School of Physics (ETDs)
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Item Optimization of Prostate Plan in a Pelvic Prosthesis Phantom(University of the Witwatersrand, Johannesburg, 2024-09) Dumela, Khombo Eunice; Oderinde, Oluwaseyi M.; Usman, IyaboT.Background: An increasing number of elderly prostate cancer patients with high-density material hip prosthesis are referred for external beam Radiotherapy (EBRT). Radiation treatment of pelvis cancer patients with high-density hip prosthesis needs special attention because of the artifacts created in the computed tomography (CT) field of view and the radiotherapy dosimetry challenges. The accuracy of the treatment planning dose calculation algorithms determines the accuracy of the dose delivered to the patient during radiation therapy. However, the most available algorithms do not accurately model the absorption of high-density metals’ scattering properties and underestimate the resulting dose perturbations. Aim: This study aims to optimize the dose distribution of prostate 3D conformal treatment, intensity-modulated radiotherapy (IMRT) and volumetric-modulated arc therapy (VMAT) in an in-house metallic hip prosthesis phantom. Methods and materials: In this study, an ionization chamber and Gafchromic (EBT3) films were used to physically measure the prostate point dose in an in-house pelvic phantom. The pelvic phantom was irradiated on the Linac with four static fields, namely, (1) anterior field, (2) posterior field, (3) right lateral field passing through the bone of the normal hip and (4) left lateral passing through the hip prosthesis. IMRT and VMATs plans were also generated on the phantom. The phantom was also irradiated with IMRT and VMATs plan. The use of single arc versus two arcs with avoidance sector were also evaluated. The phantom consists of different materials; Nylon-12 (a solid water-equivalent material) to simulate the prostate with a central cavity to accommodate an ionization chamber and film, superflab gel bolus to simulate human soft tissue, dental wax to simulate human soft tissue, bone anatomy for the right hip and a titanium implant to replace the bony structure of the left hip. For the static fields, an in-house pelvic phantom was simulated using the EGSnrc Monte Carlo code, and 6 and 15 MV photon energies were employed as in an experimental setting. The prostate point doses computed by the Treatment Planning System (TPS), measured using ionisation chamber, and Gafchromic EBT3 film were compared with the prostate point doses simulated by Monte Carlo code. Results and discussion: The novel phantom was constructed using superflab gel bolus, Nylon-12, dental wax, pig bone insert and a titanium alloy hip replacement. The radiological equivalence of the superflab gel bolus and dental wax was determined employing linear attenuation coefficients and then compared to an RW3 Solid water phantom. EGSnrc Monte Carlo (MC) code was used in this study. Before using Monte Carlo codes, they need to be validated by comparing the Linear accelerator Monte Carlo simulated dose distribution with the experimental data measured in a Linear accelerator using water and ionization chamber for 6 MV and 15 MV photon beams of different field sizes. The EGSnrc dose distributions were compared with the experimental measurements using a gamma analysis, employing a 2 %/2 mm distance-to-agreement criterion. The EGSnrc Monte Carlo calculated dose distribution agreed well with experimental measurements within 2 %. The MC beam model was then used to compute the dose distribution in an in-house pelvic phantom. The comparison of the measurements between the TPS calculated prostate point dose and ionization chamber for the 6 MV and 15 MV photon beams was: anterior (gantry 0°) 1.8 % and -0.5 %; posterior (gantry 180°) 1.7 % and -0.2 %; left lateral (gantry 90°) 6.3% and 4.2 %; right lateral (gantry 270°) -2.2 % and -2.1 % respectively. Results obtained for Gafchromic EBT3 film measured doses were: anterior 2.3 % and 1.3 %; posterior -0.9 % and 0.2 %, left lateral 4.5 % and 3.5 %; right lateral -2.1 % and -2.5%, for the 6 MV and 15 MV photon beams, respectively. Consequently, results obtained for comparison of TPS, ion chamber and Film with MC simulated doses were: anterior 3.9 %, -2.1 and -1.6% %; posterior 1.8 %, -0.1% and -2.7 %; left lateral -0.2 %, 6.5 % and 4.7 %; right lateral 0.4 %, -2.6% and -2.5 %, for the 6 MV photon beam. And for 15 MV photon beam the results were: anterior 1.9 %, -3.8 and -0.6%; posterior 2.0 %, -2.3 % and -2.2 %; left lateral 0.5 %, 3.7 % and 2.9 %; right lateral 0.4 %, -2.4 % and -2.9 %. Monte Carlo simulations and film measurements have a statistically significant difference of p<0.001, with the film measurements having a higher value than MC simulations except on the left lateral field. Monte Carlo simulations and ionization chamber measurements also show a significant difference of p<0.001, with the ionization chamber having a higher value than the MC simulation, except for the left lateral field passing through the hip prosthesis. The comparison of the measurements between the TPS calculated prostate point dose with ionization chamber and Gafchromic EBT3 film for the 6 MV IMRT plan of the beam passing through the prosthesis was 2.2 % and 3.3%, respectively. While the IMRT plan with avoided beam was 1.9 % and 3.1% for ionization chamber and Gafchromic EBT3 film, respectively. The comparison of the measurements between the TPS calculated prostate point dose for the 6 MV VMAT plan without avoiding for the beam passing through the prosthesis was 1.1 % and 2.2 % for ionization chamber and Gafchromic EBT3 film, respectively. While for VMAT plan with avoided sector as 3.0 % and 4.0% for ionization chamber and Gafchromic EBT3 film, respectively. The test suggested a significant difference of p=0.0001 between the distribution of film measurements and TPS calculated dose. Meanwhile, for ionization chamber measurements and TPS calculated dose; the test indicated a significant difference between ion chamber measurements and TPS calculated dose with a significant level of less than 0.001. in addition, MC simulated dose and TPS calculated dose; the test shows a percentage difference of -0.2 % and 0.5 % for 6 MV and 15 MV photon beams in the lateral field that passes through the prosthesis. The test indicated the significant difference of p=0.001 which is slightly lower compared to the other comparisons. Conclusion: The dual dosimetric pelvic prosthesis phantom is easy to assembly and is more convenient for second dose check for patients with hip prostheses. Through the use of the pelvic phantom, it was possible to measure the prostate point dose using ionization chamber and films. The TPS overestimated the prostate point dose because the treatment planning algorithm could not accurately determine the CT number and the electron density of the prosthesis due to the limitation on the CT scanner. The maximum deviation calculated in this study for TPS, ionization chamber Gafchromic EBT3 films when compared to Monte Carlo simulated dose comes from the lateral fields passing through the prosthesis for both 6 MV and 15 MV photon beams.Item Exploring the 95 GeV Excess with Extended Scalar Models(University of the Witwatersrand, Johannesburg, 2024-10) Mulaudzi, Anza-Tshilidzi; Mellado, Bruce; Kumar, MukeshThis thesis focuses on three interconnected studies investigating the presence of an additional scalar particle, S, of mass around mS ≈ 95 GeV. In the initial study, we explore the notion that an SU(2)L triplet scalar, characterised by a hypercharge Y = 0, could be the origin of the observed 95 GeV di-photon (γγ) excesses seen at ATLAS and CMS. By thoroughly examining its properties, particularly the neutral component, and considering a small mixing angle with the Standard Model Higgs boson, we uncover that this scalar naturally exhibits a substantial branching ratio to γγ. Additionally, we find that its Drell-Yan production via pp → W∗ → HH± adequately accounts for the observed excess. The second study examines how recent measurements of the W bosons’s mass by experiments such as ATLAS and CDF affect the theoretical predictions of the Two Higgs Doublet Model augmented with a Singlet Scalar (2HDM+S) model. It addresses how this model’s parameter space is further constrained by the inclusion of vector-like leptons, focusing on their impact on the muon g − 2 measurements. The third study involves exploring the potential discovery of the aforementioned scalar at future electron-positron colliders. Employing several methodologies, including the recoil mass method in e + e − collisions (e + e − → ZS, where Z → µ + µ − and S → b ¯ b), we leverage a Deep Neural Network to refine the differentiation between the Standard Model background and the targeted signal. The outcomes not only reinforce the potential for detecting the proposed scalar, but also enhance the scientific argument for the establishment of future electron-positron colliders like CEPC, FCC-ee or ILC. Together, these studies contribute valuable insights into the evolving landscape of particle physics.Item Low-temperature electronic transport of metal doped carbon nanotube molecular hybrids and Nitrogen-doped nanocrystalline diamond(University of the Witwatersrand, Johannesburg, 2024-08) Sodisetti, Venkateswara Rao; Bhattacharyya, SomnathThis thesis explores the magnetism and spin-related properties in carbon-based molecular hybrid materials, with a focus on expanding our understanding of low-dimensional carbon structures and their potential electronic applications. The investigation spans from one-dimensional systems, such as carbon nanotubes (CNTs) functionalized with single-molecule magnets (SMMs), to three-dimensional systems like nitrogen-doped ultra nanocrystalline diamond (UNCD). In these carbon structures, electronic transport is intricately tied to microstructural features, such as grain boundaries and impurity clusters, which hold significant potential for the development of all-carbon electronic devices. The research begins with a detailed examination of the chemical functionalization of multi-walled carbon nanotubes (MWCNTs) through controlled acid treatment to achieve precise metal doping. Using Raman spectroscopy and complementary techniques like ICP-MS and ToF-SIMS, we successfully demonstrate how functionalization levels influence the magnetic properties of CNT hybrids loaded with magnetic metals from the lanthanide series (Gd, Tb, Dy). The study reveals that low percentages of metal doping (0.5% to 1.0%) preserve the magnetic bistability of SMMs post-grafting, while higher doping levels lead to complex magnetic behaviors including super paramagnetism, quasi-ferromagnetism, and potential Kondo lattice behavior inCNT-heavy metal systems. We also explore the spin-phonon coupling in Gd-filled double-walled CNTs, where the onset of superparamagnetic properties at low temperatures is coupled with phonon mode stiffening observed via Raman spectroscopy. This enhanced coupling offers promising pathways for developing efficient molecular qubits through the modulation of spin-phonon interactions in one-dimensional systems. The second part of the thesis investigates into the microwave plasma-assisted chemical vapor deposition (MWCVD) growth of nitrogen-doped nanocrystalline diamond (NCD) thin films on different substrates. By pioneering upgrades to the MWCVD system, I was able to achieve reliable growth of high-quality nanocrystalline diamond thin films. Notably, I observed a novel nanostructure, termed Diaphite-a previously unreported feature, in these NCD films, consisting of nanodiamond grains coherently linked with graphene-like rings. This structure, along with the non-equilibrium growth conditions induced by nitrogen doping and secondary nucleation, presents unique polymorphic features in artificially grown diamonds. Detailed low-temperature transport measurements on four different samples—ranging from 7.5% to 20% nitrogen doping—uncovered complex transport phenomena such as 3D weak localization (WL), variable-range hopping (VRH), and unusual magnetoresistance (MR) behavior. In particular, the 7.5% N2-doped UNCD film on quartz exhibited 3D weak localization (WL) at low fields and anti-weak localization (AWL) at higher fields, with distinct magnetoresistance characteristics depending on the direction of the applied magnetic field. The 20% N2-doped films on both quartz and silicon showed more metallic-like behavior, with magneto-resistance characterized by a B1/2 dependence at low temperatures, suggesting an intricate relationship between doping level, microstructure, and electron transport. These findings significantly expand our understanding of the role that microstructural and chemical modifications play in determining the electronic and magnetic properties of carbon-based materials. This work provides a foundational platform for future research into carbon electronics, offering potential breakthroughs in spintronics, molecular transistors, quantum computing, and other advanced electronic applications.Item Digital toolbox for the generation and detection of vectorial structured light(University of the Witwatersrand, Johannesburg, 2023-06) Singh, Keshaan; Dudley, Angela; Forbes, AndrewLight has been an invaluable tool in the development of the modern world, with the myriad of applications increasing along with our degree of control over it. From the development of coherent light sources, to the shaping of amplitude and phase, this development has not ceased for the past half century. The field of structured light, borne out of the necessity and desire for control over light, has been growing steadily in recent years. In the spatial domain, the control over light’s polarization (i.e., the local planes in which the electric and magnetic fields oscillate) has been the most recent avenue of improvement, providing enhancements to a variety of applications ranging form microscopy and communication to materials processing and metrology. This class of light, commonly referred to as vectorial light, often requires specialised equipment in order for its its creation before its numerous benefits can be exploited. These tools often incur high costs and suffer from limitations relating to the diversity of vectorial light they can create, wavelength dependence and slow refresh rates. This thesis follows the development of a series of digital tools for the versatile generation and analysis of vectorial light using low-cost core technologies which can operate at high rates over a broad wavelength range. We follow the development of the generation tool in the context of its application in generating novel accelerating polarization structures, emulating vectorially apertured optics, generating probes to measure birefringence and chirality and creating synthetic spin dynamics. The development of the analysis tool is explored by investigating its application in performing automated digital Stokes polarimetry measurements, completely characterizing the internal degrees of freedom of arbitrary vectorial light and acting as a polarization and wavelength independent wavefront sensor. We then demonstrate how these tools can be used, in conjunction, to investigate the fundamental invariance of vectorial light to perturbing channels and how this invariance can be exploited in a highly robust novel communication scheme. In addition to demonstrating the applicability and versatility of these vectorial light tools, the applications offered a means to highlight areas for the optimization for the design. This culminated in the ongoing prototyping of versatile, fast, broadband devices which operate stably and have a small physical footprint.Item The Large N Limit of Heavy Operator Excitations(University of the Witwatersrand, Johannesburg, 2023-07) Carlson, Warren Anthony; De Mello Koch, RobertOperators 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.Item 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 differentiationItem Skyrmions and vectorial wavefunctions(University of the Witwatersrand, Johannesburg, 2024) Ornelas, Pedro; Forbes , AndrewThe 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.