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Bacillus subtilis and Clostridioides difficile are Gram-positive bacteria that may adapt to unfavourable conditions by forming a dormant spore. Sporulation involves an asymmetric cell division resulting in a larger mother cell and a smaller forespore. The forespore is later engulfed by the mother cell in a phagocytosis like process. Activation of the sporulation pathway is tightly regulated through complex sensor systems, crucial to which are peptides imported into the cell through peptide transport systems belonging to the ATP-binding cassette (ABC) family. Peptides have an important nutritional role as well as the signalling role and B. subtilis has three ABC peptide transporters with overlapping specificity, a dipeptide permease (Dpp) and two oligopeptide permeases (Opp and App). Here the crystal structures of the receptors for two of these transporters OppA and DppE are described revealing unexpectedly that DppE is a murein tripeptide binding protein whilst the OppA structure reveals a tetrapeptide bound whose average electron density closely resembles Ser-Asn-Ser-Ser. Crystallographic and peptide binding studies of OppA and AppA from C. difficile have led us to conclude that neither of these proteins is a receptor for peptide transport as previously reported. OppA is more likely to serve as a receptor for the uptake of nickel ions. Upon completion of engulfment, a channel is formed between mother cell and forespore at the heart of which is an intercellular interaction between SpoIIIAH and SpoIIQ that has been described structurally. The stoichiometry of this complex in vivo is unknown though models of rings containing 15-24 molecules have been proposed. Here experiments are described to fuse fluorescent reporters to SpoIIQ and SpoIIIAH in order to perform super resolution microscopy to determine the stoichiometry of the complex in live cells for the first time.

This thesis investigates the wetting of simple liquids using two density functional theory (DFT) models. The first model is a discrete lattice-gas model and the second a continuum DFT model of a hard-sphere reference system with an additional attractive perturbation. The wetting properties of liquids are principally investigated by studying the binding, or interface, potential of the fluid and this thesis presents a method by which a binding potential can be fully calculated from the microscopic DFT. The binding potentials are used to investigate the behaviour of the model fluid depending on the range to which particle interactions are truncated. Long ranged particle interactions are commonly truncated to increase computational efficiency but the work in this thesis shows that in making this truncation some important aspects of the interfacial phase behaviour are changed. It is demonstrated that in some instances by reducing the interaction range of fluid particles a shift in phase behaviour from wetting to non wetting occurs. The binding potential is an input to larger scale coarse grained models and this is traditionally given as an asymptotic approximation of the binding potential. By using the full binding potential, calculated from the DFT model, as an input, excellent agreement can be found between the results from the microscopic DFT model and the larger scale models. This is first verified with the discrete lattice-gas model where the discrete nature of the model causes some non-physical behaviour in the binding potentials. The continuum DFT model is then applied which corrects this behaviour. An adaptation to this continuum model is used to study short ranged systems at high liquid densities at state points below the `Fisher-Widom' line. The form of the decay of the density profiles and binding potentials now switches from monotonic to oscillatory. This model leads to highly structured liquid droplets exhibiting a step-like structure.

Understanding the trophic relationships between organisms is crucial to understanding ecosystem functioning and as such regular echinoids have been termed keystone through the action of their grazing. Much research has focused on this group’s action as herbivores, but as a group omnivory is common. The aim of this study was to investigate the trophic ecology of the locally super abundant regular echinoid species Psammechinus miliaris within Scottish sea lochs. To do this the study used manipulative field experiments combined with biochemical analysis of trophic proxies. The manipulative field experiments involved either the hand removal or the caging of P. miliaris to determine the impact the sea urchin grazinghas on benthic community structure. These studies revealed that grazing of P. miliaris can have a major influence on the biomass and structure of the benthic invertebrate communities. The biochemical analysis of trophic proxies was used to quantify the spatial and temporal variations in the trophic interactions of P. miliaris. These studies focused on the urchin gonad and compared differences in the gonadal somatic indices (reflecting nutritional and reproductive state) with the fatty acid biochemistry and stable isotope ratios of Carbon and Nitrogen. These studies revealed high levels of spatial and temporal heterogeneity in the trophic interactions of P. miliaris and suggested that the populations exhibited significant levels of omnivory. The combination of these studies showed that P.miliaris plays an important role in structuring benthic invertebrate communities and in the flow of energy through ecosystems and through this, ecosystem functioning.

Experimental and computational techniques have been used to study the performance of a tip-driven propeller (TDP) and a waterjet intake duct for the purpose of assessing the practical implications of using a tip-driven impeller in a waterjet propulsion system. A prototype electromagnetic tip-driven propeller has been successfully designed and built for the specific purpose of experimental analysis. This unit has been tested in towing tanks for a range of propeller speeds, advance speeds and duct shapes. In conjunction with the towing tank tests a potential-flow panel model (with viscous coupled duct) has been developed in order to predict the likely performance of the prototype thruster. The model has been validated against both the towing tank results, and against published data for standard ducted propeller units. A representative waterjet intake duct has been tested using an open-circuit wind tunnel. Velocity proffles and surface pressure distributions have been obtained for three different flow regimes. In addition, a CFD model of the same inlet duct geometry has been developed using a fully viscous, commercial RANS flow solver. This model is validated against the wind tunnel test data and has been further developed to study the influence of trim and drift on the flow through the duct. In addition, a brief study on duct-hull interaction is presented. Results from the experimental and computational tests on both the tip-driven propeller and waterjet intake duct are presented. The two validated CFD models are subsequently coupled together to investigate the performance implications of using a tip-driven, rather than shaft-driven, axial-flow waterjet impeller. It is shown that the use of a tip-driven impeller in a waterjet propulsion system has the potential to increase hydrodynamic performance. Removing the drive shaft from the system resulted in an increase in predicted impeller thrust of approximately KT=0.1. Finally, the practical implications of such a drive mechanism are discussed. It is seen that the use of an electromagnetic tip-drive is limited by the physical size of the motor.