The presentation will discuss the use of traditional computational methods, machine and deep learning, as well as quantum computing and quantum machine learning (as a new frontier) in addressing challenges in fluid dynamics, dynamical systems, and high-energy physics research. And the talk will highlight the role of the CHPC in democratising access to critical resources and the enablement of...
For over two decades I have been developing new interatomic potentials, e.g., implemented the AOM within GULP that can be employed to model non-spherical Jahn Teller Mn(III) ions, successfully refined potential parameters to model numerous systems including the Peierls' phase transition of VO2, and I am the author of a [published interatomic potential parameter database][1]. My...
The global pandemic, initiated by the SARS-CoV-2 virus and emerging in 2020, has profoundly influenced humanity, resulting in 772.4 million confirmed cases and approximately 7 million fatalities as of December 2023. The resultant negative impacts of travel restrictions and lockdowns have highlighted the critical need for enhanced preparedness for future pandemics. This study primarily...
The spotted hyena (Crocuta crocuta) is a highly social carnivore with a complex behavioural and ecological functions, making it an important model for studying genetic diversity, adaptation, and evolution. However, previous draft genomes for C. crocuta have been incomplete and derived from captive individuals, limiting insights into natural genetic variation. Here, we present a high-quality de...
TBC
Heavy rainfall events are among the most damaging weather hazards worldwide, yet they remain difficult to simulate accurately. One key source of uncertainty is the choice of input data used to initialize weather and climate models. In this study, we tested how sensitive the Conformal Cubic Atmospheric Model (CCAM) is to different initialization datasets, including ERA5, GFS, GDAS, and JRA-3Q....
Running large-scale bioinformatics analyses on high-performance computing (HPC) infrastructure like the CHPC can significantly accelerate research, but comes with technical challenges—especially for researchers aiming to deploy complex workflows such as those built with Nextflow. In this talk, I present practical recommendations and lessons learned from testing and running various...
Room-temperature ionic liquids (ILs) are molten salts with negligible vapour pressure and wide electrochemical windows, making them attractive electrolytes for beyond-lithium batteries [1]. Optimising transport properties—such as conductivity, self-diffusion, and the working-ion transference number (the fraction of the total ionic current carried by Li⁺/Na⁺/K⁺ from the added salt)—requires...
TBC
The evolution and progress of humanity are closely linked to our ways of energy use. Reliable energy sources are vital for driving economic growth, especially as society's demand for energy keeps rising. The rapid development of zinc-air batteries (ZABs) makes them an appealing alternative to standard lithium-ion batteries for energy storage needs. However, the slow kinetics of the air cathode...
This paper explores the benefits of integrating Earth Observation (EO) techniques with Artificial Intelligence (AI) to enhance the capabilities of Numerical Weather Prediction (NWP) models, particularly in the context of severe weather and environmental hazards over South Africa. NWP models often employ EO that lacks real-time resolution, which may lead to increased uncertainty in short-term...
Three-dimensional (3D) computational fluid dynamics (CFD) has emerged as a powerful tool for studying cardiovascular haemodynamics and informing the treatment of cardiovascular diseases. Patient-specific CFD models rely on boundary conditions derived from medical imaging, yet uncertainties in imaging measurements can propagate through the model and affect clinically relevant outputs such as...
This presentation chronicles the journey of an older-generation computational chemist and a young HPC expert, mediated via AI assistance, culminating in the successful deployment of a multi-node research computing cluster. The cluster supports molecular modeling and drug design, enabling large-scale molecular dynamics and quantum chemistry calculations. The senior researcher's four-decade...
Africa has traditionally lagged behind in life sciences research due to limited funding, infrastructure, and human capacity. Yet the growth of genomics and other large-scale data-driven projects now demands robust cyber-infrastructure for data storage, processing, and sharing. H3ABioNet made a significant contribution to building bioinformatics capacity across Africa over 12 years, but its...
Direct-current (DC) electric arc furnaces are used extensively in the recycling of steel as well as primary production of many industrial commodities such as ferrochromium, titanium dioxide, cobalt, and platinum group metals. This typically involves a process called carbothermic smelting, in which raw materials are reacted with a carbon-based reductant such as metallurgical coke to make the...
In an age where AI is permeating every field of engineering and science, it is essential for researchers to quickly embrace technologies that can drive breakthroughs and accelerate innovation. Tools like MATLAB are specifically designed to lower the barriers to entry into the world of AI, making advanced capabilities more accessible to engineers and scientists.
Integrating truly AI-enabled...
All CHPC Users, Principal Investigators and anyone interested in practical use of CHPC computational resources are invited to attend this informal Birds-of-a-Feather Session.
At the start overviews will be presented of the recent usage of the CHPC compute resources (HPC Cluster, GPU Cluster and Sebowa Cloud infrastructure), discussion of new resources available to users and discussion of...
The spinel LiMn2O4 cathode material has attractive candidates for the design and engineering of cost-effective and thermally sustainable lithium-ion batteries for optimal utilisation in electric vehicles and smart grid technologies. Despite its electrochemical qualities, its commercialization is delayed by the widely reported capacity loss during battery operation. The capacity attenuation is...
The proliferation of Artificial Intelligence (AI), data-driven research, and digital transformation has increased the global demand for powerful computing infrastructures capable of processing and analyzing enormous volumes of data. High-Performance Computing (HPC) has emerged as the cornerstone of this evolution, enabling researchers to perform complex simulations, accelerate model training,...
The mechanical properties of materials change when subjected to dynamically conditions of high pressure and temperature. Such materials are those applied in cutting and shaping resulting in twisting and tensile forces. Results of selected MAX phases are presented to show variations in elastic constants as a function of dynamically pressure and temperature. Another situation where materials are...
The presentation showcases recent developments and applications of the ChemShell software in the field of energy materials by the Materials Chemistry HPC Consortium (UK), focusing on defect properties. This work capitalizes on the software engineering and methodological advances in recent years (including the UK Excalibur PAX project highlighted in the last year CHPC conference) by the groups...
The cheetah is a pinnacle of adaptation in the context of the natural world. It is the fastest land mammal and has multiple morphological specialisations for prey-tracking during high-speed manoeuvres, such as vestibular adaptations to facilitate gaze and head stabilisation [1]. Understanding the cheetah’s head stabilisation techniques is useful in field such as biomechanics, conservation, and...
We describe the development of a new library, libGint, for the calculation of the four-centre, two electron integrals required by local basis set ab initio electronic structure codes such as CP2K and CRYSTAL. The focus of this new work is the acceleration of the calculation via Graphical Processing Units (GPUs), particularly for codes that employ periodic boundary conditions. The core kernels...
The core-shell architecture has garnered significant interest for electrode materials owing to the ability to enhance conductivity, stability and enhanced surface functionality. Due to its high capacity and energy density, the O3-type Li2MnO3 layered cathode material is a potential candidate electrode for large-scale energy storage. However, it tends to undergo structural transformation from...
All CHPC Users, Principal Investigators and anyone interested in practical use of CHPC computational resources are invited to attend this informal Birds-of-a-Feather Session.
At the start overviews will be presented of the recent usage of the CHPC compute resources (HPC Cluster, GPU Cluster and Sebowa Cloud infrastructure), discussion of new resources to be made available to users and...
Extreme weather events' escalating frequency and severity underscore the urgent need for high-resolution climate modelling. Developing countries, often with limited resources, face unique challenges in implementing kilometre-scale Earth System Models (ESMs) to simulate local-scale climate projections accurately. Here, I will explore the computational challenges associated with running such...
The largest user community at the Centre for High Performance Computing (CHPC) are those that belong to the domains of computational chemistry and material science (CCMM). The CCMM special interest group (SIG) was established by several senior academic staff members in the computational chemistry and material science domains that make use of the CHPC resources, to have a forum where the...
As technology advances, field researchers increasingly apply sophisticated computational methods to study biological systems, enabling insights across individual, population, and ecosystem scales that were previously challenging to obtain through traditional observational approaches. The present study focused on the impact of wind patterns on sub-Antarctic Marion Island’s ecology, combining...
Quantum chemical methods, in particular, those based on density functional theory (DFT), can be successfully used to achieve a mechanistic understanding of reactivity at the microscopic level, which is required to optimise functional materials (such as catalysts, electrocatalysts, semiconductors, optoelectronic materials) with respect to their target properties.
The presentation will...
High performance computing (HPC) has been a crucial factor in the development of cosmology in the past few years. The tension between increasing precision and computing limitations drives a lot of our research work in the development of new algorithms. I will review the research done by my group in the context of HPC focusing on 3 main topics: 1) large scale simulations of the early Universe;...
Thermoelectricity is the phenomenon direct and thermodynamically reversible conversion of heat to electricity and vice versa. Graphene is one of the carbon-based materials with a low dimensions and mechanically robust, and it tend to have better performance in thermoelectric. Electronic and thermoelectric properties were computed and analysed using density functional theory with a...
One major health challenge in the Continent is the underrepresentation of African populations in the various aspects of drug development. Firstly, drug development is a long and expensive process. Hence, the focus of drug companies is often towards more profitable markets, leaving the specific needs of Africa populations out of their scope. This results in limited development of treatments for...
Computational Material Science is a well established field in South Africa. A great many presentations during the annual conference of the South African Institute of Physics are dedicated to materials simulations with Density Functional Theory. There are however few contributions which go beyond the application of existing codes and algorithms.
This can be attributed in part to the perceived...
The field of materials science has seen a significant increase in the use of computational techniques to study the properties and behaviour of different materials at the atomic and molecular level. A key computational method employed in the study of solid-state materials is Density Functional Theory (DFT), which accurately forecasts the electronic structure, mechanical properties, and...
Experiments rely on models and theory to study the properties of physical systems. Consequently, computer experiments or simulations complement experiments and have enabled theoretical studies of properties of physical systems through the implementation of models and theory. Interatomic potentials have been successfully applied to computational studies involving up to millions of atoms....
Parts of southern Africa and Madagascar are majorly impacted by landfalling tropical cyclones (TCs). Despite the devastating impacts associated with these systems, little is known about the changing attributes of TCs in a warmer world, especially in this region. Therefore, we are undertaking novel, bespoke high resolution climate simulations to generate the first convective-scale (km-scale)...
The envisaged hydrogen economy cannot be realized without a proactive approach to novel materials design. Hydrogen is emerging as a game changer in the grand realm of clean energy value chain mainly because, as an energy vector, hydrogen is both an energy carrier and an energy source. However, despite this potential, several challenges limit large scale adoption of hydrogen including the fact...
Our research group utilizes High-Performance Computing (HPC) infrastructure to implement software programs facilitating calculations including, but not limited to, molecular docking, Quantum Mechanics/Molecular Mechanics (QM/MM), Molecular Dynamics Simulations (MDS), Molecular Mechanics Generalized Born Solvent Accessible Surface Area (MM-GB/SA), Quantitative Structure-Activity Relationships...
Multiscale quantum mechanical/molecular mechanical (QM/MM) techniques are a well established approach for simulating chemical reactivity including a realistic description of the surrounding environment. The [ChemShell project][1] is a leading software package for performing QM/MM simulations, developed at the UK’s Daresbury Laboratory and collaborating research groups around the world. The...
High-performance computing is critical for understanding the ocean’s role in Earth’s climate system. The Southern Ocean, in particular, plays a vital role in regulating global climate through the transport and exchange of heat and carbon, yet it is one of the most computationally demanding regions to model.
The Southern Ocean Carbon-Climate Observatory (SOCCO), CSIR, has developed a...
The SARS-CoV-2 main protease (Mpro) is crucial for the coronavirus’s replication cycle and pathogenesis. Due to its high conservation and absence of human analogues, it is an attractive drug target whose inhibition promises therapeutic relief against COVID-19 morbidity. The present study aimed to profile the Mpro catalytic mechanism by characterising and leveraging key mechanistic events for...
Increased greenhouse gas emissions continue to warm the planet, fuelling climate extremes such as heatwaves, floods, and droughts. These events devastate socio-economic activities globally, but their impacts are even more severe in Africa, where people are more vulnerable. International negotiations on reducing greenhouse gas emissions are slow, while emissions themselves continue to rise....
Increased greenhouse gas emissions continue to warm the planet, fuelling climate extremes such as heatwaves, floods, and droughts. These events devastate socio-economic activities globally, but their impacts are even more severe in Africa, where people are more vulnerable. International negotiations on reducing greenhouse gas emissions are slow, while emissions themselves continue to rise....
The South African Weather Service (SAWS) operates under the SAWS Act (Act No. 8 of 2001), which mandates it to provide essential weather forecasts and warnings to safeguard lives and property. To meet this mandate, SAWS runs numerical weather prediction (NWP) models on its high-performance computing (HPC) system to simulate atmospheric processes.
The current NWP configurations generate...
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...
Major discoveries in molecular biology, along with advances in bioinformatics technologies, have resulted in an exponential increase in the biological data supplied by the scientific community over the past few decades. Genomics, transcriptomics, proteomics, and metabolomics are four of the techniques that have impacted studies in plant-biotic/abiotic stress. When used singly, each of these...
“Science and Fun” Session at 2024 CHPC- Women in HPC
Location
Boardwalk International Convention Centre
Gqeberha (Port Elizabeth)
Date & Time: 04 December 2024, 15:30 -16:30
General Information
Title: “Women in High Performance Computing South Africa (WHPC-South Africa)”
Duration: 60 minutes
Type of session: Science and Fun Session
Organiser(s):
Name Affiliation...
