Dye sensitised solar cells (DSSCs) mimic charge excitation and transfer processes found in natural photosynthesis to directly convert sunlight into electricity. Combining easy assembly with relatively cheap materials they offer a potentially cost effective solution to our energy requirements. Numerous physical processes are at work within a DSSC and the underlying complexity of these competing processes has meant that, despite considerable research effort, advances in obtaining a viable device efficiency have stagnated. The aim of this thesis is to examine, by density functional theory calculations, some of the processes at work in DSSCs with the motivation being to provide insight that informs the design of more efficient devices by experimentalists. Our calculations study some of the key factors affecting device efficiency, in particular the interaction of binding moieties with titanium dioxide surfaces, the role intrinsic and extrinsic defects have in defining the properties of semiconductors, the molecular design of sensitising dyes and the effect this has on both dye-dye and dye-semiconductor interactions. Finally we implement and test the excited state formalism of time dependent density functional theory (TDDFT) within the linear scaling DFT code CONQUEST, allowing excited state properties of large systems to be examined computationally. Our approach propagates the density matrix in real time (RT-TDDFT), and finally we use our implementation to model the real time response of titanium dioxide clusters and dyes to external electric fields.

Atomic force microscopy is an advanced imaging technique for viewing biological structures and dynamic biological mechanisms at the nanometre scale. This thesis describes a high-resolution atomic force microscope designed for imaging biological samples in physiological solution. This microscope includes a highly sensitive interferometric cantilever detector, along with a home-built frequency/phase and amplitude detector. The initial chapters of this thesis begin with a description of the experimental set-up, as well as various tests carried out to characterise the fast frequency detector. Following this is a description of the interferometric cantilever detector, which possess a noise floor at a mere 5 fm/√Hz, making it particularly suited for detecting cantilevers in liquids. Results chapters then go on to demonstrate the capability of this instrument to image at nanometre and atomic-scale resolution. Images of the atomic structure of muscovite mica in buffer solution are presented. Images of chaperonin protein GroEL were also acquired, which contain features of the protein's apical domain. Most importantly, for the first time AFM was used to track the pore-formation of pore forming protein pneumolysin in buffer solution. Supported lipid bilayers were prepared and images were captured of the proteins oligomerising on their surface. The initial stage of pore-formation was investigated by comparing the height of pneumolysin before and after pores were formed. Details of the monomers making up the structure of the protein were also imaged, as well as pores created within the supported lipid bilayers.

The low degree of processing of the interstellar medium (ISM) in nearby metal-poor galaxies, such as NGC 4449, allow them to be viewed as local analogues of the first galaxies formed in the Universe. In this work we present a study of dust and star formation in NGC 4449, both on global and local scales. We present the spectral energy distribution (SED) of NGC 4449 from the FUV to the sub-mm. Our analysis of a global optical spectrum of NGC 4449 suggests an early onset of star formation, while our results from a chemical evolution dust model provide an indication of the chemical composition of dust globally. These results were used as constraints in constructing a photoionization and radiative transfer MOCASSIN model of NGC 4449. The presented iterative scheme allowed us to infer a total mass of the youngest stellar population which is likely to reside in the centre, in the SW and in the N of NGC 4449. The derived global recent star formation rate is in good agreement with previous estimates. We conclude that our scheme is a new tool, which is particularly suitable for deriving integrated properties of galaxies. Based on spectroscopic observations from the Spitzer Space Telescope and the Herschel Space Telescope we obtained a detailed view of the ionized regions, the photo-dissociation regions and the dust emission within NGC 4449. Our results suggest a deficit of ionized polycyclic aromatic hydrocarbons (PAHs) near the centre of NGC 4449 and bright [OIII]88 emission dominating the ISM cooling locally. Additionally, we examined a sample of type Ibc supernovae to assess their possible contribution to dust formation in the early Universe. We found that the estimated dust masses are too low to consider type Ibc supernovae as major dust producers.

Two novel methods in strong-field and attosecond physics are studied in this thesis: Bohmian trajectories and initial-value representations (IVRs). Both methods describe the system dynamics in terms of trajectories of electrons, and include the binding potential and the laser field. The full solution of the time-dependent Schrodinger equation (TDSE) is used as a benchmark. First, Bohmian trajectories are applied to high-order harmonic generation (HHG). We find that the trajectory located at the innermost region of the atomic core is the most important for HHG and yields spectra with a well defined plateau and cutoff. Using time-frequency analysis, we associate this trajectory to an ensemble of unbound classical trajectories leaving and returning to the core, and observe arch-like patterns that build up in the phase of the wave function. Furthermore, we relate the Bohmian trajectories to the short and long trajectories encountered in the strong-field approximation (SFA) and show that the central Bohmian trajectory overestimates the contribution of the long SFA trajectory. Second, IVRs, namely the Herman-Kluk (HK) propagator and the coupled coherent states (CCS) method, are employed in the study of strong-field ionization dynamics. This study is performed in phase space, where signatures of tunneling and over-the-barrier ionization are identified for an initially bound wave packet. Our results indicate that the HK propagator does not fully account for tunneling and over-the-barrier refections, but partly reproduces features associated with the wave packet crossing classically forbidden regions. In contrast, the CCS method accurately reproduces the results from the time-dependent Schrodinger equation (TDSE). The original CCS, compared with the TDSE, works well in short time propagation. If reprojection of the wave function to the initial grid is employed quantitative agreement between these two methods, and the first ever CCS computation of HHG spectra, with a plateau and sharp cutoff, is obtained in long time propagation.

This thesis addresses the problem of collaboration among experimental biologists and modelers in the study of systems biology by using ontology and Semantic Web Services techniques. Modeling in systems biology is concerned with using experimental information and mathematical methods to build quantitative models across different biological scales. This requires interoperation among various knowledge sources and services. Ontology and Semantic Web Services potentially provide an infrastructure to meet this requirement. In our study, we propose an ontology-centered framework within the Semantic Web infrastructure that aims at standardizing various areas of knowledge involved in the biological modeling processes. In this framework, first we specify an ontology-based meta-model for building biological models. This meta-model supports using shared biological ontologies to annotate biological entities in the models, allows semantic queries and automatic discoveries, enables easy model reuse and composition, and serves as a basis to embed external knowledge. We also develop means of transforming biological data sources and data analysis methods into Web Services. These Web Services can then be composed together to perform parameterization in biological modeling. The knowledge of decision-making and workflow of parameterization processes are then recorded by the semantic descriptions of these Web Services, and embedded in model instances built on our proposed meta-model. We use three cases of biological modeling to evaluate our framework. By examining our ontology-centered framework in practice, we conclude that by using ontology to represent biological models and using Semantic Web Services to standardize knowledge components in modeling processes, greater capabilities of knowledge sharing, reuse and collaboration can be achieved. We also conclude that ontology-based biological models with formal semantics are essential to standardize knowledge in compliance with the Semantic Web vision.

The Main Injector Neutrino Oscillation Search (MINOS) is a long-baseline accelerator neutrino experiment designed to measure properties of neutrino oscillation. Using a high intensity muon neutrino beam, produced by the Neutrinos at Main Injector (NuMI) complex at Fermilab, MINOS makes two measurements of neutrino interactions. The first measurement is made using the Near Detector situated at Fermilab and the second is made using the Far Detector located in the Soudan Underground laboratory in northern Minnesota. The primary goal of MINOS is to verify, and measure the properties of, neutrino oscillation between the two detectors using the muon neutrino to tau neutrino transition. A complementary measurement can be made to search for the existence of sterile neutrinos; an oft theorized, but experimentally unvalidated particle. The following thesis will show the results of a sterile neutrino search using MINOS RunI and RunII data totaling ~2.5x10^20 protons on target. Due to the theoretical nature of sterile neutrinos, complete formalism that covers transition probabilities for the three known active states with the addition of a sterile state is also presented. The formulation of the transition probabilities was done in concert with Stephen Parke

The search for extrasolar planets is strongly motivated by the goal of characterizing how frequent habitable worlds and life may be within the Galaxy. Whilst much effort has been spent on searching for Earth-like planets, large moons may also be common, temperate abodes for life as well. The methods to detect extrasolar moons, or “exomoons” are more subtle than their planetary counterparts and in this thesis I aim to provide a method to find such bodies in transiting systems, which offer the greatest potential for detection. Before one can search for the tiny perturbations to the planetary signal, an understanding of the planetary transit must be established. Therefore, in Chapters 3 to 5 I discuss the transit model and provide several new insights. Chapter 4 presents new analytic expressions for the times of transit minima and the transit duration, which will be critical in the later search for exomoons. Chapter 5 discusses two sources of distortion to the transit signal, namely blending (with a focus on the previously unconsidered self-blending scenario) and light curve smearing due to long integration times. I provide methods to compensate for both of these effects, thus permitting for the accurate modelling of the planetary transit light curve. In Chapter 6, I discuss methods to detect exomoons through their gravitational influence on the host planet, giving rise to transit timing and duration variations (TTV and TDV). The previously known TTV effect is updated with a new model and the associated critical problems are outlined. I then predict a new effect, TDV, which solves these problems, making exomoon detection viable. Chapter 7 presents a feasibility study for detecting habitable-zone exomoons with Kepler, where it is found that moons down to 0.2M⊕ are detectable. Finally, conclusions and future work are discussed in Chapter 8.

Developing epithelial tissues are characterised by the disordered cell packing caused by ongoing cell proliferation and changes in tissue size. However, cell packing in adult epithelial tissues exhibits a high level of order, and typically, the apical tissue surface resembles a regular hexagonal lattice of planar polygons. One of the central questions in tissue development concerns the mechanisms which induce cells to repack. The change in packing may transform the tissue into a regular pattern of hexagonal cells, as seen during the renement of Drosophila M. wing and notum tissue, or it can occur as a mechanism which drives tissue shape change, as seen during embryonal axis elongation during Drosophila convergent extension. We study cell repacking in epithelia eected by the forces that act at the interface between adjacent cells. To this end, we develop a mechanical model of epithelial tissue based on the ideas of the cellular Potts model and building on previous vertex models. Analysing expanding and xed-size tissues, we nd that steady state packing geometries depend on the regularity in the timing of cell divisions. We predict that cells in topologically active epithelia leave the tissue in response to mechanical compression and geometric anisotropy. Through a collaboration with biologists Eliana Marinari and Buzz Baum, we nd that such mechanically driven cell delamination indeed occurs in the Drosophila notum. We thus identify a novel process of tissue homeostasis, whereby live cells delaminate from developing epithelium in order to limit overcrowding. Analysing the relation between stable packing geometries and the mechanical parameters, we suggest that an increase in the strength of acto-myosin contractility alone could cause tissue to repack into a regular lattice. Modifying the model to describe polarised acto-myosin localisation, we computationally reproduce cell intercalation and actin cable and rosette formation during convergent extension in Drosophila.

By applying a magnetic field across a trapped ultracold gas of alkali metal atoms, it is possible to alter the binding energies of near threshold molecular states. The proximity of molecular states to the scattering threshold has a strong effect on the threshold scattering characteristics. Because of this the magnetic field strength can be used to control low energy scattering within the gas. This resonant phenomena is referred to as a magnetically tuneable Feshbach resonance. This thesis looks at these and related phenomena in the context of trapped potassium atoms. First, we perform coupled-channels calculations in order to characterise a group of previously unreported Feshbach resonances, occurring in a host of different collision channels. Next, we compare these characterisations to empirical data, and more simplified models. Second, a detailed investigation into the photodissociation of weakly bound Feshbach molecules is carried out. This allows us to gain new insights into the structure of the exit channel interaction. We make semi-classical arguments which enable experimentalists to directly measure the height of potential barriers. We also perform detailed numerical calculations which, in conjunction with experimental data, allow us to develop a fine-tuned potential model for the exit state. Third, we model weakly bound triatomic states and their impact on near threshold scattering. Then, we discuss the use of three body recombination as a tool for observing Efimov states. Furthermore, we model the three body recombination rate using a simplified two channel model. Finally we suggest a method intended to provide the basis for numerical calculations using realistic Born-Oppenheimer potentials. It could also be used to analytically study near threshold three body physics.

CH+ is one of many molecules important in astrophysics observations and is of interest for the formation of large hydrocarbons. A key feature of work on CH+ has being its observed overabundance in the interstellar medium compared to calculated predictions. The molecular R-Matrix with Pseudo-States (RMPS) method is applied to CH+ for internuclear separations of 0.7-3.2 Angstrom using the UK Polyatomic R-Matrix codes. These calculations show the potential energy curves for the four lowest states and we identify resonances below the 3\prod threshold. We perform an initial calculation of the dissociative recombination cross sections from the resonance curves. We also detail our contributions to the UKRmol initiative, involving the creation of a consistent core of R-matrix codes.