Physically interesting behaviour can arise when soft matter is confined to nanoscale dimensions. A highly relevant biological example of such a phenomenon is the Nuclear Pore Complex (NPC), found perforating the Nuclear Envelope of all eukaryotic cells. In the central conduit of the NPC, of 30-60 nm diameter, a disordered arrangement of proteins regulates all macromolecular transport between the nucleus and the cytoplasm. Its selectivity for larger macromolecules relies on changes in a permeability barrier that is formed by these unstructured proteins, induced by interactions of these proteins with molecules called Nuclear Transport Receptors (NTRs), which can chaperone larger macromolecules through the NPC. The exact mechanism for the transport selectivity is unknown. To model these unstructured proteins in the nanoscale channel of the NPC, a density functional theory approach is developed that treats the proteins as interacting polymers. This new method is tested against Monte Carlo to show its validity. A detailed comparison between this model system and those previously proposed in the literature is provided. In a parameter range relevant for the NPC, the system shows bimodal behaviour The polymers can alternate between two condensed states: An open state, in which this condensation takes place at the channel wall, and a closed state in which it occurs at the channel centre. We then extend this model by including explicitly the effect of Nuclear Transport Receptors on the conformations of the polymers. The model takes into account the finite size of the transport receptors relative to the NPC diameter. Mapping the polymer and transport receptor behaviour over a set of physiologically relevant parameters gives different structural scenarios for the various hypothesized transport mechanisms. Further to this, the transport rates for each parameter set can be obtained, showing whether such parameters are consistent with experimental evidence. In addition to this, we study the effect of relaxing some of the assumptions of our model, specifically by looking at azimuthal symmetry breaking effects in two dimensions. We also compare our model to experimental results measuring the thickness of planar polymer brushes comprised of NPC proteins to further justify parameter choices.

A new class of hydrogen storage material (HSM), the swelling clay minerals, is introduced by the investigation of laponite, a representative smectite. Simple ion exchange allows for a diverse range of charged species to be studied as possible adsorption sites for H2 within the laponite interlayer, while a sub-monolayer of water pillars the interlayers apart by 2.85 Å, close to the kinetic diameter of H2. Neutron diffraction shows that the 001 peak, representing the clay d-spacing, is directly affected by the introduction of H2 or D2, confirming intercalation into the interlayers. Volumetric adsorption isotherms and neutron scattering show that laponites with 3 wt% H2O rapidly physisorb 0.5-1 wt% H2 at 77 K and 80 bar, with low binding enthalpies (3.40-8.74 kJ mol-1) and consequently low room temperature uptake (0.1 wt% at 100 bar). The higher structural density of clays results in lower H2 densities than MOFs and activated carbons, however some cation-exchanged forms, such as Mg and Cs, show promise for improvement having capacities of 22.8 g H2 per litre at 77K, 80 bar, intermediate between AX-21 and IRMOF-20. At low coverage, INS spectra reveal up to five adsorption sites with low rotational energy barriers (0.7-4.8 kJ mol-1), persisting up to at least 50 K. Analysis of quasielastic neutron scattering (QENS) spectra for Ca-laponite expanded with 3 wt% H2O reveals two populations of interlayer H2: one immobile up to 100 K and localised to the Ca2+ cations, while the other diffuses by jump diffusion at a rate of 1.93 0.23 Å2 ps-1 at 80 K, 60% slower than in the bulk (Dbulk = 4.90 0.84 Å2 ps-1). Arrhenius analysis gives activation energies of 188 28 K for the calcium and 120 32 K for the sodium form, comparable to the range for activated carbons. The adsorbate phase density of H2 in laponite interlayers at 40 K is 67.08 kg m-3, close to the bulk liquid density of 70.6 kg m-3. Jump lengths of 3.2 0.4 Å for Ca-laponite measured by QENS at 40 K are similar to the H2-H2 nearest neighbour distance in condensed H2 (3.79 Å). Thus data from a variety of techniques provides a coherent model for the structure and behaviour of H2 in laponite. The experimental achievement of a two-dimensional film of liquidlike H2 confined within the interlayers up to 40 K is of great interest for the field of superfluidics, since it may be possible to supercool liquid hydrogen confined in laponite interlayers below the predicted Bose-Einstein condensation temperature at 1 K.

The goal of this thesis was to determine the nature of phosphatidylcholine self assembly within hydrocarbon liquids. This study was enacted in order to investigate the potential use of amphiphiles in compartmentalisation strategies for putative organisms inhabiting the hydrocarbon lakes of Titan (the largest moon of Saturn). The backbone of terrestrial cell membranes are vesicular structures composed of a phospholipid bilayer, with the hydrophilic head groups arranged around the periphery, and simple lipid vesicles are thought to be akin to the first terrestrial protocells. It may be possible that reverse vesicles, surrounding a nonpolar core and composed of a bilayer with the hydrophilic head groups arranged internally, may be ideal model cell membranes for putative hydrocarbon-based biota inhabiting Titan‟s hydrocarbon lakes. Compounds that are shown to form reverse vesicles in conditions comparable to those of Titan„s lakes could be potential „biomarkers‟ and searched for in future missions to Titan. In order to discover whether certain phosphatidylcholines can exhibit vesicular behaviour within hydrocarbon liquids, and to analyse their structure, I have carried out experimental studies using environmental conditions that are increasing comparable to those found on the surface of Titan. Studies of macroscopic and microscopic phase behaviours were used to determine the presence of self assembled particles, including reverse vesicles. These studies included the use of microscopy, confocal laser scanning fluorescence microscopy, transmission electron microscopy (TEM), dynamic light scattering (DLS), small-angle neutron scattering (SANS) and small-angle x-ray scattering (SAXS). The systems studied included: the hydrocarbon solvents cyclohexane, octane, heptane, hexane, pentane and butane; various amphiphilic ratios of PC4:0, PC18:2 and lysoPC18 at dilute, ≤30 mM, concentrations; inclusion or exclusion of NaCl as a stabiliser; methanol or direct preparation methods; variation of sonication intensities and times; and a variety of temperatures. Results of this research demonstrate that unilamellar, multilamellar and multi-chambered reverse vesicles can form in a wide range of phosphatidylcholine-hydrocarbon systems. Small concentrations of NaCl and lyso-phosphatidylcholines were found to facilitate reverse vesicle formation. A reduction in temperature (down to the freezing point of the solvent) did not change the structural phase behaviour of most systems, but often increased the size of reverse vesicles. Decreasing the molecular weight of the alkanes was found to effect which amphiphilic ratios formed reverse vesicles; pentane solvent molecules were particularly effective at bilayer penetration. These results support the feasibility of further cryogenic self assembly experiments as analogues to the hydrocarbon environments found on Titan.

Molecules are essential to the formation of stars, by allowing radiation to escape the cloud and cooling to occur. Over 180 molecules have been detected in interstellar environments, ranging from comets to interstellar clouds. Their spectra are useful probes of the conditions in which these molecules form. Comparison of rest frequencies to observed frequencies can provide information about the velocity of gas and indicate physical structures. The density, temperature, and excitation conditions of gas can be determined directly from the spectra of molecules. Furthermore, by taking a chemical inventory of a particular object, one can gain an understanding of the chemical processes occurring within a cloud. The class of molecules known as complex molecules (>6 atoms), are of particular interest when probing the conditions in massive starforming environments, as they are observed to trace a more compact region than smaller molecules. This thesis details the work of my PhD, to explore how complex molecules can be used to trace the physical and chemical conditions in hot cores (HCs), one of the earliest stages of massive star formation. This work combines both the observations and chemical modelling of several different massive star-forming regions. We identify molecular transitions observed in the spectra of these regions, and calculate column densities and rotation temperatures of these molecules (Chapters 2 and 3). In Chapter 4, we chemically model the HCs, and perform a comparison between observational column densities and chemical modelling column densities. In Chapter 5, we look at the abundance ratio of three isomers, acetic acid, glycolaldehyde, and methyl formate, to ascertain whether this ratio can be used as an indicator of HC evolution. Finally, we explore the chemistry of the HC IRAS 17233–3606, to identify emission features in the spectra, and determine column densities and rotation temperatures of the detected molecules.

Understanding the role of star formation and its feedback effects at high redshift is extremely important, as this greatly influences the nature of the first galaxies. This knowledge will also allow us to resolve the formation conditions of hyper-metal poor stars such as SDSS J102915+172927 (Caffau et al. 2011). This star is thought to be the first ‘truly’ low metallicity star, as it possesses a total metallicity between 10..5 .. 10..7 Z (Caffau et al. 2012). Hence it’s formation was probably triggered by a single primordial supernova (SN) event. Fragmentation studies that only include metal-line cooling, cannot reproduce the conditions in which such a star could form (Klessen et al. 2012). Therefore it is critical to simulate the physical processes that occur on the small scale as reliably as possible, as they impact large scale dynamics. At present early universe supernova shock models only include non-equilibrium chemistry and its associated cooling for temperatures below 104 K (Machida et al. 2005; Kitayama & Yoshida 2005; Nagakura et al. 2009; Chiaki et al. 2013). The metal-line cooling is often calculated separately assuming the collisional equilibrium. If we want to obtain realistic results, it is important to incorporate a complete chemistry (which includes metals, molecules and dust) and therefore evaluate the non-equilibrium cooling that occurs at all temperatures. In Chapter 2, we first try to understand the chemistry that would occur in a low metallicity gas. We investigate the chemical evolution of a metal-free cloud that has been mixed with ejecta from a single supernova. The very first stars would have been massive and simulations predict a range of masses (Bromm & Yoshida 2011). The initial mass of the star dictates the type of supernova explosion it will undergo. As each type of SN produces a different elemental yield, we would like to ascertain if it is possible to constrain molecular tracers of progenitor mass from a primordial cloud that interacted with that particular SN ejecta. A metal-free chemical network with its associated cooling is coupled to a hydrodynamics code in Chapter 3. Previous studies (Machida et al. 2005; Kitayama & Yoshida 2005; Nagakura et al. 2009; Chiaki et al. 2013) have focused on the fragmentation of the shell that forms as early universe supernova remnant interacts with an interstellar medium of a uniform density. Our model has improved upon these studies by modelling a multiphase medium with multidimensional simulations, with the goal to investigate the shock-driven fragmentation of a metal-free clump. We also investigate the effect of cosmic rays, CMB ionisation and deuterium chemistry on clumping and fragmentation of a neutral clump. Vasiliev et al. (2008) highlighted an important link between the formation of extremely metal poor stars and the radial distribution of primordial gas within a first galaxy, prior to the supernova explosion. This distribution is heavily dependent on the size of the metal-free star and its HII region prior the explosion. Hence in Chapter 4 we extend our metal-free model by simulating the formation of a HII region around a 40 M star in a number of gas clouds with differing density profiles. As the explosion mechanism for this star is not well understood, we explore a range of explosion energies and their impact on compression and fragmentation of the clump. The impact of metal and dust cooling on the fragmentation of low metallicity gas has been highlighted by a number os studies (e.g. Bromm & Loeb 2003; Santoro & Shull 2006; Omukai et al. 2005; Schneider et al. 2012). In Chapter 5 we consider the effect of cooling from metals, metal bearing molecules and dust. The nature and production of high redshift dust is not well constrained. Assuming dust-to-gas ratio can be scaled with metallicity, a simple dust model is implemented which includes cooling induced by gas-grain collisions is evaluated at all temperatures. The observational properties of dust and the physical consequences of its presence in the interstellar medium are extremely well-known and well-documented (Draine 2003). However its composition, structure and size-distribution are still subjects of much discussion. In Chapter 6 we have carried out an investigation of the chemical evolution of gas in different carbon-rich circumstellar environments. We pay careful attention to the accurate calculation of the molecular photoreaction rate coefficients to ascertain whether there is a universal formation mechanism for carbon dust in strongly irradiated astrophysical environments.

Astonishingly for a discipline that did not even exist twenty years ago, the science of Exoplanets has arguably evolved exponentially, delivering transformational science. Planetary formation theories had to be completely revisited. The critical step yet to take is the determination of the chemical composition of the atmospheres of these exotic worlds. Detecting atmospheric features, which have a contrast of about 10^(-4) compared to the host stars radiation, is a challenge, especially since none of the instruments available can provide an absolute calibration at that level. To measure even the smallest flux variations, the data reduction techniques adopted are therefore critical. In particular, instrument systematics and stochastic errors need meticulous corrections. The menagerie of parametric correction models used in the field, has often led to fierce debates due to the high level of degeneracy between the correction model and the scientific result. However, some of these concerns can be addressed by adopting more robust and objective statistical techniques to remove instrumental systematics. In this thesis, I present two robust methods to extract the planetary signal out of instrumental and astrophysical noise with no required knowledge of the data or instrument itself. The first method uses Fourier analyses to enhance the astrophysical signal in a condition of low signal-to-noise. It benefits from the sparsity of the signal itself in the Fourier domain. I tested the procedure on ground-based data of the transit of HD-189733b, presenting for the first time the planetary spectrum at 0.94-1.4 micron. The second one makes use of a supervised machine-learning algorithm to de-trend the long- term stellar activity. The algorithm constrains a probability distribution over the function space by using a Gaussian Process prior and conditioning it with the data. This allows the extrapolation of the long-term information even when the star is not continuously monitored. I proved the effectiveness of the technique by applying it to the high precision photometric lightcurves of the NASA/Kepler space observatory. Both these two methods can be applied to other datasets recorded by different instruments. In particular I plan to analyse stellar light curves observed by CoRoT and Spitzer or ground-based facilities. Given the experience I have developed with the exoplanet spectra observed by IRTF I will be in a strong position to study the advantages and pitfalls of future facilities such as James Webb Space Telescope and the ELT.

Magnetic nanoparticles (MNPs) are intensively researched due to their high potential in biomedicine, catalysis and high density information storage. FePt NPs are a potential alternative magnetic material to commonly used magnetite NPs for biomedical applications and the synthesis of FePt NPs is an active area of research. The purpose of this thesis has been to develop wet chemical synthetic methods to tune and improve the properties of FePt magnetic nanoparticles. The morphology of magnetic nanoparticles affects the way they interact with each other, and with their surroundings. Changes in shape and composition with varying synthetic conditions can also give clues to the mechanism of formation. Changes in volume, solvent and the nature of the stabiliser have been shown to yield varying morphology in the FePt system. Multicore FePt nanoparticles up to 44 nm in diameter and composed of Pt rich FePt nanocrystals within an iron rich FePt matrix not previously seen in the literature are presented here. Magnetic properties of multicore nanoparticles are size dependent; in dioctyl ether and dibenzyl ether and with decreasing amount of oleic acid, saturation magnetisation and blocking temperature increase with size. The results indicate that coordination of Fe and Pt intermediates with oleic acid and oleylamine respectively hinders deposition of each respective metal in the growth of discrete and multicore nanoparticles. L-glutathione and albumin immediately transferred 20 nm multicore nanoparticles into water and show that large FePt nanoparticles may be stable under physiological conditions following stability tests. The use of an autoclave is shown to increase the Fe content, crystallinity and subsequent magnetic properties of FePt pseudo cube nanoparticles compared to those synthesised under atmospheric pressure. Decreasing amount of oleic acid is also shown to increase the iron content and can lead to elongated FePt nanoparticles under normal pressure. Infra-red studies indicate mono and bi dentate coordination with oleic acid, however shifts of spectra show that the strength of the bi-dentate interactions weaken with increasing oleic acid amount.

This thesis studies photogrammetric techniques applied to the ATSR instruments for the extraction of atmospheric parameters with the objective of generating new scientific datasets. The atmospheric parameters under observation are cloud top height, smoke plume injection height, and tropospheric wind components. All have important applications in various tasks, including the initialisation and validation of climate models. To generate accurate stereo measurements from the ATSR imagery the forward and nadir views need to be accurately co-registered. Currently this is not the case, with differences of up to 2 pixels in both axes recorded. In this thesis an automated image tie-pointing and image warping algorithm that improves ATSR co-registration to ≤1 pixel is presented. This thesis also identifies the census stereo matching algorithm for application to the ATSR instruments. When compared against a collocated DEM, census outperforms the previous stereo matching algorithm applied to the ATSR instrument, known as M4, significantly: RMSE ~700m vs. ~1200m; bias ~60m vs ~600m; R2 ~0.9 vs ~0.7. Furthermore, this thesis reviews the M6 algorithm developed for application within the ESA ALANIS Smoke Plume project. Using census a climatological cloud fraction by altitude dataset over Greenland is generated and demonstrated to agree well with current observational datasets from MISR, MODIS and AATSR. The 11μm channel stereo output provides insights into high cloud characteristics over Greenland and appears to be, in comparison with CALIOP, practically unbiased. The ALANIS Smoke plume project is introduced and the inter-comparison of the M6 algorithm against MISR and CALIOP is presented. M6 demonstrates some ability for determining smoke plumes injection heights above 1km in elevation. However, the smoke plume masking approach currently employed is demonstrated to be lacking in quality. Finally, this thesis presents the determination of cloud tracked tropospheric winds from the ATSR2-AATSR tandem operation using the Farneback optical flow algorithm. This algorithm offers accuracy on the order of 0.5 ms-1 at full image resolution, which is unprecedented in comparison to similarly derived datasets.

This thesis describes the development and applications of the continuum-atomistic molecular dynamics (MD) model in the context of radiation damage. By extending the classical MD method to incorporate the electronic excitations represented as an electron fluid and coupled to the ions in the two-temperature (2T) formalism, we have been able to correctly capture the physics governing the atomistic dynamics under huge electronic excitations. The integrated 2T-MD model has been specifically adapted to study three types of non-equilibrium scenarios: laser excitations, swift heavy ion impacts and large-scale high energy collision cascades. Using the 2T-MD model we have estimated the impact of the electron-phonon coupling and the electronic stopping power on the primary radiation damage yield in bcc iron. We have found that the cascade dynamics and the resultant damage from 50-100 keV primary knock-on atom impacts is highly sensitive to the electronic stopping treatment at low projectile velocities, which represents the first rigorous study of this type. By examining the temporal evolution of the structure factor of laser-irradiated gold thin films, we have been able to directly compare the 2T-MD results with Bragg peaks measured by ultrafast electron diffraction and have achieved an excellent agreement between theory and experiment with no fitting parameters. This has enabled us to elucidate the melting dynamics following laser irradiation at a picosecond resolution for the first time and also to validate the two-temperature approach. To simulate semiconductors under electronic excitations, the continuum part of the 2T-MD model, which represents electrons, has been replaced by two continuum equations: one for carrier density and one for their energy, to account for the finite band-gap effects. We have applied such extended method to simulate ion tracks, which result from swift heavy ion impacts. We have achieved a very good agreement with the experimental results on the ion track radii, provided that we are free to adjust the strength of the electron-phonon coupling. We propose future studies in the field of non-equilibrium atomistic modelling. In particular, we discuss ab initio methods and further improvements to hybrid MD to study the effects of the interatomic potential changes in response to high electronic excitations.

The spectroscopy of trace atmospheric species covered in this thesis is of wide and varied interest to the scientific community. The atmospheric applications of spectroscopic data include atmospheric modelling, remote sensing, and water vapour transport studies which are increasingly relevant to studies of our environmental impact as a species. Aside from the atmospheric applications, several of the molecules studied here are relevant in astronomical contexts, including ammonia, which was the first polyatomic molecule observed in the interstellar medium. In all these fields accurate rovibrational assignment of empirical molecular spectra is imperative, and where it is not available high quality variational line lists can provide vital information to take its place. This thesis sets out to improve the state of knowledge of spectroscopic parameters for the trace atmospheric species, 14NH3, HD16O, HD17O, HD18O, and HTO. The results comprise many new assignments and several new line lists which I hope to be of value to the wider scientific community. The ammonia assignments come as part of a complete re-analysis of the HITRAN ammonia data, in which we also recommend a new labelling scheme for ammonia in order to uniquely specify multiply-excited degenerate states. We also provide new composite line lists for several previously unobserved hot bands of ammonia. Significant HD18O and HTO assignments are obtained via analysis of two laboratory spectra due to Orphal et al. and Kobayashi et al. respectively. This work made use of new variational line lists for the HDO, D2O, HTO and T2O isotopologues of water which are also presented herein. For the three HDO isotopologues new line lists are used in combination with the highly accurate empirical energy levels of the IUPAC Task Group in order to provide high quality composite line lists. I believe that these line lists represent the best compilation of spectroscopic parameters available at present for these species.