School of Physics (ETDs)

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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
Development of TileCoM firmware and software for the off-detector electronics of the ATLAS Tile Calorimeter at the HL-LHC
(University of the Witwatersrand, Johannesburg, 2023-08) Gololo, Mpho Gift Doctor; Argos, Fernando Carrio; Mellado, Bruce
In 2010 the LHC started to operate as the energy frontier particle accelerator in the world, situated close to Geneva and 100 m below the French and Swiss border in a circular tunnel of 27 km. The HL-LHC which is an upgrade of the LHC is envisioned to maximize the instantaneous luminosity of L = 1 × 1034 cm−2s −1 by a factor of 5 to fully exploit the physics potential at the energy frontier. During 10 years of operation, an improved TDAQ system architecture will have the capability to accommodate the trigger rates and the amount of data generated from the HL-LHC. TileCal is the ATLAS central hadronic calorimeter, a sampling calorimeter with iron as passive medium and plastic scintillator tiles as active medium. The ATLAS TileCal Phase-II upgrades will prepare the ATLAS experiment for the HL-LHC and includes new requirements in terms of radiation levels, an increase in data bandwidth, and clock distribution. To meet the requirements of the HL-LHC, a completely new readout electronics is designed to support the data acquisition system of TileCal. As part of the new readout electronics, this thesis is focused on the design of the TileCoM and Tile GbE Switch. The Tile GbE Switch PCB is manufactured by two South African companies, Trax Interconnect and Jemstech. The PCBs are fully func tional and have been integrated with new readout electronics. Three main function alities are implemented on the TileCoM in software and firmware implementation as key elements of the TDAQ and DCS of the ATLAS TileCal at the HL-LHC. The TileCoM and Tile GbE Switch are successfully integrated with the ATLAS Phase II TileCal upgrade electronics. This is achieved by successful remote control and monitoring of the ATLAS TileCal Phase-II upgrade electronics. This thesis shows monitoring results based on voltage, current and other parameters.
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.
Hunting dark matter with faint radio halos
(University of the Witwatersrand, Johannesburg, 2023-10) Sarkis, Michael David; Beck, Geoff
The nature of Dark Matter (DM), the elusive substance that constitutes a significant amount of the total matter in the universe, remains an unsolved problem in modern physics despite a decades-long search effort. One approach to this problem has been to search for faint emission signatures that are produced indirectly from the DM present in large astrophysical structures, and thus infer properties about theoretical DM models from observational data. In recent years, the results from studies that use this type of indirect search have produced stringent constraints on the most popular DM particle candidate parameter spaces, ruling out swathes of viable DM models. These compelling results have been enabled by the arrival of sophisticated interferometric radio telescopes, which are excellent DM hunters due to their high sensitivity and resolution. In this thesis, we focus on the use of the latest data from the MeerKAT radio interferometry telescope, through the first public release of the MeerKAT Galaxy Cluster Legacy Survey, to search for DM emissions in a set of nearby galaxy clusters. Each step of this process, from the creation of theoretical DM emission models to the statistical analysis of the observational data, has been described in detail in this thesis. With this data, we find an almost universal improvement to results found with corresponding modelling scenarios in the literature. Since this work is among the first to use MeerKAT data in astrophysical DM searches, these results present a strong argument for continued work in this field. Another central focus of this thesis is the accurate modelling of the physical processes involved in the production of the DM-induced radio emissions, as the quality of current radio data requires theoretical models that are sufficiently accurate to describe the emission at such high resolutions. One aspect of the modelling that has lacked this accuracy has been the solution to the diffusion-loss equation, which is a crucial factor in determining indirect DM emissions. A new algorithm for solving this equation, which provides higher accuracy and computational efficiency than previous public methods, has thus been developed and presented in this thesis. These aspects of DM indirect detection study will become ever more important as we approach the inauguration of the Square Kilometre Array (SKA), which will provide data with unprecedented potential with which to continue the hunt for DM.
Implementation of the DAQ software for the ALTI module in the ATLAS TileCal and the search for new physics in the four lepton final state
(University of the Witwatersrand, Johannesburg, 2023-06) Tlou, Humphry Sijiye; Wilkens, Henric; Ruan, Xifeng; Mellado, Bruce
The discovery of the Standard Model (SM) Higgs boson in 2012 presents new challenges and opportunities for the Large Hadron Collider (LHC) experiments. After a long period of operation, the LHC experiments needed to maintain and upgrade their detectors in order to continue and conduct research beyond the SM. As part of the upgrades, the Tile Calorimeter (TileCal) participated in Phase-I of the upgrades (December 2018 - March 2022). TileCal, the central hadronic calorimeter (|η| < 1.7) of the ATLAS experiment uses a set of Trigger and Data Acquisition (TDAQ) software to readout, transport and store physics data resulting from collisions at the LHC. In preparation for the Phase-I upgrades, the ATLAS Local Trigger Interface (ALTI) module was designed for the ATLAS experiment at CERN for TDAQ purposes. It is a 6U VME electronics board, which is a part of the Timing, Trigger and Control (TTC) system. It integrates the functionalities of four legacy modules, currently used in the experiment: Local Trigger Processor, Local Trigger Processor interface, TTC VME bus interface and the TTC emitter. The ALTI module provides the interface between the Level-1 Central Trigger Processor and the TTC optical broadcasting network to the front-end electronics of each of the ATLAS sub-detectors. This thesis discusses the development, validation and integration of the TileCal specific ALTI software in the TileCal online software by the author. A set of ALTI boards were installed in the back-end electronics of the sub-detector and fully validated for the ATLAS detector at CERN. Performance testing and maintenance of the ALTI modules and software were performed during the second half of the upgrade period, in preparation for Run 3 (2022–2025) data-taking period. The thesis also discusses the search for the presence of a new heavy resonance produced via gluon-gluon fusion and decaying to the four-lepton (4ℓ) final state, in association with missing transverse energy (EmissT), with ℓ = e, µ (where ℓ is the lepton, e is the electron and µ is the muon). The search uses 2015–2018 proton-proton collision data at √s = 13 TeV, corresponding to an integrated luminosity of 139 fb−1, collected by the ATLAS detector. The data are interpreted in terms of two models, firstly the R → SH → 4ℓ + EmissT , where R is a scalar boson, which decays to two lighter scalar bosons (S and H). The S decays to a pair of neutrinos and the H decays into 4ℓ, through ZZ bosons. The second model is the A → Z(νν)H(ZZ) → 4ℓ + X, where A is considered to be a CP-odd scalar which decays to a CP-even scalar H and the Z boson. The Z boson decays to X, which can be a pair of neutrinos or jets, and the H decays to the 4ℓ final state.
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.
Modification of boron nitride nanostructures induced by medium energy ion irradiation
(University of the Witwatersrand, Johannesburg, 2023-08) Lisema, Lehlohonolo Innocent; Madhuku, Morgan; Derry, Trevor
This research focused on using Chemical Vapour Deposition (CVD) to synthesize boron nitride nanostructures, particularly nanotubes, and selectively introducing defects into them through ion implantation. Boron ion implantations were carried out at ambient temperature at 150 keV energy and fluences 1x1014 and 5x1014 ions/cm2. The synthesized samples were analyzed using scanning electron microscopy (SEM), Raman spectroscopy, and Grazing incidence X-ray diffraction (GIXRD). Ion implantation was found to introduce defects into the surface of the samples, resulting in increased stress levels and a higher local density that favoured more crystallized nanostructures. SEM images showed clear evidence of BN nanostructures and boron nitride nanotubes (BNNTs), with the latter appearing as long, thin structures with diameters ranging from ⁓30-90nm. After ion implantation, the Raman spectra of samples implanted with ion fluence 5×1014 ions/cm2 at 1000oC, show an amorphous h-BN peak, and a narrower, intense E2g vibrational mode of h-BN is observed around 1366 cm-1 for samples synthesized at 1100oC and 1200oC. Raman analysis did not show any E2g mode of vibration of h-BN for all samples at implanted with ion fluence 1×1014 ions/cm2. The samples synthesized at 900 ºC had no active 1366 cm-1 Raman peak present. Grazing incidence X-ray diffraction (GIXRD) spectra revealed a prominent peak between 54 and 56 ° 2θ, corresponding to the (004) h-BN reflection, which was used to determine the average a and c lattice parameters 0.249 ± 0.0002 nm and 0.662 ± 0.001 nm, respectively, yielding an interplanar distance of 0.166 ± 0.0001 nm representing the stacking direction of the BN layers. The majority of the samples had broad peaks, indicative of a nanocrystalline material. The only exception was the sample grown at 1200 °C, which was found to have a Scherrer crystallite size >100 nm. In contrast, the rest of the samples had an average size of 3.5 ± 0.3nm. The average crystalline domain size values confirmed that after ion implantation, the phonon lifetime would be longer due to a large domain size, indicating that the BN nanostructures were more crystallized. The fluence of 5x1014 ions/cm2 showed to be the optimal growth condition for BNNTs. Overall, BNNTs and BN nanostructures were effectively synthesized at 900°C, 1000°C, 1100°C, and 1200°C CVD temperatures, and insights into the influence of ion implantation on the composition as well as properties of BN nanostructures are presented. The most noteworthy finding of the experiment was the substantial increase in the size of the Raman derived crystallite domains in the 1100°C and 1200°C samples following ion implantation with boron ions at a fluence of 5x1014 ions/cm2.
Optimization of gallium oxide (ga2o3) nanomaterials for gas sensing applications
(University of the Witwatersrand, Johannesburg, 2024) Gatsi, Nyepudzai Charsline
Gas sensors are needed for monitoring different gases in indoor and outdoor environments, food quality assessment, and health diagnostics. Among materials studied for these applications, semiconducting metal oxides (SMOs) have generated a lot of interest due to their excellent sensitivity, simple circuit, and low cost. One-dimensional (1𝐷) 𝐺𝑎2𝑂3 nanomaterials are part of the promising candidates explored for the sensing of different gases due to their excellent electrical conductivity, high catalytic behavior, and chemical and thermal stability. This study reports the optimization of crystal structure, morphology, and surface chemistry of 𝐺𝑎2𝑂3 nanostructures for use in the detection of various gases. A set of unmodified and noble metal modified 1𝐷 𝐺𝑎2𝑂3 nanomaterials were synthesized by microwave-assisted hydrothermal method followed by heat-treatment at different temperatures and their gas sensing performances were systematically studied. The samples were characterized by thermogravimetric analysis (TGA), X-ray diffraction (XRD), Raman analysis, scanning electron microscope (SEM), transmission electron microscope (TEM), Brunauer-Emmett-Teller (BET), photoluminescence (PL), diffuse reflectance spectroscopy (DRS), and X-ray photoelectron spectroscopy (XPS) methods. The effects of heat-treatment temperatures on phase transformations and gas sensing performances of various 𝐺𝑎2𝑂3 polymorphs were investigated. The 𝛼 − 𝐺𝑎2𝑂3, 𝛽 − 𝐺𝑎2𝑂3 and 𝛼/𝛽 − 𝐺𝑎2𝑂3 crystal structures were synthesized and evaluated for gas sensing. The 𝛽 − 𝐺𝑎2𝑂3 sensing layers presented selective response coupled with fast response/recovery times towards carbon monoxide (𝐶𝑂) compared to the 𝛼 − 𝐺𝑎2𝑂3 and 𝛼/𝛽 − 𝐺𝑎2𝑂3 crystal structures. The observed variations in the gas sensing performances of these three crystal structures were attributed to controlled properties of different 𝐺𝑎2𝑂3 polymorphs. Furthermore, the 𝛽 − 𝐺𝑎2𝑂3 polymorph was prepared in the form of regular and hierarchical nanorod-based morphological features which demonstrated different gas sensing behaviors. The 𝛽 − 𝐺𝑎2𝑂3 regular nanorods showed better capabilities of detecting isopropanol than the nanobundle-like and nanodandelion-like features, and these differences were attributed to changes in textural, porosity, and compositional properties related to different morphologies. The effects of incorporating 𝐴𝑔 and 𝐴𝑢 noble metal nanocrystals on regular 𝛽 − 𝐺𝑎2𝑂3 nanorods surfaces on their gas sensing behaviour were also investigated. The results revealed that surface modification of 𝛽 − 𝐺𝑎2𝑂3 nanorods with 0.5 and 1.0 𝑚𝑜𝑙% 𝐴𝑔 and 𝐴𝑢 noble metals significantly lowered the sensor operating temperature compared to that of unmodified 𝛽 − 𝐺𝑎2𝑂3 nanorods towards the detection of ethylene. In addition, surface incorporation of 1.0 𝑚𝑜𝑙% 𝐴𝑔 dramatically increased the sensor sensitivity and selectivity and reduced the response/recovery times towards ethylene gas, and these positive changes were attributed to the electronic and chemical sensitization effects stimulated by the catalytic activity of 𝐴𝑔 nanocrystals incorporated on the surface of 𝛽 − 𝐺𝑎2𝑂3 nanorods. This study unambiguously optimized the crystal structure, morphology, and surface chemistry of 𝐺𝑎2𝑂3 nanostructures for the detection of carbon monoxide, ethylene and isopropanol gases. These sensors may potentially be used in real-time detection of carbon monoxide and isopropanol for indoor air quality monitoring to improve human health. In additional they have also demonstrated capabilities for the precise and economical detection of ethylene around plants and fruits, which could be beneficial to the horticultural and agricultural industries
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.
Search for new resonances in the four-lepton channel and implementation of the LED integrator panel for the PROMETEO system in the ATLAS Tile Calorimeter
(University of the Witwatersrand, Johannesburg, 2024) Mtintsilana, Onesimo; Kumar, Mukesh; Mellado, Bruce
The Large Hadron Collider (LHC) has transformed our understanding of fundamental particles and forces, notably with the seminal discovery of the Higgs boson in 2012, which completed the Standard Model (SM) of particle physics. Despite its success, the SM leaves numerous unanswered questions, motivating a quest for new physics. This thesis explores three main avenues: Firstly, it investigates the possibility of an extended Higgs sector or alternative SM extensions, focusing on heavy ZZ resonances that decay into four leptons. Using a dataset of 139 fb−1 from proton-proton collisions at the LHC, this study explores both gluon-gluon fusion and vector-boson fusion production mechanisms. Although no significant signal for a new resonance is observed, upper limits on the production cross section of spin-0 or spin-2 particles are established. These limits provide constraints on specific theoretical models, such as Type-I and Type-II two-Higgs doublet models for spin-0 resonances, and the Randall-Sundrum model for spin-2 resonances. Intriguingly, the combined results of ATLAS and CMS for Run 2 and Run 3 data in the final state of 4 leptons exhibit an excess around 250 GeV, reaching a significance of 2.4σ which is in the region of interest of the multi-lepton anomalies.. In the second part, the analysis extends to heavy boson decays resulting in a final state with four leptons, specifically focusing on the R boson or the A boson decays into a combination of the SM Higgs boson and another boson, denoted S, which further decays into dark-matter candidates. No evidence contradicting SM predictions is found, yielding stringent upper limits on the production cross-sections of these hypothesised bosons and their branching ratios at a 95% confidence level. Lastly, the thesis highlights advancements in Higgs boson studies and new particle discovery potential in the upcoming High-Luminosity LHC era starting in 2029, emphasising improvements to the ATLAS detector electronics, particularly the integration of a new LED Integrator Panel within the Prometeo portable readout module system, enabling precise calibration and monitoring of individual detector components
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
Study on the influence of Nuclear Deformation on the Pygmy Dipole Resonance in Samarium isotopes
(University of the Witwatersrand, Johannesburg, 2023) Jivan, Harshna; Sideras-Haddad, Elias; Pellegri, Luna
The past decade has seen an increase in studies dedicated to understanding the low-lying electric dipole (E1) response, commonly referred to as the Pygmy Dipole Resonance (PDR). These studies revealed that the PDR has a mixed isospin nature, and that the use of complimentary probes is needed to fully understand this response. Since majority of studies on the PDR focused on spherical nuclei, the influence that deformation has on the PDR response is yet to be understood. Preliminary relativistic proton scattering studies on 154Sm performed at RCNP (Japan), showed potential evidence for a splitting in the PDR responses similar to that of the Giant Dipole Resonance with deformation. A tentative interpretation suggested that this splitting could be connected to the splitting of the resonance structure with respect to the K quantum number. Theoretical studies considering the deformed HFB+QRPA model however, suggest that this splitting is connected to the isospin mixed character of these states as observed in spherical nuclei. The isoscalar responses of the spherical 144Sm and axially deformed 154Sm isotopes were investigated for the first time using the inelastic scattering of alpha particles at 120 MeV. The comparative experiments were performed at iThemba LABS in South Africa, coupling together for the first time, the K600 magnetic spectrometer in zero-degree mode with the BaGeL (Ball of Germanium and LaBr3:Ce detectors) array. The particle-gamma coincidence measurement was used to obtain the cross section for the population of the pygmy states. In both nuclei, the region of the PDR was excited and the E1 multipolarity of the transitions was supported by the angular correlation between the α-particles and the co-incident γ-rays measured. The total exclusive cross section measured for 144Sm amounted to 24.3 ± 3.8 mb/sr while for 154Sm to 18.8 ± 2mb/sr. The experimental results were compared with the prediction of the RQTBA and the deformed HFB+QRPA theories, respectively. The theoretical cross sections were extracted within a semiclassical coupled-channel approach. The fragmentation observed in the experiment for the 144Sm was underestimated by the calculations, although good agreement with the total cross section measured was found. In the case of the deformed 154Sm however, the experimental cross section accounted for only 52% of the predicted cross section in the same excitation region. The isoscalar response extracted in this thesis was compared with the isovector strength obtain from an experiment performed at RCNP using the relativistic proton scattering at forward angles. The double hump observed in the isovector channel was not found in the case of the isoscalar strength. This implies that the difference obtained between these two experiments is related to the “isospin splitting” of the PDR rather than a splitting of thestrength connected with the K quantum number.
The application of weakly supervised learning in the search for heavy resonances at the LHC
(University of the Witwatersrand, Johannesburg, 2023-06) Choma, Nalamotse Joshua; Ruan, Xifeng; Mellado, Bruce
The discovery of the Higgs boson at the Large Hadron Collider by the ATLAS and CMS experiments has made the search for new physics beyond the Standard Model a priority in the field of High Energy Particle Physics. New resonances have yet to be discovered using inclusive and model-dependent searches, which means they may be driven by subtle topologies. Rapid improvements in Machine Learning techniques have led to their increasing application in High Energy Particle physics. Unlike supervised learning, which is known to assume full knowledge of the underlying model, semi-supervised learning, in particular weakly supervised learning, allows the extraction of new information from data with partial knowledge. The goal of this study is to set up searches for heavy resonances at the electroweak scale with topological requirements performed in both inclusive and exclusive regions of phase-space tailored to a particular production mode. These resonances could be generated with different production mechanisms. In this work, we describe search procedures based on weakly supervised learning applied to mixed samples and used to search for resonances with little or no prior knowledge of the production mechanism. This approach has the advantage that sidebands or control regions can be used to effectively model backgrounds without relying on models. The effectiveness of this method is measured by the production of the Standard Model Higgs boson, which decays into a pair of photons in both inclusive and exclusive regions of phase-space at the LHC. Having confirmed the ability of the method to extract various Standard Model Higgs boson signal processes, the search for new phenomena in high mass final states will be set up at the LHC. Subsequently, the approach is used in the search for new resonances in the Zγ final state with Z → e +e − or Z → µ +µ −, using the Monte Carlo simulated signal samples for 139 fb−1 of integrated luminosity for Run 2 collected at the LHC. The weakly supervised learning approach is implemented and compared to the performance of the fully supervised approach, which is then used to calculate the production limit for Higgs-like particles for Zγ where the significance of the signal is maximal.
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
The Large N Limit of Heavy Operator Excitations
(University of the Witwatersrand, Johannesburg, 2023-07) Carlson, Warren Anthony; De Mello Koch, Robert
Operators with bare dimension of order N are studied. These are restricted Schur polynomials labeled by Young diagrams with two long rows or two long columns and are heavy operators in the large N limit. A dramatic simplification of the action of the dilatation operator on these states is found, where the diagonalization of the dilatation operator reduces to solving three-term recursion relations. The solutions to these recursion relations reduce the spectrum of the dilatation operator to that of decoupled harmonic oscillators, showing that these systems are integrable at large N. Then, generating functions for bound states of two giant gravitons are constructed and an extension to more than two giant gravitons is sketched. These generating functions are integrals over auxiliary variables that encode the symmetrization and anti-symmetrization of the fields in the restricted Schur polynomials and give a simple construction of eigenfunctions of the dilatation operator. These generating functions are shown to be eigenfunctions of the dilatation operator in the large N limit. As a byproduct, this construction gives a natural starting point for systematic 1/N expansions of these operators. This includes the prospect to generate asymptotic representations of the symmetric group and its characters via the restricted Schur polynomials. Finally, the asymptotic expansion of the three-point function is computed in three BMN limits by varying one parameter in the large N limit. It is argued that these asymptotic expansions encode non-perturbative effects and are related by a parametric Stokes phenomenon.

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