Theses and Dissertations (Physics)

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Neutral hydrogen lensing simulations in the hubble frontier fields
(Oxford University Press, 2024-07) Blecher, Tariq; Deane, Roger; Obreschkow, Danail; Heywood, Ian
Cold gas evolution ties the formation of dark matter haloes to the star formation history of the universe. A primary component of cold gas, neutral atomic hydrogen (HI), can be traced by its 21-cm emission line. However, the faintness of this emission typically limits individual detections to low redshifts ( z 0 . 2). To address this limitation, we investigate the potential of targeting gravitationally lensed systems. Building on our prior galaxy–galaxy simulations, we have developed a ray-tracing code to simulate lensed HI images for known galaxies situated behind the massive hubble frontier field galaxy clusters. Our findings reveal the existence of high HI mass, high HI magnification systems in these cluster-lensing scenarios. Through simulations of hundreds of sources, we have identified compelling targets within the redshift range z ≈0 . 7 −1 . 5. The most promising candidate from our simulations is the Great Arc at z = 0.725 in Abell 370, which should be detectable by MeerKAT in approximately 50 h. Importantly, the derived HI mass is predicted to be relatively insensitive to systematic uncertainties in the lensing model, and should be constrained within a factor of ∼2 . 5 for a 95 per cent confidence interval.
Microwave-assisted hydrothermal synthesis and energy storage application of nickel-aluminum layered double hydroxide-graphene foam nanocomposites
(University of Pretoria, 2015-10) Manyala, Ncholu I.; Dangbegnon, Julien K.; fatemehtaghizadeh86@gmail.com; Taghizadeh, Fatemeh
The graphene foam (GF) was synthesized by chemical vapor deposition (CVD) and different mass of GF were added to the LDH. The morphological, structural and compositional properties of LDH and LDH/GF composites were investigated by scanning electron microscopy (SEM), X-ray diffraction (XRD), Raman spectroscopy, Fourier transform infrared (FTIR) spectroscopy and Brunauer - Emmett – Teller (BET). The results show the presence of interlaced sheets of LDH/GF composites. The electrochemical properties of the synthesized composite electrode system (with Ag/AgCl as reference electrode) displayed excellent electrochemical performance. All results clearly show and demonstrated excellent potential of graphene based composites electrode materials for energy storage applications.
Synthesis and characterization of transparent conducting oxides for Stark e ect applications in single molecule spectroscopy
(University of Pretoria, 2019-09) Diale, M. (Mmantsae Moche); Kruger, T.P.J. (Tjaart); joramskaap@gmail.com; Cronje, Abraham Johannes
The desire to study the characteristics of transparent conducting oxides (TCOs) for Stark application in single molecule spectroscopy (SMS) stemmed from our interest in the dark states of light harvesting complex II (LHCII) of plants. Investigation of this mechanism requires a Stark cell. The high optical quality required by the SMS procedure demands a very speci c thickness microscope slide at the objective to sample interface. Since no commercial TCOs of this standard were available, we had to synthesize our own and spincoat our SMS setup's stock microscope slides. As a rst attempt, uorine doped tin oxide (FTO) thin lms were synthesized at 0 to 3 percent atomic doping levels. The optical quality of the lms were low, as they appeared almost burned (blackish). X-ray di raction (XRD) con rmed the lms to be FTO by the FTO powder di raction le (PDF 00-041-1445). The average optical band gap achieved was 3.860 eV, in good agreement to literature. A minimum resistivity of 0.37 :cm􀀀�1 was obtained for the 2% sample. Scanning electron microscopy revealed that the poor optical quality of the lms was due to agglomeration of tin, most likely due to a too high tin concentration in the solution. Due to availability and experience in the department with zinc oxide thin lms, the following study was on the synthesis of aluminium doped zinc oxide (AZO). Thin lms of atomic doping percentages ranging from 0 to 5 percent in steps of 1 percent were fabricated. A new deposition of layer procedure was also used, described in the next paragraph. AZO was successfully synthesized, con rmed by XRD correspondence to zinc oxide's PDF (00- 036-1451) and the average optical band gap of 3.2873 eV agreement to literature. SEM revealed polycrystalline morphology in all lms. All lms had high transparency in the visible, as showcased by ultraviolet to visible (UV-Vis) spectroscopy. A minimum resistivity of 8.61 :cm􀀀�1 was obtained for the 2% sample. From experience gained in the FTO study, we hypothesized that a di erent Deposition of thin lm layer technique could have a signi cant impact on the quality of TCO lms. Simply drying a layer before addition of a new layer would not solidify the layer in a signi cant way. Addition of new solution would then solubilize a good amount of dried particles of the previous layers. This would result in a new pseudo-solution of much higher concentration, resulting in aggregation and low reproducibility. Our results indicated that the Deposition of thin lm layer technique had little impact on the optical quality of the lms, however, the crystalline and electrical qualities were both signi cantly better for TCO application. This procedure was used for the AZO study.
Single molecule spectroscopy on photosynthetic light-harvesting complexes
(University of Pretoria, 2020-02) Kruger, T.P.J. (Tjaart); Diale, M. (Mmantsae Moche); farooq.kyeyune@up.ac.za; Kyeyune, Farooq
Single molecule spectroscopy (SMS) is a powerful approach to study subtle, fundamental properties of biological systems generally obscured by the ensemble average. SMS allows for a detailed understanding of the molecular mechanisms underlying the biological function of many systems. In this thesis, SMS was used to investigate the photophysical properties of photosynthetic light-harvesting complexes (LHCs) under different environments. The two LHCs studied are LHCII, the major lightharvesting complex of higher plants (specifically Spinacia oleracea), and LH2, one of the major light-harvesting complexes of purple bacteria (specifically Rhodopseudomonas acidophila). In the first part, the photodynamics of LHCII in two different oxygen-depleted environments, i.e., in the presence of enzymatic oxygen scavengers and under nitrogen gas purging, were investigated. In the presence of oxygen scavengers, we observed at least two distinct states, which are characterized as unquenched and quenched, where quenching refers to energy dissipation in the form of heat. Under the nitrogen gas atmosphere, the majority of LHCII complexes exhibited only an unquenched state, with a negligible probability of switching to the quenched stated. Moreover, we found that the rate at which LHCII switches between the unquenched and quenched states was two orders of magnitude lower compared to that in the presence of oxygen scavengers. We speculate that the quenched state in LHCII could be activated by molecular oxygen, which, in turn, might play a key role in regulating light harvesting in oxygenic photosynthesis. Surprisingly, LH2, a pigment-protein from an anoxygenic organism, was also found to be incredibly stable under nitrogen gas purging. Overall, these results will help to increase our understanding of the photophysical mechanisms underlying the regulation of light harvesting, with a view of developing robust bio-solar devices as well as improving biomass yields. In the second part, the effects of plasmonic coupling on the fluorescence dynamics of LHCII were explored. We demonstrated that the brightness (fluorescence intensity) of a single LHCII can be significantly enhanced when coupled to a gold nanorod (AuNR). The increase in brightness is due to the enhanced rate of excitation and increased decay rate of LHCII placed near the nanorod. The AuNRs utilized in this study were chemically synthesized, and the LHCII/AuNR hybrid system was constructed using a simple and economical spin-assisted layer-by-layer technique. A fluorescence brightness increment of up to 240-fold was obtained, accompanied by a two orders of magnitude decrease in the average (amplitude-weighted) fluorescence lifetime down to a few picoseconds. This large fluorescence enhancement is explained by the strong spectral overlap of the longitudinal localized surface plasmon resonance of the utilized AuNRs and the absorption or emission bands of LHCII. In principle, these results provide an effective strategy to study the fluorescence dynamics of weakly emitting photosynthetic LHCs, especially at the single-molecule level where the fluorescence signal is usually overwhelmed by the background noise.
The study of transparent hematite films using ultrafast and Raman spectroscopies
(University of Pretoria, 2019-11) Diale, M. (Mmantsae Moche); Kruger, T.P.J. (Tjaart); sipho.congolo@gmail.com; Congolo, Sipho
Hematite (Fe2O3) is a promising photoanode material that is being studied immensely for its application in solar water splitting to produce hydrogen and oxygen as fuels. It has attractive properties such as a narrow bandgap that allows for absorption of visible light, it is earth-abundant and is an easily processable photocatalytic material. In this study, we report on hematite thin films prepared by spray pyrolysis on fluorine-doped tin oxide (FTO) coated glass substrates. The samples were prepared by spray pyrolysis and treated with tetraethoxysilane as well as post-annealed. We employed ultrafast transient absorption spectroscopy and high-resolution confocal Raman microscopy for analysis of the hematite thin films. For all the films, Raman spectroscopy confirmed the characteristic spectrum of the hematite. The high-resolution Raman mapping showed a uniform intensity over the analyzed areas which suggests a uniform coating of the hematite films on the FTO substrates. Ultrafast transient absorption spectroscopy was used to investigate the effect of three experimental parameters; the effect of the spray volume, tetraethoxysilicate treatment of the hematite and post-annealing at 500 ºC for 2 hours with 10 ºC/min ramping. All three parameters gave a positive result. Ultrafast transient absorption spectroscopy indicates that all three experimental parameters slowed down electron-hole recombination. Global analysis of the difference absorption data resolved the spectra and associated decay lifetimes of three distinct processes, operating on the ultrafast, tens of picoseconds and hundreds of picoseconds timescales. Thus, understanding these properties will aid in the engineering of this material to prolong recombination and, as a result, improve its solar to hydrogen conversion efficiency in photoelectrochemical cells.
The effect of palladium deposition on electrically active defects in irradiated silicon
(University of Pretoria, 2023-12) Meyer, W.E. (Walter Ernst); Auret, F.D. (Francois Danie); abrahamwillembarnard@gmail.com; Barnard, Abraham Willem
DLTS was used to study the effect of resistive physical vapour deposition of Pd Schottky contacts on the defects observed in an n-type Si substrate that was irradiated before deposition (“pre-irradiated”) and compared to defects in a diode that was irradiated after deposition (“post-irradiated”). In the post-irradiated samples, the familiar radiation-induced defects were observed. However, in the pre-irradiated samples, 13 new defects were observed, with DLTS signatures differing from those of the defects in the post-irradiated diodes. Out of the 13 newly observed defects, four defects, with activation energy of 0.180, 0.220, 0.360 and 0.607 eV, had DLTS signatures corresponding to defects previously observed in Pt-containing Si, while no match was found for other defects. The effect (referred to as the Pd Effect) was carefully studied, and it was found that the effect was only observed with Pd, and not when other metals including Au, Ni, Al, Ag were used. Careful experiments ruled out annealing during evaporation of the contact as a possible cause. Different sources of Pd were used in un-used crucibles in an attempt to avoid contamination, but the effect was observed in all cases. It was found that this phenomenon was inhibited by the presence of a thin intermediate layer, irrespective of the layer being Pd or Au. We therefore conclude that the effect is only observed when Pd is deposited directly on the irradiated Si surface. We believe that these defects are produced by defect-enhanced diffusion of Pd. Overall, the study enhances our understanding of defect behaviour in silicon-based devices, particularly under irradiation and metal deposition conditions, and reveals the unique properties and effects of Pd.
Probing the Association of Galaxy Clusters with Bent-Tailed Radio Sources Using the MeerKAT Galaxy Cluster Legacy Survey
(University of Pretoria, 2024-03) Thorat, Kshitij; Dean, Roger; toivosamuel@gmail.com; Mabote, Toivo Samuel
A bent-tailed radio galaxy (BT) is an active radio-loud galaxy in which its double jet presents a bend in the same direction, possibly as a result of interaction with the intracluster medium (ICM). Our dataset was extracted from the MeerKAT Galaxy Cluster Legacy Survey (MGCLS). The MGCLS is a survey consisting of observations of 116 clusters at declinations ranging from -85° to ∼ 0°. Through visual inspection of the continuum images aided by an automated source finder, we have separated BT radio sources from other extended radio sources in the MGCLS images. As a result of the study, we present the largest catalogue of BTs to date using the MGCLS sample, from which we extracted 1292 BTs, of which 83% are wide-angle-tailed radio galaxies (WATs) and 17% are narrow-angle-tailed radio galaxies (NATs). As expected, most of the BT sources are estimated to fall below the traditional Fanaroff-Riley divide. We find that around 65% of BTs are associated with massive clusters (1014.5 to 1015 h−1 MJ) for a subsample of 37 galaxy clusters, within which we identified 401 BTs. Contrary to expectations, we do not observe a significant increase in the number of BTs in merging clusters; 45% of the clusters in MGCLS that we have confirmed as merging also contain 45% of the BTs. This may be due to MeerKAT presenting a more complete picture of the BT population. We observed a high number density of BTs in the cluster center region, with an exponential decrease as the distance from the cluster center increases. This pilot study provides the largest sample of BT sources and is well-suited for future studies, including machine-learning-based exploration, as well as highlighting the requirements of future studies using SKA precursors and pathfinders.
Migration and aggregation of ruthenium implanted in glassy carbon
(University of Pretoria, 2023-12-15) Malherbe, Johan B.; Thabethe, Thabsile T.; Odutemowo, Ope; tasabeeh.jafer@gmail.com; Osman Jafer, Tasabeeh Alabid
Glassy carbon is a continuous, isotropic and non-graphitizing carbon that combines the properties of glass and ceramic with those of graphite. It has excellent properties such as high tensile strength, high hardness, good thermal and electrical conductivity, and combined resistance to high temperatures, wear, and corrosion. Glassy carbon is also highly impermeable to gases and liquids. These outstanding properties of glassy carbon make it a good choice for nuclear applications. Glassy carbon has been proposed as a containment material for radioactive fission products. For glassy carbon to be considered a suitable candidate for fission products containment, it must be an effective diffusion barrier for fission products, such as ruthenium (Ru), and its microstructure should not change dramatically under ion bombardment and extreme heat conditions. In summary, this study thoroughly investigated the impact of implantation and annealing temperatures on the microstructure and migration behaviour of Ru implanted in glassy carbon, with a focus on assessing its suitability as a diffusion barrier for Ru fission products. Raman and XRD results revealed amorphization of glassy carbon and structural changes induced by ion bombardment and subsequent annealing, showcasing the transition from tensile to compressive stress. RBS and SIMS elucidated Ru migration, with notable aggregation and segregation at higher annealing temperatures. Remarkably, both low and high-temperature annealing did not lead to significant Ru loss, affirming glassy carbon's efficacy as a storage container for Ru. Surface analyses through SEM and AFM showed a reduction in roughness post-implantation, while annealing-induced variations in roughness were linked to Ru migration or aggregation, surface diffusion and cluster formation. This comprehensive investigation provides valuable insights into Ru migration in glassy carbon, laying the foundation for its potential application as an effective diffusion barrier for Ru fission products.
Studying single plant light-harvesting complexes in near-native environments
(University of Pretoria, 2023-12-14) Krüger, Tjaart P.J.; Kirchhoff, Helmut; bertus.mooikloof@gmail.com; van Heerden, Bertus
Photosynthesis in plants begins with light absorption by light-harvesting complexes, the main one being light-harvesting complex II (LHCII). This protein is a key component of a critical photoprotective process called non-photochemical quenching (NPQ). Single-molecule spectroscopy (SMS) has revealed that isolated LHCII complexes have complex, individual behaviour, and this behaviour can be directy related to NPQ. The physiological applicability of these findings is, however, limited by the artificial environment typically used for SMS. Applying SMS in vivo is immensely challenging, however, in part because the complexes are crowded and in constant motion. New approaches are therefore needed which enable the study of LHCII (and similar proteins) in controllable environments that mimic the native one. This thesis develops two such approaches, namely real-time feedback-driven single-particle tracking (RT-FD-SPT) and proteoliposomes, and applies them to LHCII. Different RT-FD-SPT methods were investigated using theoretical modeling, illuminating fundamental aspects of performance and aiding in the selection of an appropriate method. New data analysis code was developed for fluorescence lifetime analysis and applied to measurements on LHCII. The first measurements of photon antibunching from LHCII are reported. An RT-FD-SPT setup with unique spectroscopic measurement capabilities was constructed and used, for the first time, on light-harvesting complexes. LHCII aggregation was investigated using fluorescence correlation spectroscopy (FCS) and RT-FD-SPT. Lastly, a proteoliposome protocol was optimised which allows protein-lipid interactions to be studied at the single-molecule level.
Application of the Jost-matrix theory to the lambda-nuclear and multi-lambda systems
(University of Pretoria, 2024-02-28) Rakitianski, Sergei; u04361482@tuks.co.za; Gopane, Ishmael Mmusi
This study involves the investigation into the hypernuclear and multi-lambda systems using the Jost-function method, as well as the recovery of the two-body potential from the two and three-body systems using the approximate(guessed) wavefunction. The Schrodinger equation describing the quantum system of interest is solved by being replaced with a system of first-order differential equations, which enable one to obtain the Jost functions. These Jost functions are multi-valued energy functions which can be treated as single-valued functions defined on a complex energy surface called the Riemann surface. Direct calculations of the Jost functions, the S-matrix, for all complex momenta of physical interests including the spectral points corresponding to the bound states and resonance states can be obtained. In this work, this method was used to locate the spectral points for the wide range of Λ-nuclear systems within the two-body ΛA-model. The S-matrix residues as well as the corresponding Nuclear-Vertex and Asymptotic-Normalization constants (NVC’s and ANC’s) for the bound states are also found. For scattering parameters the Jost functions were factorized in such a way that they contain certain combination of the channel momenta times an analytic single-valued function of the energy E. The remaining energy-dependent factors were now defined on single energy plane which does not have any branching points anymore. For these energydependent functions, a system of first-order differential equations is obtained. Then, using the fact that the functions are analytic, they were expanded in the power series to obtain a system of differential equations that determine the expansion coefficients. When the expansion coefficients are obtained for the expansion around the energy E0 = 0,the coefficients are then used to calculate the effective range parameters. For the same hypernuclear systems, the scattering lengths, effective radii, and the other effective-range parameters (up to the order ∼ k8) for the angular momentum ℓ = 0, 1, 2 are calculated. Possible bound and resonant states of the multi-lambda systems ΛΛ(0+), ΛΛΛ(12 −) and ΛΛΛΛ(0+, 1+, 2+) are sought as zeros of the corresponding Jost functions calculated within the framework of the hyperspherical approach with local two-body S-wave potentials describing the ΛΛ interactions. Bound ΛΛ(0+), ΛΛΛ(1 2 −) and states only appears if the two-body potentials are multiplied by a minimum factor of ∼ 1.461 and 3.449. For ΛΛΛΛ(0+, 1+, 2+) systems the bound states appear when the two-body potentials aremultiplied by the factors ∼ 3.018, 4.360 and 3.419. A method for deducing the two-body potential from a given two- or three-body wave function is suggested. This method makes it possible to numerically obtain an unknown potential acting between the particles A and B when we know the potentials of their interaction with a third particle C and know the characteristics of the three-body bound state (ABC). The systems (nnp) and (ΛΛα) were used to show that a three-body wave functions can be constructed using the knowledge of the binding energies and sizes of these systems to deduce reasonable and realistic nn and ΛΛ potentials.
Effects of irradiation-induced defects in germanium
(University of Pretoria, 2023) Diale, Mmantsae; Auret, F.D. (Francois Danie); U20791152@tuks.co.za; Thaba, Cambel Rashia
In this study, we investigated the electrical characteristics of defects in germanium produced by alpha particle radiation using conventional deep level transient spectroscopy (DLTS) and Laplace deep-level transient spectroscopy (L-DLTS). Resistive deposition was used to fabricate palladium (Pd) and silver-gold (Ag/Au) Schottky contacts. I-V and C-V measurements were used to determine the suitability of the device by calculating the ideality factor (n) and carrier concentration (Nd). The Pd/n-Ge Schottky diodes were of high quality with ideality factor n = 1.159 before irradiation. After irradiation, ideality factor increased to n = 1.383, showing that exposing the device to irradiation, Schottky diodes of the device degraded. The carrier concentration of the devices from the C-V graphs, where the plot representing the samples before irradiation, was observed to be steeper compared to the plot before irradiation, indicating a decrease in free carrier density from 1.52×1016 cm-3 for an unirradiated sample to a 6.37×1015 cm-3 irradiated sample. A DLTS spectrum of the unirradiated germanium did not show any electrically active defects in detectable concentrations. After irradiation, DLTS spectrum illustrated the presence of several defects: E07+04, E10, E16+17, E23+25, and E37 (E+Eʹ). Peaks E and E’ were separated at 185 K by L-DLTS using manual regularization parameters, allowing the inversion routine to take into consideration the possibility of two or more closely spaced peaks. Conventional DLTS spectrum were also recorded for different pulse widths, and the peak height was reduced with a shorter pulse width, indicating that partial trap recharge was hardly observed for defects with pulse widths of 100 ns and 1 µs. The peak height started intensifying from 10 µs to 1 ms, which is a longer pulse width until it reaches saturation, meaning that all traps were now filled. The activation energies for all observed defects were calculated from the Arrhenius plot. Defects E25, E23, E10, E0.07, and E0.04 were observed after irradiation, but they were not all fully characterized. AuAg/Ge samples measurements illustrated the presence of 6 peaks after irradiation, which revealed an additional peak with an activation energy of 0.21 eV, defect E21 when compared to Pd/Ge samples. The electrical properties of E and E’ defects in germanium (Ge) introduced by alpha particle radiation were studied using high-resolution Laplace deep-level transient spectroscopy (L-DLTS). From the Arrhenius plot, it was observed that the E-centre consists of two components with similar DLTS signatures, but they have different properties, given that they have different activation energies of Et 0.375 eV and 0.370 eV. Electric field dependence of the E defect was measured at different temperatures to distinguish between Poole-Frenkel and phonon-assisted tunnelling, it was observed that the emission of carriers was described by phonon-assisted tunnelling for all measurements at different temperatures. The defect's depth profile measurements for the E-centre showed that as we probe deeper into the bulk of the semiconductor, the concentration of the E-centre defect decreases. The DLTS amplitude of the combined E and E' defects increased as the filling pulse width increased from a few microseconds to a millisecond. However, the DLTS amplitude of E was observed to be 4 times bigger than the DLTS amplitude of E' and both defects are structurally different
Laplace deep-level transient spectroscopy studies of the divacancy in alpha-particle irradiated silicon
(University of Pretoria, 2024-02-15) Meyer, W.E. (Walter Ernst); Auret, F.D. (Francois Danie); u10539362@tuks.co.za; Weideman, H.J.S.
Defects in semiconductors are usually detrimental to the device operation. Particularly in space, the high levels of radiation induce defects that damage electronics in satellites and space craft. However, in some devices defects are crucial to device operation and they are purposely introduced into the semiconductor during manufacture. In both cases it is important to be able to characterize these defects in order to find ways to remove defects that are detrimental and to introduce or keep those defects that are useful. During this research, the deep-level transient spectroscopy (DLTS) technique was performed on Schottky diodes fabricated on n-type silicon, which were irradiated by alpha particles from an Am241 source. In contrast to gamma and electron irradiation, which practically induce only point defects, alpha particles produce some defect clusters as well, especially in the region just before coming to rest. In particular, the two charged states of the divacancy were investigated. These investigations included the determination of the DLTS signature (the ionization enthalpy and apparent capture cross-section) of the observed defects. The depth profile and introduction rate of the defects were also determined. This was then compared to previously done research on electron irradiated silicon to determine if any other unknown defects arose from alpha-particle irradiation. The conventional deep-level transient spectroscopy spectrum showed three discrete peaks at 90 K, 125 K and 225 K, when recorded at a rate window of 80 s-1. By comparison with literature, it was determined that the peak at 90 K was due to both the CiCs defect and the VOi defect, while the peak at 125 K was due to V2 (=/-) defect level and the peak at 225 K was due to the PV defect and the V2 (-/0) defect level. The annealing profile of both charge states of the peaks due to the divacancy showed annealing in the range 350 K to 400 K, which was not observed in electron-irradiated diodes. We suggest that this is due to defect clusters annealing out, releasing interstitials that combine with the divacancies thereby converting them to highly mobile vacancies. It was also observed that, in the region 550 K to 620 K, where the divacancy anneals, the two peaks annealed by different amounts. This is not the case in electron-irradiated material. We therefore suggest that the V2 (=/-) charge transition level is suppressed by cluster effects.
Fluorescence correlation spectroscopy of the main plant light-harvresting complex
(University of Pretoria, 2023-12-07) Kruger, T.P.J. (Tjaart); nsfconradie@gmail.com; Conradie, Francois
Light-harvesting complex II, LHCII, is vital for the light-dependent reaction of photosynthesis in higher plants. It acts as the starting point for photosynthesis in Photosystem II (PS II) by increasing the absorption of sunlight and efficiently transferring excitation energy to reaction centres, where water-splitting takes place. On top of this, LHCII acts as a molecular switch for a fast photo-protective mechanism that protects PS II from over-absorption of solar energy. This protective non-photochemical quenching (NPQ) is linked to a pH gradient over the thylakoid lipid membranes in which LHCII resides. Aggregation of LHCII is also caused by a drop in pH accompanying an increased pH gradient and has been proposed to be a useful model with which NPQ can be studied. This dissertation describes an experimental study on LHCII aggregation using Bio-Beads adsorbent to remove detergent from solutions containing isolated LHCII at two pH levels, namely pH 7.5 and pH 5.5. Two experimental techniques were combined to investigate the sizes of LHCII aggregates and fluorescence lifetimes simultaneously: fluorescence correlation spectroscopy (FCS) and time-correlated single-photon counting (TCSPC). FCS calibration was done by measuring the effective detection volume of a microscope using two different methods. NPQ measurements of LHCII fluorescence during detergent removal showed that LHCII aggregation was not ultrasensitive to the adsorption of detergent to Bio-Beads. Results from applying FCS showed an increase in hydrodynamic radii of LHCII over detergent adsorption time, from single trimeric radius to aggregate level radii, with the increase being more dramatic for pH 5.5. A sudden increase in radii after 45 minutes of detergent removal for all samples was found. Two-component fluorescence decays were analysed, showing a decrease in average fluorescence lifetimes from 3.6 – 4.0 ns to < 2.1 ns at pH 7.5 and to < 1.3 ns at pH 5.5. A comparison between fluorescence intensities and particle sizes as well as between fluorescence lifetimes and particle sizes was obtained for two separate repetitions of the study.
Computational studies of doped tin disulphide monolayer for photoelectrochemical water splitting
(University of Pretoria, 2023-05-25) Mapasha, Edwin; Diale, Mmantsae; onkegqiba@yahoo.com; Gqiba, Onke Lwazi
In this ab initio study, density functional theory, including a Hubbard U correction term (DFT+U), calculations were performed to investigate the photoelectrochemical (PEC) water splitting possibility of SnS2 monolayer. Initially, the thermodynamic stability and photocatalytic (PC) properties of pristine SnS2 were studied and it was found that it suffers poor electrical conductivity and the bottom of conduction band minimum (CBM) is below the reduction potential of H^(+/) H_2 level, limiting the PC performance. To improve performance for PEC water splitting, various doping strategies were performed on a large 5×5 SnS2 supercell. These doping strategies are: C adsorbed onto an interstitial position, C adsorbed on a S atom, C adsorbed on a Sn atom, C substituting a S atom and C substituting a Sn atom.
Synthesis and characterization of tin dioxide coated gold nanocomposites for applications in thermal heat conduction
(University of Pretoria, 2023-11-16) Diale, Mmantsae M; Kyesmen, Pannan I; u14007739@tuks.co.za; Makgale, Tshepho Trevor
In this work, we synthesized three nanofluids based on tin dioxide-coated gold nanocomposites (Au@SnO2) using a two-step method. First, we synthesized gold (Au) nanomaterials, then encapsulated them with tin dioxide (SnO2) through spontaneous hydrothermal encapsulation. Finally, we dispersed them into an ethylene glycol base fluid. The materials were analysed using various physicochemical techniques, such as Powder X- Ray diffraction (XRD), Transmission and Scanning electron microscopy (TEM and SEM), and Ultraviolet-Visible spectroscopy (UV-Vis). The diffraction patterns of the materials showed that the composite structures consisted of an FCC Au core and a mesoporous SnO2 shell. TEM and SEM micrographs showed that the Au@SnO2 nanocomposites had spherical, rod-like, and prism-like shapes. To assess the structural stability of these different types of Au@SnO2 nanocomposites, their TEM micrographs were collected and analysed over a three-month period. The results showed that the Au@SnO2 nanocomposites had better structural stability than their counterparts that were not coated with SnO2 and were exposed to the same conditions. During an additional evaluation of the materials' structural stability, their ultraviolet- visible absorption spectra were analysed over a three-month period. The results indicated that by encapsulating the Au nanostructures with SnO2 with an appropriate coating thickness size in the range from 50 nm to 150 nm, both the structural stability and optical properties of the materials can be significantly improved. The study was based on the observation of localized surface plasmonic resonance absorption peaks at a wavelength of 550 nm, which showed an increase in intensity and a narrower bandwidth upon the encapsulation of the gold nanostructures with SnO2. In contrast, the pure uncoated Au nanostructures showed low intensity and broad absorption peaks at the same wavelength. Furthermore, for the last two months of the study, a red shift to a higher wavelength of 600 nm was observed for the high intensity absorption peaks of the coated nanostructures, while the uncoated ones did not show any such shift. Thermal conductivity of the Au-based nanofluids, both coated and uncoated with tin dioxide, was measured using the transient hot-wire method. The results showed that the thermal conductivity of the nanofluids made up of SnO2-coated gold nanostructures increased by more than 10%. Additionally, the thermal conductivity of the SnO2-coated Au 2 nanofluids was observed to rise with an increase in the thickness of the SnO2 layer encapsulating the Au nanostructures. These findings suggest that the Au-based nanofluids coated with SnO2 have potential applications in thermal energy management and electronic cooling systems.
Quantum wasserstein distance of order 1 between channels
(University of Pretoria, 2023-10-26) Duvenhage, Rocco; mapayawitnesss@gmail.com; Mapaya, Mathumo
We analyse a formulation of the quantum Wasserstein distance of order $1$ and set up a general theory leading to a Wasserstein distance of order $1$ between the unital maps from one specific algebra to another specified algebra. This gives us a metric on the set of unital maps from one composite system to another, which is deeply connected to the reductions of the unital maps. We use the fact that channels are unital maps with extra structure, to systematically define a quantum Wasserstein distance of order $1$ between channels, i.e., a metric on the set of channels. Lastly, the additivity and stability properties of this metric are studied.
Statistical approaches to the selection of strong gravitationally lensed spectral line sources in the Square Kilometre Array era
(University of Pretoria, 2023) Deane, Roger; charissa@imago-web.co.za; Button, Charissa Bronwyn
Neutral atomic hydrogen (HI) and hydroxyl (OH) are important gas components within the context of galaxy evolution. HI is a key transitory phase in the baryon cycle and, hence, has a crucial role in star formation. Extragalactic OH is typically found in highly luminous infrared emission, as well as dense molecular hydrogen gas regions, associated with extreme star formation activity and gas-rich major galaxy mergers. Currently, both HI and OH emission are only directly detected at low redshifts (z < 0.2). Strong gravitational lensing, together with the upcoming large spectral line surveys of the SKA1-Mid, will offer opportunities to study HI and OH sources out to intermediate and high redshifts, which is not possible with current radio telescopes. A large number of HI and OH sources are predicted to be detected with these surveys, of which only a fraction will be lensed. This thesis investigates a statistical approach to select these lensed sources in the upcoming surveys. The approach is based on the distortion that the magnification bias has on the source number counts at high HI masses or high OH luminosities and uses this effect to find a flux density selection threshold above which gravitationally lensed sources are preferentially selected. This thesis finds that the surface density of lensed HI galaxies and lensed OH megamasers are low and that the flux density selection thresholds are faint, requiring deep and wide observations in order to select lensed HI galaxies and OH megamasers in this way, in the absence of any other information. This thesis also starts to investigate whether it will be possible to remove these lensed contaminants using ancillary optical/near infrared data from the Legacy Survey of Space and Time. These results indicate that a large fraction of these sources could be removed in this way. Future work will extend this investigation. The results of this thesis will provide valuable input to the increase of the scientific yield of the SKA1-Mid surveys by combining high sensitivity observations with the natural amplification of strong gravitational lensing to directly observe both HI and OH at cosmological epochs well beyond the peak of cosmic star formation and AGN activity.
Development of a waste management process for naturally occurring radioactive material in the South African mining industry
(University of Pretoria, 2022) Malherbe, Johan B.; Theron, Chris C.; riaan@upsilonconsulting.co.za; Van der Westhuizen, Abraham Jozua
The South African Naturally Occurring Radioactive Material (NORM) regulatory framework provides guidance on most matters associated with radiation protection within the mining and minerals processing sphere, but definitive guidance on radiation protection for NORM waste post closure is lacking. This thesis suggests a structured process for the justification of radiation protection decisions and offers guidance on the utilisation of management systems and possible sources of information available to the radiation protection professional. The structured process is applied to a copper mine and smelter (Palabora Mining Company or PMC), thereby demonstrating its effectiveness.
First-principles study of the enhancement of electrochemical performance of a SnS2 monolayer for lithium/sodium-ion batteries via vacancy defects
(University of Pretoria, 2023) Mapasha, Refilwe Edwin; bekeurca@gmail.com; Bekeur, Craig Arthur
Various transition metal dichalcogenides materials have been investigated from bulk to monolayer phases for different advanced technological applications. Tin disulfide monolayer offers advantages as an anode material for Li/Na-ion batteries, although it cannot be considered an ideal for direct exploitation. We systematically performed a comparative study of the adsorption and diffusion behaviour of Li/Na on a pristine SnS2 monolayer and on a SnS2 monolayer with a S-vacancy for enhancement of electrochemical performance, using the density functional theory approach. Although all the adsorption sites are exothermic, it was established that Li/Na adatoms mostly prefer to bind strongly on a SnS2 monolayer with a S-vacancy but avoiding the S-vacancy site. It was established that avoiding the S-vacancy site along the path, an excellent diffusion barriers of 0.19 eV for Li and 0.13 eV for Na were achieved, suggesting possible ultrafast charge/discharge rate. Due to reduced molar mass, the SnS2 monolayer with a S-vacancy has a slightly higher storage capacity than its pristine counterparts for both Li and Na adatoms. The obtained open circuit voltage values are within the range of 0.25–3.00 V assuring that the formation of dendrites can surely be averted for the envisaged battery operation. Understanding the effects of an S-vacancy on the electrochemical properties of Li/Na on the SnS2 monolayer allows us to consider possible improvements to energy storage devices that can be applied as a result of improved anode material.
The effect of implantation and heat treatment on the structural evolution and migration behaviour of Selenium in glassy carbon
(University of Pretoria, 2023) Hlatshwayo, Thulani Thokozani; Njoroge, Eric G.; Malherbe, Johan B.; adeojo_sam@yahoo.com; Adeojo, Samuel Adedigba
The storage and management of nuclear waste is perhaps the most controversial aspect of nuclear power production, as there is no permanent solution to this problem that has existed for centuries. In the last decade, our group at the University of Pretoria, South Africa, has been studying the suitability of glassy carbon (GC) as a nuclear waste storage material. Some of these studies focused on investigating the migration of strontium, caesium, silver, cadmium, indium, europium, and xenon in GC. No research information on the migration of selenium (Se) in GC in the literature, hence this study. A radioisotope of Se, 79Se is a fission product found in spent fuel and reprocessed nuclear fuel. Its release into the environment has associated health hazards. In this study, Se ions of 150 keV were implanted into GC substrates to a fluence of 1 × 1016 ions/cm2 at room temperature (RT), 100, 150 and 200 °C. The samples implanted at RT and 200 °C were characterised by transmission electron microscopy (TEM) to compare the radiation damage level with respect to the implantation temperatures. Some as-implanted samples were sequentially annealed at the low-temperature regime (300 – 700 °C) and high-temperature regime (1000 – 1200 °C) for 5 h in steps of 100 °C. A new set of as-implanted samples were isochronally annealed at 1000, 1100 and 1200 °C for 5 h cycles. The migration of Se was monitored by Rutherford backscattering spectrometry (RBS) and secondary ion mass spectroscopy (SIMS). Raman spectroscopy was used to monitor the microstructural changes in the GC substrates. Se implantation induces radiation damage at relatively comparable depths in the GC samples implanted at RT and 200 °C. The damaged layer in the RT sample corresponds to about 8.5 dpa, greater than 0.2 critical dpa, which will totally distort the GC microstructure. The microstructures of the as-implanted GC samples were damaged by Se ion implantation, which increases with increasing implantation temperatures. The sample implanted at RT has a more graphitic disorder and the 200 °C sample has the least damaged microstructure and is less graphitic. Annealing the as-implanted samples at 300 – 700 °C resulted in a limited recovery of the GC substrate and appreciable recovery was observed at the high-temperature regime, 1000 – 1200 °C. No measurable diffusion of Se atoms occurred in all the as-implanted samples after annealing at the low-temperature regime (300 – 700 °C). At 1000 °C, the RT Se profile broadens, indicating the diffusion of Se atoms. Further annealing at 1100 and 1200 °C resulted in the asymmetrical broadening of Se profiles towards the surface of the RT sample, accompanied by about 5 and 32 % losses of Se atoms, respectively. The Se profiles of the RT sample at 1100 and 1200 °C exhibited tailing towards the bulk, indicating the migration of Se in the bulk of the GC substrate. The diffusion coefficients of Se were calculated to be 4.79 × 10-20 and 5.90 × 10-20 m2s-1 after annealing at 1000 and 1100 °C, respectively. No measurable diffusion of Se occurred in the sample implanted at 100 °C at the high-temperature regime, 1000 – 1200 °C. Segregation of Se at the surfaces of the samples implanted at 150 and 200 °C and sequentially annealed at 1000 – 1200 °C was observed, accompanied by the loss of Se and migration in the bulk of these substrates. Overall, the SIMS profiles of the new sets of as-implanted samples isochronally annealed at the high-temperature regime were somewhat similar to those obtained by RBS, with minor differences. The differences in the RBS and SIMS profiles were attributed to the resulting different microstructures of these two samples (i.e., the sequentially and isochronally annealed sample types). Generally, the migration behaviour exhibited by Se atoms in the bulk region of the as-implanted samples (after annealing) can be explained in terms of trapping and de-trapping of the Se atoms by defects induced during implantation. The high-temperature annealing caused the annealing of defects in the less radiation damage region, creating pathways for Se atoms to migrate deeper into the bulk of the as-implanted and annealed GC samples. One of the initial concerns in this research was the migration of Se atoms in the bulk of the GC substrates, as this will limit the use of GC as a potential nuclear waste storage container. With a minute concentration of Se atoms estimated in the bulk region of the GC, the integrity of GC (as a nuclear storage container) cannot be limited.

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