Machine Learning (ML) algorithms have been used extensively in the classification and characterization of protein sequences and proteome data. However, the functional annotation of newly identified proteins relies heavily on sequence similarity analyses, i.e. functional annotations of characterized proteins are transferred to novel protein sequences based on amino acid sequence conservation....
The hybrid sulphur (HyS) cycle[1] has shown potential to be a viable hydrogen producing process via the electro-oxidation of aqueous SO$_2$. The process makes use of a platinum electrocatalyst. Hence research conducted by Falch [2], into reducing the amount of Pt in the catalyst was done at the North-West University. They achieved promising results by vapour deposition of Pt onto a glassy...
Li2MnO3 has been considered a potential cathode material due to its high theoretical capacity, nontoxicity and natural abundance of Mn. However, it has not been commercialized due to poor structural stability during cycling that results in capacity fade. Doping Li2MnO3 with transition metals is one of the ways that are extensively explored to optimize its properties and stability. To study...
The Diels-Alder (DA) reaction is one of the most important reactions in organic chemistry, which has found so many applications in a variety of domains such as in the total synthesis of natural products, in polymer chemistry as well as in the industrial preparation of agrochemicals and fragrances. Over the past few years, numerous computational studies have been investigating the mechanism of...
The precious metals are extracted as valuable by-products from sulphides and arsenides- platinum group minerals (PGMs). The growing use of precious metals in the mineral processing industry has developed a deep interest in extracting them from the PGMs. The structure and thermodynamic properties of arsenopyrite (FeAsS) and sperrylite (PtAs2) must be better understood in order to extract the...
This content along with corresponding figures can be found in the uploaded PDF version of this abstract.
HPC applications that use message passing programmer interfaces like MPI rely on asynchronous communication to achieve scalable performance. Asynchronous communication often produces non-deterministic software executions. Non-determinism in MPI applications can negatively impact...
Rooibos (Aspalathus linearis) is an economically important medicinal plant endemic to South Africa. It provides diverse pharmacological and nutraceutical benefits, and was shown to alleviate stress, allergy, diabetes and cardiovascular disease symptoms, and to boost the immune system. To understand the genomic background of these medicinal properties, diverse transcriptomes and the nuclear...
In South Africa, more than 3000 plant species are used in traditional medicine. Medicinally active compounds have been identified from diverse endemic South African plant species, but so far close to nothing is known about the genomic background of these plants. Plant genome sequencing can provide information on the genes and biosynthetic pathways that are relevant for plant growth (e.g....
The recent movement towards renewable and sustainable sources of energy has received significant interest of late. Among others, solar, wind and hydrogen have been identified as viable alternatives for fossil fuels whereof the latter proposed alternative receiving particular attention. Among others, the HyS cycle serves as one process for the obtainment of hydrogen. Herein a metal catalyst,...
The covalent inhibition mechanism of action, which overcomes competition with high-affinity, high-abundance substrates of challenging protein targets, can deliver effective chemical probes and drugs. Heat shock protein 72 (HSP72) expressed in cancer cells may be responsible for tumorigenesis and tumor progression by providing resistance to chemotherapy. In this study, we explore the most...
SOMOSPIE [1] is a modular workflow that predicts fine-grained soil moisture from coarse-grained satellite data and terrain parameters. Soil moisture is important for environmental sciences, precise agriculture, and wildfire detection. Depending on the resolution, the data of SOMOSPIE for a region of interest such as Oklahoma (a rich agriculture area) can range from 4.5 GB to 42 TB. The large...
Abstract:
Nickel manganese cobalt batteries, also known as lithium-ion batteries, because of their higher energy capacity and high power, extended cycle life, improved rate stability, superior safety efficiency density, and low cost of nickel and manganese raw materials, have the potential to ensure energy storage. Li-ion batteries are rechargeable batteries that have shown to be one of...
Microorganisms use efflux pumps to regulate their internal environment by removing toxic substances including antimicrobial agents. Studies have supported drug efflux pumps (EP) as a participant in the emergence of resistance towards antimicrobial drugs. Of the EPs, the NorA remains the most studied druggable target. In this study, the shikimate pathway-derived phenolic acids were evaluated...
Electronic devices play an integral role in our daily lives. It changes the way we approach problems such as, communication, transport, health care and many more. The ever-increasing need for high-performance electronic devices created a multibillion-dollar industry to keep up with the demand of high-performance semiconductors. The thermal management of these devices is essential for the...
Toll-like receptors (TLRs) primarily involved in recognizing pathogen-associated molecular patterns (PAMPs) and innate immune activation against invading pathogens. Simultaneous cytokine storm generated through uncontrolled activation of TLRs remains a challenge in management of certain disease conditions, such as sepsis. Very few studies have reported peptide binding partners for TLR-2 as...
Magnesium-ion batteries are a promising energy storage technology of our time due to their higher theoretical energy density and low raw materials. Now among the major setbacks has been the identification of cathode materials that will demonstrate capacities and voltages identical to lithium-ion systems. Then, in this study, we make use of first-principle based calculations to study the...
COMPUTATIONAL MODELLING STUDIES ON SCALING OF BULK AND SURFACES OF SPERRYLITE AND COOPERITE USING CASTEP AND ONETEP CODES
Thato Manyama, Peace Mkhonto and Phuti Ngoepe
University of Limpopo, Materials Modelling Centre, Private Bag x1106, Sovenga, 0727
e-mail address: thatosammuel50@gmail.com
Abstract
We have employed the CASTEP and ONETEP codes to investigate their scaling on the bulk...
Due to the rising demand of renewable energy, lithium-ion batteries have attracted much attention with Li2MnO3 being a perfect candidate to use as the cathode material. This is due to its high energy density and specific capacity. However, Li2MnO3 suffers from poor cycling stability and voltage fade which limits its practical application. In this work the built monoclinic Li1.2Mn0.8O2 is doped...
see attachement.
please see attachement
The search for the next affordable, environmentally friendly, and high-energy-density cathode material is an integral part of the betterment of lithium-ion batteries, in a quest to address the grievous challenges confronting energy storage systems. Density Functional Theory (DFT) has made significant progress in this search, however, it is found wanting at unravelling the electronic structure...
Nowadays, ionic liquids have gained wide usage as green corrosion inhibitors due to their effectiveness, eco-friendliness and outstanding physiochemical characteristics. The present study investigates the computational analysis of thirty ionic liquids used as green corrosion inhibitors of metallic dissolution in molar HCl environment. Density functional theory was employed to study the...
In this work Kohn-Sham density functional theory (KS-DFT) calculations have been used to get a better understanding of the re-mining efforts of pyrite and tailings. In refractory ores the precious metal gold occurs as micro/nano-inclusion encapsulated within the crystal lattice of host mineral pyrite (FeS2). Therefore, the encapsulated gold is inaccessible to the reagent for extraction. Since...
PDF file uploaded
Dimethylsulfoxide (DMSO) is one of the most used solvents in industries and in Chemistry. Despite its importance, a very few studies have been reported on DMSO clusters. In this work, we have explored thoroughly the potential energy surfaces (PESs) of the DMSO clusters from dimer to tetramer at the MP2/aug-cc-pVDZ level of theory. In order to understand the non-covalent interactions in DMSO...
The importance of organic crystals in drug development, technology advancement, and the development of materials owing to their unique properties cannot be over-emphasized. But growing good-quality crystals has been a challenge, particularly since the invention of X-ray crystallography due to the complexity that surrounds crystal formation. Synthetic chemists often have an intuitive feeling...
Lithium-air batteries, based on their high theoretical specific energy, are a particularly attractive technology for electrical energy storage that promises a long-range electric vehicle extensively affordable. However, they suffer from the production of unstable discharge products which leads to capacity fading of the battery. Several catalysts have been used to improve Oxygen Reduction...
MOF-508 with Zn as the metal is a good candidate for CO$_2$ adsorption.$^{[1]}$ This seemingly non-porous material, without obvious pores in the as-synthesized form, shows a flexible response to CO$_2$ pressure. To utilize this material for other applications, such as gas separation, storage and catalysis, a deeper insight is required into the underlying mechanism driving the dynamic...
First-principles density functional theory calculations were performed to study the energetic stability, electronic and electrochemical properties of Li atoms on the H vacancies (VH) in graphane. On a single VH, Li relaxes to a height (dLi-C) of 2.07Å with a binding energy (Eb) of 1.82eV/Li. The obtained Eb value is more than the Li standard bulk cohesive energy of 1.63eV suggesting a possible...
Rooibos (Aspalathus linearis) is a medicinal plant endemic to South Africa, commonly used to make herbal tea. It produces a wide range of phenolic compounds, including the rare aspalathin and PPAC that have anti-diabetic and cardio-protective properties; therefore rooibos is considered a hot target for medical research. Due to the effects of climate change, such as increasing periods of...
Catalysis is one of the most effective techniques used to improve electrochemical performance and influence the production of stable discharge products during cycling in lithium-air batteries. Despite several studies addressing the effectiveness of catalysts in Li-air batteries, the reactivity and catalytic effect of ruthenium oxide (RuO2) are not fully understood. In this study, we used the...
The oxide-garnet tetragonal Li7La3Zr2O12 (t-LLZO) is a candidate material for use as a solid electrolyte in Li-ion batteries. In order to use t-LLZO in practical devices, it must be able to withstand high temperatures with good phase stability. Thus, doping with a supervalent cation, such as Ta, at the Zr-site of t-LLZO is an effective way to enhance the low-temperature tetragonal crystal...
Monazite is an important mineral in the mining industry and contains non trivial amounts of rare earth elements (REEs), thorium (Th) and uranium (U). These components are exceptionally significant and find application in numerous areas of modern technology and are generally used in catalysis, metallurgy and magnetic sector. The thermal plasma treatment is a new process of high-temperature...
Protein tyrosine phosphatase 1B (PTP1B), a negative regulator of the insulin signaling pathway has gained attention as a validated druggable target in the management of type 2 diabetes mellitus (T2DM), a global epidemic threatening human health. The lack of a clinically approved PTP1B inhibitors has continued to prompt research in plant-derived therapeutics possibly due to their relatively...
Force Field Parametrization of the Fe2+4S2−4 Clusters in Dihydropyrimidine Dehydrogenase, the 5-Fluorouracil Cancer Drug Metabolizer: Facilitating In Silico Pharmacogenomic Studies
Maureen Bilinga Tendwa1,, Lorna Chebon-Bore1,, Kevin Lobb1,2, Thommas Mutemi Musyoka1, and Özlem Tastan Bishop1
1Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes...
Nanoparticles with diameter 1.0 nm plays a significant role in catalysis because they constitute a new type of material possessing properties, which are distinct from individual atoms, molecules and bulk matter. Doped nanoparticles offers ways to explore fundamental properties of nanoparticles, in addition to a vastly greater range of parameters that can be tuned to obtain nanoparticles with...
Genome-wide association studies ( GWAS) have been applied to various organisms, including fungi. These studies have successfully identified gene regions associated with traits such as pathogenicity and virulence. The plant pathogen Ceratocystis albifundus is infecting non-native Acacia mearnsii trees and has recently been found to infect native cultivated Protea cynaroides plants in...
Cancer is one of the leading causes of death globally, accounting for 10 million deaths in 2020 with lung, stomach, colon, liver and breast cancers remaining the leading causes.
A hallmark common to these cancers is the altered sugar attachment or glycosylation of the MUC1 protein. In healthy cells, the MUC1 consists of long, branched sugars, whereas in cancer cells, these sugars are...
The problem addressed in this talk is that of suitable concentrating solar (CS) plant site selection in the vicinity of a ferromanganese smelter. Proper CS site selection is important if a CS plant supplying process heat to an industrial application is to perform properly. The focus will be on the numerical work conducted during the course of this investigation, which included large scale CFD...
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Zakiena Hoossen (2nd year PhD student at WITS/CSIR, zakiena.h@gmail.com)
Supervisors: Wits: Prof F Engelbrecht, Prof T Celic; CSIR: Dr P Monteiro, Dr S Nicholson
The exchange of carbon and heat fluxes occurs between the atmosphere and the ocean on different scales. In particular, the upper ocean called the mixed layer is involved in these exchanges. This mixed layer is affected by eddies....
A plasma discharge in a Helium gas reactor at different pressures and at low currents (0.25 to 0.45 A) has been investigated by Computational Fluid Dynamics (CFD) modelling coupled with the Maxwell’s equations. This topic is of interest because plasma is known to contain chemically active species and charged particles, which can be used in a wastewater treatment application. There is a need to...
COMPUTATIONAL CHEMISTRY
Spinel LiMn2O4 has attracted tremendous attention and is the Li-ion battery research hotspot for the potential facilitation of a constant energy supply and storage. This is due to LiMn2O4 being cost-effective, having good structural stability with improved safety conditions and environmental affinity. Furthermore, it has an excellent rate performance with 3D Li+ diffusion channels. However,...
Precious metals nanoparticles play a crucial role in the delivery of drugs to the human body. As such, various sizes of gold nanosphere particles have been modelled through classical molecular dynamics. Temperatures including 0, 100, and 300 K have been set as the initial starting temperatures in the NVT ensemble. The many-body Sutton-Chen potential was used to describe the interactions...
Automatic speech recognition (ASR) is a field of research that use statistical computing and machine learning to convert human speech into text. The United Nations is currently actively using ASR systems developed in our previous work to support their humanitarian relief programmes in rural Africa. These systems monitor community radio broadcasts in local languages to obtain information that...
Code-switching in South African languages is common but data for language modelling remains extremely scarce. We present techniques that allow recurrent neural networks (LSTMs) to be better applied as generative models to the task of producing artificial code-switched text that can be used to augment the small training sets. We propose the application of prompting to favour the generation of...
In recent years, stochastic numerical solvers for the Parker cosmic-ray transport equation have become indispensable in cosmic ray modulation studies. Such codes, however, rely heavily on the quality of the pseudo-random number generation(PRNG) algorithm implemented in their calculations to model the Weiner processes required in the stochastic differential equations to be solved. The current...
Keywords: CASTEP, Ni-Al, Ni-Cr, phase stability, mechanical properties
The structural properties, phase stability and elastic properties of Ni-Al and Ni-Cr compounds were systemically investigated using first principle calculations based on density functional theory. The calculations were calculated using CASTEP supercell approach with ultrasoft pseudopotential. The structures comprised of 16...
Alloy-based Fe-Al intermetallic are important for high-temperature applications and are corrosion resistant to oxygen. This is due to a well-adherent protective oxide layer that forms on the surface of the metal interface. These alloys are a major driver as a component for better infrastructure, industrial coating and the improvement of automotive parts. The automotive industry is a major user...
The Plasmodium falciparum phosphatidylinositol 4-kinase type III beta (PfPI4KIIIβ), a protease kinase enzyme, has been shown to be vitally important for the survival of the malaria parasite, both in the host and the vector. However, the lack of the three-dimensional structure and the full structural characterisation of its binding pocket limits its utility and subsequently the development of...
Probing the Structural Dynamics of the Malaria Parasite Plasmodium falciparum GTP-cyclohydrolase I to Reveal Potential Allosteric Drug Targeting Sites
Computer-aided drug discovery based on high-performance computing (HPC) has become an essential approach in drug discovery research. HPC remarkably improved the efficiency of discovering new drugs and metabolic targets by reducing the...
Proposed DFT study for the N-alkylation of amines via the ‘borrowing hydrogen’ mechanism
Shivania Naidoo
209521862@stu.ukzn.ac.za
Student Number: 209521862
School of Chemistry and Physics
Supervised by Dr Thishana Singh and Prof Neil Koorbanally
Amines are an important class of compounds used in the agrochemical, additives and dye industry as well as in the fine chemical industries (in the...
Transition-metal-mediated oxygen transfer reactions are of great importance in both industry and academia; thus, a series of group VII B oxo complexes of the type MO3L (L =O−, F−) and their effects as oxidation catalysts on ethylene have been studied on the singlet and triplet PES at the DFT B3LYP/LACVP* level of theory.
Molecular structures were stable on the singlet reaction surface except...
Next-generation computing systems are expected to have dramatically higher performance than current systems. However, I/O bandwidth and parallel file system capacity will not grow at the same rate. This I/O bottleneck constitutes a major challenge for the analysis of data-intensive high-performance computing (HPC) simulations.
This work targets one of the most common applications on...
Malaria has been targeted by the WHO for elimination for well over a decade now. The emergence of resistance to widely used antimalarials combined with the persistence and lack of drugs that target other Plasmodium species like P. vivax has made it challenging to eradicate malaria.
The main aim of this research is to find drugs that inhibit the function of a lipocalin that has been shown to...
Titanium in its metal and powder form can be produced through thermochemical processes involving the reduction of a precursor such as titanium dioxide. However, the reduction process occurs extremely fast and results in the agglomeration of crystalline particles. This reduction process occurs in the presence of alkali metal and alkali earth metal salt mediums. In this study, we employ...
Abstract:
Pharmacogenomics is a field of study that involves the association of genes involved in drug metabolism with drug response. The CYP2D6 gene is important for drug metabolism. Different studies have identified a number of variations in the CYP2D6 gene in African populations with potential functional impact. The aim was to gain insights of how missense variants found in sub-Saharan...
Investigating the adsorption behavior and reactivity of catalytically relevant molecules on well-defined gold surfaces provides great information for understanding the catalytic activity of gold-based nanocatalysts, such as nanoporous gold (np-Au). Within this project we aim to deliver a comprehensive picture of surface reactivity, where an idealized picture of a perfect clean and rigid...
Researchers over the past four decades have argued that on the one hand, small businesses are significant drivers of economic growth and employment globally while on the other hand, they have a high rate of failure. In South Africa for instance, 91% of businesses, 57% of the GDP and 61% of the employment reportedly come from small businesses. Conversely, South Africa has recorded a high rate...
The separation of valuable minerals from the gangue minerals is still a challenge, in particular the extraction of arsenides platinum group minerals (PGMs). It has been reported that the flotation of PGMs resulted in low recovery when using traditional xanthates. This was owed to the report that the arsenides hosting the platinum group elements (PGEs) minerals are not amiable to flotation....
Lithium manganese oxide (LiMn2O4) is one of the promising cathode materials for lithium-ion batteries (LIBs), however, it suffers from capacity fading mainly due to surface manganese (Mn2+) ion dissolution during Charge/discharge processes. Although many studies focused on reducing Mn-dissolution, surface modification has proven to be an ideal method of...
The layered Li2MnO3 has attracted tremendous research interest as a cathode material for high capacity lithium-ion batteries due to its high theoretical capacity of 459 mAh.g-1 and the ability to reversibly intercalate more lithium. However, voltage decaying and poor rate capability during cycling pose serious problems in its practical application. To solve this problem, sodium-ion...
Malaria is caused by Plasmodium parasites, spread to people through the bites of infected female Anopheles mosquitoes. The study focused on all 5 (Plasmodium falciparum, P. knowlesi, P. malariae, P. ovale and P. vivax) parasites that causes malaria in humans. Africa is a developing continent, and it is the most affected with an estimation of 90% of more than 400 000 deaths reported by the...
FeCo alloy plays an important role in soft magnetic materials with a wide range of technological applications due to their high saturation magnetization and Curie temperature. However, this binary alloy displays poor ductility at room temperature. The ductility of this alloy can be improved by the ternary addition of V. In this study, the HPC application code VASP was used and a supercell was...
Keywords: Large Scale Graphs, Graph Comparison, Shared Memory Implementation
Authors: Krishna Sai Ujwal Kambhumpati(1), Patrick Bell(2)), Michela Taufer(2)
, and Sanjukta Bhowmick(1)
Affiliations:
1. The University of North Texas
2. The University of Tennessee, Knoxville
Corresponding Email Address: krishnasaiujwalkambhumpati@my.unt.edu
Comparing the structure of a pair or a group of graphs is...
Southern Ocean Carbon and Climate Observatory (SOCCO, CSIR)
University of Witwatersrand (wits), Global Change Institute (GCI)
Supervisors: Prof. F. Engelbrecht (wits, GCI), Dr P. Monteiro and Dr S. Nicholson (SOCCO)
The Southern Ocean plays a critical role in mitigating some of the effects of climate change through its heat and carbon uptake. Models are the most useful tool to...
Abstract
The TiPd alloy is one of the promising candidate for high temperature shape memory applications with the martensitic transformation temperature from B2 to B19 at 823 K. Previous studies showed that the B2 TiPd is unstable since it displays negative C′ which resulted in poor shape memory behaviour. In order to enhance the properties, the effects of partial substitution of Pd with...
We investigate the use of silhouette coefficients in cluster analysis for speaker diarisation, with the dual purpose of unsupervised fine-tuning during domain adaptation and determining the number of speakers in an audio file. Our main contribution is to demonstrate the use of silhouette coefficients to perform per-file domain adaptation, which we show to deliver an improvement over per-corpus...
