Conference Publications

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AmLight - Maximizing Technological Advancements in Research and Education; Network Connectivity for Open Science between South Africa, the US, and South America
(2024) Morgan, H; Inarra, J; Bezerra, J; Lopez, LF; Chergarova, V; Cox III, DAC; Alvarez, GE; Hazin, A; Pillay, Kasandra; Makan, Ajay K; Greaves, D; Shariff, A; Sullivan, P
Connecting South and North America with Africa via a South Atlantic high performance Research & Education Network (REN) has become a strategic priority. Africa offers unique biological, astronomical, environmental, geological, anthropological, and cultural resources, making it a valuable partner in global research and education. Enhanced technological and social connections between the United States, Brazil, and Africa are advancing research in multiple disciplines. The high-performance networking infrastructure of AmLight-ExP, in collaboration with the South African National Research and Education Network, provides unprecedented resources for open science research and education communities. This paper presents the architecture, capabilities, and impact of the AmLight-ExP network, highlighting its role in fostering international collaboration and addressing significant scientific challenges.
Computational study of the mechanistic pathway of hydroxyl radical-initiated degradation of disperse red 73 dye
(2022-02) Wahab, OO; Olasunkanmi, LO; Govender, Krishna K; Govender, PP
The mechanisms of hydroxyl radical (·OH) degradation of disperse red 73 (DR73) dye were investigated using density functional theory (DFT) calculations. Comparative feasibility of ·OH attack at the azo (N=N) site or on a > C–N group was examined based on their energies with a view to determine the more preferred pathway for DR73 degradation and predict its degradation products. Further decomposition of the cleavage products by ·OH radical through processes such as deamination and loss of molecular nitrogen was also examined. The results showed that ·OH radical attack on DR73 is more favourable via the azo (N=N) site. However, subsequent rupture of the N=N bond was found to be kinetically and thermodynamically less favourable compared to the C–N bond rupture arising from the attack of the radical on a ring carbon attached to the azo group. Introduction of water (as a solvent) was found to produce an accelerating and stabilising effects on the N=N bond cleavage mechanism, but an inhibitory and destabilising effects on the C–N counterpart. Deamination and nitrogen evolution reactions of the primary degradation products upon further ·OH radical attack were found to be kinetically and thermodynamically feasible.
A DFT study of the chemical reactivity properties, spectroscopy and bioactivity scores of bioactive flavonols
(2022-02) Akintemi, EO; Govender, Krishna K; Singh, T
Density function theory calculations was used to determine the molecular parameters, electronic and chemical reactivity descriptors, spectroscopy, and non-linear optical properties, electronic dipole moment, polarizability and hyperpolarizability of fifteen (15) flavonol aglycones (no sugar moiety) from plant sources to investigate their possible application as drug candidates. Geometry optimisations was carried out using the hybrid functional and basis set: M06-2X/6-31+G(d,p). Our calculations show that all the flavonols investigated are chemically reactive. Their reactivity is greatest in water hence making them suitable drug candidates since this is the ideal medium for drug delivery. The highest negative charge on the oxygen atom of the hydroxyl and high positive charge on the H atom of C5-OH are vital for antioxidant activity. The most reactive species, from reactivity descriptor calculations, is Gossypetin. All the flavonols are active as enzyme inhibitors and moderately active as G-protein-coupled receptors, ion channel modulators and protease inhibitors. The physicochemical properties show the flavonols have good bioavailability. All the compounds agree with Lipinski’s rule of 5, signifying potential use as oral active drugs.
Exploring compatibility and accuracy of functionals on structural and electronic properties of manganese oxide cathode materials: A dft and dft+u study
(2024-07) Kgasago, MZ; Ngoepe, PE; Phoshoko, Katlego W; Ledwaba, RS
Lithium manganese oxides (LMO) have gained significant interest as positive electrode materials for lithium-ion batteries, owing to their high capacity and suitability for achieving remarkable energy densities thus positioning them as promising candidates for advancing LIB technology. Among these materials, Li2MnO3 and LiMnO2 exhibit unique structural and electronic properties that are crucial for their performance in LIBs. This study aims to assess the structural and electronic characteristics of layered lithium manganese oxide cathode materials for lithium-ion batteries using DFT-based computational simulations. Through comparison with experimental data, our findings demonstrate the reliability of computational predictions, with calculated lattice parameters showing excellent agreement with measured values (within 0.5% for Li2MnO3 and 3.5% for LiMnO2). Band structure analysis reveals a moderate direct band-gap of approximately 1.439 eV for Li2MnO3, matching the experimental value of 1.64 eV, and 1.379 eV for LiMnO2, aligning closely with the experimental value of 1.58 eV. These findings shows the reliability of computational simulations in predicting the properties of manganese oxide cathode materials for lithium-ion batteries, paving the way for their future implementation as shells in a core-shell design.
Friend or Foe – The impact of ChatGPT on capture the flag competitions
(2024-03) Meyer, Heloise
ChatGPT, an artificial intelligence (AI)-based chatbot, has taken the world by storm since the technology's release to the public in November 2022. The first reactions were awe and amazement as ChatGPT presented the capability to instantly respond to various text-based questions following a conversational approach. However, it is ChatGPT's ability to complete more advanced tasks, such as supplying source code to programming-related questions or generating complete articles focusing on a specific topic, which has caused eyebrows to be raised. The capabilities offered by ChatGPT, fuelled by popularity and easy accessibility, have introduced several new challenges for the academic sector. One such challenge is the concept of AI-assisted cheating, where students utilise chatbots, such as ChatGPT, to answer specific questions or complete assignments. Although various research studies have explored the impact of ChatGPT on university education, few studies have discussed the influence of ChatGPT on Capture the Flag (CTF) competitions. CTF competitions offer a popular platform to promote cybersecurity education, allowing students to gain hands-on experience solving cybersecurity challenges in a fun but controlled environment. The typical style of CTF challenges usually follows a question-answer format, which offers students the ideal opportunity to enlist the assistance of ChatGPT. This paper investigates the ability of ChatGPT to assist and aid students in solving CTF challenges. The exploratory study involves past CTF challenges across various categories and the questioning of ChatGPT in an attempt to solve the challenges. The outcome of the study reveals that although ChatGPT can assist students with challenges during CTF competitions, the assistance that can be offered is minimal. Instead of producing answers to CTF challenges, ChatGPT can merely offer insight or guidance regarding the questions asked.
Origin of electrochemical activity in nano-Li2MnO3; stabilization via a ‘point defect scaffold’
(2015) Sayle, TXT; Caddeo, F; Monama, Nkwe O; Kgatwane, KM; Ngoepe, PE; Sayle, DC
Molecular dynamics (MD) simulations of the charging of Li2MnO3 reveal that the reason nanocrystalline-Li2MnO3 is electrochemically active, in contrast to the parent bulk-Li2MnO3, is because in the nanomaterial the tunnels, in which the Li ions reside, are held apart by Mn ions, which act as a pseudo ‘point defect scaffold’. The Li ions are then able to diffuse, via a vacancy driven mechanism, throughout the nanomaterial in all spatial dimensions while the ‘Mn defect scaffold’ maintains the structural integrity of the layered structure during charging. Our findings reveal that oxides, which comprise cation disorder, can be potential candidates for electrodes in rechargeable Li-ion batteries. Moreover, we propose that the concept of a ‘point defect scaffold’ might manifest as a more general phenomenon, which can be exploited to engineer, for example, two or three-dimensional strain within a host material and can be fine-tuned to optimize properties, such as ionic conductivity.
Proceedings of the 27th International Conference on Information Visualisation (IV 2023), Tampere, Finland, 25-28 July 2023
(2023-07) Banissi, E; Siirtola, H; Ursyn, A; Pires, J; Datia, J; Nazemi, N; Kovalerchuk, B; Andonie, R; Nakayama, M; Mabakane, Mabule S
This collection of papers on this year's information visualization forum, compiled for the 27th conference on Information Visualization incorporating the following: Artificial Intelligence analytics, machine-, deep-learning, and Learning Analytics - IV2023, advocates that a new conceptual framework will emerge from information-rich disciplines like the Humanities, Psychology, Sociology, Business of everyday activities as well as the science-rich disciplines. To facilitate this, IV2023 provides the opportunity to resonate with many international and collaborative research projects, lectures, and panel discussions from distinguished speakers that channel how this new framework conceptually and practically has been realized. This year's theme is enhanced further by AI's impact on all aspects of life and learning analysis of today's multifaceted and data-rich environment. Joining us in this search are some 70-plus researchers who reflect and share a chapter of their thoughts with fellow researchers. The papers collected, peer-reviewed by the international reviewing committee, reflect the vibrant state of information visualization, analytics, applications, and results of researchers, artists, and professionals from more than 25 countries. It has allowed us to address the scope of visualization from a much broader perspective as we step into the age of AI. Each contributor to this conference has added a new view and thoughts that challenge our beliefs and further encourage our adventure of innovation.
SANReN’s 100 Gbps Data Transfer Service: Transferring data fast!
(2024-11) Pillay, Kasandra; Hugo, Jones O; Makan, Ajay K; Khwela, Thokozani E; Bogopa, Koloto T; Shabalala, Manqoba V
This paper presents the new 100Gbps large data transfer infrastructure of the South African National Research Network (SANReN). In 2018, SANReN piloted the deployment of 10 Gbps capable Data Transfer Nodes (DTNs) in an effort to increase the transfer speeds and reliability for the movement of large datasets. The pilot result showed that there was a need to have national infrastructure available to support large data transfers for use by South African researchers and scientists. The initial pilot evolved to committing resources towards implementing the SANReN Data Transfer Service (DTS). With the national upgrade of the core SANReN backbone network capacity, 100 Gbps DTNs have been implemented in Cape Town and Johannesburg, South Africa, with Globus data transfer software installed. Traditionally, the DTNs and perfSONAR nodes are implemented as two separate devices, which leads to increased hardware cost and maintenance and becomes more difficult to implement at locations with limited rack space, or high rack space costs. The SANReN Performance Enhancement and Response Team have been novel in their approach to implementing shared infrastructure for South African researchers, as it is costly in the South African research and education context for institutions to implement on their own infrastructure. SANReN is also one of the first National Research and Education Networks (NRENs) to implement the combined DTN/perfSONAR node successfully. Several
Second Life: Enabling a Student Special Interest Group through Decommissioned HPC Systems
(2024) Beukman, M; Jumoorty, S; Faller, J; De Beste, E; Johnston, Bryan J
The prevalence of High Performance Computing (HPC) in scientific research continues to grow, and with this growth, the importance of HPC education and training also increases. However, limited access to advanced research computing resources continues to impede workforce development in resource-constrained environments. In this poster, we describe our student-run HPC special interest group at the University of the Witwatersrand in South Africa, and provide an overview of the practical benefits it provides for students. Our group leverages repurposed decommissioned HPC systems to enable practical hands-on experience with HPC and computing clusters for undergraduate students at our university. We further discuss our group’s approach to selecting and preparing teams for student cluster competitions, where historically we have enjoyed notable success.
Ten years of the HPC Ecosystems Project: Transforming HPC in Africa for the past decade
(2024) Johnston, Bryan J; Timm, Lara C; Macleod, David N; Poole, J
The Council for Scientific and Industrial Research (CSIR)’s National Integrated Cyberinfrastructure System (NICIS) plays a pivotal role in advancing two key initiatives that focus on developing cyberinfrastructure across the African continent: the Southern African Development Community (SADC) Cyberinfrastructure Framework, and the Square Kilometre Array (SKA) Partner Countries Big Data initiative. Within NICIS these initiatives are managed through the HPC Ecosystems Project, which has two primary objectives: dis tributing entry level High Performance Computing (HPC) systems by repurposing decommissioned tier-1 HPC systems, and cultivat ing a skilled HPC workforce across Africa. The first deployment of HPC systems under the project occurred in 2013, using repurposed hardware from the Texas Advanced Computing Center’s decom missioned Ranger HPC system. These systems were allocated to bolster research capabilities at local research institutes in South Africa and within partner countries of the SKA project across Africa. A decade later, at the close of 2023, the HPC Ecosystems Project has deployed 35 HPC systems in 11 countries and delivered more than 30 formal HPC training workshops to over 700 participants, surpassing 21000 total participation hours. There is an active and growing virtual community exceeding 230 HPC practitioners glob ally. This paper provides a high-level overview of the first ten years of the project’s lifespan; outlining the various approaches towards establishing sustainable cyberinfrastructure and HPC workforces in Africa. Included is a reflection on the challenges experienced, lessons learned, and progress made towards delivering cyberin frastructure resources and HPC training to resource-constrained environments.
The use of amino acids in gold leaching; the FTIR and DFT approach
(2024-09) Tapfuma, A; Akdogan, G; Luckay, RC; Lopis, Anton S
The drive towards environmentally benign gold mining, often referred to as ‘green mining’, has gained momentum as a response to the escalating environmental concerns linked to cyanide usage in gold processing. Recently, amino acids have emerged as promising gold-leaching lixiviants, offering advantages over the conventional cyanide methods. However, the bulk of research has predominantly focused on glycine, the first member of the alpha-amino acid group, leaving other amino acids unresearched. In a novel approach, this study shifts the focus to the use of alanine in gold leaching and associated gold-alanine complexation at both experimental and computational levels, coupled with dissolution work. Experimental analyses through Fourier Transform Infrared Spectroscopy (FTIR) showed that alanine, in either its neutral or deprotonated state, effectively bonds with gold through donor electrons from nitrogen (N) and oxygen (O) at the amine and carboxylic end, respectively. In addition, the complexes of deprotonated alanine, compared to neutral (zwitterion) alanine, exhibited higher characteristic peak shifts during complexation. Furthermore, quantum computational calculations revealed that deprotonated alanine formed the most stable gold complex compared to the neutral amino acid, characterized by the N-Au-N bonding. The complexation of gold and deprotonated alanine exhibits the larger complexation energy compared to the neutral form, as revealed by the computational analyses. The third part of the study involved the dissolution of gold using both the deprotonated and neutral molecules, and the results showed that gold dissolution was more pronounced using the deprotonated molecule. This study showed that the gold dissolution is connected to the complexation as shown by FTIR and DFT, and this can be seen in high gold dissolution corresponding to a high peak shift at deprotonation pH and high complexation energy for the gold with the deprotonated alanine compared to the neutral alanine. Lastly, the study suggests that deprotonated alanine can be a possible lixiviant to leach gold from secondary gold sources such as tailings.
Using digital forensics for Android smartphone devices to aid criminal investigations
(2024-03) Agenbag, S; Henney, A; Pieterse, Heloise
In the past decade, there has been an exponential adoption and ownership of smartphones by billions of users worldwide. However, as smartphone usage increases, criminals have taken advantage of them for illicit or criminal purposes. In criminal investigations, smartphone data has become an invaluable source of information. This study focuses on constructing a snapshot of Android-operated smartphone data to assist investigators in answering critical investigative questions. A thorough review of the literature with regard to the use of smartphone evidence in criminal cases, with the goal of emphasising the investigative phase and the supportive role of mobile data evidence in guiding investigations will be performed. In order to identify additional persons of interest and develop a thorough understanding of the case, the methodology will entail analysing user profiles, smartphone usage patterns, communication logs, application usage, geographic lookups, and device interactions. By conducting a thorough examination of relevant literature, designing a suitable model, and executing a case study, the study intends to offer valuable perspectives on the creation of timelines or visual representations derived from smartphone data. The results of this study will contribute to improving the efficacy of mobile forensics in assisting investigators and facilitating the use of Android-operated smartphone data as supporting evidence in criminal investigations.

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