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This thesis presents information on the subcellular localisation of two important trace elements, selenium and arsenic, in wheat, rice and rice roots for what is believed to be the first time. The general aim of this work was to illustrate the potential of using physical science techniques to solve biological problems. High resolution secondary ion mass spectrometry was undertaken using the CAMECA NanoSIMS50 with a sensitivity down to ppm concentrations and a lateral resolution of less than 100 nm. Selenium in wheat grain was found to be distributed across both the bran layer and the endosperm region with Se-rich hotspots found in the aleurone cells and a higher intensity of Se in the subaleurone region. Arsenic in rice grain was found in two key regions. In grains with high As and high dimethylarsinic acid (DMA) content, As was predominantly localised to the subaleurone region yet in lower concentration, hydroponically grown As(III)-treated grains the As was only localised to the aleurone layer near the ovular vascular trace (OVT). A combined NanoSIMS and S-XRF experiment revealed As hotspots near the OVT. A combination of high pressure freezing, high resolution secondary ion mass spectrometry and TEM was used to localise As in the roots of rice plants revealing a contrasting subcellular distribution of As and Si in the roots even though arsenite and silicic acid are transported across the plasma membranes by the same transporters. Fe plaque forms only on the root epidermis and was shown to be a strong sink for As. Colocalisation of S with As in the vacuoles of the endodermis, pericycle and xylem parenchyma supports the notion that As is stored as arsenite-phytochelatin complexes in the roots while Si is localised in the endodermis cell walls and is not strongly affected by the Lsi2 mutation.

Reduced-activation ferritic steels are considered as the primary candidate materials for structural applications within nuclear fusion power plants. It is known that by mechanically alloying ferritic steel powder with Y (usually in the form of Y₂O₃) then consolidating the material by hot isostatic pressing, a nanoscale dispersion of oxygen rich nanoclusters as small as ~2nm is introduced into the microstructure. This vastly improves high temperature strength and creep resistance, and the nanoclusters also act as trapping sites for helium and point defects produced under irradiation. In this thesis, the evolution of the oxide nanoclusters in a Fe-14Cr-2W-0.3Ti & 0.3Y₂O₃ ODS alloy was investigated primarily using atom probe tomography. The microstructure was characterised at various points during processing to give an insight into the factors influencing the formation of the nanoclusters. It was found that the nanoclusters nucleated during the mechanical alloying stage, then followed near classical nucleation and growth mechanisms keeping the same composition of ~8%Y, ~12%Ti,~25%O and ~45%Cr throughout. The formation and evolution of 5-15nm grain boundary oxides was also observed, and these were shown to form first as Cr₂O₃ particles that subsequently transform into a Y-Ti-O based oxide on further processing. The influence of mechanical alloying with 0.5wt.%Fe₂Y rather than 0.3wt.%Y₂O₃ was also investigated, and this showed that there was no difference in the final microstructure produced provided the level of Ti in the starting powder was tightly controlled. Without sufficient Ti, the nanoclusters were Y-O based and ~6nm diameter. Both the Y-O and Y-Ti-O nanoclusters were moderately stable on annealing at 1200°C for up to 100 hours, with only minimal coarsening observed. Ti was found not to influence the coarsening rate of the nanoclusters significantly. The stability of the oxide nanoclusters under irradiation was investigated by using Fe²⁺ ion irradiation to simulate displacement cascade damage in the ODS-Eurofer material (the official European candidate material for testing in the ITER fusion test reactor). Doses up to ~6 dpa at 400°C were used, and there was no significant change to the nanocluster distribution. However segregation of Mn to dislocations was observed after irradiation. These results indicate that ODS steels are good candidate structural materials, as the microstructure is stable at high temperature and under irradiation. The starting powders, and processing parameters need to be tightly controlled in order to produce the optimal material for use in service.

The design, construction and characterisation of a novel, arrayed, open-access optical microcavity is described. Included in this thesis are the precise fabrication details, making use of the focused ion beam. A technique for analysing and optimising the microcavities constructed, making use of an atomic force microscope is also included. Results from the optical characterisation of the fabricated microcavities are presented, including quality factors of around 104, and fitnesses of around 400. The optical analysis then progressed onto coupling colloidal semiconductor nanocrystals to the microcavity modes. This yielded room temperature Purcell enhancements, single particle sensing, and also allowed for the characterisation of a second iteration of cavities. This improved set was shown to achieve fitnesses in excess of 1800 and quality factors with a lower limit of 15000. The optical identification of single NV centres in nanodiamond is discussed, along with the development of an optical apparatus to couple them to microcavities at cryogenic temperatures. Finally several results from finite difference time domain simulations will be presented, showing ultimate mode volumes of less than 0.5 cubic wavelengths are possible for this approach.

Maintaining the safe operation of nuclear power plants (NPPs) is crucial. This requires fully understanding the mechanism of long term irradiation and thermal ageing, as well as their effects, on components including the reactor pressure vessel (RPV). The research community is collecting data that will be required to support the case for extending the operation of western-type NPPs beyond that of 60 years. One of the current dilemmas faced by the long-term operation of RPVs is the formation of nanometre scale precipitates. These precipitates are known to cause embrittlement where it increases the ductile-to-brittle transition temperature of the RPV steels. The chemistry of these precipitates is strongly dependent on the chemistry of the RPV steels. In general, these precipitates can be categorised into two types, copper-rich precipitates (CRPs) and manganese-nickel (-enriched) precipitates (MNPs) [1, 2]. The concentration of copper in the precipitates depends on the bulk content of the steel [3]. The formation mechanism of the precipitates under neutron irradiation and thermal ageing, and their influence on material degradation at high neutron fluence (Φt), is still unclear. To understand the long term precipitation under irradiation and thermal ageing, high nickel and copper containing RPV steels with a similar microstructure an chemical composition as those currently in service were subjected to either neutron irradiation (to high neutron fluences, Φt ≥ 5 x 10²³ neutrons.m^-2) or thermal ageing (for as long as ≈ 50,000 hours). CRPs and MNPs were both detected. The co-precipitation of the CRPs and MNPs were observed in thermally aged steels. The development of crystal structures in the CRPs is believed to be dependent on the size of the precipitates and the ambient temperature. When the CRPs reached a critical size, they underwent the martensitic transformation from BCC→9R→3R→FCC or FCT. The CRPs preferentially nucleate heterogeneously at the dislocation lines. Chemical analysis suggests that most of the CRPs are iron free. Under thermal ageing, the MNPs were found to precipitate at the interface of the CRPs and the matrix. These MNPs are found to be iron free too. Larger MNPs were often found to be at CPRs that were associated with dislocation lines. Also, based on the volume fraction observed, it is possible to suggest that the kinetics of nucleation and growth of the MNPs are relatively slow compared to the CRPs. This is in good agreement with the simulations reported in Refs. [4, 5]. It is the first time the MNPs are directly imaged from neutron irradiation low copper steels using electron microscopy. These irradiation-induced MNPs are densely populated in the neutron irradiated samples. It was found that the irradiation-induced MNPs are more sensitive to electron beams. It was thought that this was due to a relatively large amount of point defects present in the irradiation-induced MNPs.

Les récepteurs AMPA (rAMPA) sont les récepteurs ionotropiques du glutamate responsables de la majeure partie des courants excitateurs rapides dans la transmission synaptique rapide. Lors de la libération de glutamate, le rAMPA passe par 3 états conformationnels majoritaires : pore fermé/agoniste non lié, pore ouvert/agoniste lié et pore fermé/agoniste lié. Le contrôle du nombre et de l’organisation dans la synapse des rAMPA, via une combinaison de diffusion latérale et d’endo/exocytose, est essentiel à la régulation de l’intensité de la transmission synaptique. Les interactions existant entre les protéines de la densité post-synaptique et les protéines partenaires des récepteurs régulent la diffusion des récepteurs, contrôlant leur nombre et leur organisation à la post-synapse. Mon travail de thèse a consisté à étudier l’impact de l’activation des rAMPA sur leur mobilité et leur organisation à la post-synapse. En effet, la fixation de glutamate sur les récepteurs ainsi que leur désensibilisation entraînent des modifications structurales majeures affectant leurs interactions avec les protéines d’échafaudage et les protéines accessoires. L’impact de telles modifications sur les propriétés de diffusion et sur l’organisation sub-synaptique de ces rAMPA était jusqu’à présent inconnu. Mes travaux démontrent une mobilisation des rAMPA synaptiques consécutivement à leur activation par le glutamate. A l’échelle moléculaire, je propose que le passage de l’état activé à l’état désensibilisé des rAMPA entraîne un changement d’affinité de ces derniers pour une de leur protéine partenaire : la Stargazin. Cette régulation glutamate dépendante de la diffusion des rAMPA participe au maintien de la fidélité de la transmission synaptique rapide. / AMPA receptors (AMPAR) are ionotropic glutamate receptors which are responsible for the vast majority of fast excitatory synaptic currents in fast transmission. Upon release of glutamate, AMPAR undergo three main conformational states: pore closed/agonist unbound, pore open/agonist bound and pore closed/agonist bound. Controlling the number of AMPAR and their organization in the synapse, through a combination of lateral diffusion and endo/exocytosis, is essential to regulate the intensity of synaptic transmission. The interactions between proteins of the post-synaptic density and accessory receptor proteins regulate the distribution of receptors, controlling their number and organization in the post-synapse. During my PhD, I studied the impact of AMPAR activation on their mobility and organization in the post-synapse. Indeed, the binding of glutamate to AMPAR and their following desensitization lead to major structural changes on the receptor which impacts on their interactions with scaffolding proteins and accessory proteins. The impact of such modifications on the lateral diffusion and sub-synaptic organization of AMPAR was not known yet. My findings show a mobilization of synaptic AMPAR following their activation by glutamate. At the molecular level, I suggest that the transition from the activated state to the desensitized state of AMPAR leads to a change in affinity of the receptor for their partner protein: Stargazin. This glutamate dependent regulation of AMPAR diffusion participates in maintaining the fidelity of fast synaptic transmission.

The pursuit of high quality, large area graphene has been a major research focus of contemporary materials science research, in the wake of the discovery of the multitude of exceptional properties exhibited by the material. The DPhil project was undertaken with the objective of developing an understanding of the growth of large graphene sheets by chemical vapour deposition (CVD), and also in the subsequent characterisation of their material properties. By conducting atmospheric pressure CVD growth at high methane flow rates, it was found that few-layered graphene (FLG) could be deposited on a copper catalyst. It is demonstrated that the self-limiting property of a copper catalyst is not universal to all deposition conditions, and shown that FLG grows in a terrace-like configuration. In depth transmission electron microscopy (TEM) studies were carried out on FLG. By selective image reconstruction from the inverse power spectrum of the TEM images, it was possible to elucidate the inter-grain connectivity of few-layer graphenes. It was determined that there were two possible inter-grain configurations possible; specifically an overlap of graphene layers or a discrete atomic bonding edge. The perturbation of the few-layer structure when subject to an out of plane distortion was found to incur a shift in the conventional AB-Bernal stacking of FLG. By utilising the aberration corrected TEM (AC-TEM) at Oxford it was possible to resolve atomic detail in CVD synthesised monolayer films, including atomic bond rotations and vacancies. The use of a high current density at low accelerating voltage (80 kV) was demonstrated to allow for the controlled defect creation in graphene sheets. This permitted the creation of monovacancies and iron doped vacancy complexes suitable for further study. The behaviour of these two defect types under electron beam irradiation was subsequently studied.

This thesis concerns the application of aberration corrected scanning transmission electron microscopy (STEM) to the quantitative analysis of industrial Pd-Pt core-shell catalyst nanoparticles. High angle annular dark field imaging (HAADF), an incoherent imaging mode, is used to determine particle size distribution and particle morphology of various particle designs with differing amounts of Pt coverage. The limitations to imaging, discrete tomography and spectral analysis imposed by the sample’s sensitivity to the beam are also explored. Since scattered intensity in HAADF is strongly dependent on both thickness and composition, determining the three dimensional structure of a particle and its bimetallic composition in each atomic column requires further analysis. A quantitative method was developed to interpret single images, obtained from commercially available microscopes, by analysis of the cross sections of HAADF scattering from individual atomic columns. This technique uses thorough detector calibrations and full dynamical simulations in order to allow comparison between experimentally measured cross section to simulated ones and is shown to be robust to many experimental parameters. Potential difficulties in its applications are discussed. The cross section approach is tested on model materials before applying it to the identification of column compositions of core-shell nanoparticles. Energy dispersive X-ray analysis is then used to provide compositional sensitivity. The potential sources of error are discussed and steps towards optimisation of experimental parameters presented. Finally, a combination of HAADF cross section analysis and EDX spectrum imaging is used to investigate the core-shell nanoparticles and the results are correlated to findings regarding structure and catalyst activity from other techniques. The results show that analysis by cross section combined with EDX spectrum mapping shows great promise in elucidating the atom-by-atom composition of individual columns in a core-shell nanoparticle. However, there is a clear need for further investigation to solve the thickness / composition dualism.

One of the most challenging goals in nanoparticle research is to develop successful protocols for the large-scale, simple and possibly low-cost preparation of morphologically pure nanoparticles with enhanced properties. The work presented in this thesis was focused on the synthesis, characterisation and testing of magnetic nanoparticles and their potential applications. There are a number of magnetic nano-materials prepared for specific applications such as metal oxide nanoparticles encapsulated with various porous materials including Fe₃O₄/Fe₂O₃ coated with soft bio-organic materials such as glycol chitosan and bovine serum albumin and hard materials such as silica (SiO₂) and zinc sulphide (ZnS). The preparation of these materials was achieved principally by bottom-up methods with different approaches including micro-emulsion, precipitation, electrostatic and thermolysis processes. The thesis also presents the uses of various analytical techniques for characterising different types of nano-materials including Attenuated Total Reflection Fourier Transformer Infrared Vibrational Spectroscopy (ATR-FTIR), Ultraviolet Visible- Near Infrared (UV-Vis-NIR) Spectroscopy, Zeta Potentiometric Surface Charge Analysis, Superconducting Quantum Interference Device (SQUID) and Vibration Sample Magnetometry (VSM) for magnetic analysis and powder X-Ray Diffraction (XRD) for crystallographic pattern analysis. There are many applications of magnetic nanoparticles, including nano-carriers for biological and catalytic reagents. The magnetic nanoparticles can facilitate separation in order to isolate the carriers from solution mixtures as compared to many inefficient and expensive classic methods, which include dialysis membrane, electrophoresis, ultracentrifugation, precipitation and column separation methods. There are six key chapters in this thesis: the first chapter introduces the up-to-date literature regarding magnetic nano-materials. The uses of magnetic nano-materials in drug binding and for protein separation are discussed in the second and third chapters. The fourth chapter presents the use of magnetic nanoparticle in conjunction with a photo-catalytic porous overlayer for the photo-catalytic reduction of organic molecules. The fifth chapter describes different analytical techniques used for the characterisation of nanoparticles and the underlying principles and the experimental details are also given. The sixth chapter summarises the results and provides an overview of the work in a wider context of future applications of magnetic nanoparticles.

Microscopic beams of penetrating synchrotron radiation provide a unique tool for the analysis of material structure and deformation. This thesis describes my contributions to the development of new synchrotron X-ray micro-beam diffraction experimental techniques and data interpretation, and the use of experimental results for the validation of material deformation models. To study deeply buried material volumes in thick samples, the micro-beam Laue technique was extended to higher photon energies. Through-thickness resolution was achieved either by a wire scanning approach similar to Differential Aperture X-ray Microscopy (DAXM), or by applying tomographic reconstruction principles to grain-specific Laue pattern intensity. Both techniques gave promising first results. For reliable micro-beam Laue diffraction measurements of elastic strains in individual grains of a polycrystal, understanding of the error sources is vital. A novel simulation-based error analysis framework allowed the assessment of individual contributions to the total measurement error. This provides a rational basis for the further improvement of experimental setups. For direct comparison of experimental measurements and dislocation dynamics simulations, diffraction post-processing of dislocation models in two and three dimensions was developed. Simulated diffraction patterns of two-dimensional dislocation cell/wall type structures captured correctly some of the features observed experimentally in reciprocal space maps of a large-grained, lightly deformed aluminium alloy sample. Crystal lattice rotations computed from three-dimensional dislocation dynamics simulations of a Frank-Read source showed anisotropic orientation spread similar to that observed in micro-beam Laue experiments. For the experimental study of crystal lattice distortion, a novel technique was proposed that combines micro-beam Laue diffraction with scanning white-beam topography. Diffraction topography allows the study of lattice rotation at scales smaller than the scanning beam size. The new technique makes it possible to apply classical topography methods to deformed samples.