Thesis (Ph. D.)--School of Chemistry, Faculty of Science, University of Sydney, 2006. / Title from title screen (viewed 13 January 2009). Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy to the School of Chemistry, Faculty of Science. Includes bibliographical references. Also available in print form.

Self-propelled particles are a class of far-from-equilibrium systems which present many complex, emergent features that are not obvious from the microscopic dynamics. Simulations of well-chosen instances of such systems are a powerful yet tractable method of investigating many real-world phenomena. The frequently non-time-reversible interactions of many cases of self-propelled particles with surfaces means that the environment has an impact on large-scale behaviour in a way that would not be true for particles close to thermal equilibrium. This work investigates several examples of such systems, and compares them with experimental results for comparable systems: firstly, the spatial distribution of smooth-swimming mutants of Eschericia Coli within water-in-oil emulsion is investigated, and its dependence on inter-bacterial interactions and the size of water droplets. The nature of bacterial collisions is inferred through data analysis and simulation. Secondly, pattern formation by chemotactic run-and-tumble bacteria due to secretion of a chemoattractant by the bacteria themselves, demonstrating a range of approaches to control the formation of biofilms by bacteria. Finally the dependence of the bulk transport properties of chemotactic self-propelled particles in porous environments, on their detailed dynamics, is probed: how they interact with obstacles, their form of chemotactic response, their ability to actively enhance their rotational noise, and their method of sensing chemical gradients.

L’Arménie se situe dans la zone de collision entre Arabie et Eurasie et est le siège d’une déformation intracontinental active comme l’atteste les nombreux tremblements de terre historiques qui s’y sont produits. Tous ces séismes, destructeurs, attestent d’une forte activité sismique régionale, et il est par conséquent important d'évaluer l’aléa sismique associé aux structures actives qui génère cette sismicité.Le travail présenté ici, expose les résultats de l’analyse de la tectonique active au niveau des terminaisons nord-ouest et sud-est de la faille de Pambak-Sevan-Syunik (PSSF), une des failles décrochant majeure qui traverse l'Arménie du NW au SE. La quantification des déformations en termes de géométrie, cinématique, vitesse de glissement et paléosismicité, en utilisant les méthodes de datation 3He cosmogénique, OSL/IRSL et radiocarbone, révèlent des comportements différents entre les deux régions.Au niveau de la terminaison nord-ouest, dans la région d’Amassia, la faille PSSF s’incurve vers l'ouest et se subdivise en deux branches de direction WNW-ESE, et de cinématique inverse, définissant une structure en pop-up. Nous estimons une vitesse de soulèvement de 0.5 ± 0.1 mm/an et une vitesse de raccourcissement NNE-SSW de 1.4 ± 0.6 mm/an. Ces résultats suggère que l’essentiel des ~2 mm/an de mouvement dextre estimés le long de la faille de PSSF sont absorbés au niveau du pop-up d’Amassia.Au niveau de la terminaison sud-est, dans la région du volcan Tsghuk, la faille PSSF semble disparaitre. Le peu d’activité tectonique est caractérisée par des failles normales sub-méridiennes associées à une légère composante décrochant dextre. Nous déterminons une vitesse de glissement vertical de ~0,2 mm/an, une vitesse d’extension ~EW de ~0,1 mm/an associée à une composante dextre de ~0,05 mm/an. Ces résultats suggèrent que le mouvement dextre observé le long de la faille de PSSF plus au nord, a été transféré sur d'autres failles plus à l'ouest dans le Karabakh (faille Hagari ou autres structures situés encore plus au NW). / The territory of Armenia was located in the collision zone between Arabia and Eurasia, and is the seat of active intercontinental deformations, which was attested by the many historical earthquakes that have occurred in this region. All these destructive earthquakes show a strong regional seismic activity, and therefore it is important to evaluate the seismic hazard associated with active structures that generates this seismicity.This study presents the results of the analysis of the active tectonics within the northwestern and southeastern extensions of the Pambak-Sevan-Syunik fault (PSSF), a major right-lateral strike-slip fault cutting through Armenia (NW - SE). Quantifying the deformations in terms of geometry, kinematics, slip rates and earthquake activity, using cosmogenic 3He, OSL/IRSL and radiocarbon dating techniques, reveal different behaviors between the two regions.Within the northwestern extension, in the region of Amassia, the PSSF bends to the west and splits into two main WNW-ESE trending reverse faults defining a compressional pop-up structure. We estimate an uplift rate and a shortening rate of 0.5 ± 0.1 mm/y and 1.4 ± 0.6 mm/y, respectively. This suggests that most of the ~2 mm/y right lateral movement of the PSSF seems to be absorbed within the Amasia pop-structure.Within the southeastern extension, in the region of Tsghuk volcano, the PSSF shows signs of dying out at the southernmost tip of the Syunik graben. A very slow NS trending normal faulting associated with a slight right-lateral movement characterizes the tectonic activity in the region of Tsghuk volcano. We estimate vertical slip rates, EW stretching rate, and right-lateral slip rate of ~0.2 mm/y, ~0.1 mm/y and ~0.05 mm/y, respectively. These results lead to the conclusion that the right lateral movement observed further north along the PSSF is mainly transferred within other active faults further west within the Karabagh (Hagari fault or other structures further northwestwards).

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In an ideal world, unwanted or undesirable effects in a system could and would be completely ignored. In fact, this was the case in mid-80s' PC design when an 80286 microprocessor running at a "blazing" 12 MHz was considered leading-edge technology. As technology continued to push the envelope and ever-faster designs were realized, more demanding software packages were developed and utilized efficiently. These increasingly sophisticated software packages in turn allowed designers of all disciplines to test systems of escalating complexity. These more complex models placed a heavier burden on the hardware, prompting a push for better and faster hardware designs. The cycle repeats to this day. As such, we are now in an environment where a 1 GHz microprocessor is considered somewhat dated. More importantly, whereas a small 1 nH (1 billionth of a Henry) inductance in a power delivery path was considered inconsequential a decade ago, it is now a barrier to implementing a design. Similarly, the equivalent series inductance (ESL) of a capacitor plays an increasing (and detrimental) role in the behavior and design of today's VRM (Voltage Regulator Module) design. In fact, it is the ESL of the capacitor that hinders proper voltage regulation at high frequencies by increasing the output impedance beyond a desired level. This dilemma has been recognized and several topologies have been proposed to overcome this problem. One category is improved passive devices, with the latest involving array capacitors to achieve near-zero ESL. As passive devices are almost always preferable to active solutions due to their lower losses, these technologies hold great promise, though they are inherently limited in small-footprint applications. A second category is the addition of active devices, which involves the use of some filtering technique to inject or absorb current during a fast transient by the use of semiconductor switches connected to a power source. These switching-state topologies have been shown to be prone to unstable oscillations, often caused by over-reactions or over-corrections of one transient prompting the opposite switch to engage its power source. The research goal is to develop a methodology to use active filters to more-seamlessly extend the control bandwidth of today's VRM technology. A hybrid active power filter is developed which uses bipolar junction transistors (BJT) in the forward-active region to connect a power supply source to the microprocessor. In this way, the switches are used in a way analogous to a dimmer switch (vs. simply 'on' or 'off'). By proper design of the compensator in the feedback loop, the active power filter can be used to suppress transients in any desired frequency range, limited only by the amplifier's current rating and bandwidth. The compensator design's derivation shows the relationship to the output impedance of the active filter. In essence, we are 'designing' a capacitor with a very low ESL, having more desirable output impedance vs. frequency relationship than either a capacitor, or a more complicated VRM with an extended bandwidth. Using this design, however, at very high frequencies (i.e., approaching 1 GHz, or one trillion cycles per second) requires state-of-the-art packaging designs to limit unwanted impedances, and also an ultra-wide GHz bandwidth, high-current operational amplifier. Both of these barriers are outside the scope of this research. As is often the case in research efforts, we have not '˜solved' the problem, but have shifted it to a frequency range where the effect isn't problematic. Experimental results show the use of a hybrid power filter with a VRM with Adaptive Voltage Positioning (AVP) can significantly suppress voltage undershoot during fast transient load current changes. In addition, the design is modified to reduce and possibly eliminate bulk output capacitors. This provides a promising alternative to a Voltage Regulator Module with a very high control bandwidth. Lastly, simulations give an estimate of the required IC design to use an APF to augment packaging capacitors. / Master of Science

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in partial fulfillment of the requirements for the degree Master of Family Medicine, October 2013 / Botswana has one of the highest HIV prevalence rates in the world, with 32% of pregnant women and 24% of adults in the general population living with HIV. Although antiretroviral therapy (ART) or HIV/AIDS treatment is widely available in the public sector in Botswana, not all treatment-eligible patients utilise the services in a timely manner. The study aims to identify the factors associated with the intention of already screened HIV positive/AIDS patients, who met the government criteria, to enrol into the HIV treatment programme in Lobatse, Botswana. Methods: A Cross-sectional descriptive study was used, conducted at the Infectious Disease Control Clinic, Athlone Hospital, Lobatse over a 6-month period. A questionnaire was administered on systematically sampled participants, who met Botswana National antiretroviral treatment or HIV/AIDS treatment guidelines. Results: A total of 342 participants were enrolled, mostly female (67.3%) and single (50%). Majority of the participants were age 35-44 years (17%), attained up to primary level education (44%) and were mostly unemployed (54%). A majority (59%) intended to enroll into ART or HIV/AIDS treatment programme due to sickness, while others were motivated by voluntary testing and counseling (24%). The majority of the respondents received post-test counseling (97.3%) and most was motivated to seek ART or HIV/AIDS treatment (88.3%). Only (60%) disclosed their status to their relative. Although most participants (59.6%) were willing to be linked to care and support, most (65.1%) were ignorant of support groups and services available for them. Discussion: Although there is increasing access to ART or HIV/AIDS treatment, most participants still wait until they are sick or have symptoms before they enroll into ART. Supportive post-test counseling and conducive family environment were some of the enabling factors. Distance to health facilities and long queues are barriers to accessing care as well as stigma and discrimination. The most significant reasons for not continuing with the treatment were health facilities being far from place of residence and queuing for a long time to see a doctor and or collect medications. Conclusion: Sickness, public education, supportive family environment and effective post-test counseling were found to be significant motivators for intention to enroll into ART. Perceived barriers to accessing treatment include distance and time spent in the health facilities. Interventions are required to reduce stigma, bring health facilities nearer to the people, and increase efficiency in health facilities and increase access and utilization of the care and support groups.

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in partial fulfilment of the requirements for the degree of Master of Science in Pharmaceutical Affairs Johannesburg, 2012 / Objective: To determine the proportion of HIV+ patients who fail treatment on a yearly basis in a 5-year treatment cohort in Tshwane District Hospital and to determine the correlation of treatment failure with variables routinely measured at the clinic namely WHO stage, CD4 count, HIV viral load, age, gender, presence of concomitant diseases, concomitant medication and distance travelled to clinic. Design: A retrospective study with an analytical component was conducted using the hospital records of adult patients receiving antiretroviral therapy in 2004 and followed for 5 years (until 2009) at the Tshwane District Hospital. Methods: All adult patients receiving antiretroviral therapy in 2004 were identified and followed for the next 5 years till 2009 at Tshwane District Hospital. The proportion of patients that failed treatment yearly was calculated. Univariate analysis was used to compare all patients who failed at any time point with the patients who did not fail at all for all variables. A repeated measures logistic regression model was developed to determine the variables that impacted on the binary outcome, namely treatment failure or not. Results: Of the 1104 adult patients who were attending the TDH Immunology clinic in 2004, 870 adults were receiving ARVs. 333 patients (38.28 %) experienced treatment failure throughout the study period. 6.9 % (60/870) of the study population failed virologically. 307 of the 870 patients (35.29 %) failed treatment immunologically. 102 patients (11.72 %) experience treatment failure at the 12 month time point, 37 patients(4.49 %) at the 24 month time point, 57 patients(6.93 %) at 36 month time point, 101 patients(12.27 %) at the 48 month time point and 140 patients (7.01 %) failed treatment at 60 month time point. Univariate analysis showed significant correlation between treatment failure and non-adherer, interrupting treatment, defaulted treatment, viral load at baseline, 12, 24, 36, 48, 60 months, and CD4 count at baseline, 12, 24, 36, 48, 60 months. In the multivariate analysis, there was a significant association between short term stoppage of treatment (STSTOP) (coefficient ratio = 1.41; p<0.001), long term stoppage of treatment (LTSTOP) (coefficient ratio = 3.24; p<0.001), transfers from other health institutions (coefficient ratio = 1.96; p<0.001), regimen (coefficient ratio = -0.1734) and treatment failure. The change in log viral load at 12 months from baseline (LOGVLBL12) (coefficient ratio =-1.7145; p<0.001) was highly significant for reaching the end point - treatment v failure. Older patients were less likely to fail treatment (coefficient ratio = -0.0517, p<0.001) and patients with an advance stage of the disease (WHO stage 3 or 4) were at a lower risk of failing treatment (coefficient ratio = -0.4175; P=0.008). The CD4 count was significant in the univariate analysis P<0.01) and XTGEE (coefficient ratio =- 0.0001; p<0.001). There was no significant correlation between gender, place of residence, employment status and treatment failure. Conclusion: More than one–third of the patients receiving treatment in TDH failed treatment within the 5 year study period. The determinants of treatment failure are age, WHO stage, transfer from other institutions, short term stoppage of treatment, long term stoppage of treatment, CD4 cell count and the level of viral suppression within the first year of treatment (LOGVLBL-12). This study reinforces the need for identifying high risk patients earlier in treatment in order to implement strategies that might strengthen adherence to treatment.

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