Research Publications/Outputs

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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 development and validation of a representative MDI-BDO–based polyurethane hard segment model
(2021-01) Karunarathna, B; Jayakody, RS; Karunanayake, L; Govender, Krishna K
Segmented polyurethanes show extraordinary physicochemical properties, mainly owing to the nature and the chemistry of the hard segment domains. There are yet many inexplicable physiochemical properties of MDI-BDO–based hard polyurethane segments such as the geometry, cis–trans isomerism, electronic structure, chemical reactivity, the inter-hard-segment interactions, and the photo-response. In the present study, it was attempted to develop and validate a model system that would facilitate further research on the structural and chemical properties of the MDI-BDO hard segments. It was found that the trans isomer of urethane bond is more stable than the cis isomer, and it is argued here that thermal transformation from trans to cis not possible due to the high rotational energy barrier. The differences between the calculated IR spectra of the cis and trans isomers are proposed as a powerful differentiation tool. The calculated Fukui indices show that cis and trans isomers are different in their chemical reactivity. The findings of the present study suggest intermolecular and intramolecular pi-stacking and highly plausible two significant types of hydrogen bond types between hard segments. In the present study, a model system for MDI-BDO hard segment was developed and successfully validated via computational experiments. Further calculations done with the new model provided an indispensable understanding of the structure, cis–trans isomerism, reactivity, and intermolecular interactions of the MDI-BDO hard segments. The proposed model can be further improved in the future by incorporating suitable soft segments. In summary, the model system developed and validated in the present study has provided new opportunities to understand and further study the structural and chemical features of the hard segments of the MDI-BDO–based polyurethane.
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.
Description of a network attack ontology presented formally
(Springer, 2021-06) Van Heerden, Renier P; Leenen, L; Irwin, B; Misra, S; Tyagi, AK
The identification of network attacks in real-time is becoming increasingly important. Most Artificial Intelligence (AI) applications use machine learning to do the classification of attack types but the advantage of an ontological approach is that automated reasoning is the underpinning theory rather than automated learning. Automated reasoners allow automated classification and this powerful feature is the basis for the developing of an early warning system for active network attacks. In this paper, the authors describe how to employ Semantic Technologies by building an ontology to identify network attack types in order to support the automated classification of current network attacks by recognising relevant properties which are then mapped to relevant attack scenarios depicted in the ontology. The ontology engineering guidelines provided by Noy and McGuinness (2001) were used to build the ontology. The classes and relationships of the ontology are described formally and implemented in Protégé, an ontology editor. A core class in the ontology is the Attack Scenario class that represents different types of network attacks, for example, a Denial of Service attack. The ontology is evaluated by showing two examples of real attacks that correctly classified by the presented ontology. The presented ontology is to be expanded in future work. The aim of this paper is not to present a complete network attack ontology, but rather to present a proof of the concept of how to formally describe such an ontology, with the view to providing a baseline for future development of details. Row examples are explored to demonstrate how specific instances of attacks are classified using the ontology.
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.
A DFT study of two-dimensional CdS/TiS2 on isotropic chalcogenide AgSbTe2 thermoelectric material: Electronic charge transfer and optical properties
(2022-08) Kiarii, EM; Govender, Krishna K; Mamo, MA; Govender, PP
Calculations of AgSbTe2 thermoelectric material and 2d CdS/TiS2 and their heterostructures were carried out using Density Functional Theory in Cambridge Serial Total Energy Package code as implemented in Material Studio 2018 software. The work function, thermal transport, electronic and optical properties were calculated. The results revealed that the heterostructures are possible to be achieved with improved properties. The electronic and thermal transport properties were likened with the description of equations derived from Boltzmann transport theory and Mott expressed in the maximum achievable Figure merit. Orbital contributions from the electron movement show valence and conduction band atomic shells.
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.
Isoniazid-loaded orodispersible strips: Methodical design, optimization and in vitro-in silico characterization
(2021-08) Adeleke, Oluwatoyin A; Tsai, P; Karry, KM; Monama, Nkwe O; Michniak-Kohn, BB
Drug treatment remains the most effective global approach to managing and preventing tuberculosis. This work focuses on formulating and evaluating an optimized polyvinyl alcohol-polyethylene glycol based orodispersible strip containing isoniazid, a first-line anti-tubercular agent. A solvent casting method guided through a Taguchi experimental design was employed in the fabrication, optimization and characterization of the orodispersible strip. The optimized strip was physically amalgamated with a monolayer, uniformly distributed surface geometry. It was 159.2 ± 3.0 µm thick, weighed 36.9 ± 0.3 mg, had an isoniazid load of 99.5 ± 0.8%w/w, disintegration and dissolution times of 17.6 ± 0.9 s and 5.5 ± 0.1 min respectively. In vitro crystallinity, thermal measurements and in silico thermodynamic predictions confirmed the strip's intrinsic miscibility, thermodynamic stability and amorphous nature. A Korsmeyer-Peppas (r = 0.99; n > 1 = 1.07) fitted kinetics typified by an initial burst release of 49.4 ± 1.9% at 4 min and a total of 99.8 ± 3.3% at 30 min was noted. Ex vivo isoniazid permeation through porcine buccal mucosa was bi-phasic and characterized by a 50.4 ± 3.8% surge and 95.6 ± 2.9% at 5 and 120 min respectively. The strip was physicomechanically robust, environmentally stable and non-cytotoxic.
Model inter-comparison for short-range forecasts over the southern African domain
(2021-09) Mulovhedzi, PT; Rambuwani, GT; Bopape, MJ; Maisha, R; Monama, Nkwe O
Numerical weather prediction (NWP) models have been increasing in skill and their capability to simulate weather systems and provide valuable information at convective scales has improved in recent years. Much effort has been put into developing NWP models across the globe. Representation of physical processes is one of the critical issues in NWP, and it differs from one model to another. We investigated the performance of three regional NWP models used by the South African Weather Service over southern Africa, to identify the model that produces the best deterministic forecasts for the study domain. The three models – Unified Model (UM), Consortium for Small-scale Modelling (COSMO) and Weather Research and Forecasting (WRF) – were run at a horizontal grid spacing of about 4.4 km. Model forecasts for precipitation, 2-m temperature, and wind speed were verified against different observations. Snow was evaluated against reported snow records. Both the temporal and spatial verification of the model forecasts showed that the three models are comparable, with slight variations. Temperature and wind speed forecasts were similar for the three different models. Accumulated precipitation was mostly similar, except where WRF captured small rainfall amounts from a coastal low, while it over-estimated rainfall over the ocean. The UM showed a bubble-like shape towards the tropics, while COSMO cut-off part of the rainfall band that extended from the tropics to the sub-tropics. The COSMO and WRF models simulated a larger spatial coverage of precipitation than UM and snow-report records.
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.
Quantum mechanistic studies of the oxidation of ethylene by rhenium oxo complexes
(2021-08) Fosu, EA; Obuah, C; Hamenu, L; Aniagyei, A; Ainooson, MK; Govender, Krishna K
Transition-metal-mediated oxygen transfer reactions are of importance in both industry and academia; thus, a series of rhenium oxo complexes of the type ReO3L (L=O-, Cl-, F-, OH-, Br-, I-) and their effects as oxidation catalysts on ethylene have been studied. The activation and reaction energies for the addition pathways involving multiple spin states (singlet and triplet) have been computed. In all cases, structures on the singlet potential energy surfaces showed higher stability compared to their counterparts on the triplet potential energy surfaces (PESs). Frontier Molecular Orbital calculations show electrons flow from the HOMO of ethylene to the LUMO of rhenium for all complexes studied except ReO4- where the reverse case occurs. In the reaction between ReO3L (L=O-, Cl-, F-, OH-, Br-, and I-) and ethylene, the concerted [3+2] addition pathway on the singlet PES leading to the formation of dioxylate intermediate is favored over the [2+2] addition pathway leading to the formation of a metallaoxetane intermediate and subsequent rearrangement to the dioxylate. The activation and the reaction energies for the formation of the dioxylate on the singlet PES for the ligands studied followed the order O->OH-I->F->Br->Cl- and O->OH->F->I->Br->Cl-, respectively. Furthermore, the activation and the reaction energies for the formation of the metallaoxetane intermediate increase in the order O->OH->I->Br->Cl->F- and O-> Br->I->Cl->OH->F-, respectively. The subsequent rearrangement of the metallaoxetane intermediate to the dioxylate is only feasible in the case of ReO4-. Of all the complexes studied, the best dioxylating catalyst is ReO3Cl (singlet surface) and the best epoxidation catalyst is ReO3F (singlet surface).
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.
A systems thinking approach to value-added services adoption in national research and education networks
(2021-09) Pillay, Kasandra; Erasmus, Louwrence D; Pretorius, JC
The growing importance of advanced or value-added services (services over and above basic connectivity services) in national research and education networks (NRENs) is well understood in the research and education community. These services are made available to further distinguish and enhance national research and education networks’ offerings from that of commercial internet service providers. Systems thinking allows a ‘bigger view’ of a situation to be analyzed. This paper presents a model that was developed, refined and validated using design science research methods and a systems thinking approach. The model is a causal diagram developed to enable the visualization of how factors in the NREN services adoption context are interrelated. The model was refined and validated with international NREN experts. As a result of the evaluation stage, a shared mental model and understanding of the NREN’s advanced services delivery ecosystem was developed. The model can be used as a communication and decision-making tool to facilitate services adoption from NRENs to their research and education communities.
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.
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.
Utilisation of a virtual honeynet to proactively secure the South African National Research and Education Network against cyberattacks
(2024-07) Meyer, Heloise; Barbour, Graham D; McDonald, Andre M; Badenhorst, Danielle P; Gertenbach, Wian P
South Africa is witnessing a significant increase in cyberattacks. Although such an increase in cyberattacks can be attributed to various factors, poor investment in cybersecurity technology and lack of awareness are causing South Africa to be a target of interest. While cyberattacks are targeting various sectors, it is the cyberattacks impacting critical infrastructure that are a growing concern. The South African National Research and Education Network (SA NREN) is a high-speed network dedicated to science, research, education and innovation traffic. With the growth of the SA NREN and the continuous increase in cyberattacks affecting South African institutions, proactive steps are required to secure and protect the SA NREN. This responsibility lies with the SA NREN Cybersecurity Incident Response Team (CSIRT), which was established in 2016 to offer protection against cyberattacks. While various proactive measures are currently in place to monitor the SA NREN, the CSIRT continues to explore alternative cost-effective solutions to secure the NREN. This paper investigates the benefits of utilising a novel low-interaction secure shell (SSH) honeynet, referred to as the Virtual Honeynet, to monitor and proactively secure the SA NREN. The Virtual Honeynet uses virtual containers to reduce resource requirements and improve performance. The investigation involved the experimental deployment of the Virtual Honeynet on the SA NREN over a twelve-day period and the evaluation of the captured data. The evaluation conducted focused on extracting behavioural and geographical intelligence from the raw data to guide the deployment of cyber measures to secure the SA NREN. The results presented in this paper confirm the value the Virtual Honeynet offers to the SA NREN as a technology to proactively secure the network.

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