We study linear and nonlinear structure formation in cosmologies where the accelerated expansion is driven by modifications to general relativity (GR). We focus on Galileon and Nonlocal gravity, which are two classes of models that have been attracting much attention. We derive the linearly perturbed model equations and solve them with suitably modified versions of Einstein-Boltzmann codes. We also derive the perturbed equations keeping the relevant nonlinear terms for small scale structure formation, which we solve using N- body codes and semi-analytical techniques that were developed for these models. Using CMB, SNIa and BAO data we find strong evidence for nonzero active neutrino masses (Σmν ≈ 0.6 eV) in all three main branches of covariant Galileon cosmologies, known as the Cubic, Quartic and Quintic models. However, in all branches, the lensing potential does not decay at late times on sub-horizon scales, which contradicts the measured positive sign of the ISW effect, thereby ruling out the Galileon model. The Nonlocal model we study should be able to fit the CMB with similar parameter values as ΛCDM. The N-body simulation results show that the covariant Galileon model admits realistic halo occupation distributions of luminous red galaxies, even for model parameters whose linear growth is noticieably enhanced (σ8 ≈ 1) relative to ΛCDM. In the Cubic Galileon model the screening mechanism is very efficient on scales smaller than 1Mpc, but in the Quartic and Quintic sectors, as well as in the Nonlocal model, we identify potential tensions with Solar System bounds. We illustrate that, despite the direct modifications to the lensing potential in the Cubic Galileon and Nonlocal models, cluster masses estimated from lensing remain the same as in GR. The lensing effects produced by cosmic voids found in the simulations of the Cubic Galileon are significanly boosted (≈ 100%) compared to GR, which strongly motivates using voids in tests of gravity. The combination of linear and nonlinear theory results presented here for Galileon and Nonlocal gravity is an example of what it could be done for any serious alternative models to ΛCDM, which will be tested by future experiments.

This thesis has been the product of three projects which are all related to depth perception, within the core discipline of vision science. The first project was collaborative work between the University of Durham and researchers at University of California, Berkeley. These included Prof. Martin S. Banks and Bill Sprague at U.C. Berkeley, and Dr. Jurgen Schmoll and Prof. Gordon Love at the University of Durham. This project built on previous research investigating the ocular adaptations in different land-dwelling vertebrate species. We found that we could strongly predict pupil shape based on the diel activity and trophic strategies of a species, and our simulations showed that multifocal pupils may extend depth of focus. The second project was also in collaboration with U.C. Berkeley; Prof. Martin S. Banks, and Paul Johnson, which involved a study into 3D displays and different approaches to reducing the vergence-accommodation conflict. Our results showed that a focus-correct adaptive system did assist in the vergence-accommodation conflict, but monovision was less efficacious and we believe this was due to a reduction in stereoacuity. The third project considered spherical aberration as a cue to the sign of defocus. We present simulations which show that the spatial frequency content of images on either side of focus differ, and suggest that this could, in principle, drive the accommodative process.

This thesis details three novel advances in instrumentation that are each related to performance improvement in wide-field visible-spectrum imaging systems. In each case our solution concerns the assessment and improvement of optical imaging quality. The three instruments are as follows: The first is a portable transmission microscope which is able to correct for artificially induced aberrations using adaptive optics (AO). The specimens and the method of introducing aberrations into the optical system can be altered to simulate the performance of AO-correction in both astronomical and biological imaging. We present the design and construction of the system alongside before-and-after AO-correction images for simulated astronomical and biological images. The second instrument is a miniature endoscope camera sensor we re-purposed for use as a quantitative beam analysis probe using a custom high dynamic range (HDR) imaging and reconstruction procedure. This allowed us to produce quantitative flux maps of the illumination beam intensity profile within several operational fluorescence microscope systems. The third and final project in this thesis was concerned with an adaptive modification to the light sheet illumination beam used in light sheet microscopy, specifically for a single plane illumination microscope (SPIM), embracing the trade-off between the thickness of the light sheet and its extent across the detection field-of-view. The focal region of the beam was made as small as possible and then matched to the shape of curved features within a biological specimen by using a spatial light modulator (SLM) to alter the light sheet focal length throughout the vertical span of the sheet. We used the HDR beam profiling camera probe mentioned earlier to assess the focal shape and quality of the beam. The resulting illumination beam may in the future be used in a modified SPIM system to produce fluorescence microscope images with enhanced optical sectioning of specific curved features.

Since the first realization of a laser source in 1960, tremendous progresses have been made in the theoretical understanding and experimental control of interacting atomic-optical systems. Optical fields can nowadays be used to engineer long-range interactions in cold atomic gases, manipulating the external degrees of freedom of the atoms via optical forces. This opens the possibility for the study of highly controllable and tunable long-range interacting systems, in which a complex dynamics for the motional properties of the gas can arise due to the effective atom-atom coupling induced by the field. In this thesis the spontaneous emergence of spatial structures in non-equilibrium atom-optical systems is theoretically and numerically investigated, for different geometries and physical configurations. Extending previous research in hot atomic gases, self-organising instabilities involving the external degrees of freedom are studied, and in contrast to other cold-atom spatial instabilities the spontaneous breaking of continuous symmetries is predicted. The main focus of the work presented in this thesis is on dynamical instabilities in cold gases. However, connections are found with other fields of nonlinear physics, such as synchronisation of coupled oscillators and phase transitions in many-body systems. Part of the research presented here has been conducted in the context of a collaboration with the Photonics group at Strathclyde and the Institut non Linéaire de Nice, in which experimental observations of self-organisation and continuous symmetry breaking were obtained.

The properties of InGaN alloys are important for many applications in optoelectronics, since the fundamental band gap of this material system spans the visible range. Calculating properties, particularly for InN, is theoretically challenging, especially obtaining accurate values for the band gap. We have developed a semiempirical parameterization for the simulation of (In,Ga)N using the density functional based tight binding method (DFTB), where the band gaps of InN and GaN have been empirically adjusted to match experiment. This is the first application of this method to In containing materials. We demonstrate the performance of this method by calculating a range of properties for both compounds and also their alloy for a range of crystal structures (wurtzite, zincblende and, for the pure compounds, rocksalt). There are several methods to model alloys of these materials, here the virtual crystal approximation and the cluster expansion method been used to study the alloy system of InGaN. While 8, 16 atom supercells are commonly used for cluster expansions, in this work these results are critically compared against the larger 32 atom cell, the effect of the ensemble used to simulate the alloy is also investigated by using both the Strictly Regular Solution and Generalised Quasi-Chemical approximations to provide limiting cases around the experimental conditions of Molecular Beam Epitaxy (MBE) and Metal-Organic Chemical Vapor Deposition (MOCVD) alloys.

The focus of this work is the effects of ions on solute association processes in solution: complex formations of aromatic carboxylic acids with a-cyclodextrin and bundle formation of carbon nanotubes in their N-methylpyrrolidone based dispersions. The work has two distinct parts: cation effects and anion effects. In one part we explain experimentally observed difference between effects of sodium and potassium cations on interactions of aromatic carboxylic acids with a-cyclodextrin. To explain this difference, we propose a molecular mechanism, which we call "competition for the guest". According to this mechanism sodium ions interact with carboxylic group of aromatic carboxylic acid, which prevents the acid from the formation of a complex with cyclodextrin. Another manifestation of ion effects explored in this work is the impact of ions on the behaviour of benzoic acid at water/vapour interface. As a consequence of ion induced changes in hydration pattern, the molecule changes its orientation at the interface as well as its affinity to the interface. The results of the molecular dynamics simulations are compared to surface sensitive technique of X-ray photoemission spectroscopy. Another part of the work studies ion effects on the stability of carbon nanotube dispersions in N-methylpyrrolidone. By evidence of spectroscopy and transmission electron microscopy, it was found that inorganic ions significantly reduce stability of carbon nanotubes dispersions in N-methylpyrrolidone. Comparing the results to molecular dynamics simulations it was suggested that the reduction of stability takes place due to the formation of ion depletion areas around carbon nanotubes. These ion depletion areas increase the free energy of the interface between the tube and the salty N-methylpyrrolidone, forcing the carbon nanotubes to associate with each other, forming bundles and larger aggregates. Overall, this work is devoted to study of ion effects in aqueous and non-aqueous liquid media, using a combination of experimental and computational tools. Here we deepen the understanding of ion effects as a subtle balance of several pairwise interactions, which take place in liquid media containing both solutes and salts.

This thesis reports on experimental and numerical investigations of relativistic electron transport in solids irradiated by intense (i.e. IL > 10p19s Wcmp-2s) laser pulses. Specifically, the effect of electrical resistivity on fast electron transport is explored. The first investigation explores fast electron transport in allotropes of carbon by measuring the spatial-intensity distribution of the beam of protons accelerated from the target rear-surface. An analytical model is developed which accounts for the rear-surface fast electron sheath dynamics, ionisation and projection of the resulting beam of protons, and is used (in conjunction with the experimental measurements) to infer annular fast electron beam transport with lamentary structure in 200 um-thick diamond targets. The important role that material lattice structure has in defining electrical resistivity, which in turn defines the fast electron transport properties, is established utilising three-dimensional hybrid pa rticle-in-cell (3D hybrid-PIC) simulations together with an analytical model of the resistive lamentation instability. The second investigation explores fast electron transport in silicon utilising both experimental measurements and 3D hybrid-PIC simulations. Annular fast electron transport is demonstrated and explained by resistively generated magnetic fields. The results indicate the potential to completely transform the beam transport pattern by tailoring the resistivity-temperature profile at temperatures as low as a few eV. Additionally, the sensitivity of annular fast electron beam transport is explored by varying the drive laser pulse parameters (i.e. energy, focal spot radius and pulse duration) and is found to be particularly sensitive to the peak laser pulse intensity. An ability to optically 'tune' the properties of an annular fast electron transport pattern may be important for applications. In the final investigation the effect that initial target temperature, and thus lattice melt, has on fast electron transport properties is demonstrated. Laser-accelerated proton beams are used to isochorically heat silicon for several tens-of-picoseconds prior to the propagation of fast electrons through the pre-heated target. This enables the influence of resistivity gradients, generated by proton-induced lattice melt, on fast electron transport properties to be explored. The experimental observation of an annular proton beam after t heat = 30 ps of proton pre-heating, which corresponds to annular electron transport within the target, is in excellent qualitative agreement with 3-D hybrid-PIC simulations of fast electron transport in a target containing an initial temperature (and thus, resistivity) gradient.

Measurements of optically significant constituent (OSCs) concentrations in shelf seas can be used as sensitive indicators of ecosystem status and function. Measuring OSC concentrations is labour intensive and a method to improve data analysis would greatly enhance our ability to monitor shelf sea environments. One option is the inversion of optical signals to recover constituent concentrations, as instrumentation already exists for measuring optical properties in situ. The feasibility of inverting measurements of inherent optical properties (IOPs) to give constituent concentrations using linear matrix algebra is considered, as previous authors reported that this gave encouraging results. Two problems were identified when IOP inversion was tested using synthetic data. First, the results obtained degraded rapidly in response to increasing levels of noise. Second, the inversion process relied on accurate values for the specific inherent optical properties of the OSCs that were unlikely to be obtained in practice. A further difficulty was encountered in the long-term deployments of instrumentation for measuring IOPs, since the equipment proved to be very susceptible to fouling. Alternative methods for optical data analysis had to be proposed which were more resistant to noise and required fewer assumptions for analysis to be completed. Two promising lines of research were initiated. One involved combining IOP measurements with other available optical and hydrographic variables to study particle populations in Scottish sea lochs. The other employed signal processing techniques to derive information on sediment transport in Liverpool Bay from measurements of beam attenuation subjected to large amounts of biofouling. Both of these methods allow ecological information to be derived from optical data that has been gathered under sub-optimal conditions. They provide a foundation for the analysis of large scale optical data sets from planned ocean observing systems, which will deploy optical instruments on moorings, floats, ocean gliders and autonomous underwater vehicles.

Very high energy electrons (VHEEs) (100-250 MeV) have the potential of becoming an alternative modality in radiotherapy because of their improved dosimetry properties compared with X-ray photons, which could confer possible radiobiological benefits. The rapid development of ultra-compact laser-plasma wakefield accelerators (LWFAs) is now providing a potential low cost device for VHEE radiotherapy. These beams have characteristics unlike any other beams currently used for radiotherapy: femotosecond radiation pulses, small field size and energies that exceed electron energies currently used in clinical applications. A set of Monte Carlo (MC) calculations have been performed to study dosimetric properties of VHEEs propagating in water. To assess radiation protection and safety handling issues, the generation of neutrons, induced activity and equivalent doses have been evaluated. A dosimetry system, consisting of EBT2 Gafchromic® film and EPSON Expression 10000XL scanner, for VHEEs has been established. EBT2 Gafchromic film turns out to be a robust dosimeter with a minor energy-dependent response over a broad range of beam energies and modalities, and can be successfully used for dosimetry of very high energy electron beams. The dosimetric measurements have been carried out using three different accelerators: a 20 MeV clinical LINAC, a 165 MeV conventional LINAC and a 135 MeV laser-plasma wakefield accelerator. The measurements have been compared with Monte Carlo simulations using the FLUKA code. Additionally, the set of dose measurements employing IBA CC04 ionisation chamber has been presented. Dosimetric measurements have been complemented by preliminary cancer cell irradiation studies to determine the toxicity and dose response to LWFA VHEEs of two lung cancer cell lines (A549 and H460). The efficacy of VHEEs on in vitro tumour cells has been assessed by clonogenic assay and γ-H2AX assay employing immunofluorescence detection of signalling molecules has been deployed to indicate DNA double-strand breaks and repair.

III-nitride micro-pixellated light-emitting diodes (micro-LEDs) are a novel format of light source capable of generating micro-scale, spatially and temporally-controllable light patterns. These devices consist of arrays of LED pixels with diameters in the range of 1 µm to 100 µm and emit light across the ultraviolet-blue-green-red part of the spectrum. In addition, compared with conventional broad-area LED devices, micro-LEDs show improved device performance in many aspects, such as high output power densities and the capability to withstand high injection current densities. For these reasons, micro-LEDs allow the study of interesting LED properties in regimes not accessible to conventional broad-area LEDs and also a wide range of novel LED applications. The research work presented in this thesis focuses on the novel applications of micro-LEDs in visible light communications (VLC) and micro-displays. Due to a reduced current crowding effect and superior thermal management capabilities, micro-LEDs can be driven at very high current densities, resulting in high modulation bandwidths of the devices. For this reason, optical data transmission was demonstrated from individual micro-LED pixels at bit rates of up to 1 Gbit/s using a high-speed probe under a binary amplitude modulation scheme. To make a more practical VLC system, micro-LED devices were integrated with specifically-designed complementary metaloxide-semiconductor (CMOS) electronics, which allow individual micro-LED pixels to be conveniently controlled via a simple computer interface. Such CMOS-controlled micro-LED devices have been demonstrated for data transmission at bit rates of up to 512 Mbit/s by modulating a single CMOS/micro-LED pixel and 1.5 Gbit/s by modulating four CMOS/micro-LED pixels simultaneously. Apart from the application in VLC, CMOS-controlled micro-LED devices can also be used to implement micro-display systems. A colour-tunable micro-display system capable of delivering high-resolution microscale dynamic images and tuning its colour from red to green has been demonstrated based on new LED epitaxial LED structures, micro-LED fabrication, and the CMOS technology. Other work reported in this thesis includes using micro-LEDs for data transmission in plastic optical fibre and investigating the modulation characteristics of colour-converters such as colloidal quantum dots and light-emitting polymer. A detailed study on size-dependent capacitance in III-nitride micro-LEDs, especially the negative capacitance (NC) effect, has also been reported in this thesis. This capacitance research sheds light on the mechanisms underlying the NC effect and is potentially useful for improving the LED performance for VLC and other applications.