Some purple bacteria species, such as Rhodopseudomonas palustris 2.1.6, produce light harvesting antenna (LH2) with unusual absorption spectra when they are grown under low-light intensities. This ability is often related to the presence of multiple genes encoding the LH2 apoproteins. This thesis describes isolation of pure stable LH2s from Rhodopseudomonas palustris 2.1.6 grown at different light intensities, determination of the polypeptide composition of high- (HL) and low-light (LL) LH2 complexes and characterisation their spectroscopic properties using various optical spectroscopies. The question of whether rings with a heterogeneous apoprotein composition exist has been addressed by single-molecule spectroscopy. For the first time, direct evidence that individual LL LH2 complexes have a heterogeneous αβ-apoprotein composition has been found. Such mixed rings feature Bchl a molecules with both B820-like and B850-like site-energies. This finding was supported by a femtosecond study on the energy transfer reactions and exciton relaxations within both HL and LL LH2 complexes. This thesis also describes attempts to crystallise the HL and LL LH2s. Even though three-dimensional crystals of both HL and LL LH2 complexes only diffracted to low resolution, it was possible to use molecular replacement to obtain structures that suggest both these types of LH2s are nonamers.

The main focus of this research was to examine the molecular complexes formed by the proton sponge material DMAN [1,8-bis(dimethylamino)naphthalene]. It is well known that DMAN will readily protonate – forming the DMANH+ – leaving the second molecule in a DMAN complex negatively charged. In addition to the preparation of materials by crystallisation techniques, full characterisation was carried out using X-ray diffraction of the single crystal samples obtained. Neutron diffraction was also carried out on some of the samples for which the hydrogen atom information was most important to obtain, though this was restricted by the amount of beamtime available on the central facilities used. Several families of DMAN complexes were studied, including DMAN : benzoic acid (chapter 4), DMAN with a wide series of halo-substituted benzoic acids (Chapter 4), DMAN with hydroxyl-, nitro- and methyl- substituted benzoic acids (Chapter 5), and its complexes with a selection of other organic acids (Chapter 6). Several general patterns are found in this work, including the following: • The DMAN is usually protonated (DMANH+), with the hydrogen atom held in a short N−H···N intramolecular hydrogen bond, as observed previously; • The carboxylic acids tend to form dimers, but with a carboxyl and a deprotonated carboxylate group involved, these DIMER− units are formed through a single, very short, strong, charge-assisted O−H···O hydrogen bond; • a wide range of C−H···O and C−H···π weaker hydrogen bonds are present, together with consistent stacking of the DMAN rings, including π···π interactions, but with additional stacking at a range of interplanar distances; • the overall packing in several complexes includes chains or sheets of DIMER− units with DMANH+ included in pockets in the structure. There are some exceptions to these patterns, for example: • varying stoichiometry, resulting in the first example of the occurrence of both protonated (DMANH+) and unprotonated DMAN in a single complex • the inclusion of solvent water in some hydrated complex, which interrupts some of the patterns of intermolecular interactions In addition to the studies of DMAN, a ternary hydrogen bonded complex was studied using X-ray and neutron diffraction and the new molecular porous material 4-phenoxyphenol, containing a range of solvents, was fully characterised using these diffraction techniques as well as the thermal methods TGA and DSC.

In this thesis electron microscopy was employed to characterise the nanoscale and atomic scale structure and chemistry of organic and inorganic materials. In chapter 4, the thin film morphology of the organic blend of [poly(9,9-dioctylfluorene- co-benzothiadiazole)] (commonly referred as F8BT) and poly[9,9-dioctyfluorene-co- N-(4-butylphenyl)-diphenylamine] (abbreviated as TFB) was investigated, mainly by bright field transmission electron microscopy (BF-TEM). F8BT and TFB are conjugated polymers, which are candidates to replace inorganic semiconductors in many applications because of their simple preparation and processing procedures. The phase separation of the F8BT:TFB blend was investigated at different compositions. Polymer domains were found in the thin film, with sub- micrometer size which varies with concentration. The 1:1 weight ratio sample showed sub-micrometer TFB rich areas in a F8BT matrix, while the 1:4 weight ratio thin film presented F8BT phases, whose areas are mostly below 0.02 μm2, in a TFB layer. Since some electronic applications, especially in optoelectronics, show increased efficiency after addition of quantum dots in the polymer blend, the effect of CdSe quantum dots on the phase separation of the organic blend was investigated together with their effect on the nanoscale morphology. The CdSe quantum dots were found to aggregate in clusters with limited dispersion within the polymer domains, which did not present significantly morphology changes as a consequence of quantum dots (QDs) addition. The atomic structure and chemistry of the inorganic Ba6−3xNd8+2xTi18O54 microwave ceramic was quantitatively investigated in chapter 4, using high resolution scanning transmission electron microscopy (HR-STEM) and electron energy loss spectroscopy (EELS). These materials are an essential part of telecommunication systems, they can be found in components such as resonators and antennas, on account of their high permittivity, temperature stability and the very low dielectric loss at microwave frequencies. The unit cell was refined with sub-Å precision based on extensive data analysis of HR-STEM images and the unit cell structure showed no significant changes as a consequence of changes in composition or cooling rate after annealing. Ba was found to substitute preferentially to specific Nd atomic columns in the structure, and these trends apply across the whole composition range. These results were confirmed by comparisons with image simulations and provided a starting point for improved refinements of X-ray data.

The hydrogenation of nitrobenzene to form aniline is a large-scale industrial process performed using a variety of heterogeneous catalysts. One variant of the process involves the application of alumina-supported Pd catalysts. Although several 0.3 wt% Pd/alumina formulations exhibit high aniline selectivity (ca. 98%), different grades of these catalysts favour different impurities. It is observed that the impurities arise from different reaction pathways depending on the provenance of the catalyst. In order to investigate whether the origins of impurity formation are connected to catalyst structure, a series of Pd catalysts active for this reaction have been characterised by a variety of techniques: chemisorption measurements, X-Ray Diffraction, Transmission Electron Microscopy, Temperature-Programmed Desorption and Infrared spectroscopy. The low metal loading industrial grade catalysts are challenging to characterise and required a degree of analytical refinement. Temperature-programmed infrared measurements of the probe molecule carbon monoxide revealed morphological and energetic information that could be correlated with catalytic performance. This information constitutes part of a valuable feedback loop that enables specifications for the next generation of ultra-selective nitrobenzene hydrogenation catalysts to be determined.

Quinol-dependent nitric oxide reductase (qNOR) is a homodimeric, membrane-bound metalloenzyme with the catalytic function of reducing two molecules of nitric oxide to nitrous oxide. In bacteria, qNOR can serve either as a respiratory enzyme, or in pathogens as a defence mechanism against cytotoxic levels of nitric oxide radicals generated by the host immune response. One such pathogen is Neisseria meningitidis, a cause of meningitis and septicaemia worldwide. Various biochemical, biophysical, and computational techniques have been applied in study of the molecular mechanism underlying the reduction of nitric oxide by nitric oxide reductase, yet clearly defined mechanics of the enzymatic reaction have yet to be concluded. Understanding of the enzymatic mechanism requires a high-resolution crystal structure of the enzyme to provide a basis for computational calculations and directed biochemical/biophysical analysis. A crystal structure of the qNOR of Geobacillus stearothermophilus was solved to a resolution of 2.5 Å, but significantly in a catalytically inert form unsuitable for reliable characterisation of the active site. By this structure, molecular dynamics studies of potential solvent channels to the active site has led to the identification of a hydrophilic pathway from the cytoplasm for transfer of protons required for catalytic turnover. This would be the first nitric oxide reductase identified to take chemical protons from the cytoplasm instead of the periplasm (as occurs in the isofunctional cytochrome c-dependent nitric oxide reductase), a striking feature in respiratory terms as this membrane separation of proton/electron uptake would infer an electrogenic property to qNOR as yet unobserved in nitric oxide reductases. This thesis presents efforts to characterise the qNOR of Neisseria meningitidis, a highly active reductase that, from preliminary analyses, appears promising in its potential to retain a catalytically active form for crystallographic studies. This qNOR was heterologously over-expressed in a bacterial host and purified into a detergent micelle suspension. Spectroscopic techniques were employed to elucidate the electronic state of the active site of qNOR, and amperometric assays were used to study the nature of the nitric oxide reductase activity. N. meningitidis qNOR was found to have nitric oxide reductase activity significantly greater than that of other qNORs and largely independent to pH changes, and displayed Raman characteristics distinct from other qNORs. Crystallography of qNOR yielded X-ray diffraction to ~4.5 Å, and a crystal structure solved to a resolution of 5 Å. From this, significant structural homology to the high-resolution G. stearothermophilus qNOR crystal structure could be observed. Based on solvent networks identified in the crystal structure of G. stearothermophilus, a cytoplasmic pathway for chemical protons to the active site has been proposed. Research described in this thesis involves site-directed mutagenesis of residues believed to play a role in proton transfer. It was found that none of the mutant variants tested significantly affected the nitric oxide reductase capability of qNOR.

The rapid depletion of fossil fuels has raised increasing attention worldwide, and initiated intensive research for sustainable alternatives for energy production. Among these, biodiesel from microalgae has appeared as one of the most promising candidate due to their ability to accumulate large amount of lipids. Indeed, microalgae can achieve a productivity up to 25 higher than other crop sources without need of cultivatable soil, therefore without competing with food production. In the meantime, microalgae have also shown promising results for the treatment of various kind of wastewaters. However, the cultivation of microalgae for energy production suffers from the large costs of harvesting and dewatering of biomass, prior to lipid extraction and biofuel production, which accounts for up to 50% of operating costs. Therefore, the search for cost-effective methods of harvesting and dewatering of microalgae biomass has become necessary to optimize their usage. This study investigates forward osmosis (FO) for the dewatering of microalgae biomass and its implementation within a photobioreactor used for wastewater treatment. FO is a cost-effective filtration process based on the differences of osmotic pressure across a semi-permeable membrane. The use of FO for microalgae dewatering is of high interest, given the high fouling ability of microalgae biomass and the low fouling promises of FO. First, the feasibility of using FO for microalgae dewatering was assessed, focusing on better understanding the fouling mechanisms involved. The filtration performances have been investigated under various operating parameters. It has been found that when Ca2+-containing draw solutions were used, microalgae responded to the back diffusion of calcium ions by an extensive excretion of carbohydrates, accelerating the formation of algal flocs, thus enhancing the rate and extent of flux decline and reducing the algae dewatering efficiency. However, most of the fouling was reversible by simple hydraulic flushing. In addition, substantial adsorption of algal biomass was observed on the feed spacer. Also, Scenedesmus obliquus and Chlamydomonas reinhardtii, with fructose and abundant glucose and mannose in its cell wall, showed strong response to the back diffusion of calcium ions which encouraged S. obliquus to produce more extracellular carbohydrates and formed a stable gel network between algal biomass and extracellular carbohydrates, leading to algae aggregation and severe loss in both water flux and algae biomass during FO dewatering with Ca2+-containing draw solution. Among the species investigated, Chlorella vulgaris without fructose was the most suitable microalgae species to be dewatered by FO with a high algae recovery and negligible flux decline regardless of which draw solution was applied. These findings improve mechanical understanding of FO membrane fouling by microalgae; have significant implications for the algae species selection; and are critical for the development and optimization of FO dewatering processes. Finally, the implementation of FO dewatering with continuous microalgae biomass production and synthetic wastewater treatment was investigated. Two systems (External FO ; Immersed FO) have been studied and compared in order to provide insights on the advantages and disadvantages of each system. Constant parameters have been set identical for both systems: operation time; photobioreactor; hydraulic retention time; biomass production; FO permeate volume. The results reveals that the wastewater treatment efficiency (nutrients removal), as well as the production of biomass were greater with the immersed system due to a greater microalgae growth. However, these may not be sustainable in a long term operation of the immersed system. The external FO system was found better in terms of salinity build-up and FO dewatering performances. Overall, an external FO dewatering is recommended due to its better flexibility and sustainability.

Introduction: One of the most critical problems of NMR is the intrinsic lack of sensitivity owing to the small energy difference between nuclear energy levels. This issue can be addressed in different ways. One possibility is to reduce the spectral noise, which to a large extent is created by the console electronics. Another approach is to actually increase the signal strength of the NMR signal. An experimental approach to achieve this is ex situ dissolution Dynamic Nuclear Polarisation. It increases the population difference of the spin states by transferring the high electron polarization to the NMR detectable nuclei. A theoretical introduction into NMR, quantum mechanical basics of spin physics and DNP are presented in Chapters 1 and 2. Methods: One of the main drawbacks of D-DNP is the necessity for a post-polarisation sample transfer to an NMR spectrometer. One of the major aims of the work presented in this thesis was to build an autonomous robotic device to transfer the sample under pressure controlled by Arduino microelectronics to overcome problems associated with the sample transfer. Chapter 3 presents how this device was constructed and. In addition applications performed using this device are presented. Results: The benefits of the application of this device for fast-relaxing nuclei are discussed in chapter 4 with the application on 2-D DNP-NMR acquisition of U-\(^1\)\(^3\)C Glucose. Novel experiments using Dissolution DNP were also performed as part of the work for this thesis. A method for analysing aminoacids of biological fluids using DNP is presented in the Chapter 5 by acetylating which creates long lived tags. An approach for extracting the maximum of information out of a single polarisation experiment is what Chapter 6 covers with an approach to perform Parallel Receiver DNP and the application on ATP and 1-13C TetraMethylPhosphonium. Finally, the future applications of the DNP and the authors’ personal ideas for further development are presented in Chapter 7, the discussion. Briefly, DNP-NMR using a fast sample transfer system can be a capable system for performing different types of analysis, but the maximum outcome is always when the system is combined with \(in-vivo\) MRI scanners.

A method for developing an optical mapping system to quantify electrical activation and repolarisation in murine left atria was created. The spread of activation is important in understanding the mechanisms for the rhythm of the heart in healthy and diseased states as cardiovascular disease is the leading cause of death worldwide. The activation spread was recorded using a novel 2nd generation high resolution (128x2048 pixels) CMOS camera with the voltage sensitive dye di-4-ANEPPS. Algorithms for automatic quantification of action potential duration and conduction velocities were implemented in MATLAB. Optical mapping results were validated against monophasic action potentials and microelectrode measurements showing comparable duration measurements. A genetic mouse model of atrial fibrillation was used (Pitx2c\(^+\)\(^/\)\(^-\)) and was found to have a shorter action potential duration in the left atrium compared to wild-type mice. The results showed a preferential antiarrhythmic effect of the sodium channel blocker, flecainide, to the left atrium of Pitx2c\(^+\)\(^/\)\(^-\) mice. A second mouse model was used to mimic arrhythmogenic right ventricular cardiomyopathy (plako\(^+\)\(^/\)\(^-\)). No significant changes were witnessed in young sedentary cohorts at baseline and flecainide slowed conduction in both WT and plako\(^+\)\(^/\)\(^-\). In endurance trained mice, a prolongation of the effective refractory period was seen after flecainide treatment. Plako\(^+\)\(^/\)\(^-\) sedentary mice treated with dihydrotestosterone showed a prolongation in action potential duration.

This thesis describes an experiment which studies a cloud of magneto-optically trapped potassium-39 atoms inside an optical ring cavity. The potassium atoms are firstly cooled in a two-dimensional magneto-optical trap (MOT) and are then transferred into a three dimensional MOT which overlaps with the cavity mode. In this thesis, the optimisation of the MOT systems and the characterisation and construction of the optical ring cavity are discussed. After exploring these two systems independently, the two systems are then coupled together to provide an atom-cavity system, which exhibits collective strong coupling. The system is shown to exhibit normal-mode splitting, with a collective Rabi splitting of G = 2π (6.25±0.50)MHz, corresponding to (4.7±0.6) x 103 atoms in the cavity. Whilst collective strong coupling has been achieved before in other experiments, we believe this is the first experiment to achieve this with potassium. The next goal in the experiment is to control the group refractive index of the atoms inside the cavity. The modification of the group index using electromagnetically-induced transparency (EIT) on hot atoms inside a vapour cell has already been previously demonstrated by this experiment; and using the same laser system we aim to demonstrate EIT on the cold intra-cavity atoms as well. Gain mechanisms could also be used to create a ring laser with a controllable group index. These techniques could lead to a range of applications such as enhanced-sensitivity laser ring gyroscopes and active optical clocks.

Plenoptic imaging is a technology by which a three dimensional representation of the world can be captured in a single image. Previous research has focused on the technology itself, with very little focusing on applications of the technology. This thesis presents an investigation into its potential application to the field of retinal imaging, with the aim of producing three dimensional images of the retina at a cheaper cost than the current gold standard of retinal imaging, optical coherence tomography. Both a theoretical and practical approach have been utilised through the means of computational simulations and plenoptic imaging through the use of a commercial camera. Significant steps have been taken towards the overall goal, forming a strong foundation from which future projects will benefit.