamuddy
Institution Name: Rhodes University
Active Member Count: 3
Allocation Start: 2024-07-29
Allocation End: 2025-01-29
Used Hours: 313546
Project Name: Structural Bioinformatics and research for tool development
Project Shortname: CBBI1658
Discipline Name: Bioinformatics

Dr Olivier Sheik Amamuddy - a Structural Bioinformaticist - is a Principal Investigator at the Department of Biochemistry, Microbiology and Bioinformatics at Rhodes University, and his group apply high-performance computing at the CHPC to study the molecular dynamics of proteins of medical interest. Recent work from his PhD student revealed novel insights into the behaviour of a key protein associated with malaria drug resistance. His MSc student identified compounds with a potential for cancer treatment, in an under-explored site of a human protein. Our research depth and its progress are made possible by our access to the computational capacity of the CHPC.

Principal Investigator: Prof Amir H Mohammadi
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2024-07-30
Allocation End: 2024-08-06
Used Hours: 27580
Project Name: Development of a new catalyst for the production of green hydrogen
Project Shortname: MATS1552
Discipline Name: Material Science

We are a Thermodynamics and Reactor technology groups from University of KwaZulu-Natal under discipline of chemical engineering. We are very happy with CHPC facility. We do modelling of electro-catalyst development for the viable production of green hydrogen. This is in-line with national government plans to green energy future. This type of modelling requires high computational power, thus, we need CHPC facility. We are about to close this project as the student is doing final corrections on the marked PhD thesis. The corrections were suggested by the examiner. We hope CHPC get more funding to extend the capacity.

Principal Investigator: Mr Randall Paton
Institution Name: University of the Witwatersrand
Active Member Count: 5
Allocation Start: 2024-07-30
Allocation End: 2025-01-31
Used Hours: 390884
Project Name: Compressible Gas Dynamics
Project Shortname: MECH0847
Discipline Name: Other

The compressible flow research group makes use of the CHPC to model flows which govern many of the benefits we enjoy of modern life. These systems require high resolution, both spatially and temporally, to describe the physics at play. The greater understanding of these fundamental flows that results will allow for application in fields ranging from personalised health care to sustainable air transport. The group is now expanding on the traditional paradigm of computational fluid dynamics by leveraging these results with machine learning to develop more efficient ways of modelling flows based on high-quality training data. This will allow the benefits of high-performance computing to be more widely spread for the betterment of all.

Principal Investigator: Dr Caleb Kibet
Institution Name: International Centre of Insect Physiology and Ecology, Nairobi, Kenya
Active Member Count: 7
Allocation Start: 2024-07-30
Allocation End: 2025-01-30
Used Hours: 194268
Project Name: Insect Genomics
Project Shortname: CBBI1470
Discipline Name: Bioinformatics

Our research group at Pwani University, in collaboration with ICIPE, investigates chemosensory gene regulation in insect vectors like tsetse flies and mosquitoes. Using machine learning and high-performance computing (CHPC), we analyze large genomic datasets to understand olfaction, aiding in better vector management strategies. This project has supported two PhD students, three MSc students, and several interns, contributing to key research outputs, including optimizing nanopore polishing with machine learning.

Principal Investigator: Dr Bubacarr Bah
Institution Name: African Institute for Mathematical Sciences
Active Member Count: 6
Allocation Start: 2024-07-30
Allocation End: 2025-02-18
Used Hours: 32858
Project Name: Large Scale Computations in Data Science
Project Shortname: CSCI0972
Discipline Name: Applied and Computational Mathematics

The main work of this period is about developing a deep learning model that can identify gibbons through their call sounds. This would enable passive monitoring of these mammals. This work is one of the first to demonstrate that this approach works and in addition to identifying individual gibbons we can identify groups of individuals due to the sounds having group signatures. The manuscript on the outcome of this work is almost completed and will soon be submitted to an appropriate journal.

Principal Investigator: Dr Uljana Hesse
Institution Name: University of Western Cape
Active Member Count: 10
Allocation Start: 2024-08-01
Allocation End: 2025-02-01
Used Hours: 80496
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 analysis 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. It is known world-wide as a beverage - rooibos tea. Rooibos produces a diverse range of phenolic compounds that contribute to its health promoting properties (e.g. anti-diabetic, anti-aging and cardioprotective effects). The species comprises several growth types that differ in morphology, biochemical profiles and niche adaptation mechanisms, but only one growth form is used for large-scale commercial production of tea. Genomic information on interesting genes (stress tolerance, plant productivity, biosynthesis of industrially relevant compounds) can substantially facilitate plant breeding and bioprospecting.
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 have characterized diverse gene families, members of which are involved in the biosynthesis of phenolic compounds in rooibos. 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 native flora.

Principal Investigator: Dr Renée Prins
Institution Name: 0 Other
Active Member Count: 2
Allocation Start: 2024-08-01
Allocation End: 2025-02-01
Used Hours: 65000
Project Name: CenGen
Project Shortname: CBBI1615
Discipline Name: Bioinformatics

CenGen, a plant and pathogen R&D lab based in Worcester, is pioneering research in agricultural plant breeding and collaborative crop studies. As a DIPLOMICS partner, CenGen is tackling the complex task of de novo sequencing and assembly of indigenous plants, focusing on environmentally significant species like Spekboom. The team has successfully produced a high-quality draft genome assembly for Spekboom and draft assemblies for 22 additional species and developed a robust pipeline to support ongoing and future research.
These genomic resources pave the way for deeper biodiversity, genetics, and genome structure exploration. However, such research generates vast amounts of data—often exceeding 1 TB per species—far beyond current computing capacities. Without CHPC resources, processing this data would not be possible.
Beyond research, CenGen is committed to education. Through the Veldkos | Field food DNA Project, Grade 11 learners contributed to sequencing efforts, successfully producing a high-quality draft genome assembly of Carissa macrocarpa (Grootnoemnoem/Natal Plum). This initiative helps inspire and train the next generation of scientists.
CenGen's work underscores the crucial role of CHPC resources in driving scientific progress that benefits both research and society.

Principal Investigator: Dr Romina Henriques
Institution Name: University of Pretoria
Active Member Count: 8
Allocation Start: 2024-08-01
Allocation End: 2025-02-01
Used Hours: 416199
Project Name: Marine Genomics
Project Shortname: CBBI1661
Discipline Name: Bioinformatics

The Marine Genomics Group at University of Pretoria uses molecular data (DNA/RNA) to understand how the interplay between oceanographic features, fisheries and climate change influence the evolution of Southern African marine fishes. We are a diverse group of postgraduate students, postdocs and PIs, all focused on generating knowledge on commercially exploited fishes in Southern Africa, to assist with conservation and management actions, that ensure the long-term persistence of these important species. We currently have several projects on-going, on red roman, blacktail, the kobs, pyjama sharks, among others. As we generate Whole Genomes sequences for all these species, the CHPC is crucially important for our jobs, and greatly help us in achieving our research goals.

Principal Investigator: Prof Rebecca Garland
Institution Name: University of Pretoria
Active Member Count: 9
Allocation Start: 2024-08-01
Allocation End: 2025-03-03
Used Hours: 89071
Project Name: Air quality and atmospheric composition
Project Shortname: ERTH1484
Discipline Name: Earth Sciences

Global assessments estimate large impacts from exposure to poor air quality in many countries in Africa. However, these estimates have large uncertainties due to lack of information, which often stems from the lack of ground-based measurements. This lack of data impacts not only the understanding and quantification of air pollution levels and impacts, but also impacts on the understanding of climate as many air pollutants impact climate as short-lived climate forcing pollutants (SCLPs; e.g. particulate matter, ozone). Multiple platforms and data streams are useful in understanding and quantifying the spatial and temporal heterogeneity in air quality and atmospheric composition. In African cities this is especially important, not only due to the large heterogeneity in urban areas, but also due to the high costs of regulatory-grade instruments, resulting in a sparse network. However, there are now more data streams available to cities that help to understand and quantify air quality. This group investigates the application of satellite, low-cost sensors and modelling individually and together, to improve the understanding of urban air quality as well as regional atmospheric composition. CHPC resources are necessary due to the large size of these datasets and the analyses required to integrate them.

Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 7
Allocation Start: 2024-08-06
Allocation End: 2025-02-06
Used Hours: 153264
Project Name: Computational and statistical methodologies for human and environmental health prediction
Project Shortname: CBBI0818
Discipline Name: Bioinformatics

The group focuses on bioinformatics, computational & Genome Data Science and Artificial Intelligence approaches, and tool development pertinent to genomic diversity to uncover the role of genetic and environmental in determining the risk and susceptibility of communicable and non-communicable diseases, and drug responses. Members of the group are mainly from the University of Cape Town, and other African institutions within the Southern African regions. The PI is affiliated with the University of Kinshasa, D..R. Congo, and Northumbria University Newcastle. The groups CBBI1039, CBBI0818, and CBBI0818_2 have recently conducted an intensive analysis of human and microbial genome variation and developed and evaluated several approaches for multi-omics data integration for both the host and pathogen perspectives to facilitate the transformation of omics-driven clinical practice. The group has currently launched a major project to investigate for the next 3 years, a novel artificial intelligence approach for disease risk prediction and stratification. This project is a computational cost and demands long-term storage and critical resources for high-speed computer processes. The group will continue to benefit from valuable CHPC resources to implement this project. For example, with such CHPC resources and support, in the last three months, the group has finalised the development of JasMAP software, a joint ancestry and genetic association method, tailored to multi-way mixed ancestry populations to efficiently unravel gene underlying ethics differences in disease risk. Without such CHPC support and resources, the group will not be able to deliver such research. The CHPC resources have been a valuable, supportive, and helpful platform to effectively enhance my research group which heavily relies on large-scale sequence datasets and complex and memory cost pipelines. CHPC enabled us to not only sustain our research but also provide support to young, early, and middle-career researchers.

Principal Investigator: Prof Emile Rugamika CHIMUSA
Institution Name: University of Kinsasha
Active Member Count: 26
Allocation Start: 2024-08-06
Allocation End: 2025-02-08
Used Hours: 5597
Project Name: African Multi-Omics Data Science
Project Shortname: CBBI1039
Discipline Name: Bioinformatics

The group focuses on bioinformatics, computational & Genome Data Science and Artificial Intelligence approaches, and tool development pertinent to genomic diversity to uncover the role of genetic and environmental in determining the risk and susceptibility of communicable and non-communicable diseases, and drug responses. Members of the group are mainly from the University of Cape Town, and other African institutions within the Southern African regions. The PI is affiliated with the University of Kinshasa, D..R. Congo, and Northumbria University Newcastle. The groups CBBI1039, CBBI0818, and CBBI0818_2 have recently conducted an intensive analysis of human and microbial genome variation and developed and evaluated several approaches for multi-omics data integration for both the host and pathogen perspectives to facilitate the transformation of omics-driven clinical practice. The group has currently launched a major project to investigate for the next 3 years, a novel artificial intelligence approach for disease risk prediction and stratification. This project is a computational cost and demands long-term storage and critical resources for high-speed computer processes. The group will continue to benefit from valuable CHPC resources to implement this project. For example, with such CHPC resources and support, in the last three months, the group has finalised the development of JasMAP software, a joint ancestry and genetic association method, tailored to multi-way mixed ancestry populations to efficiently unravel gene underlying ethics differences in disease risk. Without such CHPC support and resources, the group will not be able to deliver such research. The CHPC resources have been a valuable, supportive, and helpful platform to effectively enhance my research group which heavily relies on large-scale sequence datasets and complex and memory cost pipelines. CHPC enabled us to not only sustain our research but also provide support to young, early, and middle-career researchers.

Principal Investigator: Dr Fortunate Mokoena
Institution Name: North-West University
Active Member Count: 4
Allocation Start: 2024-08-06
Allocation End: 2025-02-06
Used Hours: 20787
Project Name: Protozoan parasites and cancer drug discovery
Project Shortname: CBBI1293
Discipline Name: Bioinformatics

Our work is developing new compounds to be used as potential antimalarial agents. We use compounds from various libraries and a protein receptor to conduct molecular docking and molecular dynamic simulations
to support our predictions. Following this, we validate the predictions using biochemical experiments.

Principal Investigator: Prof Sharon Prince
Institution Name: University of Cape Town
Active Member Count: 2
Allocation Start: 2024-08-06
Allocation End: 2025-01-28
Used Hours: 3367
Project Name: The investigation of small molecule interactions with TBX2/TBX3 transcription factors
Project Shortname: HEAL1643
Discipline Name: Health Sciences

The Prince Cancer Laboratory at UCT has shown that the TBX2/3 transcription factors play an important role in cancer progression and prevention. To this end, we have investigated the interplay of these transcription factors with various proteins and drug candidates and have recently shown that a drug currently used for tapeworm infections, niclosamide, directly interacts with TBX3 and possesses potent anticancer activity. To better understand this relationship, we used molecular docking software subscribed to by the CHPC to investigate the drug-TBX3 interactions. Our current results will be used to inform our future synthesis campaigns. By targeting TBX3, we can find selective cancer treatments that pose fewer adverse effects.
This project will now expand to other drug candidates and TBX3-protein interactions.

Principal Investigator: Prof Robyn van Zyl
Institution Name: University of the Witwatersrand
Active Member Count: 4
Allocation Start: 2024-08-06
Allocation End: 2025-01-28
Used Hours: 16269
Project Name: Targeting Protozoal Infections
Project Shortname: HEAL1398
Discipline Name: Health Sciences

Climate warming has highlighted the need for continued research into diseases which are influenced by temperature increases. Climate warming has allowed Anopheles species not normally found in South Africa to be documented within our borders. These changes can increase the spread of malaria and increase the number of infections. This has highlighted the need for alternative preventative and treatment measures to ensure the population in Africa are protected against malaria. To tackle this a two pronged approach has been undertaken by researchers at WITS Research Institute for Malaria (WRIM) and the WITS Pharmacology Division lead by Professor Robyn van Zyl, by targeting both the malaria parasite and Anopheles mosquito. Firstly, compounds with a similar structure and target as atovaquone, a highly effective preventative antimalarial drug, have been evaluated in silico to identify lead compounds for further investigation using the CHPC facilitated platform to access Schrondiger drug docking programme. This has lead to the design and in silico evaluation of new novel compounds against atovaquone-sensitive and -resistant targets with improved efficacy, with in vitro efficacy still to be tested. Similarly, plant-derived compounds have been evaluated in silico against the olifactory sensors in Anopheles to investigate their potential as repellents that may be more effective than citronella or DEET. The potential efficacy of the latter compounds need to be verified when used by human volunteers, but show initial promising. The search for new and novel compounds targeting Plasmodium malaria and Anopheles mosquitoes should continue as resistant strains are being reported worldwide and alternative therapies are required to protect our communities.

Principal Investigator: Prof Amir H Mohammadi
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2024-08-06
Allocation End: 2025-01-28
Used Hours: 2904966
Project Name: Development of a new catalyst for the production of green hydrogen
Project Shortname: MATS1552
Discipline Name: Material Science

We are a Thermodynamics and Reactor technology groups from University of KwaZulu-Natal under discipline of chemical engineering. We are very happy with CHPC facility. We do modelling of electro-catalyst development for the viable production of green hydrogen. This is in-line with national government plans to green energy future. This type of modelling requires high computational power, thus, we need CHPC facility. We are about to close this project as the student is doing final corrections on the marked PhD thesis. The corrections were suggested by the examiner. We hope CHPC get more funding to extend the capacity and to resolve current issues on Material Studio.

Principal Investigator: Mr Asad Jeewa
Institution Name: University of KwaZulu-Natal
Active Member Count: 4
Allocation Start: 2024-08-07
Allocation End: 2025-02-20
Used Hours: 32602
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, but has already graduated Honours students and will soon graduate published MSc students. We expect further growth in 2025, elcoming new MSc and Honours students.

Principal Investigator: Prof Marelie Davel
Institution Name: North-West University
Active Member Count: 8
Allocation Start: 2024-08-07
Allocation End: 2025-02-19
Used Hours: 23786
Project Name: DNN Analysis
Project Shortname: CSCI1191
Discipline Name: Computer Science

MUST Deep Learning is a research niche area that studies the theory and application of deep learning. Deep learning is a family of machine learning techniques (originally inspired by the idea of artificial neural networks) that nowadays consist of large, complex, layered models that excel at solving 'human-like' tasks. It is one of the core technologies driving current innovation in Artificial Intelligence.

MUST is a technology-focused group: by growing skills and expertise within a narrow technology focus, it produces researchers that solve complex tasks across a variety of domains. Applications are developed with domain partners from industry and government. Current application domains include speech and language modelling, space weather modelling, and industrial applications of deep learning (for example, airfoil design, telecommunications, and intelligent transport systems). Current theoretical work focuses on generalisation in deep learning and interpretability of deep learning models.

The MUST research group slots into larger collaborative initiatives such as the Centre for Artificial Intelligence Research (CAIR) and the current NITheCS, coordinating a research programme in each. It forms the CAIR Deep Learning node, and coordinates the 'Machine learning in support of theoretical and computational sciences' research programme in NITheCS. MUST regularly participates in national and international conferences, including prestigious conferences such as the Association for the Advancement of Artificial Intelligence (AAAI) Conference on Artificial Intelligence, and the International Joint Conference on Artificial Intelligence (IJCAI). The group has a distributed model: research activities include student labs in Potchefstroom, linking with remote students nationally, as well as a satellite research office in the Western Cape.

Principal Investigator: Prof SANTHOSH KUMAR KUTTAN PILLAI
Institution Name: Durban University of Technology
Active Member Count: 7
Allocation Start: 2024-08-08
Allocation End: 2025-02-28
Used Hours: 26170
Project Name: Environmental Pollutants
Project Shortname: CBBI1646
Discipline Name: Bioinformatics

In a world where biotechnology drives innovation, the research group led by Prof. Santhosh Pillai at the Durban University of Technology is making significant strides in enzyme technology. The team is focused on various microbial enzymes such as carbohydrases and proteases, including cellulases, xylanases, keratinases, collagenases and fibrinolytic enzymes, alongside a wide array of peptides and their practical applications. The research also extends to the valorization of biomass to value added products in a sustainable manner using microbial fermentation and enzyme systems. The significance of this work lies in its potential to revolutionize multiple industries. Proteases and peptides, the current focus of the group, have far-reaching applications. For instance, they are vital in managing poultry waste, enhancing the cosmetic and textile industries, and advancing medical and food technologies. By developing a deeper understanding of these biomolecules, the research aims to create innovative solutions that can be applied across diverse sectors. The group's research is greatly supported by the computational resources provided by the Centre for High-Performance Computing (CHPC). Alongside conventional methods, the team utilizes advanced detection techniques and molecular simulation studies, which are made feasible by CHPC's free access. This support is crucial in pushing the boundaries of scientific exploration, allowing the team to delve deeper into the complexities of enzyme technology. Currently, the CHPC resources are being employed for degradation studies and the microbial analysis of various environmental sources. These studies are crucial for detecting and identifying microbial diversity, further enhancing our understanding of microbial processes and their applications in Environmental biotechnology. As the research progresses, the team is confident that their work will significantly advance scientific knowledge, providing new insights and solutions that could benefit a broad range of industries and contribute to environmental sustainability.

Principal Investigator: Prof MESFIN ABAYNEH KEBEDE
Institution Name: University of South Africa
Active Member Count: 7
Allocation Start: 2024-08-12
Allocation End: 2025-02-12
Used Hours: 67029
Project Name: Electrode materials for energy storage systems
Project Shortname: MATS0855
Discipline Name: Material Science

Electrode materials for energy storage systems is a research program which focuses on modeling of electrode materials for energy storage systems such as lithium-ion battery, sodium ion battery, supercapacitors, etc. We will study the electrode materials structural, mechanical, thermal and electrochemical properties. Currently the program comprises of postdocs, PhD students in my supervision and myself as PI. The program has a plan to include more postgraduate students in future. I am based in University of South Africa and my research group consists of Postdocs and PhD students. I also co-supervise PhD students from other Universities through collaborative projects.
In the research program we simulate computationally the structural and visualization of the materials and use for the supporting the experimental research works.
The CHPC resource helps us to get comprehensive data both computationally and experimentally which results in the publication on high impact journal.
The project is progressing in a promising direction, at this moment there are manuscripts being ready for submission for publication.

Principal Investigator: Dr Sphelele Sosibo
Institution Name: North-West University
Active Member Count: 8
Allocation Start: 2024-08-12
Allocation End: 2025-02-12
Used Hours: 12414
Project Name: Molecular Dynamics of target enzymes
Project Shortname: HEAL1414
Discipline Name: Chemistry

The Computational and Medicinal Chemistry Research Group at NWU utilises computer software in the CHPC to predict protein-ligand interactions as a means of drug discovery. Computational chemistry offers a valuable alternative by enabling the study of chemical entities without the need for physical chemicals. This approach reduces the reliance on in vitro and in vivo experiments, ultimately accelerating research.

We are leveraging the CHPC's parallel computing facilities to scale up projects initially developed on personal computers. Our work utilizing CHPC resources has already led to successful publications.

The CHPC services are highly regarded by students, and we anticipate that the majority of our ongoing research will result in published work.

Principal Investigator: Dr ADEDAPO ADEYINKA
Institution Name: University of Johannesburg
Active Member Count: 12
Allocation Start: 2024-08-12
Allocation End: 2025-03-12
Used Hours: 572097
Project Name: Computational Design of Molecules
Project Shortname: CHEM1221
Discipline Name: Chemistry

The Computational Design of Molecules Research Group is located within the Department of Chemical Sciences at the University of Johannesburg. We aim to design and investigate new or improved molecules, compounds 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 High­Performance 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: Prof Gerard Tromp
Institution Name: Stellenbosch University
Active Member Count: 9
Allocation Start: 2024-08-13
Allocation End: 2025-02-13
Used Hours: 20915
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 Ndumiso Mhlongo
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2024-08-14
Allocation End: 2025-02-18
Used Hours: 75349
Project Name: Biomolecular Modelling Research Unit
Project Shortname: HEAL1002
Discipline Name: Health Sciences

Biomolecular Modelling Research Unit is located at the University of KwaZulu-Natal, Howard College Campus and headed by Dr Ndumiso N. Mhlongo. This research group perfoms molecular modelling simulations to study dynamic properties of macro-molecules such as protein folding and allosteric regulations; ligand-receptor interactions; atom-to-atom interactions; protein-protein interaction;virtual screening and molecular docking of molecules to understand their structure and function for the design and development of inhibitors against drug targets in diseases. Through the use of CHPC resources, we have designed potential inhibitors against M. tuberculosis and cancer treatment. These have made contributions to discovery new inhibitors & new knowledge which could directly translate into real health benefits of the society.

Principal Investigator: Mr Mokgerwa Monama
Institution Name: University of Limpopo
Active Member Count: 2
Allocation Start: 2024-08-14
Allocation End: 2025-02-14
Used Hours: 266795
Project Name: Application of Bioinformatics Towards Drug Discovery
Project Shortname: CBBI1665
Discipline Name: Bioinformatics

As a bioinformatics researcher based at the University of Limpopo Department of Biochemistry, Micorbiology and Biotechnology (BMBT), I am amazed and excited to receive immense and dedicated support from the CHPC. Our current research focus lies in discovering potential drugs and combating antimicrobial resistance, particularly given the recent prevalence of extremely resistant strains. With the CHPC's generosity, we are able to train future scientists who might one day solve some of these urgent problems. With that said, we have been able to utilize the comprehensible computational resources to allow students to learn about Linux-based High-Performance Computing (HPC) systems that make use of command-line programs to generate insightful biological data. Thanks to the students' eagerness to learn, their determination, and hard work, they will be graduating in 2025 with their Honours degrees. We are very proud and look forward to seeing their future achievements.

Principal Investigator: Dr Lonnie van Zyl
Institution Name: University of Western Cape
Active Member Count: 2
Allocation Start: 2024-08-14
Allocation End: 2025-02-14
Used Hours: 5318
Project Name: Engineering bacterial pyruvate decarboxylase for increased thermostability
Project Shortname: CBBI1265
Discipline Name: Bioinformatics

As part of the 1KSA programme (https://www.1ksa.org.za/), the microbial biobank hosted by the Institute for Microbial Biotechnology and Metagenomics (IMBM) at the University of the Western Cape has committed to determining the genome sequence of 500 bacteria from their collection. As of December 2024, IMBM have sequenced 470 genomes from their collection which represents an important, growing resource for South African researchers to tap into. Early 2025 should see completion of IMBM's contribution to 1KSA, however the biobank will continue to grow with the inclusion of bacterial isolates from several research labs across South Africa. Those interested in more information about the biobank, how to request strains and/or genomic information can contact Dr. Anita Burger (alburger@uwc.ac.za; 0219592083), Ms. Stephanie Lawrence (slawrence@uwc.ac.za; 0219592460) or Dr. Lonnie van Zyl (lvanzyl@uwc.ac.za; Tel: 0219592325).

Principal Investigator: Mr Adebayo Azeez Adeniyi
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2024-08-14
Allocation End: 2025-02-18
Used Hours: 141049
Project Name: Drug Discovery Research Using Quantum and Molecular Dynamic Simulation
Project Shortname: CHEM0958
Discipline Name: Chemistry

This report summarizes our research progress, highlighting the crucial role of South Africa's CHPC resources in our recent achievements.
Since our last update, we've made significant strides, culminating in the publication of two new articles. These publications underscore the direct impact of South Africa's CHPC environment on our expanding research portfolio.
CHPC support has been transformative, allowing us to broaden our research focus. We've successfully integrated machine learning and deep neural networks into our work, alongside explorations in vaccine development, photochemistry, and polymer chemistry. These new areas complement our ongoing research in drug development and the electrochemical properties of small molecules, demonstrating our commitment to addressing real-world challenges.
Access to South Africa's CHPC resources has been essential for these advancements. The parallel computing capabilities have significantly accelerated our research timelines and enabled us to tackle more complex problems. Specifically, we've leveraged these resources for:
• Bioinformatics: Analyzing large datasets related to vaccine development and drug discovery.
• Quantum Computing: Performing high-level calculations to understand the chemical and spectroscopic properties of small molecules, validating experimental results and guiding further research. We've utilized packages like Gaussian, Orca, GAMESS, and NewChem extensively.
• Molecular Dynamics Simulations: Modeling the behaviour of complex molecular systems using GROMACS, Amber, and LAMMPS, providing insights into molecular interactions and dynamics.
A key aspect of our research methodology is theoretical modelling. South Africa's CHPC resources have been invaluable, allowing us to perform the computationally intensive simulations necessary to gain deeper insights and design effective experimental strategies.
The availability of CHPC resources has accelerated our research and enabled us to pursue new and impactful research directions. Without their support, our recent publications and overall progress would not have been possible. We are deeply grateful for the access to these critical resources and the excellent technical support provided by CHPC.
Looking forward, we plan to continue leveraging CHPC resources to further our research in drug design. We are confident that with continued access to these resources, we will be able to make significant contributions to drug design and vaccine development.

Principal Investigator: Dr Albert Aniagyei
Institution Name: University of Health and Allied Sciences, Ghana
Active Member Count: 1
Allocation Start: 2024-08-14
Allocation End: 2025-02-18
Used Hours: 1929
Project Name: Hydroxylation and Epoxidation Reaction by High Valent metal oxo complexes
Project Shortname: CHEM1610
Discipline Name: Chemistry

The Aniagyei Research Group is in the Department of Basic Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana.

To address the fundamental issues of molecular structure, function, interaction, and design, my research interests are primarily in the application of quantum mechanical simulation techniques to model chemical systems at the atomic and electronic levels, such as mechanistic and structural questions in organic, inorganic, organometallic, and materials chemistry.

The oxo complexes of high valent metal oxo complexes are of great interest for their potential toward epoxidation and dihydroxylation. The application of such reagents in chemical synthesis has spurred considerable interest in the underlying activation mechanisms.
Although the broad mechanistic framework for the addition of metal-oxo complexes is known, most of the key steps remain unresolved. A mechanistic understanding of catalytic reactions is crucial for designing new catalysts and modes of reactivity and developing greener and more sustainable chemical processes.
To elucidate the mechanism of metal oxo addition to olefinic bonds, one requires the use of computers to calculate and predict the energy of atoms and molecules to understand the behaviour and structure of materials and molecules.

However, the accuracy required to do such calculations goes beyond the power of your laptop. Therefore, simulations must be carried out within the quantum mechanics in highly efficient software such as Gaussian and Quantum Espresso and large-scale HPC machines provided for CHPC.

The project seeks to develop a new highly efficient catalyst system that characterizes epoxidation and dihydroxylation reactions

Principal Investigator: Prof Eric van Steen
Institution Name: University of Cape Town
Active Member Count: 6
Allocation Start: 2024-08-14
Allocation End: 2025-03-19
Used Hours: 121855
Project Name: Lateral interactions on surfaces
Project Shortname: CHEM0780
Discipline Name: Chemistry

Hydrogen is the fuel of the future, but it cannot be stored easily as it requires either low temperatures or high pressures. However, it can be converted into a high-density energy carrier, such as diesel or kerosene, through its catalytic conversion with the greenhouse gas CO2. The latter may be obtained from difficult to decarbonize sources such as the cement manufacturing process or even waste.

The optimal catalyst(s) for the conversion of hydrogen into storable liquid fuels, typically comprises of an active metal, a support and promoters. Hydrogen and CO2 adsorb on the active metal and react further in multiple reaction steps. The support and promoters affect these reactions, and the interaction between the support/promoters, active metal and adsobed species is investigated using high performance computing, so that novel, more efficient catalysts can be developed.

Principal Investigator: Dr Chris Oosthuizen
Institution Name: University of Cape Town
Active Member Count: 3
Allocation Start: 2024-08-15
Allocation End: 2025-03-13
Used Hours: 27341
Project Name: Bayesian Integrated Population Modelling of Southern Elephant Seals
Project Shortname: CBBI1533
Discipline Name: Environmental Sciences

Tagen de Wet, a research Masters student in Statistical Sciences at the University of Cape Town, used the HPC cluster to train and fine-tune hyperparameters for various deep-learning models, particularly image classification and object detection models. The HPC was instrumental in training models for analyzing penguin-borne video data, specifically in tasks such as penguin head tracking, penguin detection, krill classification, and surface event classification. His work aims to streamline penguin video analysis, reducing the manual effort required to annotate the data.
This research is part of a broader effort to enhance the analysis of bio-logging data collected from foraging penguins. While these biologgers valuable movement and location data, video loggers offer direct visual confirmation of behaviors such as prey capture and social interactions, as well as environmental information. By automating video analysis, Tagen's work aims to reduce the bottleneck in this research and provide a more complete picture of penguin foraging ecology.
Beyond hyperparameter tuning, the HPC allowed for large-scale experimentation with different model architectures, optimizing trade-offs between accuracy and computational efficiency. Tagen also explored methods for handling challenging underwater video conditions, such as fluctuating lighting and occlusions. The computational power of the HPC was crucial for comparing data augmentation techniques, improving model robustness, and ensuring reliable detection in real-world scenarios. Tagen is in the final months of his MSc and expects to graduate soon.

Principal Investigator: Dr Brigitte Glanzmann
Institution Name: Stellenbosch University
Active Member Count: 18
Allocation Start: 2024-08-16
Allocation End: 2025-02-16
Used Hours: 155466
Project Name: SAMRC Precision Medicine African Genomics Centre
Project Shortname: CBBI1195
Discipline Name: Bioinformatics

The SAMRC Genomics Platform was established in July 2019 through a partnership between the SAMRC and the Beijing Genomics Institute (BGI) to provide next generation sequencing (NGS) to African scientists. The SAMRC's investment to establish one of the first African genomics sequencing facilities was well timed with global funding initiatives to promote African genomics, guidelines incorporating NGS into routine diagnostics and the acceleration of precision medicine. The SAMRC Genomics Platform is a purpose-built NGS facility consisting of multiple laboratories capable of generating large "omics" datasets. It is situated on the first floor of the SAMRC NIVS building on the Tygerberg Hospital Campus.

The SAMRC Genomics Platform operates in two distinct, but interconnected arms. The first arm is the service delivery arm which will be responsible for providing NGS services to paying clients. The second arm is the research arm, which generates independent and collaborative research outputs and builds NGS capacity in South Africa. We currently support infrastructure for short- and long read NGS from MGI and Oxford Nanopore Technologies.

Principal Investigator: Mr Ernest Opoku
Institution Name: Nesvard Institute of Molecular Sciences, Ghana
Active Member Count: 15
Allocation Start: 2024-08-16
Allocation End: 2025-02-18
Used Hours: 93796
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: Dr Adeola Rotimi
Institution Name: Agricultural Research Council
Active Member Count: 7
Allocation Start: 2024-08-19
Allocation End: 2025-02-19
Used Hours: 11184
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: Dr Kshitij Thorat
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2024-08-19
Allocation End: 2025-02-17
Used Hours: 184280
Project Name: An AI-and-Simulations driven exploration of Extragalactic Radio Sources
Project Shortname: ASTR1707
Discipline Name: Astrophysics

This project is aimed at simulating jets shot by very massive black holes which are found in the centres of galaxies. These objects are called "radio galaxies". These jets shine in radio wave electromagnetic waves which can be "seen" by radio telescopes like the South African built MeerKAT radio telescope. These jets can extend for millions of light years and therefore the astrophysics behind them requires detailed simulation-based modelling. The astronomy group based in the University of Pretoria has been investigating some of the more peculiar cases of such astrophysical jets. The project is led by MSc student Tumisho Gabanangata, who will be simulating X-shaped radio galaxies, which form some of the most unusual cases of radio galaxy jets and these sources have been among the most spectacular images made by the MeerKAT telescope. These simulations ensure the physics behind the observations made by radio telescopes is well understood. The project has already made impressive progress and is expected to lead to publications.

Principal Investigator: Dr Patricia Swart
Institution Name: 0 Other
Active Member Count: 6
Allocation Start: 2024-08-21
Allocation End: 2025-02-21
Used Hours: 100547
Project Name: DIPLOMICS_CLARITY
Project Shortname: CBBI1617
Discipline Name: Bioinformatics

Scientists are becoming more and more aware that the analysis, transfer, storage and management of omics data requires specific skills, knowledge and infrastructure; and actually this usually makes up a substantial proportion of an omics-related project, in terms of time and resources. This is increasing the need for bioinformaticians and the required infrastructure and researchers are now slowly starting to factor in those costs (both people time and infrastructure, e.g. data storage costs) into their project budgets. This is a welcome change. CLARITY, made possible by DIPLOMICS, along with the CHPC has been able promote the importance of bioinformatics and provide part-time job opportunities to those with bioinformatics expertise.

Principal Investigator: Dr Rian Pierneef
Institution Name: University of Pretoria
Active Member Count: 33
Allocation Start: 2024-08-21
Allocation End: 2025-02-21
Used Hours: 267660
Project Name: Bioinformatic and Computational Biology analyses of organisms
Project Shortname: CBBI1124
Discipline Name: Bioinformatics

The Bioinformatic and Computational Biology analyses of organisms programme is primarily based at the University of Pretoria with Dr Rian Pierneef the principal investigator. The programme is active in diverse and multi-disciplinary research projects and relies heavily on the CHPC as primary provider of computational resources. The programme aims to build human capacity in the field of bioinformatics and computational biology and empower the scientific leaders of tomorrow with the required competencies. Research endeavors span human, plant, animal, and environmental research topics and the programme prides itself in the continuous growth and expansion, all made possible due to access to the CHPC.

Principal Investigator: Dr Shane Murray
Institution Name: 0 Other
Active Member Count: 8
Allocation Start: 2024-08-22
Allocation End: 2025-02-22
Used Hours: 91928
Project Name: DIPLOMICS 1KSA
Project Shortname: CBBI1622
Discipline Name: Bioinformatics

The 1KSA Project, a DIPLOMICS initiative, aims to sequence the genomes of over 1000 South African species. South Africa's biodiversity belongs to her and her people. Therefore, this biodiversity project is fully conducted in South Africa - from sample collection, genome sequencing to data storage - from start to finish. The NICIS infrastructure makes this possible. 1KSA can transfer data to and from the CHPC cluster, assemble genomes, and then securely store the data in country. Assembled genomes are published on the 1KSA website in the form of a species card (www.1ksa.org.za). Project documentation, methods and workflows are also available on Zenodo in the spirit of open science. To date, 48 species cards have been published on the website, along with videos from the sample contributors about the importance of their research and the 1KSA project.

Principal Investigator: Prof Ken Craig
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2024-08-22
Allocation End: 2025-02-28
Used Hours: 59317
Project Name: CFD modelling of falling-film bioreactors
Project Shortname: MECH1001
Discipline Name: Computational Mechanics

Falling-film bioreactors have many applications that include algae grown for animal feed or for use as biofuels as a sustainable alternative to fossil-based fuels. In addition, produced algae can also be used in the production of pharmaceuticals, nutraceuticals, cosmetics and in the aquaculture industry. A key limitation to the efficient production of algae in falling films is the absorption of carbon dioxide into the film layer, requiring enhancement techniques to increase production. This is typically done using structured surfaces. As a method of studying the performance of falling-film bioreactors, Computational Fluid Dynamics (CFD) incorporating the Volume of Fluid (VOF) method to capture the gas-liquid interface, is used to quantify film thickness, waviness, and the mass transfer of CO2 into the film. The research is carried out in the Department of Mechanical and Aeronautical Engineering at the University of Pretoria. The CFD work is coordinated by Prof Ken Craig while the experimental part of the research is led by Dr Bradley Bock. The focus of the work is to develop validated simulation techniques of falling films that can be used for the optimal design of falling-film applications. Initially, the CFD models are validated against experimental data from literature. As part of the collaboration, there is the development of experimental measurement techniques to estimate film thickness, gas absorption, etc., activities that are crucial in supporting the simulation effort. Because of the computationally resource-intensive nature of the VOF technique, the resources of the CHPC are critical to the success of this programme.

Principal Investigator: Dr Ernest Odhiambo
Institution Name: University of Nairobi
Active Member Count: 1
Allocation Start: 2024-08-22
Allocation End: 2025-02-28
Used Hours: 4105
Project Name: Computational Modeling of Heat Containment Systems
Project Shortname: MECH1178
Discipline Name: Computational Mechanics

The MECH 1178 research programme is currently championed by Ernest Odhiambo and Peter Odhiambo. The main focus of this research is the modeling of a novel wind turbine known as the magnus lift wind turbine. What distinguishes this wind turbine from the classical type is the fact that rotating cylinders rather than aerofoil blades are used. Given the nature of the assembly, that is cylinders rotating about their axes and then the resulting lift forces forcing the whole assembly to rotate, it proved quite challenging to get us to the stage where the whole assembly is know responding to wind forces, thanks to the use of the LENGAU CHPC. The cluster made it possible to get results faster and shorten the whole process of fine tuning the driving code. The project is useful because we can now model effectively wind turbines where the wind speeds are significantly low. The project is at 70% completion.

Principal Investigator: Prof Craig Law
Institution Name: University of the Witwatersrand
Active Member Count: 7
Allocation Start: 2024-08-23
Allocation End: 2025-02-28
Used Hours: 490385
Project Name: Aerothermodynamics with vortices, vorticity and shear
Project Shortname: MECH1532
Discipline Name: Other

The scope of the Aerodynamic investigations of vortices and vorticity has grown to include a number of projects which have produced some very interesting pictures. We are currently working on trying to better understand what these pictures are telling us so that we can design better rocket engines, more stable supersonic aircraft and insect like drones in the near future.

The contribution of the CHPC is critical to helping us understand our experimental results and improve our understanding of what the flow field does and how we can manipulate it to build better rockets, planes and drones. We want to extend this work to look at birds in flight as well, so that we can learn from nature and ensure a greener future for aviation.

Principal Investigator: Prof Liliana Mammino
Institution Name: University of Venda
Active Member Count: 4
Allocation Start: 2024-08-23
Allocation End: 2025-02-25
Used Hours: 19111
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 molecules, which were isolated from plants used in traditional medicine and have proven to be promising for the treatment or prevention of diseases.
We choose these molecules because they are ideal for the development of more powerful drugs for the treatment of the same disease, because traditional medicine has already proved that they are able to reach "the right place" within the body, where their activity can be effective.

WHY IT IS INTERESTING TO STUDY MOLECULES COMPUTATIONALLY
The biological activity of a substance depends on the properties of its molecules. Computational studies provide information about the properties of a molecule. This helps understand the chemical behaviour of the molecule, including its pharmaceutical activity.
For instance, we have studied a certain number of molecules pertaining to the same class (called acylphloroglucinols) and having anticancer activity and have compared their properties. Then, we have studied how each of them can interact with some proteins that are important for a cancer to grow, and block their functions. Blocking their functions means that the cancer cannot continue growing or spreading. We have compared the ways and strength with which each molecule interacts with that protein and identified the more effective ones.

WHY USING THE CHPC IS ESSENTIAL FOR US
The calculation of the properties of molecules is very demanding in terms of computer power. Using the CHPC enables us to obtain results in a reasonable time. Using it is therefore essential for us to conduct our research efficiently.

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: Dr Johannes Pretorius
Institution Name: Stellenbosch University
Active Member Count: 1
Allocation Start: 2024-08-26
Allocation End: 2025-02-28
Used Hours: 104275
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 three research topics: The performance of natural draft direct dry cooling systems (NDDDCS), the performance of forced draft cooling systems for supercritical carbon-dioxide (sCO2) applications and the optimization of a heat exchanger for the NDDDCS. We do this by one-dimensional (1D) calculation, three-dimensional (3D) Computational Fluid Dynamics (CFD) simulations, or co-simulations where we link the 1D codes to the 3D CFD for simultaneous simulation.
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 and unsteady 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 in the final stages of our simulations on this topic. In a related topic, we have simulated various configurations of a finned-tube heat exchanger using 3D CFD in order to optimize its design, specifically for its use in a NDDDCS. From these simulations, we have produced a reduced-order model. This study has recently been completed.
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. This study has recently been completed.

Principal Investigator: Prof Kevin Naidoo
Institution Name: University of Cape Town
Active Member Count: 13
Allocation Start: 2024-08-23
Allocation End: 2025-04-09
Used Hours: 1012057
Project Name: Reaction Dynamics of Complex Systems
Project Shortname: CHEM0840
Discipline Name: Chemistry

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 Mahmoud soliman
Institution Name: University of KwaZulu-Natal
Active Member Count: 35
Allocation Start: 2024-08-27
Allocation End: 2024-08-30
Used Hours: 33562
Project Name: Drug Design, development and modelling
Project Shortname: HEAL0790
Discipline Name: Health Sciences

The research scope of Molecular Bio-Computation and Drug Design Laboratory (http://soliman.ukzn.ac.za/) 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. In my research group (http://soliman.ukzn.ac.za/) we rely extensively on the computational support from CHPC for the last 13 years. With such amazing support from CHPC, the lab has successfully grown significantly and manged to publish more than 350 publications in high impact factor journal with more than 100 student graduations. The impact of CHPC on developing research and human capacity as evident from research publications and student graduations is commended and highly appreciated.

Principal Investigator: Prof Rajshekhar Karpoormath
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2024-08-27
Allocation End: 2025-02-27
Used Hours: 111430
Project Name: Design of small novel organic compounds as potential drug candidates
Project Shortname: HEAL0835
Discipline Name: Health Sciences

SMCRG at UKZN: Advancing Drug Discovery Under Prof. Rajshekhar Karpoormath's Leadership
The Synthetic and Medicinal Chemistry Research Group (SMCRG) at the University of KwaZulu-Natal (UKZN), led by Professor Rajshekhar Karpoormath, continues to make valuable contributions to drug discovery and medicinal chemistry. Established in 2014, SMCRG has emerged as a premier research group dedicated to developing novel therapeutic agents targeting infectious diseases, including tuberculosis (TB) and other global health threats.
Under Prof. Karpoormath's leadership, the group has secured significant funding, including a prestigious grant from the Bill and Melinda Gates Foundation in 2023(Co-PI) and 2024 (PI) for anti-TB drug discovery. With a strong focus on translational research, SMCRG has successfully developed five anti-TB drug leads currently in pre-clinical investigations. The group's synthetic and medicinal chemistry efforts have resulted in over 190 peer-reviewed publications and three patents, underscoring its commitment to innovation and excellence.
Prof. Karpoormath has played a pivotal role in mentoring the next generation of scientists, having supervised 48 postgraduate students (22 PhD's and 26 Masters) and 18 postdoctoral scholars. The current SMCRG team comprises five Master's, 10 PhD, and two postdoctoral researchers, fostering a dynamic and collaborative research environment.
Prof. Karpoormath is recognized among the top researchers at UKZN. In 2017, 2021, 2022 and 2023, his research group was featured in the university's top 30 researchers list. His international collaborations and multidisciplinary approach have strengthened SMCRG's impact on drug discovery.
SMCRG remains committed to advancing medicinal chemistry and addressing global health challenges through innovative research, setting new benchmarks in pharmaceutical sciences.

Principal Investigator: Prof Sybrand van der Spuy
Institution Name: Stellenbosch University
Active Member Count: 7
Allocation Start: 2024-08-27
Allocation End: 2025-02-28
Used Hours: 775854
Project Name: CFD simulation of turbomachinery
Project Shortname: MECH1187
Discipline Name: Computational Mechanics

The turbomachinery research group at Stellenbosch University consists of five to seven postgraduate (master's and PhD) students that are all doing CFD simulations of rotating machinery. The work stretches from modelling the noise and performance of large diameter cooling fans (used by Eskom), to the performance of small centrifugal compressors (used in a solar Brayton cycle) to the development of rocket engine turbines (used by the ASRI group). The focus of the work is on supporting local technology and in all the cases, the simulations have been coupled to actual experimental evaluations.

The group has been making use of the CHPC for its 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, fan noise and blade tip leakage flow that have not previously been possible within our group. Mesh sizes of 20 million + are now common and the information gained from these simulations give researchers the ability to present their work next to researchers from much more famous entities like Cambridge and MIT.

The results achieved to date have been world class and a number of theses, journal papers and conference publications have stemmed form this work. The group is continuously trying to increase the complexity of its outputs and it is hoped that they will shortly be able to model 100 million + size meshes.

Principal Investigator: Dr Nikhil Agrawal
Institution Name: University of KwaZulu-Natal
Active Member Count: 2
Allocation Start: 2024-08-27
Allocation End: 2025-02-27
Used Hours: 84374
Project Name: Molecular Modeling of proteins using different computational tools
Project Shortname: HEAL1189
Discipline Name: Health Sciences

We are Molecular Modeling Group based at the University of KwaZulu-Natal, we are using powerful supercomputers to study how certain proteins, linked to HIV, stick together to form harmful structures called amyloids. These structures play a role in various diseases, so understanding them could help in developing new treatments.

By running computer simulations, we can see how these proteins interact at a very tiny, atomic level. This helps us understand why they clump together and what factors drive this process.

Thanks to the CHPC's resources, we have made important discoveries. We are now finishing a research paper and will share our findings at international conferences. Our work could lead to better ways to target amyloid-related diseases, including those linked to viruses like HIV.

Principal Investigator: Dr Wilhelm Johann van den Bergh
Institution Name: University of Pretoria
Active Member Count: 2
Allocation Start: 2024-08-27
Allocation End: 2025-02-28
Used Hours: 11388
Project Name: CFD investigation into heat transfer
Project Shortname: MECH1672
Discipline Name: Computational Mechanics

The University of Pretoria is renowned worldwide for its contributions in the field of experimental and computational heat transfer research.
Specifically, the Clean Energy Research Group has in recent years been investigating mixed convection heat transfer. The increased heat transfer ability of mixed convection over pure forced convection in internal laminar flow has been one of the key research questions. For specific applications, achieving mixed convection is very attractive, since it increases the heat transfer ability two- or three-fold.
High viscosity fluid, such as glycol, is being investigated as a possible candidate for these applications. Increasing the efficiency of heat transfer in exchangers (such as radiators) is of practical importance.
These fluids exhibit an extremely long thermal entry length, which makes experimental facilities problematic. Computationally, investigating these fluids requires large mesh sizes to model the long thermal development lengths necessitated by the high viscosity. Concomitantly, sizeable computational resources are required if the results are to be obtained in a reasonable timeframe. Thus far, the project has delivered some surprising results, and it is progressing at a fair pace. An article is being prepared for peer-review, and should be submitted before April 2025.

Principal Investigator: Dr Ofentse Pooe
Institution Name: University of KwaZulu-Natal
Active Member Count: 3
Allocation Start: 2024-08-27
Allocation End: 2025-02-27
Used Hours: 8487
Project Name: Computational and biochemical Characterisation of recombinant protein interactions using bioinformatics approaches
Project Shortname: CBBI0983
Discipline Name: Chemistry

Our research work aims to deliver potential antimalaria drugs (hybrids) with dual therapeutic action with enhanced efficacy.
The designed and synthesised selected drugs are essentially investigated against malarial glycolytic pathway proteins, specifically lactate dehydrogenase and hexokinase.
Due to the emerged resistant malaria strains and the efficiency of the RTS,S/AS01 vaccine which is approximately 32 % against severe malaria, thus drug treatment remains a most viable option to manage malaria.
Therefore, CHPC essentially assist us as a group to conduct in silico work (molecular docking and dynamics simulation) which is our vital first step in investigating possible interactions of the drugs against our target diseases.

Currently, we are working on designing a multi-epitope vaccine which could be used against malaria. Therefore, clear understanding of how this vaccine could behave within the human body, in silico work must be conducted.

Principal Investigator: Prof Paulette Bloomer
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2024-08-27
Allocation End: 2025-02-27
Used Hours: 188047
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, bryde's whale, cape grysbok) that make use of the CHPC resources, with additional projects in the pipeline.

Principal Investigator: Dr Joseph Simfukwe
Institution Name: Copperbelt University
Active Member Count: 6
Allocation Start: 2024-08-28
Allocation End: 2025-03-12
Used Hours: 49564
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 is 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. Photoelectrochemical (PEC) water splitting using suitable semiconductors to decompose water into hydrogen (H2) and oxygen is a promising route. Our research work is mainly computational and therefore, 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 Gebremedhn Gebreyesus Hagoss
Institution Name: University of Ghana
Active Member Count: 7
Allocation Start: 2024-08-30
Allocation End: 2025-04-03
Used Hours: 605396
Project Name: Atomistic simulations and condensed matter
Project Shortname: MATS1031
Discipline Name: Physics

My research group at the Department of Physics, University of Ghana, conducts cutting-edge simulations to investigate the structural, electronic, magnetic, and optical properties of both 2D and bulk materials. These computational studies rely on density functional theory (DFT) and extended Hubbard functionals as implemented in Quantum ESPRESSO, the GW approximation of many-body perturbation theory (MBPT), and the Bethe-Salpeter equation (BSE). Our research would not be possible without the high-performance computing resources provided by the CHPC in South Africa. Typically, we prepare input files on our laptops and workstations, submit the jobs to the CHPC cluster, monitor them at least once a day, and download the results upon completion.

Our research focuses on five key areas:

1. Transition-Metal Oxides
We study the electronic, magnetic, structural, and optical properties of doped and undoped materials, comparing computational results with experimental data.
2. Perovskite Materials for Energy Applications
We investigate the structural, electronic, dielectric, and vibrational properties of double perovskite materials using extended DFT approaches (DFT+U and DFT+U+V) while also searching for lead-free double perovskites. In addition, we employ the HSE06 hybrid functional and the GW+BSE approach to study their electronic properties.
3. Cathode Materials
We explore cathode materials for metal-ion batteries, with a particular focus on Na-ion and Mg-ion batteries, using extended Hubbard functionals.
4. Ruddlesden-Popper Perovskite Ruthenates
We calculate electron-phonon couplings in Sr₄Ru₃O₁₀ and Sr₃Ru₂O₇ using DFT+U and spin-orbit coupling. Additionally, we plan to incorporate the dynamical mean-field theory (DMFT) approach to gain deeper insights into the metamagnetic properties of these materials.
5. Magnetic Materials
We investigate the magnetic and electronic structures of DyFeO₃ and LaFeO₃ using near-edge X-ray absorption fine structure (NEXAFS) spectra and first-principles calculations.
Our work continues to push the boundaries of computational materials science, and we are grateful for the support of CHPC in enabling our research.

Principal Investigator: Prof Mahmoud soliman
Institution Name: University of KwaZulu-Natal
Active Member Count: 23
Allocation Start: 2024-08-30
Allocation End: 2025-03-04
Used Hours: 697109
Project Name: Drug Design, development and modelling
Project Shortname: HEAL0790
Discipline Name: Health Sciences

The research scope of Molecular Bio-Computation and Drug Design Laboratory (http://soliman.ukzn.ac.za/) 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. In my research group (http://soliman.ukzn.ac.za/) we rely extensively on the computational support from CHPC for the last 13 years. With such amazing support from CHPC, the lab has successfully grown significantly and manged to publish more than 350 publications in high impact factor journal with more than 100 student graduations. The impact of CHPC on developing research and human capacity as evident from research publications and student graduations is commended and highly appreciated.

Principal Investigator: Dr Mohau Mateyisi
Institution Name: Council for Scientific and Industrial Research
Active Member Count: 16
Allocation Start: 2024-09-02
Allocation End: 2025-04-08
Used Hours: 1608549
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

Climate Model forecasts and projection provide scientific evidence of day-to-day weather events and possible future changes. The understanding of what climate patterns would shift going into the future is critical for sustainable development. The underlying science is computationally expensive and demands high performance computational resources to advance. The CSIR supported by the CHPC high performance computing successfully developed climate change model evidence using internationally accepted best practices.

All sectors of development stand a chance to benefit from the research and development investment in support of climate resilience strategies nationally. The developed climate model evidence allows for production tailored information on climate change extremes. This is the kind of information which is extremely beneficial to the general public, industries and the government.

Going forward, the investment stand a chance lead enhanced climate service for the benefit of agriculture, water resource allocation, biodiversity, food security and sustainable settlements. The need for South Africa to make its development strategies informed by the best available science is more important than ever before due to the alarming rate of Global Warming which is disproportionately affecting all regions in South Africa. The investment ensures that climate scientist in the country can respond to the climate change induced threats by contributing scientific developments from the Southern Ocean lens.

Principal Investigator: Dr Fabio Cinti
Institution Name: NITHEP
Active Member Count: 7
Allocation Start: 2024-09-02
Allocation End: 2025-03-14
Used Hours: 51884
Project Name: Quantum Monte Carlo for ultra-cold atoms
Project Shortname: PHYS0892
Discipline Name: Physics

The investigation of properties of quantum materials and the necessary tools to engineer them are at the forefront of condensed-matter physics. These materials present fascinating properties due to the macroscopic manifestation of quantum mechanics. Particular examples are superfluids and superconductors where particles flow without friction. The simulation of these systems with state-of-the-art Quantum Monte Carlo methods requires powerful superconductors such as CHPC and allows a better understanding of quantum many-body systems.

Principal Investigator: Dr Sarah Roffe
Institution Name: Agricultural Research Council
Active Member Count: 12
Allocation Start: 2024-09-02
Allocation End: 2025-03-14
Used Hours: 3467453
Project Name: ARC-NRE Agrometeorology
Project Shortname: ERTH1556
Discipline Name: Earth Sciences

The Agricultural Research Council (ARC) Agrometeorology Division is at the forefront of climate research in South Africa. Our research group is dedicated to studying how climate change and variability affect agriculture in the region, with a focus on improving climate services for farmers and agricultural decision-makers. By combining scientific expertise with cutting-edge technology, we aim to better understand weather patterns, extreme climate events, and their impact on food security. Our work focuses on a wide range of research areas, including the analysis of weather systems, climate modelling, and developing indices that help predict agricultural conditions. One of the key projects involves using high-performance computing (HPC) to run advanced simulations and process large datasets. These simulations help us improve our understanding of weather patterns, such as extreme cold events, and predict their effects on crops and livestock. The use of HPC resources, provided by the Centre for High-Performance Computing (CHPC), is essential to the success of our research. These resources allow us to analyse vast amounts of data and run complex models that would otherwise be impossible with conventional computing methods. The CHPC's support has enabled us to develop more accurate predictions, providing critical insights into climate risks faced by farmers and helping them make better-informed decisions. Since starting our collaboration with the CHPC, our research has made significant progress. We have successfully completed analyses and presented our findings at major conferences. Our work is helping shape the future of agricultural planning and climate resilience in southern Africa. Thanks to the powerful HPC capabilities, we are confident that our research will continue to make a positive impact on food security and climate adaptation strategies across the region.

Principal Investigator: Prof Mpho Sithole
Institution Name: Sefaku Makgatho Health Sciences University
Active Member Count: 12
Allocation Start: 2024-09-02
Allocation End: 2025-03-06
Used Hours: 6357
Project Name: Computational modeling of titanium based alloys
Project Shortname: MATS1228
Discipline Name: Physics

The material modelling group is housed at Sefako Makgatho Health Sciences University. Our niche area is to investigate the properties of materials/alloys at the atomic level. The properties of interest are lattice parameters, structural, mechanical, thermodynamic, and electronic. The research focuses on titanium alloys, shape memory alloys for biomedical applications, and permanent magnets for electronic devices, disc drives, and turbine generators.
The group employs the first-principles method during their investigations. This is a computational approach that uses physical laws to predict material properties. The method uses Density Functional Theory (DFT), which is based on quantum mechanics to determine the material's properties at the atomic level.
The CHPC facilities play an important role in our research. We need CHPC for their high speed processing capabilities, to perform complex computations and data analysis, which is faster than traditional computers.

Principal Investigator: Dr Benjamin Victor Odari Ombwayo
Institution Name: Masinde Muliro University of Science and Technology, Kakamega, Kenya
Active Member Count: 9
Allocation Start: 2024-09-04
Allocation End: 2025-03-12
Used Hours: 1805791
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 Double and 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 with over 80 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: Mr Paul Tarwireyi
Institution Name: University of Zululand
Active Member Count: 1
Allocation Start: 2024-09-04
Allocation End: 2025-03-26
Used Hours: 2710
Project Name: Machine Learning-Enhanced Cybersecurity for Emerging Technologies
Project Shortname: CSCI1621
Discipline Name: Computer Science

The Machine Learning-Enhanced Cybersecurity for Emerging Technologies project, led by the Networks and Security research group at the University of Zululand's Department of Computer Science, focuses on detecting network intrusions and malware threats across platforms like desktops, mobile devices, IoT, and cloud computing. By applying machine learning techniques, including classic and deep learning for classification and metaheuristic algorithms for optimization, the project aims to enhance system security against evolving cyber threats. A key challenge is optimizing solutions for resource-constrained devices without compromising detection accuracy. Additionally, the project is training honours students, contributing to the next generation of cybersecurity experts. This research seeks to deliver scalable, adaptive solutions to protect critical digital infrastructures.

We intend to use the CHPC to optimize our results using either feature selection or hyperparameter tuning.

Principal Investigator: Dr Khuthala Mnika
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2024-09-10
Allocation End: 2025-03-11
Used Hours: 1884
Project Name: Genetics of Inherited Kidney Disease
Project Shortname: CBBI1713
Discipline Name: Bioinformatics

Our group is dedicated to studying inherited kidney disease. We aim to identify pathogenic variants among participants to better understand the genomic and genetic landscape of kidney disease, with a particular focus on the African population. Our ultimate goal is to develop a diagnostic panel for this purpose.

Principal Investigator: Prof Tjaart Krüger
Institution Name: University of Pretoria
Active Member Count: 6
Allocation Start: 2024-09-10
Allocation End: 2025-04-16
Used Hours: 132162
Project Name: A DFT study of bio-inspired organic solar cells
Project Shortname: MATS1498
Discipline Name: Material Science

Bioinspiration from photosynthetic protein complexes

Polymers and proteins have a lot in common. Being molecular machines – i.e., macromolecular robots – proteins execute their designed functions in a finely regulated way with extraordinary efficiency, despite ample environmental disorder and densely crowded, heterogeneous environments. This serves as a significant source of inspiration for polymer synthesis. Photosynthetic pigment-protein complexes offer a lot of formidable design principles for organic solar cells.

Prof. Tjaart Krüger from the University of Pretoria has teamed up with Dr Newayemedhin Tegegne from Addis Ababa University to shed more light on new sets of organic solar-cell materials that have partly been inspired by photosynthetic light-harvesting complexes. Their research sheds light on the molecular design of organic solar cells and the properties that enhance their stability and efficiency.

Due to the complexity of both the natural, photosynthetic molecules and 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 Geoff Nitschke
Institution Name: University of Cape Town
Active Member Count: 18
Allocation Start: 2024-09-11
Allocation End: 2025-03-11
Used Hours: 214525
Project Name: Evolving Complexity
Project Shortname: CSCI1142
Discipline Name: Computer Science

The main focus of the research is to devise new methods using techniques from a broad range of biologically inspired machine learning sub-fields such as evolutionary computation and artificial neural networks (neuro-evolution) as well as statistical machine learning and apply such methods to evolve and adapt artificial brains on various experimental platforms, such as: evolutionary-robotic, artificial life and agent-based systems. Within the broad purview of artificial intelligence, the guiding research goal is to use adaptive artificial systems in order elucidate open how and why questions in the evolution and adaptive behaviour of counter-part natural systems as well as to apply novel adaptive algorithms to the synthesis of problem-solving computational tools and the engineering of robotic systems.

Principal Investigator: Prof Lyudmila Moskaleva
Institution Name: University of the Free State
Active Member Count: 9
Allocation Start: 2024-09-11
Allocation End: 2025-04-03
Used Hours: 1321520
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 (np-Au), a versatile material with interesting mechanical, optical, and catalytic properties. Recently, we published on the topic in a top-ranked journal ACS Catalysis (Eltayeb et al. ACS Catal., 2024, 14, 7901-7906) and contributed two invited papers to a special issue of Journal of Physical Chemistry C (Eltayeb et al. J. Phys. Chem. C, 2024, 128, 14978-14988, and Eltayeb et al. J. Phys. Chem. C, 2025, 129, 1611-1626). Our studies are focused on the remarkable low-temperature catalytic activity of np-Au and its high selectivity toward partial oxidation reactions. A dynamic behavior of the catalytic surface (including the diffusion and restructuring processes under the influence of adsorbates) has been studied with the help of ab initio molecular dynamics simulations. Static DFT computations revealed new mechanisms for methanol overoxidation in dry and wet environments explaining decreased selectivity of partial oxidation. The calculations are very computationally expensive and possible only through the use of HPC resources.
In another subproject, we investigate the hydrocarbon combustion chemical reactions using density functional theory (DFT), high-level ab initio quantum chemistry methods and statistical theory. 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, 6716–6792, and presented at the 27th International Symposium on Gas Kinetics and Related Phenomena, in Leeds, UK, 2024. A PhD student, Ms. KP Otukile, is finalizing her dissertation on this topic.
In a third subproject, we have been modelling cis-trans isomerism in square-planar d8 complexes of group VIII metals with cyanoximes. Computational modelling of the complexes helped us to explain different preferences of Ni compared to Pt and Pd observed experimentally.

Principal Investigator: Dr RAMONTSHENG RAPOLAKI
Institution Name: South African Weather Service
Active Member Count: 4
Allocation Start: 2024-09-12
Allocation End: 2025-03-12
Used Hours: 121533
Project Name: WAVE AND WATER LEVEL MODELLING
Project Shortname: ERTH1609
Discipline Name: Earth Sciences

A pioneering project is underway to install and test the Delft3D model to run the South African Weather Service's (SAWS) Storm Surge and Wave Forecasting System (SWaSS) to investigate climate change scenarios, particularly focusing on wind and wave projections.

SWaSS will be utilised to downscale CMIP6 wind and wave projections, providing high-resolution insights into future climate conditions. As South Africa's only operational, high-resolution, public-good storm surge and wave forecasting system, SWaSS offers an invaluable opportunity to model future water levels and regional wave patterns with exceptional precision.
By integrating Delft3D with SWaSS, the project aims to enhance the accuracy and reliability of climate impact assessments, ensuring a more comprehensive understanding of coastal risks and extreme weather events. This initiative will not only improve forecasting capabilities but also contribute to long-term climate adaptation strategies.

Principal Investigator: Prof Charalampos (Haris) Skokos
Institution Name: University of Cape Town
Active Member Count: 13
Allocation Start: 2024-09-12
Allocation End: 2025-03-12
Used Hours: 164008
Project Name: Chaotic behavior of Hamiltonian systems
Project Shortname: CSCI1007
Discipline Name: Applied and Computational Mathematics

Using modern numerical techniques of Nonlinear Dynamics and Chaos Theory we investigate in a unified mathematical way the behavior of models describing the energy transport in disordered and granular media, as well as the properties of new elastic materials like graphene and molecules like the DNA. This research is performed by members of the 'Nonlinear Dynamics and Chaos Group' in the Department of Mathematics and Applied Mathematics at the University of Cape Town. The performed investigations constitute an innovative combination of Applied Mathematics, Chaos Theory, Hamiltonian Dynamics and Nonlinear Lattice Dynamics. Their outcomes will provide answers to some fundamental questions about the effect of chaos on the energy transport in disordered and granular media, and on the behavior of graphene and DNA. Some of the questions we try to address are: Does the presence of impurities and nonlinearities enhance or suppress the propagation of energy (e.g. heat) in solids, of light in crystals, and of vibrations in granular material? How does the ratio of the different base pairs in DNA chains affect their structural stability and the temperature at which the double-stranded DNA breaks to single-stranded DNA?

Principal Investigator: Prof Clement Nyirenda
Institution Name: University of Western Cape
Active Member Count: 4
Allocation Start: 2024-09-16
Allocation End: 2025-03-17
Used Hours: 81255
Project Name: Computational Intelligence Algorithms for Smart Environments
Project Shortname: CSCI1631
Discipline Name: Computer Science

This project focuses on developing nature-inspired computational intelligence algorithms for applications in smart healthcare, smart energy, astronomy, and other fields. The research team is led by Principal Investigator Clement Nyirenda and includes three MSc students from the University of the Western Cape: Jeremiah Taguta, Liyakhanya Tabata, and Jessica Randall. Their work can be summarized as follows:

1. Jeremiah Taguta is leveraging artificial intelligence to predict temperature fluctuations in the cold storage of fresh produce. This research aims to reduce food spoilage and maintain product quality during transportation.

2. Liyakhanya Tabata is developing an AI-powered system for automatic banking check verification. His study compares two types of deep learning models—one inspired by how the human brain processes visual information (CNN) and another that mimics attention mechanisms in language models (Transformers).

3. Jessica Randall is using the CHPC facility to run Python scripts for Topological Data Analysis (TDA), generating Persistent Barcodes and Persistence Diagrams to identify topological patterns across different datasets.

Principal Investigator: Prof Fourie Joubert
Institution Name: University of Pretoria
Active Member Count: 48
Allocation Start: 2024-09-16
Allocation End: 2025-03-16
Used Hours: 3448
Project Name: NGS Bioinformatics
Project Shortname: CBBI0905
Discipline Name: Bioinformatics

In South Africa and may other countries, Mycobacterium tuberculosis (which causes Tb) undergoes changes in its genome. Some of these changes interfere with the action of the drugs used for Tb treatment. Dillon Muzondiwa's project analyzed large available datasets, so be able to predict which changed would lead to drug resistance.

Principal Investigator: Dr Lynndle Square
Institution Name: North-West University
Active Member Count: 7
Allocation Start: 2024-09-17
Allocation End: 2025-04-16
Used Hours: 188024
Project Name: Exploring poly(2,5)benzimidazole enhanced with carbon nanotubes for space applications
Project Shortname: MATS1088
Discipline Name: Physics

A research team led by Associate Professor Lynndle Square from North-West University's Centre for Space Research is using South Africa's national high-performance computing (HPC) infrastructure to explore innovative materials designed to survive the harsh environment of space. Supported by the NRF Thuthuka programme (2022–2024), this cutting-edge research is focused on developing lightweight polymer composites that can withstand intense radiation and temperature extremes in Low Earth Orbit.
The group's work centers on a unique polymer, poly(2,5-benzimidazole), which is enhanced with nanofillers to improve strength, thermal stability, and resistance to ion bombardment—factors critical for space missions. The aim is to create affordable, efficient shielding materials that can lower launch costs by reducing payload weight, a major factor in space travel economics.
To achieve this, the research relies heavily on the computational power provided by the Centre for High Performance Computing (CHPC). Using advanced simulation software and material modelling techniques, the team can model how these novel materials behave under space-like conditions—something that would be costly and difficult to replicate in a lab environment.
This work is progressing exceptionally well. Multiple students have completed postgraduate degrees as part of the project, and several findings have already been published in high-impact journals. The group has also presented their results at international conferences, with one student winning second prize at IEEE NANO 2023.
With new computational and fabrication labs now in place, the group is set to continue pushing the boundaries of space materials research—firmly establishing South Africa as a contributor to global innovation in aerospace science.

Principal Investigator: Prof Serestina Viriri
Institution Name: University of KwaZulu-Natal
Active Member Count: 25
Allocation Start: 2024-09-17
Allocation End: 2025-04-15
Used Hours: 20488
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 provides state-of-the-art High-Performance Computing, enabling 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: Dr Kiprono Kiptiemoi Korir
Institution Name: Moi University, Eldoret, Kenya
Active Member Count: 13
Allocation Start: 2024-09-19
Allocation End: 2025-02-18
Used Hours: 295281
Project Name: Thermal characterization of MoS2 nanostructures: an ab initio study
Project Shortname: MATS0868
Discipline Name: Material Science

Our research group, based at Moi University's Computational Material Science Group (CMSG), collaborates with Dr. Haffad from the University of Bejaia, Algeria, and Dr. Re Fiorentin from Istituto Italiano di Tecnologia (IIT), Italy. Our work focuses on materials for energy, optoelectronics, and ultra-hard industrial applications.
Two-dimensional (2D) materials exhibit unique properties, including quantum effects, high flexibility, and superior electron mobility, distinguishing them from their bulk counterparts. Zinc sulfide (ZnS) is particularly promising for green hydrogen production via water splitting. To enhance its photocatalytic efficiency, we investigate doping and defect engineering using Density Functional Theory (DFT) simulations. These predictive approaches, rooted in quantum and classical mechanics, require substantial computational resources, making High-Performance Computing (HPC) facilities like CHPC indispensable.
In our recent study, we employed ab initio DFT calculations to examine how 3d transition metal doping influences the water-splitting potential of ZnS (1100). Our findings indicate that dopant stability depends on the d-electron character, concentration, and doping site. Zn-rich conditions were found to favor dopant incorporation over S-rich conditions. Among the dopants, copper exhibited the highest stability, while cobalt, manganese, and iron showed decreasing stability. At doping concentrations of 1–6%, manganese and iron reduced the band gap by 15–60% and 19–51%, respectively, while Cu and Co achieved greater reductions of 37–78% and 26–75%. Band-edge alignment analysis revealed that ZnS (1100) doped with 4% Cu and 2% Co falls below water's redox potential, suggesting enhanced photoelectrochemical (PEC) activity. These results highlight the potential of Cu and Co dopants in improving ZnS-based water-splitting efficiency, paving the way for sustainable hydrogen production.

Principal Investigator: Prof Thirumala Govender
Institution Name: University of KwaZulu-Natal
Active Member Count: 10
Allocation Start: 2024-09-19
Allocation End: 2025-03-20
Used Hours: 347072
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: Prof George Amolo
Institution Name: Technical University of Kenya, Nairobi, Kenya
Active Member Count: 15
Allocation Start: 2024-09-19
Allocation End: 2025-04-03
Used Hours: 977631
Project Name: Properties of Materials for Green Energy Harnessing
Project Shortname: MATS862
Discipline Name: Material Science

The MATS862 group is a Kenyan based group at the Department of Physics, Earth and Environmental Sciences, Technical University of Kenya, Nairobi. The group initially focused on the science and technology of materials for energy conversion but has slowly embraced a multidisciplinary approach. Our students and faculty are now channeling support to other themes that need computing resources in Health & Nutrition, Mineral Science.

Our work involves employing fundamental science to understand properties of matter at the atomic as well as extended scales. Materials here range from those is use in physical, chemical and biological sciences and now extended to applied science and technology. This is done using computer programs that simulate interactions at the atomic scale.

What is measured at the bulk level originates from the atomic scale. Being able to simulate properties of interest provides insights of actual situations. Recent simulation techniques now involving effects of temperature and pressure, thus becoming crucial as part of decision support tools for sectors manufacturing, development of drugs and vaccines, among others. Simulation to support these sectors reduces trial and error, thus saving costs.

Investigations of a property of interest of a material such as Sodium chloride, would require one to use information of the constituent atoms (Sodium and Chloride), placing them in a known computer program and using basic science (formula) to extract the desired information. We have full time support of High Performance Computing (HPC) resources available to faculty and graduate students from the CHPC, South Africa, for which we are very grateful.

MATS862 is doing well and now pioneering at the national and regional levels, as observed in the launch of the Advanced Physics tRaining in collaboration with Africa (APhRICA) at our institution in December 2024. This has not extended to support other thematic areas, which is essential for development of products and services for possible commercial utility.

Principal Investigator: Prof Francois Engelbrecht
Institution Name: University of the Witwatersrand
Active Member Count: 3
Allocation Start: 2024-09-20
Allocation End: 2025-03-20
Used Hours: 4995801
Project Name: WITS Climate Modelling
Project Shortname: ERTH1200
Discipline Name: Earth Sciences

Making use of the allocation on the CHPC, in recent months the Wits Global Change Institute has made substantial progress with two major climate modelling experiments. These climate modelling experiments involve generating novel and unique simulations on the Lengau cluster. Specifically: 1) We have continued to develop the first ensemble of convective-permitting climate change simulations focused on the southwest Indian Ocean, providing valuable insights into tropical cyclone landfall patterns in Madagascar, Mozambique, and Malawi. These pioneering high-resolution simulations, generated using an African-based HPC facility, are the first to be conducted for this region. We have finalized the present-day and future downscalings for four GCMs and are currently processing the last (fifth) GCM. 2) We are producing projected climate change simulations for southern Africa to investigate regional tipping points (Engelbrecht et al., 2024). Thus far, we have completed the downscaling of two GCMs and made significant progress with three additional GCMs. The goal of this experiment is to downscale a total of ten GCMs. This represents the largest climate change modelling initiative ever conducted in Africa, utilizing an African-based HPC system.

Principal Investigator: Dr Gerhard Venter
Institution Name: University of Cape Town
Active Member Count: 5
Allocation Start: 2024-09-20
Allocation End: 2025-04-09
Used Hours: 79905
Project Name: Simulation of Ionic Liquids
Project Shortname: CHEM0791
Discipline Name: Chemistry

Gerhard Venter's research group at the University of Cape Town uses quantum chemistry, classical molecular dynamics computer simulation and machine learning methods to study and predict the properties of room temperature ionic liquids, high temperature molten salts and energetic materials in general. The properties of molten salts play a crucial role in various industrial processes, particularly in fields such as metallurgy, as well as energy production and storage. Whereas molten salts relevant to metallurgy typically have high melting points making the study of their properties challenging, room temperature ionic liquids on the other hand 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.

Thermodynamic properties of molten slags are important to optimize industrial processes, whereas 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 these systems, 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: Dr Francis Opoku
Institution Name: Kwame Nkrumah University of Science and Technology
Active Member Count: 16
Allocation Start: 2024-09-23
Allocation End: 2025-04-02
Used Hours: 3031245
Project Name: High-Throughput theoretical design of two-dimensional materials as an ultrasensitive toxic gas sensor
Project Shortname: MATS1423
Discipline Name: Chemistry

The Mafa and Opoku Research Groups have announced a groundbreaking advancement in the fight against water pollution caused by pharmaceutical drugs. Their latest study, published in a leading scientific journal, introduces a highly efficient photocatalytic material designed to degrade harmful pharmaceutical contaminants in water, addressing a critical global environmental and public health challenge. The research team developed a zinc-cobalt molybdate-based photocatalyst with oxygen vacancies (ZCMx-OV), which demonstrates exceptional efficiency in degrading tetracycline (TC), a common antibiotic contaminant in water.
High-performance computing (HPC) and density functional theory (DFT) calculations were utilized to predict and validate the vulnerable bonds in tetracycline attacked by oxygen radicals, providing deep insights into the degradation mechanism.
Pharmaceutical drugs in water systems pose significant risks to human health and ecological balance. Conventional water treatment methods often fail to remove these persistent pollutants, leading to their accumulation in the environment. The innovative ZCMx-OV photocatalyst offers a sustainable and effective solution to this growing problem, paving the way for cleaner water and healthier ecosystems.
High-performance computing (HPC) and density functional theory (DFT) calculations were utilized to predict and validate the vulnerable bonds in tetracycline attacked by oxygen radicals, providing deep insights into the degradation mechanism.
Dr. Mafa, co-lead researcher, stated, "Our work represents a significant step forward in the quest for sustainable water purification technologies. By leveraging heteroatom inclusion and advanced computational tools, we have created a material that is both highly efficient and adaptable to real-world conditions."
Dr. Opoku, co-lead researcher, added, "This study underscores the importance of interdisciplinary collaboration in solving complex environmental challenges. The integration of experimental and computational approaches has been instrumental in achieving these results."

Principal Investigator: Dr Jennifer Veitch
Institution Name: SAEON
Active Member Count: 16
Allocation Start: 2024-09-23
Allocation End: 2025-04-09
Used Hours: 103340
Project Name: SAEON Coastal and Regional Ocean Modelling Programme
Project Shortname: ERTH1103
Discipline Name: Earth Sciences