Marine habitats have undergone dramatic changes, particularly over the last few decades. Human-related causes, such as habitat alteration, overexploitation, pollution, climate change and introduction of alien species have affected marine ecosystems worldwide, with severe impacts on many species, including several seabirds. Seabirds, and particularly (but not exclusively) those species that act as top-predators, are excellent monitors of the health of marine ecosystems. However, in order to make use of them as bioindicators, we have to understand how potential limiting factors influence their ecology. In turn, this information is also useful for the conservation of their populations. In this thesis I study a diversity of limiting factors of potential importance for the breeding ecology of two threatened seabirds, the southern rockhopper penguin and the black-browed albatross, at a mixed seabird colony on the Falkland Islands. An analysis of nesting habitat quality (Chapter 2) indicated that this did not explain variation in rockhopper penguin breeding success, which was most likely influenced by predation. An analysis of spatial and temporal variability of nesting success of black-browed albatrosses has shown that disease (Chapter 3), possibly coupled with parasites (Chapter 4) was the main cause for chick mortality differences between areas and years, whilst the consequences of a diet (Chapter 5) with a strong fisheries-related component for breeding success and chick development are still to be determined conclusively. This multi factor approach together with a relatively long-term set of data are important to produce more robust conclusions (with atypical years put into context), and to tentatively assign changes in breeding parameters to individual factors. My results help to provide a more complete insight of the potential factors threatening two species of conservation importance at this colony and in the context of the Falklands.

In this thesis, we revisit the seventeen year old question of how hot Jupiters got to their short period orbits, given that gas-giant planet building is supposed to take place beyond the ice-line at about 3 AU. Two major theories are generally used to explain this mystery. Firstly, exchange of energy and angular momentum between the newly-built planet and the progenitor dust and gas disk could result in planetary migration to a short period. This is generally believed to result in planets on circular orbits, with orbital angular momenta that are aligned with the host star spin. The competing theory which has gained more support in recent years, is that gravitational interactions leading to planet-planet scattering and/or Kozai interactions with massive and distant objects caused the planets to migrate violently (scattering) or slowly (Kozai) to short period, eccentric and misaligned orbits. These orbits are then expected to circularise and align under tidal interactions with the host star. In addition, the host star is expected to show evidence of spin-up if the tide on the star is strong enough. Our contribution to this field is to provide additional support for the scenario involving dynamical interaction and tidal damping. We present observational evidence in the form of 158 new radial velocity measurements for 12 planets and a reanalysis of existing radial velocity data and photometric constraints from the literature for a total of 64 planetary systems. We also critically consider a further 30 newly announced planets from the literature. We show that there is no evidence for a finite eccentricity in several cases that were previously claimed to be “exceptions” to the observed trend that close-in planets are on circular orbits and the generally accepted reason that they underwent strong tidal interactions. We also show that the dissipative effect of tides raised in the planet by the star and vice versa explain all the eccentricity and spin-orbit alignment measurements available for transiting planets. We find evidence for excess rotation of the star in 6 systems, showing that heavy and close-in objects can exert strong tidal effects on the star. Hot Jupiters on circular orbits clump on the mass-period relation, which thus appears to be related to the stopping mechanism of orbital migration for hot Jupiters.

Glutathione S-transferases (GST) are a superfamily of detoxifying enzymes present in most life forms. They catalyse the conjugation of the tripeptide glutathione (GSH) to a wide variety of exogenous and endogenous compounds with electrophilic functional groups to form more soluble and non-toxic peptide derivatives. The over-expression of the human class Pi enzyme (hGSTP1) in tumours has been associated with multi-drug resistance. The work presented in this thesis is focused on the four polymorphisms of the hGSTP1 enzyme and their reactivity towards five anticancer nitrosourea drugs. The coding sequences of hGSTP1-A, -C and -D enzymes were obtained from the hGSTP1-B cDNA through successive cloning into the pGEM-T and pET-28a vectors, and site directed mutagenesis. This was followed by protein over-expression and purification by nickel affinity chromatography and gel filtration. Activity and inhibition assays, wavelength scans, mass spectrometry, denitrosation and thermofluor shift assays were performed to investigate the relationship between the four isozymes and the anticancer drugs (carmustine, lomustine, semustine, streptozocin and ethylnitrosourea). The enzymes were assayed for activity with 1-clhoro-2,4-dinitrobenzene (CDNB) and hGSTP1-A and -D were found to be more active towards this substrate than the other hGSTP1 variants. These two variants share residue Ile104 which could influence catalysis towards different substrates. The mass spectrometry and denitrosation assays have shown that these drugs do not constitute substrates for the hGSTP1 enzymes. The inhibition assays suggested that the four drugs may be weak inhibitors of the hGSTP1 variants. However, the thermal shift assays did not show increased protein stability in the presence of the drugs. The hGSTP1-D protein was successfully crystallised which allowed determination of the first crystallographic structure of this variant. This has allowed a detailed comparison of hGSTP1-D with other hGSTP1 protein structures available. The side chains of both amino acid residues Ile104 and Val113 of hGSTP1-D appear to occupy positions in the same orientation as the side chains of equivalent residues of other hGSTP1 enzymes. The use of the same crystallisation conditions for co-crystallisation studies with hGSTP1-D and glutathione or the nitrosourea drugs did not result in protein crystals but further optimisation should be carried out. Nonetheless, the findings of this project have helped to understand the relationship of the hGSTP1 natural variant enzymes with the five nitrosourea anticancer drugs and to realise that drug resistance in tumours over-expressing this class of hGSTs is not due to the fast metabolism of these drugs but most probably to the role that these enzymes play in cell apoptosis and survival.

Surface waves and their applications have been extensively studied by the photonics and radio engineering communities throughout the whole of the twentieth century. This thesis details briefly the history of both approaches and highlights their signi cance with regard to the subject of this thesis; laterally confining a surface wave in the microwave regime. Detailed within are the experimental, analytical and numerical methods used to ascertain what, if any, effect a change in the dimension of a guiding structure has on the dispersion of a mode supported by a metamaterial. The method of experimentally determining the dispersion of a microwave surface wave is discussed. The insensitivity of a mode supported on a one-dimensional corrugated array to the lateral width of the supporting array, even when the width is much less than the wavelength of radiation incident upon it, is investigated. Spatial dependent reduction of group velocity associated with a microwave surface wave is also detailed. Local electric-field and phase measurements are used to probe this condition. In particular, the measurement of phase associated with the supported microwave surface wave is shown to indicate the trapping location of a surface wave more accurately when compared to local electric-field measurement. The channelling of surface waves via the addition of dielectric overlayers to a metamaterial surface is investigated. By progressively narrowing the width of the channel, the interaction of the electric fields associated with the mode supported in the channel with the bordering dielectric overlayer increases. This investigation leads to a discussion of the electric field overlap between two regions of differing surface impedance.

The dynamics of atoms and hydrogen molecules in ultrafast intense laser pulses are studied experimentally using time of flight mass spectroscopy and fast ion beam techniques. The content of the study can be split naturally into two parts; the first dealing with the interaction of noble gas atoms and ions with laser pulses of between 40 and 50 fs in duration and around 20 mJ of energy per pulse, the second dealing with a time-resolved investigation of the nuclear dynamics of hydrogen molecules and their corresponding molecular ions with laser pulses of approximately 10 fs duration and an energy per pulse of 50 μJ. Within the first section of the study the technique of Intensity Selective Scanning with Effective Intensity Matching (ISS-EIM) has been used to observe Multi Electron Tunnelling Ionisation (METI) for the first time. These experiments were conducted with laser pulses focussed on neutral targets of argon and krypton. Also within the first section, the recombination of ionised electrons with their residual atomic cores has been observed for the first time in the atomic channel. This recombination occurs in the metastable ion population of singly charged ion beams of krypton and argon, provided by a fast ion beam apparatus. In the second section of the study, a pump-probe technique is employed using few cycle laser pulses to initiate (pump) and then image (probe) the nuclear dynamics of hydrogenic molecules and their molecular ions. In the ions, vibrational wavepackets have been studied and the phenomena of dephasing and revival observed. Additionally signatures of rotational wavepacket dynamics have been isolated in the neutral molecules. A technique to verify the laser pulse duration at the focus has also been introduced using xenon atoms and the same pump-probe technique.

In this thesis, observations of the Earth's magnetotail from ESA's four Cluster and the two Sino-European Double Star spacecraft are presented. The observations are of intervals where data from the combination of Cluster and Double Star provide insights into the dynamics of the magnetotail that are not possible using data from one mission alone. In the first study, observations of three magnetic flux ropes are presented, two of which were detected near-simultaneously at Cluster and Double Star TC-1, while the third was detected by Cluster, along with a TCR a few minutes later. The observations represent the first observations of multiple flux ropes existing in the magnetotail simultaneously, providing evidence that flux rope orientation is influenced by neutral sheet tilt and provide further evidence that TCRs in the lobes are caused by the passage of flux ropes in the plasma sheet. In the second study, a detailed analysis of a plasma bubble is presented, including the first direct observations of the return flows around the flanks of the plasma bubble that are expected from theory and simulation. Furthermore a partially stagnant depleted wake behind the plasma bubble, not predicted by theory or simulation was discovered and the cross-tail extent of the bubble was measured to be 3RE. The first observations of near-Earth bubble features are also reported. Finally, in the third study, the substorm onset process itself is investigated using a wide array of space- and ground-based instrumentation. A pseudobreakup and later substorm onset are distinguished using both geomagnetic and auroral data and the establishment of the substorm current wedge is observed in-situ using the TC-2 and GOES12 spacecraft. A link between higher latitude geomagnetic activity and the fast flows and plasma sheet expansion related to the reconnection of lobe field lines is also posited.

Described within is the design, manufacture, metrology and X-ray testing of an active X-ray prototype intended for the next generation of X-ray telescopes. One of the challenges faced by the X-ray telescope community is how to combine high resolution and high sensitivity into one system, as weight limitations place constraints on the optics that can be launched. Therefore the mandate of the active X-ray prototype is to provide high sensitivity through the ability of the optics to be nested and to deliver high angular resolution through the active control of the optic’s form. Piezoelectric unimorph actuators provide the active component: it is intended that they will correct for figure errors within the optic and therefore increase the angular resolution capability. The prototype’s design is based upon an ellipsoidal segment which provides point-to-point focussing of an X-ray source. The prototype itself is composed of an electroformed nickel optic where the non-reflective surface is populated with 30 piezoelectric actuators and it is the production of the prototype that is the core of the presented research. Metrology of the actuators’ influence functions is presented and highlight the prototype’s ability to deform its optic surface by microns. In addition, the measured influence functions are compared against finite element models and a distinct similarity between the functions is observed. The prototype was tested at an X-ray beamline facility in November 2008 and the results showed the prototype’s ability to correct the optic to achieve an improved angular resolution: from 0.786 arc-minutes to 0.686 arc-minutes in terms of full width half maximum. Finally, difficulties in the manufacture of the prototype and X-ray testing shall be presented alongside future work in conclusion to this thesis.

The measurement of forests is essential for monitoring and predicting the role and response of the land surface to global climate change. Globally consistent and frequent measurements can only be made by satellites; unfortunately many current system’s measurements saturate at moderate canopy densities and are not directly related to forest properties, requiring tenuous empirical relationships that are insensitive to many of the Earth’s most important, Carbon rich forests. Lidar (laser radar) is a relatively new technology that offers the potential to make direct measurements of forest height, vertical density and, when ground based, explicit measurements of structure. In addition measurements do not saturate until much higher forest densities. In recent years there has been much interest in the measurement of forests by lidar, with a number of airborne and terrestrial and one spaceborne lidar developed. Measuring a forest leaf by leaf is impractical and very tedious, so more rapid ground based methods are needed to collect data to validate satellite derived estimates. These rapid methods are themselves not directly related to forest properties causing uncertainty in any validation of remotely sensed estimates. This thesis uses Monte Carlo ray tracing to simulate the measurement of forests by full waveform lidars over explicit geometric forest models for both above and below canopy instruments. Existing methods for deriving forest properties from measurements are tested against the known truth of these simulated forests, a process impossible in reality. Causes of disagreements are explored and new methods developed to attempt to overcome any shortcomings. These new methods include dual wavelength lidar for correcting satellite based measurements for topography and a voxel based method for more directly relating terrestrial lidar signals to forest properties.

Simulations of the Martian upper atmosphere have been conducted with ‘MarTIM’, University College London’s Martian thermosphere and ionosphere general circulation model (GCM). MarTIM, a finite difference model, solves the coupled non-linear Navier-Stokes equations of continuity and momentum as well as an energy equation with calculations conducted on a fixed co-rotating grid of variable size in the pressure coordinate system. From its lower boundary of 0.883 Pa (~60 km) to its upper boundary of 9.9×10−8 Pa (~200−350 km), it evaluates the main sources of solar forcing (EUV/UV and IR absorption) while self-consistently determining the composition of four of the major gas species, CO2, N2, CO and O. These four major gases are mutually diffused throughout the model in a typical run. Development of MarTIM includes a consideration of the importance of neutral species diffusion and advection on the thermodynamics of the modelled Martian atmosphere. The influence on the modelled atmosphere of including additional neutral species is investigated. Next, a new infrared heating parameterization has been introduced from background research of detailed non-LTE modelling. This has allowed MarTIM to study thermospheric polar warming features as found in Mars Odyssey accelerometer data. MarTIM’s lower boundary is coupled to the Mars Climate Database (MCD v4.3) developed by the University of Oxford, the Open University and Laboratoire de Météorologie Dynamique. This database of GCM results provides MarTIM a physically self-consistent lower boundary derived from multiple runs of the aforementioned circulation models. Consequently the effects of dust storms, non-migrating tides and the influence of Martian topography are studied by prescription of MarTIM’s lower boundary. MarTIM is also compared against density and temperature measurements derived from SPICAM stellar occultation profiles. Lastly, a new ionospheric code has been developed through collaboration with Laboratoire de Planétologie de Grenoble. This has provided a more sophisticated ionosphere model that solves a one-dimensional kinetic Boltzmann transport equation for the suprathermal population of electrons present in the Martian ionosphere. MarTIM can now self-consistently describe an ionosphere produced by both primary (photoionisation) and secondary ionisation (suprathermal electron propagation). This new ionospheric model has been used to study the variation in secondary ionization efficiency (ratio of secondary to primary ion production) through a large range of seasonal and solar conditions.

The aim of this thesis has been to help elucidate the potential contribution of core-collapse supernovae (SNe) to the dust-enrichment of galaxies. It has long been hypothesised that SNe are a major source of dust in the Universe, an assumption that has gained support with the discovery that many of the earliest-formed galaxies are extremely dusty and infrared-luminous, as evidenced by the efficient detection of their redshifted infrared emission at submillimeter wavelengths. Massive-star, core-collapse SNe, of Types II, Ib and Ic, arising from the starbursts that power these galaxies, are plausible sources of this dust. However, very little is currently known about how much dust forms in SN outflows. To this end, sensitive mid-infrared surveys for thermal dust emission from recent core-collapse SNe have been conducted with the Spitzer Space Telescope and mid-infrared detectors on the Gemini telescopes, in order to seek evidence for dust formation and evolution in SN ejecta. Of the 30 SNe observed, only five were robustly detected. These were comprised of four Type II-P SNe: SN 2002hh, SN 2003gd, SN 2004dj and SN 2004et; and the Type IIn SN 1999bw. The mid-infrared data of SN 2004et were incorporated with optical and near-infrared data to provide a comprehensive study of this SN from days 64 to 2151 post explosion. Radiative transfer models predict up to 1.5x10^-3M\bigodot of dust had condensed in the ejecta of SN 2004et by day 690. Upper limits to mid-infrared fluxes are presented for 25 supernova and used to obtain upper limits to their dust masses in the mid-infrared. The results from this research add to the weight of observational evidence which suggests the ejecta of core-collapse SNe do not produce sufficient dust, at least during the first 3 or 4 years after outburst, to explain the masses of dust derived for some galaxies in the early Universe.