South Africa has recently experienced challenges regarding electricity consumption and availability. As part of the country's Integrated Resource Plan, these challenges are to be addressed. This involves a 20 year plan which aims to increase electricity supply capacity as well as reduce the reliance on coal power as part of the global trend to become more environmentally friendly. Wind power, specifically, is to account for a large portion of the renewable energy that is expected to become available by 2030. This results in the need for the understanding of wind turbine design by South African engineers. The dynamic analysis of wind turbine structures, is of particular interest to Civil Engineers. Wind turbine towers are recently of the monopole or tubular type tower, predominantly constructed of either concrete or steel or a combination of both. Steel tubular towers above a height of 80m are generally not recommended for wind turbines owing to cost concerns as well as difficulties in meeting dynamic behaviour requirements. Concrete towers and steel-concrete hybrid towers are recommended for this height regime. The aim of this study was to assess the prospective use of steel tubular towers of varying geometric shape for wind turbines with tower heights of 80m or greater. The study focussed on the analysis of natural frequency and assessing the applicability of steel tubular towers of geometric shapes that have not been previously explored or reported. The turbine of choice for this study was the Vestas V112 3MW type as this is one of the most commonly used and more efficient turbines for towers of this height regime. The results of this study showed that steel monopole towers of heights of 80m and more are still viable options for wind turbine towers. Various geometric tower cases of heights varying from 80m to 120m, produced acceptable fundamental natural frequencies within the allowable frequency range for a Vestas V112 3MW turbine.

This study explores the membrane stresses of hydrostatically loaded elliptical and circular toroidal tanks. Equations are derived, using the membrane theory of shells, to obtain equations which can accurately describe the meridional and hoop stress behaviour at locations sufficiently far away from any bending disturbance occurring within the shell. The derived expressions are validated using the finite element software ADINA, indicating excellent agreement between the analytical and numerical solutions. A parametric study is undertaken, whereby the membrane profiles for prolate, oblate and circular toroidal shells is investigated. Parameters which are varied are the opening and aspect ratio of toroidal shells. Stress resultant profiles are shown for numerous cases in order to aid designers on suitable ratios to minimise membrane stresses for use when designing hydrostatically loaded toroidal shells. Lastly, numerical examples are investigated, keeping the volume constant and comparing the surface area due to a variation of opening and aspect ratios. It was found that when investigating toroidal shells, considerations are required when choosing the aspect ratio and opening ratios. Based on the results obtained, compromises between prolate and circular cross-sections with relatively small opening ratios are recommended in order to minimise the cost and maximise the structural efficiency, based on the membrane stresses occurring within the shell.

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Includes bibliographical references. / Maize streak virus (MSV), circular single stranded DNA (ssDNA) virus (~2.7kb), is the causative agent of Maize streak disease, and is a devastating pathogen that causes severe crop losses to subsistence farmers in sub-Saharan Africa. MSV is transmitted by the leafhopper Cicadulina mbila, and is the type member of the Mastrevirus genus (family Geminiviridae). MSV shares a unique twinned icosahedral ("geminate") virion architecture (22 x 38 nm) with all other family members. Geminate particles consist of 110 coat protein (CP) subunits that assemble onto a circular single-stranded DNA (ssDNA) genome. Each T= I unit is an incomplete icosahedron assembled from 55 CPs. The structures of MSV and African cassava mosaic virus (ACMV, genus Begomovirus) have been studied by electron cryo- microscopy (cryo-EM) previously. While these investigations revealed some details about the geminate architecture, the interactions of capsid components have not yet been adequately modelled. The two incomplete icosahedral "heads" of the geminate particle are offset from one another and apparently make distinct CP:CP contacts at this region of the virion. Information regarding the nature of quasi- equivalent CP conformers or the sets of amino acid residues that mediate these interactions has not been forthcoming. Since the experimental results of these previous studies are not available in a public database, we were motivated to revisit the structure of MSV in order to obtain a 3D experimental density that might aid pseudo-atomic modelling. The MSV CP:ssDNA interaction has also been shown to be crucial for systemic movement through the host. Hence, quasi-atomic modelling may inform development of antiviral strategies which aim to interfere with virion assembly. MSV virions were isolated from the leaves of maize plants infected by agro-inoculation and visualized in both heavy metal stain and vitreous ice after they had been adsorbed to a thin-layer of continuous carbon to prevent virion aggregation. Virus preparations consisted of distinct CP assemblies consisting of multiples of the incomplete T=I icosahedral unit. Monopartite (icosahedral), bipartite (geminate), tripartite, and higher assemblies were observed suggesting the MSV CP is not only multifunctional but also structurally versatile being able to package ssDNA of variable sizes. Low-dose images were recorded on film, and 3D reconstruction of both monopartite and bipartite capsid species carried out using standard single-particle image processing methodology. The resolution of the bipartite reconstructions was 26 A for the negative-stain dataset, and 23 A for cryo-EM dataset, while the resolution of the monopartite reconstruction was estimated to be ~15 A. Comparative modelling of the MSV CP was undertaken using the pentamer (CPs) of Satellite tobacco necrosis virus (STNV) as a structural template. Correlation-based fitting of icosahedral and geminate atomic models that varied in geometric arrangement of MSV CPs allowed the geometric parameters of the bipartite capsid to be determined. Fitting ofMSV CPs into the EM densities informed our understanding of interfaces which allow the CP to self-associate, and showed that CPs is in fact displaced within the icosahedral geometry of the heads by a 10° rotation about the 5-fold axes of symmetry in comparison to STNV; hence, while quaternary structure of the pentameric capsomer is conserved between these viruses, the quaternary interactions between capsomers of the T=I unit has diverged considerably. This study shows that the offset between the geminate heads of the MSV virion is ~-11°, and that this geometry appears to arise owing to a distinct set of CP:CP interfaces which occur across the equator between two quasi-icosahedral heads and involve regions that would interact to form the CPs: CPs interfaces within each of the heads (across 2-fold and 3-fold symmetry axes). Notably this offset differs from that reported for ACMV, which has a reported offset of 20°. Additionally, the resolution afforded by the icosahedral monopartite reconstruction provided the first structural evidence to suggest that the calcium ion binding site of the STNV CPs (located on the CS axis) is likely to be conserved in MSV. This result suggests that in common with other plant viruses, depletion of calcium ions may be required for genome egress in a newly infected host cell. This study highlights the importance of future high-resolution studies of this unique virion morphology by both X-ray crystallography and cryo-EM.

Includes bibliographical references. / Angiotensin-converting enzyme (ACE), a zinc metalloprotease, is a key regulator of the mammalian renin-angiotensin system (RAS) Primarily, ACF is a dipeptidl peptidase which cleaves angiotensin I to produce angiotensin II, a potent vasoconstrictor. By the same enzymatic mechanism, ACE also inactivates the vasodilator bradykinin. The main overall effect of these actions is an increase in blood pressure. Several ACF inhibitors have been developed as drugs for the treatment of myocardial infarction, hypertension, kidney failure and heart failure.

Includes bibliographical references (leaves 123-136). / Amidases are a group of carbon-nitrogen hydrolysing enzymes that catalyze the conversion of amides to corresponding carboxylic acids and ammonia. These enzymes are of great interest in synthetic industries where they are used for mass production of acidic products. Aliphatic amidase from Geobacillus pallidus RAPcS (RAPcS amidase), which belongs to the nitrilase superfamily of enzymes, has recently been characterised biochemically. It shows both amide hydrolysis and acyl transfer activities, and also exhibits stereo selectivity for some enantiomeric substrates. This enzyme can therefore be exploited in large-scale production of enantio-pure compounds. Structural characterization of this amidase would yield insights into the basis of this substrate selectivity and activity. This would inform future experiments that aims at modifying this enzyme to alter its substrate specificity. This work presents structural characterization of RAPcS amidase. Gel filtration chromatography and electron microscopic analyses provided useful information on the quaternary structure of RAPcS amidase. Crystals were grown, and an X-ray diffraction dataset to 1.9 Å collected using an in-house X-ray source. The space group of this data was determined to be primitive cubic P4₂32, and the structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB ID, Ij31) that had all non-identical side chains substituted with alanines, as a search probe. The molecular replacement rotational and translational searches were performed using PHASER. The model was rebuilt with PHENIX before refinement using REFMAC5. The final model was of high quality with minimal errors. RAPcS amidase is homohexameric in solution and has a four-layer α-β-β-α structural fold that highly resembles nitrilase superfamily enzymes. It has an extended C-terminal tail that is essential for strengthening the interacting dimer interfaces by participating in domain swapping. The active site pocket has Glu, Lys, Cys catalytic triad that is conserved in the nitrilase superfamily. The substrate binding pocket is small in size, explaining the specificity of this enzyme for short aliphatic amides. These findings have made steps towards understanding the catalytic mechanism, and the basis for substrate specificity in this enzyme. It has also provided useful information on the overall structure, as well as the structure of the active site, not only for RAPcS amidase but also for related enzymes, which will form the basis for designing future structural characterization work in the nitrilase-related amidases.

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When continuously welded rails are placed over a bridge, the track and the bridge interact via the ballast in the case of ballasted track or track slab in the case of non-ballasted track. This interaction, commonly referred to as track-bridge interaction results in force transfer between the track and the bridge. With the demand to increase freight haulage on heavy haul railway lines intensifying to meet mineral export demands, there is a need to understand the manifestation of rail bridge interactions in heavy haul railway bridges. Understanding the manifestation of these forces is critical for the management of the infrastructure during operation. Whilst track-bridge interactions effects design limits in high-speed rail have been documented, to the author's knowledge there has been no documented report that addresses track bridge interactions in the design of new heavy haul railway bridges and the management old heavy haul railway bridges. Resultantly, this study explored the observed patterns of rail forces, longitudinal deck displacements, ambient temperature, concrete temperature and rail temperature on the Olifants River Railway Bridge. Thereafter, the observed patterns were used investigate the effect of rail temperature variation on rail forces and the longitudinal displacement of the deck. Examine the effect of variation in concrete temperature on the longitudinal deck displacement, rail forces and variation in rail temperature as well as the effect of longitudinal deck displacement on rail forces. The effects of the presence of a train on the longitudinal displacement of the deck, rail forces and concrete temperature will also be investigated. Finally, this study developed a predictive multiple linear regression model that will assist in the management and maintenance heavy haul railway bridges. This study demonstrated that rail temperature variation is inversely proportion to the rail forces in the rail, longitudinal deck displacement is directly proportional to concrete temperature variation and that longitudinal deck displacement of the bridge deck and rail forces in the rail are inversely proportional. However, the correlation between the longitudinal deck displacement and the rail temperature, rail temperature in the track and concrete temperature in the deck, concrete temperature in the deck and the rail forces in the track could not be established conclusively. The effect of the presence of the train on the longitudinal displacement of the deck, rail forces and concrete temperature could also not be established conclusively