The combination of brittle material with ductile fibres can produce competent composites. The fibres transmit tensile forces across cracks that form in the brittle matrix at relatively low tensile strains. The fibre reinforcing, therefore, acts to both increase the maximum stress a structural section can support and improve the post maximum stress behaviour from brittle to ductile failure. An essential aspect of defining the effectiveness of fibre reinforcing is resolving the behaviour of the interface between the fibre and the matrix as the load being transmitted between the matrix and fibre increases. The interface behaviour for simple fibres is understood analytically, and several models exist that can predict the stresses in the interface. Numerical models using finite element methods (FEM) have been used to investigate this problem in a more general way. FEM, being inherently a description of a continuum, does not elegantly describe the debonding process that occurs during the debonding of fibres from the surrounding matrix. Discrete Element Methods (DEM) describe continuous and discontinuous materials as the interaction between multiple independent particles and are well suited for modelling fracture and evolving contacts. For this study two different DEM contact models are compared to investigate the model complexity that is required to describe fibre/matrix interface stresses and debonding accurately. A simple model (a linear spring model that only transmits normal and tangential forces) and a more complex model (parallel bonds which transmit normal and tangential forces, moments, and torsion) were used. Two stages of fibre pull-out were modelled independently using a GPU accelerated DEM simulator developed by the author: a fully bonded stage and the de-bonding stage. It was found that both models were able to simulate all stages when compared to analytical solutions. No improvement to the model behaviour was evident from using a complex contact model; for this reason, a simpler, faster contact model should be used to analyse this problem. The DEM code is written relying heavily on the Numba module which allows the compilation of Python syntax for execution on a GPU. Non-reversible bond damage is simulated, and each bond must, therefore, be stored and bond damage updated at each time step. The implementation of collision detection, particle force determination and equation of motion integration written for execution on GPU are discussed. The data structure and memory use are described. The method used to apply boundary conditions is described. The performance of the developed code is investigated by comparison with similar codes, using Numpy and Numba Python modules, written for serial execution on CPU only. It was found that the developed code was 1000 times faster than the Numpy+Python implementation and 4 times faster than the Numba+Python implementation for force determination and equation of motion integration. Collision detection was 900 times faster compared to Numpy+Python but performed slower compared to Numba+Python. / Dissertation (MEng)--University of Pretoria, 2020. / Mechanical and Aeronautical Engineering / MEng / Unrestricted

Infectious diseases continue to be major health concerns worldwide. Although major advances have led to accumulation of genomic data about human pathogens, there clearly exists a gap between genome information and studies aiming at identifying potential drug targets. Here, constraint-based modeling (CBM) was deployed to integrate disparate data types with genome-scale metabolic models (GEMs) to advance our understanding of the pathogenesis of infectious agents with respect to identifying and prioritizing drug targets. Specifically, genome-scale metabolic modeling of multiple stages and species of Plasmodium, the causative agent of malaria, was used to prioritize potential drug targets that could be used to simultaneously treat (anti-malarials) and block transmission of the parasite. In addition, species-specific metabolic models were used to guide translation of findings from non-human experimental disease models to human-infecting species. Further, comparative analysis of the essentiality of metabolic genes for V. cholerae, the causative agent of cholera, growth and survival in single and co-infections with other enteric pathogens led to prioritizing conditionally independent essential genes that would be potential drug targets in both single and co-infection scenarios. Taken together, our findings highlight the utility of using genome-scale metabolic models to prioritize druggable targets that would be of broader spectrum against human pathogens.

This work describes the development and validation of a computational model for vertical borehole heat exchangers in residential ground-source heat pump energy systems. Due to the size and shape of vertical borehole heat exchangers, their operation thermally impacts a large volume of surrounding soil and thus discretized models have largely been confined to short-term transient simulations, such as the case of a thermal response test. The proposed model employs a computationally efficient physics-based models at variable spatial dimensions which can be used for long-time simulation of the ground heat transfer. The model can generally be considered as a composition of three separate domains: the borehole domain, which combines one-dimensional, three-dimensional and equations-based physics, the near-field soil domain, which resolves three-dimensional transient heat conduction and the far-field soil domain which is modelled as one-dimensional axisymmetric transient heat conduction. The main purpose of this work is to present each component of the model and validate their behaviours and assumptions through a combination of comparison to experimental data, highly cited published works, and well-known analytical models. The complete composite model ignores the three-dimensional effects of fluid heat transfer, and the axial heat transfer in the far-field in order to reduce the computational effort, and the level of uncertainty introduced by each simplification is explored. Finally, to support the composite model, a new method determining the thermal impact of the borehole operation mentioned previously was devised and presented alongside the model development and validations. This method, based on the previously defined thermal impacting radius, improves the consistency and theoretical foundation of the value’s definition based on a system energy balance, rather than local temperature conditions. / Thesis / Master of Applied Science (MASc)

No / A series of structurally related citric acid-ciprofloxacin conjugates was synthesised to investigate the influence of the linker between citric acid and ciprofloxacin on antibacterial activities. Minimum inhibitory concentrations (MICs) were determined against a panel of reference strains and clinical isolates of bacteria associated with infection in humans and correlated with the DNA gyrase inhibitory activity. The observed trend was rationalised by computational modelling.

Dry powder inhalers (DPIs) are a common therapeutic modality for lung diseases such as asthma, but they are also used to treat systemic diseases such as diabetes. Advantages of DPIs include their portable design and low manufacturing costs. Another advantage of DPIs is their breath activation, which makes them popular among patients. In a passive DPI drug is only released when the patient inhales. When the patient inhales, air flows through the device. The flow of air entrains a dry powder formulation inside the device and carries it to the lung. Currently, no DPI exists which can deliver drug independent of the patient to the desired target site in the lung. This is because drug release depends on the patient’s inhalation manoeuvre. To maximize the effect of the treatment it is necessary to optimize DPIs to achieve drug delivery that (A) is independent of the inhalation manoeuvre and (B) is targeted to the correct site in the lung. Therefore, this thesis aims to apply numerical and experimental methods to optimize DPIs systematically. First, two clinically justifiable cost functions have been developed corresponding to the DPI design objectives (A) and (B). An Eulerian-Eulerian (EE) computational fluid dynamics (CFD) approach has then been used to optimize a DPI entrainment geometry. Three different optimized entrainment geometries have been found corresponding to three different therapeutic applications. Second, the CFD approach has been validated experimentally. This is the first experimental study to validate an EE CFD approach for DPI modelling. Third, a personalized medicine approach to DPI design has been proposed. The development of this approach makes it possible to achieve the design objectives for patients with highly different lung functions. Finally, an adaptive DPI with a variable bypass element has been developed. This DPI achieves design objectives (A) and (B) for patients with highly different lung functions with a single device. In contrast to the personalized medicine approach, there is no need to select the optimal amount of bypass, since the device adapts automatically.

Understanding of visual scenes takes place within very brief episodes known as fixations. To explore the extent of the scene, the eye shifts between fixation locations at intervals of roughly 300 ms. Currently, it is a matter of open inquiry as to what factors influence the timing of these movements. This thesis focuses on understanding the mechanisms that govern the rapid adjustment of fixation and saccade timings when novel stimulus information is encountered during a fixation. In part I, I use an experimental technique known as the fixation-contingent scene quality paradigm to control the quality of incoming visual scene information. This approach is used to assess how fixation timing adapts to moment-by-moment changes in the quality level of the stimulus. I find that quality changes tend to result in an increase in fixation durations and this occurs whether the quality is increased or decreased. Using distributional analytic techniques, I argue that these results reflect the combined influence of a rapid surprise related process and a slower acting encoding related influence. In part II, I study how fixation durations are influenced by the underlying saccade programming mechanisms. An important assumption within the eye-movement control literature is that there exists a threshold called the point-of-no-return. Once this point has been reached, a saccade may no longer be modified or cancelled. I adapt a classic psychophysical technique known as the double-step procedure to study the point-of-no-return within scene viewing tasks. I also provide a measurement of the saccadic dead time, the last point in time that a saccade may be modified. In Part III, a formal model of fixation durations in high-level tasks is presented. I build on recent modelling work and develop a formal account for the early-surprise late-encoding modulation account of fixation durations in scene viewing tasks. The model is tested against data observed in Part I of the thesis. I demonstrate that the model does a very good job of predicting these distributions with relatively few assumptions. In summary, I use experimental techniques in combination with computational modelling to reveal how a composite of low-level (saccade programming) and high-level (information processing) considerations can, and must, be taken into consideration when understanding eye-movement control behaviour in scene viewing tasks.

Thesis (MSc. (Physics)) -- University of Limpopo, 2016 / The stabilities of PtS to PdS and PdS to PtS were investigated using density functional theory within the generalized gradient approximation. Their structural, electronic and mechanical properties were determined to show their stability and the effect of pressure on different compositions. We found good correlation of calculations with available ex-perimental data. The lattice parameters were observed to fluctuate with increasing con-centration for both systems. Furthermore, heats of formation were calculated to deter-mine the relative structural stability of the systems. They predict that the most stable structure is Pd50S50 P42/mmc and Pt25Pd25S50 P42/mmc being the least stable. Pd12.5Pt37.5S50 P42/m is the most stable and Pd50S50 P42/m being the least stable struc-ture. The Pt37.5Pd12.5S50 P1 was said to be the most stable structure and Pd50S50 P1 be-ing the least stable. The phonon dispersion calculations show that Pt50S50 P42/mmc, Pd50S50 P42/mmc, Pd12.5Pt37.5S50 P42/m and Pt50S50 P1 (derived from P42/mmc) are me-chanically stable, consistent with calculated elastic constants. The Pt25Pd25S50 P42/mmc show soft modes, which are due to vibrations of Pt and Pd atoms in the x - y plane which suggests the instability of the structure, in agreement with C66 being negative, and consistent with heats of formation. The lattice parameters decreased steadily with increasing pressure. An anomaly was observed in Pt50S50 P1 (derived from P42/mmc), where the c lattice parameter was found to increase with increasing pressure. The elec-tronic density of states (DOS) were performed on all compositions. The DOS were sub-jected to pressure and it was generally noted that the band gap increases with increas-ing pressure. It was observed that the smaller the band gap, the more stable the struc-ture. Furthermore, phonon dispersions under pressure show that compounds with the P42/mmc and P1 (from P42/mmc) symmetries display the mixing of lower and upper en-ergy bands at pressures above 30 GPa. / National Research Foundation

The effect of that the tire has on the overall aerodynamic drag in a car-tire assembly has been studied and deemed considerable from past studies. It has been shown that to know how tire parameters affect the drag on the car-tire assembly, it is important to understand how the vehicle body and the tires influence the flow structures. Previous studies have focused on the tire attributes that have some impact on the aerodynamic performance of the vehicle. These tire attributes, however, haven't been studied to the extent where one can get a better understanding of the impact of each of these attributes. This paper studies the impact that specific tire attributes have on the overall aerodynamic drag on the vehicle based on a thorough and systematic sensitivity study. The effect of tire attributes in a vehicle assembly as well as the sensitivity study of a rim protector on a standalone tire is conducted. This helps in better understanding the flow structures around the car body and around the tire for the improvement in the aerodynamic performance of the vehicle. This is a two-part study. One component of this study is a parametric sensitivity analysis of a tire in a tire – vehicle assembly. The other component is a parametric sensitivity analysis of the rim protector design on a standalone tire. / Master of Science / The drag performance is one of the most important factors that contributes to the overall efficiency of a vehicle. There has always been a huge demand in the automotive industry for such studies. Over the years, experimental studies conducted have shown to be invaluable to the industry. But a big downside to experimental studies is that they are extremely expensive. Experimental studies on Vehicle bodies require a wind tunnel and expensive measurement equipment. This has led to a high demand for more computational studies in this field. Various authors over the past few years have studied and challenged various solution procedures used in computational studies. The trade-off for these studies is always cost vs. accuracy. This thesis attempts to simulate both for a vehicle assembly as well as a standalone tire model to come up with a robust solution method for the computational analysis of flow over a vehicle body. The goal of this thesis is to conduct a parametric sensitivity study for the cross-section profile of the tire in vehicle assembly as well as a parametric sensitivity study for the rim protector profile of the tire in a standalone tire. At the end of the study, we will get a better understanding of the impact that each of the parameters have on the drag performance of the vehicle and the standalone tire.

This thesis investigates the role of phonetic biases and systemic effects in the actuation of sound change through computer simulations and experimental methods. Phonetic biases are physiological and psychoacoustic constraints on speech. One example is vowel undershoot: vowels sometimes fail to reach their phonetic targets due to limitations on the speed of the articulators. Phonetic biases are often paralleled by phonological patterns. For instance, many languages exhibit vowel reduction, a phonologised version of undershoot. To account for these parallels, a number of researchers have proposed that phonetic biases are the causal drive behind sound change. Although this proposal seems to solve the problem of actuation, its success is only apparent: while it might be able to explain situations where sound change occurs, it cannot easily explain the lack of sound change, that is, stasis. Since stability in sound systems seems to be the rule rather than the exception, the bias-based approach cannot provide an adequate account of their diachronic development on its own. The problem of bias-based accounts stems from their focus on changes affecting individual sound categories, and their neglect of system-wide interactions. The factors that affect speech production and perception define an adaptive landscape. The development of sound systems follows the topology of this landscape. When only a single category is investigated, it is easy to take an overly simplistic view of this landscape, and assume that phonetic biases are the only relevant factor. It is natural that the predicted outcomes will be simple and deterministic if such an approach is adopted. However, when we look at an entire sound system, other pressures such as contrast maintenance also become relevant, and the range of possible outcomes is much more diverse. Phonetic biases can still skew the adaptive landscape towards themselves, making phonetically natural outcomes more likely. However, their effects will often be countered by other pressures, which means that they will not be satisfied in every case. Sound systems move towards peaks in the adaptive landscape, or local optima, where the different pressures balance each other out. As a result, the system-based approach predicts stability. This stability can be broken by changes in the pressures that define the adaptive landscape. For instance, an increase or a decrease in functional load or a change in lexical distributions can create a situation where the sound system is knocked out of an equilibrium and starts evolving towards a new stable state. In essence, the adaptive landscape can create a moving target for the sound system. This ensures that both stability and change are observed. Therefore, this account makes realistic predictions with respect to the actuation problem. This argument is developed through a series of computer simulations that follow changes in artificial sound systems. All of these simulations are based on four theoretical assumptions: (i) speech production and perception are based on probabilistic category representations; (ii) these category representations are subject to continuous update throughout the lifetime of an individual; (iii) speech production and perception are affected by low-level universal phonetic biases; and (iv) category update is inhibited in cases where too many ambiguous tokens are produced due to category overlap. Special care is taken to anchor each of these assumptions in empirical results from a variety of fields including phonetics, sociolinguistics and psycholinguistics. Moreover, in order to show that the results described above follow directly from these theoretical assumptions and not other aspects of these models, the thesis demonstrates that exemplar and prototype models produce the same dynamics with respect to the observations above, and that the number of speakers in the model also does not have a significant influence on the outcomes. Much of the thesis focuses on rather abstract properties of simulated systems, which are difficult to test in a systematic way. The last chapter complements this by presenting a concrete example, which shows how the simulations can be linked to empirical data. Specifically, I look at the effect of lexical factors on the strength of contextual effects in sound categories, using the example of the voicing effect, whereby vowels are longer before voiced obstruents than they are before voiceless ones. The simulations implemented in this chapter predict a larger effect in cases where a given vowel category occurs equally frequently in voiced and voiceless environments, and a smaller difference where one of the environments dominates the lexical distribution of the vowel. This prediction is borne out in a small cross-linguistic production experiment looking at voicingconditioned vowel length patterns in French, Hungarian and English. Although this is only one of many predictions that fall out of the theory of sound change developed in this thesis, the success of this experiment is a strong indication that the research questions it brings into focus are worth investigating.

Widespread access to renewable electricity is seen as a viable method to mitigate carbon emissions, although problematic are the issues associated with the integration of the generation systems within current power system configurations. Wind power plants are the primary large-scale renewable generation technology applied globally, but display considerable short-term supply variability that is difficult to predict. Power systems are currently not designed to operate under these conditions, and results in the need to increase operating reserve in order to guarantee stability. Often, operating conventional generation as reserve is both technically and economically inefficient, which can overshadow positive benefits associated with renewable energy exploitation. The purpose of this thesis is to introduce and assess an alternative method of enhancing power system operations through the control of electric loads. In particular, this thesis focuses on managing highly-distributed sustainable demand-side infrastructure, in the form of heat pumps, electric vehicles, and electrolyzers, as dispatchable short-term energy balancing resources. The main contribution of the thesis is an optimal control strategy capable of simultaneously balancing grid- and demand-side objectives. The viability of the load control strategy is assessed through model-based simulations that explicitly track end-use functionality of responsive devices within a power systems analysis typically implemented to observe the effects of integrated wind energy systems. Results indicate that there is great potential for the proposed method to displace the need for increased reserve capacity in systems considering a high penetration of wind energy, thereby allowing conventional generation to operate more efficiently and avoid the need for possible capacity expansions. / Graduate