Narrow Line Type-1 Seyfert active galaxies can exhibit a high degree of variability in the X-ray regime. This thesis examines that variability in the context of reverberation models, in which a flare in activity has an extended, energy dependent, response. A novel method is developed for estimating the response function in different energy bands. This method is then applied to three AGN: Ark 564, 1H 0707{495, and NGC 4051. The striking evidence for reverberation revealed in Ark 564 leads to a more thorough examination of that object, combining spectral and temporal approaches to develop a plausible physical model for its behaviour. The preferred model is one in which the reverberation is due to scattering from hot Comptonizing material approximately 1500 light-seconds from the central source. This conclusion is reinforced by a simulation of the angular dependence of reflection by Comptonizing gas.

To elucidate the intrinsic broadband infrared (IR) emission properties of active galactic nuclei (AGNs), we analyze the spectral energy distributions (SEDs) of 87 z less than or similar to 0.5 Palomar-Green (PG) quasars. While the Elvis AGN template with a moderate far-IR correction can reasonably match the SEDs of the AGN components in similar to 60% of the sample (and is superior to alternatives such as that by Assef), it fails on two quasar populations: (1) hot-dustdeficient (HDD) quasars that show very weak emission thoroughly from the near-IR to the far-IR, and (2) warm-dust- deficient (WDD) quasars that have similar hot dust emission as normal quasars but are relatively faint in the mid-and far-IR. After building composite AGN templates for these dust-deficient quasars, we successfully fit the 0.3-500 mu m SEDs of the PG sample with the appropriate AGN template, an infrared template of a star-forming galaxy, and a host galaxy stellar template. 20 HDD and 12 WDD quasars are identified from the SED decomposition, including seven ambiguous cases. Compared with normal quasars, the HDD quasars have AGNs with relatively low Eddington ratios and the fraction of WDD quasars increases with AGN luminosity. Moreover, both the HDD and WDD quasar populations show relatively stronger mid-IR silicate emission. Virtually identical SED properties are also found in some quasars from z = 0.5 to 6. We propose a conceptual model to demonstrate that the observed dust deficiency of quasars can result from a change of structures of the circumnuclear tori that can occur at any cosmic epoch.

The range of currently proposed active galactic nucleus (AGN) far-infrared templates results in uncertainties in retrieving host galaxy information from infrared observations and also undermines constraints on the outer part of the AGN torus. We discuss how to test and reconcile these templates. Physically, the fraction of the intrinsic AGN IR-processed luminosity compared with that from the central engine should be consistent with the dust-covering factor. In addition, besides reproducing the composite spectral energy distributions (SEDs) of quasars, a correct AGN IR template combined with an accurate library of star-forming galaxy templates should be able to reproduce the IR properties of the host galaxies, such as the luminosity-dependent SED shapes and aromatic feature strengths. We develop tests based on these expected behaviors and find that the shape of the AGN intrinsic far-IR emission drops off rapidly starting at similar to 20 mu m and can be matched by an Elvis et al.-like template with a. minor modification. Despite the variations in the near- to mid-IR bands, AGNs in quasars and Seyfert galaxies have remarkably similar intrinsic far-IR SEDs at lambda similar to 20-100 mu m, suggesting a similar emission character of the outermost region of the circumnuclear torus. The variations of the intrinsic AGN IR SEDs among the type-1 quasar population can be explained by the changing relative strengths of four major dust components with similar characteristic temperatures, and there is evidence for compact AGN-heated dusty structures at sub-kiloparsec scales in the far-IR.

In this thesis we study the physics of colloidal dispersions in active and passive liquid crystals by computer simulations. Liquid crystals are materials that exhibit long-range orientational order, with characteristics intermediate between the ones of simple, isotropic fluids and the ones of crystalline solids. Active fluids are suspensions of particles that continuously stir their ambient fluid. Like liquid crystals, active fluids undergo phase transitions to orientationally ordered phases. The framework that we apply here to describe them extends hydrodynamic equations for liquid crystals to the active case, in which their constituent particles exert local stresses on the simple fluid in which they are embedded. Studying systems of colloids embedded in these materials can be done with multiple aims. Here we use colloids as probe particles to investigate the rheological properties of active nematics. To do so we apply a constant force to a spherical particle embedded therein and define an effective viscosity, which we determine by measuring the velocity in steady state. We find an important dependence of the effective viscosity on the size of the particle, and a regime characterised by a steady state of negative drag. We also consider collective properties for systems of many colloids and analyse how they are affected by activity. We find that spontaneous flow can either hinder or favour colloidal aggregation, depending mainly on whether a fixed orientation of the liquid crystal is imposed close to the colloidal surface. This remains true independently of the initial condition chosen for the liquid crystal, which only affects the transition to spontaneous flow.

The construction of mechanically interlocked molecules has been the subject of decades of research. The efficiency of strategies for preparing these molecules has increased continuously. In recent years, the transition metal templation strategy has played quite a remarkable role in the synthesis of entwined or mechanically bonded structures due to the metals’ diverse coordination chemistry and ability to chelate ligands. In the early stages of this method’s development, the metal ions were used as integral part of the scaffold for such components as rings and stoppers to generate the interlocked structures. In newly developed active metal templation strategies, metal ions are used to promote covalent bond forming reactions while simultaneously acting as structural supports. In this thesis, three main aspects are expanded for the discussion of the application of metal template strategies. First of all, the newly developed strategy - active metal template - will be described and exemplified using the Huisgen-Meldal-Fokin Cu(I)- catalyzed 1,3-cycloaddition of azides with terminal alkynes (the CuAAC “click” reaction), the Cu(I)-mediated Cadiot-Chodkiewicz heterocoupling of an alkyne halide with a terminal alkyne, and the Ni(II)-catalyzed Csp3-Csp3 homocoupling reaction. Secondly, the thesis discusses the use of these strategies to obtain several hard-to-access structures, including the first high-yielding doubly threaded [3]rotaxanes, heterocircuitcatenanes and the one pot synthesis of homocircuit-catenanes, and the smallest molecular trefoil knot prepared to date. Lastly, as an extension of the metal temptation strategy, the final chapter of this thesis will discuss the assembly of inorganic metal-organic catenanes by metal coordination.

Climate change has brought about legally-binding targets for Scotland, the U.K. and the E.U. to reduce greenhouse gas emissions and source a share of overall energy consumption from renewable energy resources by 2020. With severe limitations in the transport and heating sectors the onus is on the electricity sector to provide a significant reduction in greenhouse gas emissions and introduce a substantial increase in renewable energy production. The most attractive renewable energy resources are located in the geographic extremes of the country, far from the large population densities and high voltage, high capacity transmission networks. This means that the majority of renewable generation technologies will need to connect to the conventionally passive, lower voltage distribution networks. The integration of Distributed Generation (DG) is severely restricted by the technical limitations of the passively managed lower voltage infrastructure. Long lead times and the capital expenditure of traditional electricity network reinforcement can significantly delay or make the economics of some renewable generation schemes unviable. To be able to quickly and cost-effectively integrate significant levels of DG, the conventional fit-and-forget approach will have to be evolved into a ‘connect-and-manage’ system using active network management (ANM) techniques. ANM considers the real-time variation in generation and demand levels and schedules electricity network control settings to alleviate system constraints and increase connectable capacity of DG. This thesis explores the extent to which real time adjustments to DG and network asset controller set-points could allow existing networks to accommodate more DG. This thesis investigates the use of a full AC OPF technique to operate and schedule in real time variables of ANM control in distribution networks. These include; DG real and reactive power output and on-load-tap-changing transformer set-points. New formulations of the full AC OPF problem including multi-objective functions, penalising unnecessary deviation of variable control settings, and a Receding-Horizon formulation are assessed. This thesis also presents a methodology and modelling environment to explore the new and innovative formulations of OPF and to assess the interactions of various control practices in real time. Continuous time sequential, single scenario, OPF analyses at a very short control cycle can lead to the discontinuous and unnecessary switching of network control set-points, particularly during the less onerous network operating conditions. Furthermore, residual current flow and voltage variation can also gave rise to undesirable network effects including over and under voltage excursion and thermal overloading of network components. For the majority of instances, the magnitude of constraint violation was not significant but the levels of occurrence gave occasional cause for concern. The new formulations of the OPF problem were successful in deterring any extreme and unsatisfactory effects. Results have shown significant improvements in the energy yield from non-firm renewable energy resources. Initial testing of the real time OPF techniques in a simple demonstration network where voltage rise restricted the headroom for installed DG capacity and energy yield, showed that the energy yield for a single DG increased by 200% from the fit-and-forget scenario. Extrapolation of the OPF technique to a network with multiple DGs from different types of renewable energy resources showed an increase of 216% from the fit-and-forget energy yield. In a much larger network case study, where thermal loading limits constrained further DG capacity and energy yield, the increase in energy yield was more modest with an average increase of 45% over the fit-and-forget approach. In the large network where thermal overloading prevailed there was no immediate alternative to real power curtailment. This work has demonstrated that the proposed ANM OPF schemes can provide an intelligent, more cost effective and quicker alternative to network upgrades. As a result, DNOs can have a better knowledge and understanding of the capabilities and technical limitations of their networks to absorb DG safely and securely, without the expense of conventional network reinforcement.

We present multi-wavelength studies of the radio galaxy 3C 120 and the blazar CTA 102 during unprecedented gamma-ray flares for both sources. In both studies the analysis of gamma-ray data has been compared with a series of 43 GHz VLBA images from the VLBA-BU-BLAZAR program, providing the necessary spatial resolution to probe the parsec scale jet evolution during the high energy events. To extend the radio dataset for 3C 120 we also used 15 GHz VLBA data from the MOJAVE sample. These two objects which represent very different classes of AGN, have similar properties during the gamma-ray events. The gamma-ray flares are associated with the passage of a new superluminal component through the mm VLBI core, but not all ejections of new components lead to gamma-ray events. In both sources gamma-ray events occurred only when the new components are moving in a direction closer to our line of sight. We locate the g-ray dissipation zone a short distance from the radio core but outside of the broad line region, suggesting synchrotron self-Compton scattering as the probable mechanism for the gamma-ray production.

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MSc (Med), Epidemiology and Biostatistics, Faculty of Health Sciences, University of the Witwatersrand / Background. South Africa is currently experiencing one of the most severe AIDS epidemics in the world. The major challenge lies in prompt identification and early initiation of treatment in those eligible for HAART. Clinical staging has previously been recommended for use in settings where CD4 + count testing is not available. We conducted secondary data analysis to determine whether clinical symptoms and signs are useful in predicting the need for HAART initiation (CD4 + count < 200 cells/μL) in South Africa. Methods. Screening data from a randomized controlled trial in women who were HIV positive were analysed. All participants were interviewed using a structured questionnaire to elicit symptom history and then physical examination was done. Participants were staged using WHO criteria. Blood was drawn for CD4 + testing. The association between signs and symptoms and a CD4 + < 200 cells/μL was assessed using logistic regression. Results. Among 589 HIV infected women aged between 18 and 58 years, 90% were assessed as WHO clinical stages I/II. The median CD4 + count was 403 cells/μL (IQR: 273-586). Among women who were WHO stage I/II, 13% had CD4 + count < 200 cells/μL and required HAART. The WHO clinical staging had a low sensitivity (4%) but high specificity for detecting those that require treatment. Conclusion: In a setting where asymptomatic patients are diagnosed with HIV, clinical assessment can not replace CD4 + count testing as a method of identifying those that need treatment.

Cervical cancer is the third most commonly diagnosed cancer globally and it has also been identified as one of three AIDS defining malignancies. Highly active antiretroviral therapy (HAART) is a combination of three or more antiretroviral drugs which are classified as nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs). HAART has been shown to play a significant role in reducing the incidence of some AIDS defining malignancies, although its effect on cervical cancer is still unclear. It is hypothesized that HAART might reduce cancer risk by interacting with different signalling molecules and pathways that are involved in cancer in order to induce cell death and thus inhibit cell proliferation. The broader aim of this study was to understand the relationship between cervical cancer and HAART. This was achieved by studying the expression of key signalling molecules in cancer; MUC1 and NFkB (P65) and morphological features using scanning electron microscopy following 24 hour treatment of a cervical cancer cell line, HCS-2 with drugs which are commonly used as part of HAART; Emtricitabine (FTC), Tenofovir disoproxil fumarate (TDF), Efavirenz (EFV), Atripla combination (ATP) and Kaletra combination (LPV/r) at their clinical plasma concentrations. Quantitative real time polymerase chain reaction (qPCR) was used in order to study the gene expression of MUC1 and P65 and the data was analysed using the 2-ΔΔCT method to calculate fold change. The statistical analysis was conducted using JMP 11 software. MUC1 and P65 gene expression was reduced following drug treatment. Protein expression was studied by means of Immunofluorescence and MUC1 and P65 protein expression was reduced following drug treatment. Scanning electron microscopy revealed characteristic features of apoptotic cell death such as loss of cell contacts, reduced density and size of microvilli, increase in surface blebbing and budding and degradation of apoptotic bodies following treatment with all the drugs. In conclusion, the drugs used in this study