High resolution satellite imagery is more readily available and in larger quantities than ever before. It has become increasingly di cult for researchers in the planetary science community to manually analyse all of these images quickly and accurately. There have been several attempts over the last decade to address this by using image classi cation techniques which structure and organise planetary image datasets. However, these attempts have focused on the creation of the method rather than the analysis of the results. This thesis expands upon previous work by exploring methods to structure planetary image datasets that will allow the structure to be compared with other information about these images. The aim is to search for, and explore, trends within the resultant structure. A Context-Based Image Retrieval (CBIR) system is created using textons, a method to model texture as a histogram. These textural histograms are compared using the Earth Movers Distance (EMD) algorithm and the relationships between them are organised using Multi-Dimensional Scaling (MDS). A method to analyse the structure is presented using Pearson's correlation coe cient. These methods were applied to images of lunar craters, highlighting the e ect that illumination has on the appearance of texture in these images. This is important as it demonstrates the necessity for careful analysis of results produced by CBIR systems, as the work conducted by previous researchers has failed to take this into account. This thesis shows that if illumination is removed, or the data has little or no variation, texture analysis can be used to provide potentially important information about planetary features. In this study, once illumination was removed, it was found that the resultant structure was highly correlated with the depth/diameter (d=D) ratio of the crater, thus providing a method of predicting the d=D ratio of craters from the texture model alone. To explore the strengths and limitations of the proposed system it was applied to the di erent, but challenging, task of estimating grassland poaching damage from digital camera images. This demonstrates its potential use beyond the planetary science community. The work undertaken in this thesis demonstrates the use of CBIR systems within the planetary science community and highlights that the results obtained must be examined carefully. CBIR systems which report good visual similarity may appear to be useful for scienti c research but it is not until the results are analysed that this can be established.

The Epitaxial nature of graphene growth on the diamond (111) surface has been investigated using real-­‐time photoelectron spectroscopy (REES), Photoemission electron microscopy (PEEM), Angle resolved photoelectron spectroscopy (ARPES), low energy electron microscopy (LEEM) and low energy electron diffraction (LEED). Graphene regions were seen to co-­‐exist on the reconstructed 2×1 diamond surface following a high temperature in vacuum anneal at ~1000 °C. The graphene regions showed a π-­‐band dispersion along Κ-­‐Μ-­‐Κ that matches well with other calculations and experimental results of quasi-­‐free-­‐standing graphene. In the presence of a thin transition metal layer, the temperature at which the diamond surface undergoes conversion from sp3 to sp2 carbon is lowered. Here ordered films of Fe allow for the graphitisation of the diamond surface at ~495 °C. The order of the Fe film allows for registry to be transferred between the diamond surface and resulting graphene formation on the surface. An important aspect of this work is, the application of real-­‐time monitoring of in-­‐situ processing. Here REES is applied as a technique, which allows for precise control of the amount of graphene grown. Whilst monitoring the growth with real-­‐time imaging techniques such as LEEM allowed for investigation of the true growth optimum parameters. It was found that growth of graphene at 500 °C results in the formation large >100 μm regions which are strongly interacting with the substrate, displaying an n-­‐type doping of ~2.6 eV at the K-­‐point. The growth of qasi-­‐free-­‐standing graphene began at 530 °C however the slow growth rate at this temperature resulted in the formation of small islands made up of many graphene layers and rotational domains. Growth at 560 °C allowed for lateral growth of free-­‐standing monolayer regions across the sample surface. The grown material showed good registry to the substrate and displayed no sign of grain boundaries in LEED. The same catalytic process has been applied to the surface of SiC 6H-­‐(0001) and monitored using REES. Further control of the amount of graphene formed can by gained by the controlling the catalyst film thickness. A ~0.75nm thick film of Fe is expected to grow precisely 1 monolayer of graphene, as a result of the formation of a complete FeSi layer which terminates the graphitisation process.

Classical feedback control and system theory are playing an important role in modelling, controlling and analysing complex devices in many branches of engineering. Recent developments like quantum computers and miniaturisation of existing applications and devices are increasing the importance of the ability to control systems with quantum effects. Efforts have been made recently to extent the simplicity and power of the language of classical control theory to quantum mechanical systems. Within this framework of “Quantum Feedback Networks” we are investigating two problems. The first problem concerns the enhancement of squeezed states. It has been observed that the squeezing effect of squeezing devices can be enhancement by measurement based feedback techniques or use of optical cavities. We are investigating the possibility of feedback enhanced squeezing using coherent feedback control. Considered is a static ideal squeezing devices interacting with a single mode cavity undergoing coherent feedback using a beam splitter. We show that the overall squeezing of the output depends on the beam-splitter’s reflectivity and that we are thus able to enhance the squeezing by choosing an appropriate configuration of the beam-splitter. In the second part we investigate the question of compatibility of a rigorous approach to the adiabatic elimination of some degrees of freedom of a quantum mechanical systems and instantaneous feed-forward and feedback limits for quantum mechanical networks. The commutativity of both limits is not obvious but frequently assumed in quantum optics. We show that both limit procedures are instances of Schur complements and prove the commutativity of both limits by generalising a statement about successive Schur complements.

Biogas is an alternative fuel source, composed of methane and carbon dioxide, formed during the microbial process of anaerobic digestion (AD). Biogas production has the potential to be used as a substitute for natural gas and ease problems associated with global warming, energy security and waste management. However, AD can often be unreliable due to the instabilities that can arise during the process. The work described in this thesis, focuses on the discovery and development of micro-organisms for use in synthetic bio-methane producing microbial communities. Two main sources of instability within AD were focused on: oxygen-sensitivity of methane-producing microbes (methanogens) and volatile fatty acid (VFA) accumulation. The estuarine tidal mudflats of the River Exe Estuary, Exmouth, Devon, UK, were chosen for the search of potentially oxygen-tolerant methanogens, due to its intermittent oxygen exposure. Initially, 16S rRNA screening indicated the presence of methanogens in the very surface layer of the sediment, which was later confirmed by enrichment experiments. Whole genome shot-gun sequencing suggested Methanosarcina mazei, a methanogen known to have oxygen-tolerant capabilities, or a closely related organism, had been successfully enriched. The second part of this investigation focused on the use of E. coli as a model organism, for the engineering of a negative feedback loop against acetate production, a common VFA. The glutamine synthetase promoter, found to be sensitive to external pH and acetate concentration, was used to control the production of antisense RNA targeting the pta gene, involved in acetate production. Results indicated that expression of pta was successfully reduced, however overall acetate production was not found to decrease.

With recent advances in metamaterials research, scientists are increasingly trying to understand how interesting wave phenomena emerge from new materials. A key branch of this subject is transformation optics: using coordinate transformations to design materials which don't scatter light, used, for example, in the design of cloaking devices. This thesis is a study of various mathematical techniques, such as transformation optics, for designing non-scattering materials. The materials studied in this thesis are characterised by their macroscopic electromagnetic material properties; their permittivity and permeability. These quantities will be assumed isotropic, and to vary smoothly in space (such media being described as `graded-index'). These inhomogeneous media can be understood as the limit of a stack of different infinitesimally thin homogeneous blocks. However, the theory of graded-index media is analytically more tractable than the theory of piecewise media than the piecewise homogeneous permittivity and permeability profiles that arise from placing blocks of different materials side by side. The first part of the thesis introduces the necessary background for the rest of the thesis. Chapter 1 introduces the background electromagnetic theory used throughout the rest of the work and chapter 2 is a review of some of the existing literature on designing non-scattering media including an introduction to metamaterials, which are one route to realising graded-index media. The second part of the thesis concerns the use of phase-integral methods for designing planar, reflectionless media, inhomogeneous in one dimension. Chapter 3 introduces the phase-integral method and describes how it can be used to understand reflection in the complex position plane. Chapter 4 uses the phase-integral method to derive a large family of index profiles reflectionless from one side for all frequencies of light and angles of incidence. Chapter 5 uses the phase-integral method to calculate exact reflection coefficients for some example index profiles. Chapter 6 is concerned with designing media which, in addition to being reflectionless, transmit all incident light. It is found that this perfect transmission property is exhibited by even very highly disordered media. Chapter 7 looks further at the reflectionless media designed in chapter 4, deriving a subfamily which, in addition to being non-reflecting, are also perfectly absorbing. The third and final part of the thesis deals with the design of planar, non-scattering media which are inhomogeneous in two dimensions. One way to handle this problem is to write the electromagnetic field in terms of its amplitude and phase, and use local conservation of energy in a lossless medium to understand how the amplitude and phase are related to each other. Chapter 8 uses this idea to find explicit expressions for non-scattering index profiles, including a generalisation of an existing version of transformation optics, and the design of a `beam-shifter'. Chapter 9 uses the characteristic method to solve the relationship between amplitude and phase and how it can be used to design non-scattering profiles, such as periodic media which don't diffract. Finally, chapter 10 discusses nodes of the electromagnetic field and how they can arise from sending a wave onto a medium, in particular looking into the possibility of diffraction of a plane wave from a periodic structure into a pair of complementary modes in transmission; the corresponding transmitted field of which contains nodes.

There are approximately 500 million smallholder farmer households worldwide, at least half of which live in poverty and food insecurity. Scientific research underpins development efforts by providing options for improved varieties, breeds, or practices (termed “interventions”); and by providing analyses of how to increase the adoption and impact of those interventions. One of the most widely used method of data collection to evaluate or predict the impact of interventions is the household survey, but critical evaluations of the effectiveness of household survey data and methodologies are rare. Lack of standardised questions make efforts to aggregate findings across datasets challenging, given that different surveys often yield widely different data, both in terms of content and quality, which severely limits the comparability of those data (see Chapters 2 and 3). Here I present an improved survey method to assess farm practices and food security for smallholder households in lower income countries, primarily tropical or sub-tropical. The tool is named the Rural Household Multi-Indicator Survey (RHoMIS). It makes use of recent advances in digital technologies, which enables quicker data collection and reporting than in previous generations of survey tools. The tool was designed to be rapid, lean, user-friendly, flexible and reliable (Chapter 3). The design ethic and advances in indicator formulation allowed data to be gathered on a wider range of topics over shorter time frames but still with adequate depth to permit effective analyses (Chapters 4, 5, and 6). During development RHoMIS was deployed by 13 organisations in 17 countries, with over 15,000 interviews conducted. The tool has the flexibility needed for application in many locations, sufficient standardisation to permit rapid analysis and data aggregation between sites, and enables more efficient characterisation of smallholder farming systems compared to previous efforts. Findings of analyses presented in this thesis stress the need to understand the heterogeneity of smallholders, and to plan or evaluate interventions for specific subsets of households. Analyses presented in the research chapters show that the farm strategy of input intensification is better suited to larger farms, crop diversification is better suited to smaller farms, and that the effects are strongly influenced by the degree of commercialisation of livelihoods (Chapter 3), the use of collected resources can strongly benefit the poorest households (Chapter 4), and that off-farm incomes in combination with farm intensification hold the potential to raise the prosperity of about 90% of the households studied in Chapter 5 . Furthermore households show different levels of interest in trialling and adopting new practices which are not necessarily related to their assets or farm types, in Chapter 2 about one quarter of households were identified as likely to trial new practices. In particular the analyses highlights that those experiencing (or at risk of) extreme food insecurity benefited most from opportunities for off-farm income, whereas moderately poor households benefited more from agricultural intensification. These findings indicate that for agricultural intensification measures to raise households out of food insecurity and poverty they must be targeted to the appropriate group of smallholders, and to succeed must be in combination with opportunities to earn off farm income.

Climate change is a global crisis facing forest management. There are risks to many ecological goods and services from forests due to changes in productivity, mortality, pathogen, and wildfire dynamics. Likewise, there are opportunities such as increases in productivity or targeted funding for climate adaptation and emission reductions. To manage those risks and opportunities, we need the fundamental knowledge of forest carbon (C) cycles. Overall, my dissertation aims to improve our understanding of forest carbon dynamics and how they may respond to natural disturbances, climate change and management activities. This purpose falls within the context of the need to adapt to and mitigate climate change for the ongoing provision of ecological goods and services from forest ecosystems such as timber and biodiversity. The thesis starts with a critical analysis of six papers I have previously published. That chapter includes a synthesis of findings, critique of methods used, and identifies some areas for future research. Each subsequent chapter represents a contributing article. The overall findings of this dissertation are (i) that although forests are often GHG sinks moderate or high intensity natural disturbances can reverse that flux. (ii) That climate change effects on productivity may increase or decrease the natural sinks or even create emission sources in forests that may otherwise have been sinks. (iii) That management strategies to increase species diversity and resilience may be effective at reducing risks of emissions, but they must be assessed for individual ecosystems and may be insufficient to fully offset disturbance or climate change effects.

Significant developments in gastropod endocrinology since 1969 are reviewed. The anatomy of the CNS, distribution of nerves and the general plan of the vascular system in Deroceras reticulatu m is described. The central ganglia are encased in a thick perineural sheath, a matrix of collagen in which muscle fibres, blood vessels, granular cells, pigment cells and vesicular cells are embedded. The fine structure of the blood vessels supplying the CNS suggests that metabolic requirements reach the neurones by diffusion from these vessels. Dorsal Body tissue (DBT) occurs on the cerebral ganglia and intercerebral commissure as well as other parts of the CNS. Synaps-like contact between neurosecretory axons and DBT was not found, but the close relationship with the blood system, suggests secretory material may be liberated directly into the blood. Distinct groups of possible neurosecretory neurons were identified in the cerebral, parietal and visceral ganglia, but specialised neurohaemal areas were not found. Axons containing large numbers of elementary granules were observed in the perinueral sheath, but axons with swollen ends or evidence of exocytosis was not found. The presence of possible neurosecretory axons close to capillaries and blood spaces suggests release of neurosecretory material into the blood can take place easily. During investigation of the CNS a tissue was discovered attached to arteries arising from the cephalic arborescence. It appeared glandular, lacked ducts and was provisionally named the arterial gland. Electron probe microanalysis revealed an accumulation of copper within the arterial gland, but immunoelectrophoresis performed using rabbit antiserum to H. aspersa haemocyanin. and homogenised arterial glands gave negative results. The arterial gland in D. reticulatu m contains secretion throughout reproductive development. Its size is extremely variable between individuals, but neither size nor histology could be related to reproductive development. Tissue similar to the arterial gland of A.reticulatus was found in four other gastropod species.

CHIPS (CHerenkov detectors In mine PitS) is an R&D project aiming to develop novel cost-effective detectors for long baseline neutrino oscillation experiments. Water Cherenkov detector modules will be submerged in an existing lake in the path of an accelerator neutrino beam, eliminating the need for expensive excavation. In a staged approach, the first detectors will be deployed in a flooded mine pit in northern Minnesota, 7 mrad off-axis from the existing NuMI beam. A small proof-of-principle model (CHIPS-M) has already been tested and the first stage of a fully functional 10 kt module (CHIPS-10) is planned for 2018. The main physics aim is to measure the CP-violating neutrino mixing phase (δCP). A sensitivity study was performed with the GLoBES package, using results from a dedicated detector simulation and a preliminary reconstruction algorithm. The predicted physics reach of CHIPS-10 and potential bigger modules is presented and compared with currently running experiments and future projects. One of the instruments submerged on board CHIPS-M in autumn 2015 was a prototype detection unit, constructed at Nikhef. The unit contains hardware borrowed from the KM3NeT experiment, including 16 3 inch photomultiplier tubes and readout electronics. In addition to testing the mechanical design and data acquisition, the detector was used to record a large sample of cosmic ray muon events. A preliminary analysis of the collected data was performed, in order to measure the cosmic background interaction rates and validate the Monte Carlo simulation used to optimise future designs. The first in situ measurement of the cosmic muon rate at the bottom of the Wentworth Pit is presented, and extrapolated values for CHIPS-10 show that the dead time due to muons is below 0.3 %.

One of the main questions in the field of quantum computation is where the quantum computational speed-up comes from. Recent studies in the field of quantum foundations have suggested which are the features to be considered as inherently non-classical. One of the major contributions in this direction comes from a result known as Spekkens' toy theory, which is a model built to reproduce quantum theory as a classical phase-space-inspired theory with restrictions on what an observer can know about reality. The model reproduces many of the features of quantum mechanics, but it does not reproduce non-locality and contextuality. In this thesis we first complete Spekkens' toy theory with measurement update rules and a mathematical framework that generalises it to systems of any finite dimensions (prime and non-prime). We also extend the operational equivalence between the toy theory and stabilizer quantum mechanics to all odd dimensions via Gross' Wigner functions. We then use the toy theory to represent the non-contextual and classically simulatable part of the computation in state-injection schemes of quantum computation where contextuality is a resource. In the case of qubits, we show that the subtheories of quantum mechanics represented in the toy model can achieve the full stabilizer theory via state-injection and we associate different proofs of contextuality to different injection processes. Stepping back from Spekkens' toy theory, we conclude by focusing on single system protocols that compute non-linear functions (similarly to the popular CHSH game) which show quantum advantages even in absence of non-locality and contextuality (in its standard notions). We analyse their performances (formalised in Bell's and Tsirelson's bounds) in relation to Landauer's principle, which associates entropic costs to irreversible computations, and to a new notion of contextuality for sequences of transformations.