Coherent scatter radars are extensively employed in the study of important geophysical processes in the Earth's upper atmosphere and magnetosphere. The science relies on the ability of coherent scatter radars to detect plasma irregularities in the Earth's ionosphere and relate their properties to the geophysical process under consideration. This thesis is concerned with the physical characteristics of the plasma irregularities deduced from coherent scatter radar observations. Data from three coherent scatter radar systems, PACE, SABRE and COSCAT, each sensitive to a different irregularity wavelength, are analysed. Statistics for the backscatter power, phase speed and spectral width at each wavelength are calculated and compared. Furthermore, the functional dependence of the irregularity parameters on each other has been investigated. Strong relationships between the spectral width and irregularity phase speed and the spectral width and backscatter power are identified. The spectral widths tend to exhibit a minimum at phase speeds close to the ion-acoustic speed. There is a decrease in the average backscatter power as the spectral width increases. A new measurement of the dependence of the spectral width on the irregularity wave number is deduced. These results have important significance for the general interpretation of coherent scatter radar measurements. Special experimental campaigns with SABRE and COSCAT in conjunction with EISCAT have been undertaken to enable the irregularity phase speed and the plasma drift speed to be compared. This is a very important relationship since the plasma drift speed is routinely estimated from the irregularity phase speed. The analysis confirms the non-linear behaviour of the relationship between these two parameters. Similar results are obtained for COSCAT and SABRE. Differences can be attributed to the expected variations with wave number and to variations in the height of the observed irregularities, consistent with the kinetic theory of Robinson and Honary (1990).

Un-hydrogenated and hydrogenated a-GexSe1-x films (0.2 x 1) have been prepared by radio-frequency sputtering at room temperature employing an r.f. power of 240 W and an Ar pressure of 3-6 mTorr. Zn-alloyed films, a-GexSeyZnz, were deposited under the same conditions, with Zn concentrations up to 27%. The compositions of the films were determined by an energy dispersive X-ray analyser (SEM-EDAX) attached to a scanning electron microscope. Optical absorption edges of the a-GexSe1-x samples have been deduced from reflection-transmission (R-T) spectra and photo-thermal deflection spectroscopy (PDS) measurements. The optical bandgaps, other parameters related to the edges, and the real part of the refractive index were determined and analysed. The effects of hydrogenation on the a-GexSe1-x films are investigated by analysing their optical absorption edges and measurements of the d.c. electrical conductivity as a function of temperature. The optical and electrical properties of a-GexSeyZnz films were studied and the effects of Zn addition to GeSe films analysed from the behaviour of the optical gap and the activation energy in the d.c. electrical conductivity. Extended X-ray absorption fine structure (EXAFS) measurements have been performed on both a-GexSe1-x and a-GexSeyZnz films. Information on the local atomic structure, e.g. the nearest-neighbour bond length and the coordination number, has been extracted from the data and is discussed in detail. In particular, the experimentally determined partial coordination numbers are compared with those predicted by two models, the chemically ordered bond network (OBN) and random bond network (RBN) structures. The results reveal that the a-GexSe1-x films have a chemically ordered 4-2 covalent bond network structure throughout the whole composition range and that Zn replaces the Ge atoms and is four-fold coordinated. The dielectric functions of the a-GexSe1-x alloys is modelled and the calculated optical properties compared with the experimental results. Good agreement is found.

Micro and nanomechanical resonators are highly sensitive, label-free analyte sensors in a range of environments. Resonant cantilevers, i.e. those operated in dynamic mode, can be considered as mechanical oscillators, with analyte adsorption creating a shift in cantilever resonance. Cantilever sensors work via a purely mechanical approach, transducing an analyte binding event into a nanomechanical signal. This response is governed by changes in sensor mass and stiffness due to adsorbed analytes, with previous theoretical work predicting the latter to produce significant effects on measured frequency shifts, counteracting effects of adsorbed mass. This highlights a particularly unsatisfactory feature of micro/nano-mechanical sensors, as an accurate interpretation of the sensor response must depend on both adsorbate mass and rigidity, which for nanometer-scale coverage can only be guessed, rather than derived from independent measurements. In this thesis, procedures to disentangle such effects in air and liquid are discussed and tested on a range of surface coatings, offering a novel method of analyte detection and analysis. The dynamic characteristics of cantilever beams are strongly dependent on the mass density and viscosity of the fluid in which the beams are immersed. The application of cantilevers in accurately determining such rheological properties is also presented, first via the use of model solutions, and then extending measurements to a range of commercial alcoholic and non-alcoholic drinks. A method to quantify alcohol content is also discussed, further demonstrating the commercial applications of cantilever sensors.

Cryogenics is increasingly required for space applications as new detector technologies emerge offering improved performance, as is exemplified by future X-ray astronomy missions. The IXO1 (International X-ray Observatory) mission will carry an X-ray Microcalorimeter Spectrometer (XMS), requiring a 50mK operating temperature. Two space-demonstrated technologies are capable of maintaining milli--Kelvin temperatures: Adiabatic Demagnetisation Refrigerators (ADRs) and open-cycle Dilution refrigerators. ADRs are simpler, more reliable, and have a longer lifetime than open-cycle dilution refrigerators which deplete their Helium stores after ~3 years. For long-life (>5 year) missions, ADRs are the best practical choice. MSSL have built an engineering model ADR for the XEUS (X-ray Evolving Universe Spectroscopy) mission. However, the ADR cannot achieve the required hold time and recycle time. This thesis shows how a magnetoresistive heat switch can improve performance such that the required hold time can be achieved. Tungsten Magnetoresistive heat switch technology is developed through experimental investigation. Heat switch performance is found to be a function of purity; the difference between an otherwise identical 99.992% and a 99.999% pure sample is very significant, with switching ratios of 437 and 1×104 respectively at ~4K. The ‘on’ state thermal conductivity is limited by sample size as it is reduced to the electron mean free path and below. A Tungsten magnetoresistive heat switch mounted in the XEUS ADR via bolted joints lined with 0.13mm thick Indium foil can improve its performance to meet the design requirements. MSSL are developing an ADR targeting the IXO XMS. The cooling chain required to support the ADR is presented. The design feasibility and compliance to requirements are verified by thermal and mechanical analyses, and it is shown that the ADR can be supported during holding and recycling for both warm and cold redundancy modes of higher temperature stage coolers in the chain. [1] NOTE: During the writing of this thesis, the IXO mission ceased to be a candidate of the L-class missions under consideration by ESA. However, due to the strong science case of IXO; ESA, Astrium and the scientific community are investigating to what extent a European-led mission could preserve the original science goals of IXO. This new study is ATHENA (Advanced Telescope for High ENergy Astrophysics).

My PhD project is on the use of coherent X-ray diffractive imaging (CDI) techniques to study strained Silicon-On-Insulator (SOI) and Strained-Silicon-On-Insulator (SSOI) nanostructures, which include nanowires and microsquares. To understand and distinguish SOI wafer properties and compare and analyze different wafer bonding techniques, various SOI wafers with different bonding techniques were measured using CDI, and analysis shows inhomogeneity across all categories of SOI wafers. Furthermore, I discovered a radiation-induced bending effect causing SOI nanowires to exhibit highly strained characteristics in diffraction patterns in reciprocal-space. There is a trend of peak splitting of the central maximum of the diffraction patterns when increasing X-ray illumination dose, i.e. time of X-ray exposure. We are able to propose a model of radiation-induced bending of SOI model and our model is confirmed by simulations of calculated diffraction patterns and by a Finite-Element-Analysis tool (COMSOL Multiphysics). The results are in agreement with experimental measurements, which indicates that our model is a generally correct description of the X-ray radiation effect. We developed a Guided-Phase-Error-Reduction (GPER) algorithm to do diffraction data inversion, obtaining direct-space amplitude and phase of strong-bent SOI nanowires. Most importantly, we observe mechanical breakdown that causes various kinds of dislocations within the nanowire structure when the X-ray irradiation dose has reached a certain level. Beyond this dose, the nanowire begins to undergo plastic deformation. The second part of my PhD project involves design and performance of experimental measurements of reflection Bragg-geometry ptychography at beamline 34-ID-C at the Advanced Photon Source. We have used both KB mirrors and zone-plate focused methods. Zone-plate based focusing method produces highly asymmetric curved-wave front X-ray illumination for studies on both Siemens-star test patterns and SOI micro- and nano squares. Our preliminary analyses have shown some promising results. We have performed series of measurements on Siemens-star test sample by using transmission-geometry Ptychography with various coherence properties of Xrays and oversampling ratios of Fourier-space diffraction intensities. In the long term, Bragg-geometry ptychography has great potential for imaging condensed matter structures and surface effects, aiming at better understanding of structural Physics, Materials sciences and Nanotechnology in general. Strains by various industrial processing of SOI based electronic devices, such as silicon-based MOSFETs, can be probed by either conventional Bragg CDI or Bragg-geometry ptychography. MOSFETs may behave differently under X-ray irradiation, because of this radiation effect, resulting to various strain states which could modify carriers mobility in semiconductor devices performance in general applications.

The Askaryan Radio Array (ARA) is a new experimental effort to develop an array of sub-detectors capable of measuring ultra-high energy neutrino-induced radio pulses in the Antarctic ice sheet. Each sub-detector is able to function as a stand alone neutrino detector, the first of which was installed during the 2011 austral summer. In the following two years a further 3 sub-detectors were installed with updated design and functionality, with more planned over the next few years. This thesis describes an analysis of the data collected by the first ARA station and presents the results of a search for ultra-high energy neutrinos. No statistically significant evidence for neutrino-induced signals is observed, with no candidate neutrino events. A limit is placed on the flux of ultra-high energy neutrinos and extrapolated to the full 37 station ARA detector operated over a 5 year period.

Transcription regulation plays a key role in determining cellular function, response to external stimuli and development. Regulatory proteins orchestrate gene expression through thousands of interactions resulting in large, complex networks. Understanding the principles on which these networks are constructed can provide insight into the way the expression patterns of different genes co-evolve. One method by which this question can be addressed is to focus on the evolution of the structure of transcription factor networks (TFNs). In order to do this, a model for their evolution through cis mutation, trans mutation, gene duplication and gene deletion is constructed. This model is used to determine the circumstances under which the asymmetrical in and out degree distributions observed in real networks are reproduced. In this way it is possible to draw conclusions about the contributions of these different evolutionary processes to the evolution of TFNs. Conclusions are also drawn on the way rates of evolution vary with the position of gene in the network. Following this, the contributions of cis mutations, which occur in the promoters of regulated genes, and trans mutations, which occur in the coding reign of transcription factors, to the evolution of TFNs are investigated. A space of neutral genotypes is constructed, and the evolution of TFNs through cis and trans mutations in this space is characterised. The results are then used to account for large scale rewiring observed in the yeast sex determination network. Finally the principles governing the evolution of autoregulatory motifs are investigated. It is shown that negative autoregulation, which functions as a noise reduction mechanism in haploid TFNs, is not evolvable in diploid TFNs. This is attributed to the effects of dominance in diploid TFNs. The fate of duplicates of autoregulating genes in haploid networks is also investigated. It is shown that such duplicates are especially prone to loss of function mutations. This is used to account for the lack of observed autoregulatory duplicates participating in network motifs. From this work, it is concluded that the relative rates of different evolutionary processes are responsible for shaping the global statistical properties of TFN structure. However, the more detailed TFN structure, such as network motif distribution, is strongly influenced by the population genetic details of the system being considered. In addition, extensive neutral evolution is shown to be possible in TFNs. However, the effects of neutral evolution on network structure are shown to depend strongly on the structure of the space on neutral genotypes in which the TFN is evolving.

T cell homeostasis describes the process through which the immune system regulates cell survival, proliferation, differentiation and death to maintain T cell numbers and diversity in a range of different conditions. The aim of this thesis is to better understand how this process leads to the development of the naive CD4+ T cell compartment during childhood. Mathematical modelling is used in combination with experimental observations to estimate naive T cell kinetics over the lifetime of an individual. The analysis described here shows that post-thymic proliferation contributes more than double the number of cells entering the pool each day from the thymus. This ratio is preserved from birth to age 20 years; as the thymus involutes, the average time between naive T-cell divisions in the periphery lengthens with age and the naive population is maintained by improved naive cell survival. Thymic output is quantified from birth to age 60 years by combining models to interpret naive T cell TRECs and Ki67 expression data. Three distinct phases of thymic T cell output are identified: (i) increasing production from birth to age 1 year; (ii) steep decline to age 8 years; (iii) slow decline from age 8 years onwards. Finally, the role of inter-cellular variation in T cell residency times is explored. It is able to explain the persistence of PTK7+ naive CD4+ T cells in thymectomised individuals. Importantly, the model predicts the accumulation of veteran PTK7+ T cells in older individuals and suggests that the residual population in thymectomised individuals will also consist predominantly of veteran PTK7+ T cells. The model has implications for the use of PTK7 as a marker of recent thymic emigration and also naturally explains improved T cell survival in older individuals.

Classical, non-equilibrium systems of diffusing species or entities undergoing depletion, evaporation and reaction processes are at the heart of many problems in Physics, Chemistry, Biology and Financial Mathematics. It is well known that fluctuations and correlations in statistical systems can have a profound influence on the macroscopic properties of the system. However, the traditional rate equations that describe the evolution of mean populations in time and space do not incorporate statistical fluctuations. This becomes an issue of great importance when population densities are low. In order to develop a stochastic description of birth-and-death processes beyond the mean field approximation I employ techniques in classical many-body Physics in a manner analogous to the treatment of quantum systems. I obtain promising results to understand and quantify the exact circumstances of the failure of the mean-field approximation in specific problems in Astrophysics, namely heterogeneous chemical reactions in interstellar clouds, and in Aerosol Science, namely heterogeneous nucleation processes, and deliver the means to manipulate the alternative stochastic framework according to the Doi-Peliti formalism. In this framework the mean population of a species is given by the average of a solution to a set of constraint equations over all realisations of the stochastic noise. The constraint equations are inhomogeneous stochastic partial differential equations with multiplicative real or complex Gaussian noise. In general, these equations cannot be solved analytically. Therefore I resort to the numerical implementation of the Doi-Peliti formalism. The main code is written in the GNU C language, some algebraic calculations are performed by means of the MapleV package. In the case of large population densities the stochastic framework renders the same results as the mean field approximation whereas for low population densities its predictions differ substantially from the calculations using the traditional model.

O stars are highly important objects in their host galaxies due to the impact of their powerful stellar winds and strong flux output. The details of their physics and evolution as individual entities and as populations have important consequences for understanding the stars themselves and their environments. Two major issues are currently challenging the successful theory of line-driven winds; that the winds are clumped and not smooth or homogeneous, and that some objects appear to have weaker mass-loss than prescribed by theory; in the case of O supergiants by a factor of a few, and for late O dwarfs by perhaps and order of magnitude or more. The key goal of this thesis is to exploit sophisticated model atmosphere calculations to explore the effects of wind-clumping and X-rays due to wind shocks in O stars in the Milky Way. The consequences for the spectral line profiles produced and the ionization balance are explored in detail. The level to which clumping and X-rays affect the observations of different classes of O star is further constrained. IUE observations of weak-wind O stars (those at spectral types O6.5-9.5 V) are examined in light of the ion balance determinations, and comment is made about the current state of the weak-wind problem in the Galaxy. This involves empirical line-synthesis matches to Civ and Nv line profiles. The influence of X-rays is found to be key in the mass-loss issue through altering the ion balance. Finally the wind-formed sulphur line profiles of a small sample of O type supergiants are fitted using model atmospheres. Sulphur is important in these O stars since the model atmospheres predict the majority of it to be found in three adjacent ion stages that all have corresponding wind lines in the ultraviolet and far-ultraviolet. When moderate clumping in the winds is assumed, the mass-loss rates are found to be approximately in line with estimates based on density-squared diagnostics, such as H-alpha.