Electronic Theses and Dissertations (Masters)

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Chromatin accessibility changes during early monocyte-to-macrophage differentiation
(University of the Witwatersrand, Johannesburg, 2024) Xu, Yi Fan; Meyer, V.; Gentle, N .
The differentiation of monocytes into macrophages is a crucial process that enhances the local immune response against infection by recruiting monocytes to local tissues and transforming them into macrophages. The changes in gene expression associated with this process are known to be regulated by various mechanisms, including the chromatin accessibility landscape. Previous in vitro studies have shown that promonocytic THP-1 cells can differentiate into macrophage-like cells following treatment with phorbol 12-myristate 13-acetate (PMA). While previous studies have attempted to track the differentiation process over time, there has been a lack of research specifically focusing on earlier time points. Therefore, in this study, we used various publicly available RNA-seq, ATAC-seq and ChIP-seq datasets to describe the early events involved in monocyte-to-macrophage differentiation, using THP-1 cells treated with 100 ng/ml PMA for 24 hours as the model system. ATAC-seq data were aligned to the reference human genome (GRCh38) using Bowtie2 and chromatin accessibility peaks were identified using HMMRATAC. Differentially accessible chromatin regions (|L2FC| > 2; FDR < 0.05) were identified using DiffBind, and were annotated based on their cis-regulatory features. These included promoter regions (based on the GENCODE v40 annotations of the human genome) and THP-1-specific enhancers (defined as known enhancers within the GeneHancer database with an overlapping, THP-1-specific, H3K27ac mark). These cis-regulatory features were then associated with genes found to be significantly differentially expressed in response to PMA treatment (|L2FC| > 2; p.adj < 0.05), following quantification of gene expression using Salmon and differential gene expression analysis using DESeq2. The results of this study revealed that the early response to PMA in THP-1 cells is linked to changes in both gene expression and chromatin accessibility. These changes in both gene expression and chromatin accessibility were shown to be linked with inflammatory responses and cell migration activities. Although there was only a limited association between changes in gene expression and chromatin accessibility at the 24-hour time point, opening of chromatin at promoter and enhancer regions and increased gene expression was observed for many genes previously reported to be involved in the process of monocyte-to-macrophage differentiation, including CSF1, CSF1R, and IL-1α/β. This suggests that changes in chromatin accessibility at cis-regulatory elements taking place early in the differentiation process drive the changes in gene expression necessary for monocyte-to-macrophage differentiation
Feasibility and the facilitation of off-site treatment planning services at Charlotte Maxeke Johannesburg Academic Hospital
(University of the Witwatersrand, Johannesburg, 2024) Otten, Joseph Johannes; Ngcezu, Sonwabile
The report encapsulates the comprehensive commissioning and validation process undertaken to integrate the Varian Eclipse treatment planning system (TPS) with Elekta Versa HD™linear accelerators, enabling off-site treatment planning services (OTPS). The initiative aimed to enhance the efficiency of treatment planning and expand access to care. The process involved meticulous collection and modelling of beam data from four Versa HD™Linacs within the Eclipse system. Measurements were conducted to characterize the beam properties, including profiles, percent depth dose (PDD) curves, and output factors (OF). A pivotal aspect of the validation was the acquisition and verification of the computed tomography (CT) to electron density curve, which is crucial for accurate dose calculations. The Anisotropic Analytical Algorithm (AAA) was employed for dose calculations, with its accuracy confirmed through point dose measurements and gamma index comparisons. Fine-tuning of multi-leaf collimator (MLC) transmission and dosimetric leaf gap (DLG) parameters was achieved through iterative plan measurements and optimisations. The culmination of the validation process was the end-to-end testing, adhering to the International Atomic Energy Agency (IAEA) audit methodology, utilising CIRS phantoms (Clark et al., 2019). This testing was conducted on the clinical servers, with patient-specific quality assurance results exhibiting gamma pass rates above 90% for distance to agreement (DTA) of 3mm and a dose difference (DD) 3%, indicative of the system’s accuracy. The study demonstrated the feasibility of remote treatment planning for Elekta Linacs using the Varian Eclipse TPS. The rigorous commissioning and validation pro- cess ensured the dosimetric accuracy and quality of the integrated system. The successful validation of the Eclipse TPS for clinical use suggests that this integration could significantly streamline the planning work, potentially alleviating treatment backlogs and enhancing the delivery of care in radiation therapy.
Leveraging Machine Learning in the Search for New Bosons at the LHC and Other Resulting Applications
(University of the Witwatersrand, Johannesburg, 2023-09) Stevenson, Finn David; Mellado, Bruce
This dissertation focuses on the use of semi-supervised machine learning for data generation in high-energy physics, specifically to aid in the search for new bosons at the Large Hadron Collider. The overarching physics analysis for this work involves the development of a generative machine learning model to assist in the search for resonances in the Zγ final state background data. A number of Variational Auto-encoder (VAE) derivatives are developed and trained to be able to generate a chosen Monte Carlo fast simulated dataset. These VAE derivatives are then evaluated using chosen metrics and plots to assess their performance in data generation. Overall, this work aims to demonstrate the utility of semi-supervised machine learning techniques in the search for new resonances in high-energy physics. Additionally, a resulting application of the use of machine learning in COVID-19 crisis management was also documented.
Modelling the Sensitivity of the KM3NeT/ARCA and KM3NeT/ORCA to Neutrinos from Quiescent Blazars
(University of the Witwatersrand, Johannesburg, 2023-09) Nkosi, Bhuti Linda; Chen, Andrew
Blazar jet emission has been modelled using two families of models, leptonic and hadronic, to explain the double-peaked SED. In hadronic models, the higher energy peak is explained by proton interactions with the jet material and external fields. Lepto-hadronic models are a type of blazar emission model that accounts for both leptonic and hadronic processes in the jet. In these models, the low-energy bump of the spectral energy distribution SED is produced by synchrotron radiation from primary electrons, while the high-energy bump is produced by a combination of radiation from protons and secondary particles. Lepto-hadronic models can explain the variability and spectral features of blazars in different states, such as flaring or quiescent. In this project, we used a one-zone lepto-hadronic model to simulate the blazar jet and calculate the neutrino emission and detection prospects with KM3NeT.
Properties of composite nanomaterials for gas sensor applications
(University of the Witwatersrand, Johannesburg, 2023-09) Diantantu, Aime Diakanwa; Usman, Ibrahim
Sensors are- important devices nowadays that have been instrumental towards the development of the Internet of Things (IoT) amongst other recent technological innovations. They are used to detect and respond to some form of input or stimulus from the environment we are living in. There are different types of sensors in the market nowadays, depending on the materials used for their manufacture and their applications, namely position sensors, pressure sensors, gas sensors, etc. Gas sensors use semiconductors as materials. Metal oxides, conducting polymers, carbon nanotubes, graphene, and transition metal chalcogenides are some semiconductors materials used in gas sensors. Metal oxides are very good gas sensors materials due to their low cost, high stability, and sensitivity but their high operating temperature disqualify them. Conducting polymers are also good sensors materials due to their flexibility and low operating temperature but they are altered by humidity. To counteract humidity problem, conducting polymers need to be modified or doped with selected elements or molecules. In this project, cellulose was drugged with carbon nanotube (CNT) to create a mechanically and chemically stable structure, which can interact and sense many gases. The chemical and physical properties of cellulose make it a potential material for the development of conductive and potential sensing stuff. This led to the focus of this investigation, which is the development of mixed cellulose nanocrystal (CNC) – CNT materials for sensor application. The CNC was synthesized through the Tempo oxidation method, and various amounts of CNT were added into the CNC below the aggregation threshold of 2.5% using ultrasonication to form a CNC – CNT rectangular sheet. The developed mixed materials were characterized using Scanning Electron Microscopes (SEM) and Transmission Electron Microscope (TEM) to determine the morphology. Fourier Transform Infrared (FTIR), Raman Spectroscopy and X-ray Diffraction (XRD) were employed to investigate the structure of the final material, while TGA has shown similar degradation temperatures of CNC and CNC – CNT. SEM images showed an interconnected network-like structure with a porous architecture assembled by curved thin sheets, and the increase in CNT resulted in aggregate formation within the CNC. TEM micrographs confirmed the structure of CNC, which was rod-like and artefactual dendrites particles, and the presence of CNT in the matrix, while FTIR confirmed the main functional groups of the mixed matrix sheet. The degree of graphitization and presence of disordered cellulose in the mixed materials were determined by Raman spectroscopy to vary between 0.98 and 1.2. The XRD pattern has shown that the crystallinity index of the CNC – CNT composite is correlated to the increase in the concentration of CNT. However, the TGA data has shown that the CNC – CNT materials exhibited similar thermal behaviour, this is expected, since the concentrations of the composites have similar bonding structure and configuration compared to the pristine CNC. It is also evident that the increase in CNT content reduces the thermal degradation (reduced slope) of the CNC. The research work has developed CNC – CNT materials for sensor applications. The composite has exhibited sensor response and thereby detected H2, CO2, NO2 and Ar gases at room temperature through the changes in their electrical conductivities. The ability of CNC-CNT to respond to these gases at room temperature opens-up the possibility for its easy use in indoor and outdoor monitoring.
Skyrmions and vectorial wavefunctions
(University of the Witwatersrand, Johannesburg, 2024) Ornelas, Pedro; Forbes , Andrew
The study and generation of robust structured light stand as compelling areas of focus in the exploration of future classical and quantum photonic technologies. While the appeal of structuring light in all its degrees of freedom (DOFs) is undeniable, achieving the generation of intricate light resilient to noise from multiple sources, such as faulty detectors, stray white light, and atmospheric turbulence, is imperative for its practical integration into forthcoming technologies. Recently, there has been a lot of interest in generating states of light with identifiable topological features which are robust to local deformations thus providing such states with a possible mechanism for noise rejection. Topological structures known as optical skyrmions have garnered a lot of interest in the optics community of late as their magnetic counterparts have shown great promise as potential low-power information carriers. It has been shown that skyrmionic structures may be realised in classical free-space optical beams where their spatial and polarization DOFs are appropriately combined and manipulated to generate what are known as vector beams. Furthermore with the emergence of quantum structured light allowing for the manipulation of an individual photon’s DOFs, such topological structures may also be utilized as a resource for photonic based quantum technologies. In this dissertation we investigate the generation of classical optical skyrmions through the use of Bessel-Gaussian optical modes possessing interesting propagation dynamics which mimic magnetic systems under the application of a magnetic field. Furthermore, we extend the study of optical skyrmions to the quantum realm by generating and characterizing the topology of the quantum analogue to classical vector beams: hybrid entangled states where the spatial DOF of one photon is entangled with the polarization DOF of another. In this case the skyrmionic topology emerges as a shared property of both photons and can be identified through investigating their mutual correlations. We postulate a novel topological characterization of entangled states with the corollary that smooth deformations of these states do not change their topology and thus do not change how they are characterized. We show that the topology remains intact even when entanglement is fragile and further discuss how a typical mechanism for entanglement decay can be characterized as a smooth deformation. Lastly, we investigate the topological resilience of hybrid entangled states in the presence of isotropic noise usually attributed to external sources. We demonstrate the invariance of the topology of these states to varying levels of isotropic noise and discuss the associated mechanism for this invariance.
Solar cell simulation using ab initio methods
(University of the Witwatersrand, Johannesburg, 2024) Zdravkovi´c, Milica; Quand, Alexander; Warmbier, Robert
Solar cells are a great source of renewable energy, but they are yet to reach their thermodynamic efficiency limits. Common commercial solar cells run at approximately 20% power conversion efficiency, and almost all efficiency loss comes from thermalisation. Ab initio simulations can reduce the need for physical experiments to quantify these losses while also providing insights into the quantum mechanical properties of materials. Note that density functional theory reformulates the expression for the ground state energy of a many particle system such that it is a functional of the electron density, thereby allowing the electronic energy to be solved for numerically. But the underlying mechanism behind thermalisation is the electron-phonon interaction. Using the theory of Green’s functions, the electron-phonon interaction self-energy and charge-carrier life times can be calculated. A method of approximating the charge-carrier lifetimes using the hydrostatic deformation potential interaction, which is only valid for longitudinal acoustic phonons, is presented. Deformation potentials of -10.125eV for Silicon and 18.663eV for Gallium Arsenide, commonly used solar cell materials, are calculated in good agreement with literature. Furthermore, the electron-phonon interaction life- times were calculated to be in the order of 2.0 × 10−15s for Si and 4.0 × 10−16s for GaAs, which could have indications that the optimal thickness of a GaAs absorption layer is much thinner than for Si. Thus the deformation potential method provides a satisfactory approximation for the electron-phonon quasiparticle lifetimes based on ab initio methods
The culprit for the termination of Mars’ magnetic field: Dark Matter
(University of the Witwatersrand, Johannesburg, 2024) Makda, Javeria
The reason for a significant change in the heat flux of the interior of Mars, leading to the termination of its magnetic dynamo, is not yet known. We present the idea that interaction of dark matter particles with the elements constituting the core of Mars is the cause for this significant heat flux change. We include resonant enhancements in the determining of the capture rate of dark matter particles by a planet, using more recent formulations. The exclusion limits for the interaction cross-sections in our work are more stringent than previous limits. We demonstrate, using Xenon1T limits, that the density of dark matter in our solar neighbourhood is insufficient to induce significant heating. However, encounters with low-mass ultra-compact mini-halos or very massive conventional sub-halos could both produce significant heating effects within terrestrial planets. We find that in 1 Gyr, there is a possibility of up to ∼ 860 interactions of Mars with an ultra-compact mini-halo, that would have the sufficient density and mass to alter the workings of the convective core of Mars, such that it would lead to the cessation of the Martian geodynamo. The interaction of Earth with these halos would not result in the cessation of its magnetic field due to mechanisms such as tectonic activity, crust recycling and the subsequent motion of molten iron in its outer core, which result in the continuous functioning of the geodynamo
The development of a burn-in test station at Wits for the Phase-II upgrade of the Tile Calorimeter of the ATLAS experiment
(University of the Witwatersrand, Johannesburg, 2023-07) Njara, Nkosiphendule; Mellado, Bruce
The University of the Witwatersrand is responsible for producing over 1200 Low Voltage Power Supply (LVPS) bricks to power the on-detector electronics of the Tile Calorimeter (TileCal) of the ATLAS detector in preparation for the Phase II upgrade. The LVPS brick is a DC/DC switch-mode power supply module that steps down a 200 VDC input to a 10 VDC output. Before being sent to CERN for installation, the LVPS bricks must undergo a quality assurance test. To ensure that these electronic devices meet the necessary standards for high-quality and reliability, the University of the Witwatersrand employs a burn-in test station that subjects them to electronic tests at elevated temperatures and other stressful conditions. The burn-in test station comprises of different Printed Circuit Boards (PCBs), each responsible for various functions, and a PIC microcontroller needs to be programmed for each board to perform its respective functions. An assembler MPLABX IDE and a compiler (CCS) are used for programming the PIC microcontroller, and the Labview software is used as the control program for the burn-in test station. A simulation was used in Proteus software to test the firmware functionality before programming the hardware. Preliminary results of the current version (version 8.4.2) of the LVPS brick are discussed.
The development of a burn-in test station for the ATLAS Tile Calorimeter Low Voltage Power Supplies for phase II upgrades
(University of the Witwatersrand, Johannesburg, 2022) Lepota, Thabo James; Mellado, Bruce
It is planned that the High Luminosity (HL) function of the Large Hadron Collider (LHC) will begin operation in 2027 with an integrated luminosity of 4000 fb−1.By using the HL-LHC scientists will be able to investigate new physics beyond the Standard Model (SM), examine electroweak symmetry in more detail, and examine the characteristics of the Higgs boson. The ATLAS Tile Calorimeter’s on and off detector electronics will be completely redesigned during phase II upgrade, run 3. Due to the high radiation levels, trigger rates, and high pile-up conditions associated with the HL-LHC era, it will be necessary to accommodate its acquisition system. The Institute of Collider Particle Physics is responsible for developing and manufacturing over a thousand transformer-coupled buck converters, known as Bricks, for the Low Voltage Power Supply (LVPS) system. The LVPS is critical to the TileCAL on detector electronics as it powers them by converting 200 V high voltage to 10 V. The Bricks are located within the inner barrel, they can only be accessed once a year. If an LVPS box fails, it can be down for up to a year, causing the Front-End electronics it supports to remain offline for the same amount of time. As a result, the Bricks’ reliability is of critical concern that must be addressed throughout their manufacturing process. In addition to the burn-in test station, the Bricks that pass the quality assurance tests are sent to the European Organization for Nuclear Research (CERN), to be installed in the ATLAS detector. In this manuscript, we show how we programmed the Peripheral Interface Controller (PIC) firmware, which is an integral part of the Brick Interface board functionality in the burn-in test station. We further give detail as to how the software framework (LabVIEW) used as a control program was modified and used to operate the burn-in test station during the burn-in process. The purpose of the test results discussed is to demonstrate the burn-in test station is functional according to the preliminary protocols prescribed for Bricks
The Eigenmodes of Complex Media
(University of the Witwatersrand, Johannesburg, 2024) Peters, Cade Ribeiro; Forbes, Andrew
Structured light refers to the tailoring of light in all of its degrees of freedom. This includes amplitude, phase, wavelength and polarisation. Structuring light allows us to create complex optical fields with many interesting and useful properties. These fields have allowed us to ask deeper and more fundamental questions about Physics and have revealed new avenues for investigating aspects of the world around us. They have allowed us to significantly increase the speed at which we communicate and make information more accessible. Additionally, they allow for increased resolution and precision in imaging and measurements, both classical and quantum. One of the primary limitations when using structured light are the effects of perturbations. Many complex media, such as the atmosphere, underwater or biological specimens have a non-uniform refractive index (varying dielectric constant). This distorts most structured light beams, limiting its performance and possible uses. This works seeks to investigate this problem and offer a solution. Much attention has been given to finding which forms of structured light perform best in certain systems or scenarios. This work focuses on offering a potential solution to this problem. We begin with a discussion on common forms of structured light and models of light propagation. We then move onto methods for generating structured light experimentally. We then propose the concept of an eigenmode: modes that are perfectly invariant through such systems. They are structured light fields that are specially tailored, using our knowledge and understanding of the Physics of the system, to ensure that they propagate through the system and exit unchanged. We achieve this by modelling our system as a linear operator and then using this to find the eigenstates of this operator. We do this for two highly topical aberrations, providing approaches that can be generalised to almost any optical system. We end off this work with a discussion on important considerations when using eigenmodes for real world applications
Vacuum Arc Propulsion Systems for In Space Refuelling and Small Satellite Applications
(University of the Witwatersrand, Johannesburg, 2023-09) Stansell, Paul Robert; Lafleur, Trevor; Ferrer, Phil
In this work a compact and low power vacuum arc ion thruster and related circuitry were built utilising a vacuum arc thruster (VAT) as the plasma source. A number of VAT designs were tested before the final ion thruster design comprising of a modified coaxial VAT with a copper cathode and an extended anode grid to reduce peak ion currents was chosen. This design was chosen as it produced the best performance and prevented excessive grid arcing which was a problem encountered throughout this work. The final ion thruster required only one liter of volume, excluding electronics, and could be operated at an average power of less than one watt. Pulsed ion beams of up to 20 ± 1.4mA of copper ions with beam energy 3.23 ± 0.22keV lasting on average 320µs were produced by the system and detected by a plate downstream of the thruster. The grid system was unable to extract the large ion currents produced by the VAT which meant the overall electrical efficiency, thrust to power ratio and specific impulse were low compared to existing gas-fueled gridded ion thrusters; 2.28%, 0.474mN/kW and 33s respectively. Finally, a metallic meteorite sample was used as the cathode in a planar VAT and the ion current was measured. It was concluded that the vacuum arc ion thruster is a promising propulsion system for small satellites and has potential for refuelling from metals present in the space environment. This study adds a novel, miniature, low power and low beam voltage design to the limited literature on vacuum arc ion thrusters.

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