Falcons and falconry have become an essential part of life in the Middle East since ancient times. In the United Arab Emirates (UAE) itself, the number of trained falcons ranges from 8,000 to 10,000. Over the last five years, falcon racing, a traditional sport, has gained momentum in the UAE where captive falcons are competing for huge prizemoney. A proportion of the UAE economy goes into their care and conservation e.g. through establishing falcon hospitals with modern facilities for disease treatment and breeding as well as centers for diagnosis and research. Being the national bird of the UAE, any research on falcons is of significant interest for the country. Most of the world's falcon species are in decline. Moreover, Saker falcons are classified as 'endangered' according to the IUCN Red List of Threatened Species. From the chromosomal perspective falcons are very interesting, as they represent birds that have undergone significant genome rearrangement compared to the "norm" of 2n=~80. 'Molecular cytogenomics' in birds includes karyotyping, cross species comparisons, nuclear organization, BAC mapping, physical mapping and telomeric DNA profiling. This thesis makes use of the above approaches to define chromosome evolution and genome organization in falcon species with the following results: Firstly, successful conventional characterization of the Saker, Peregrine and Gyr falcon karyotypes (2n=50-52) was achieved producing improved karyotypes and ideograms than those previously published. Comparative genomic analyses among these three species using molecular cytogenetic approaches revealed differences between Peregrine and the other two species, but none between Saker falcon and Gyrfalcon. Also, this study has supported upgrading the fragmented Saker genome assembly to chromosome level using a novel approach hitherto only published for the Peregrine falcon (and pigeon). Secondly, a comparison of genome-wide BAC-based studies and bioinformatic analysis Multiple Genomes Rearrangement Algorithm 2 (MGRA2) revealed the chromosomal changes (inter- and intra-) that led to the falcon lineage. Also, the present study established that common mechanisms of chromosomal fusion do not recur in two different groups of species with rearranged karyotypes (falcons and parrots). This thesis also provided an overview of the telomeric DNA profile in the three species of interest. It established that the highly rearranged karyotypes studied (plus those of the budgerigar and crocodile) do not appear to possess interstitial telomeres at evolutionary fusion points. Also, this study demonstrated the existence of megatelomeres in falcon species, their nature differing between the Peregrine and the other two species studied. Finally, this thesis produced the first detailed description of nuclear organization in a bird species (Peregrine falcon) other than the Galloanserae. Non-fused macro and microchromosomes behave the same way in chickens and falcons. This implies that the same general nuclear organization mechanisms are present in falcons as well as in chickens, ducks and turkeys whose last common ancestor existed around 89 million years ago. Most notably, fused microchromosomes in the Peregrine falcon retain the same nuclear organization pattern despite being fused to a larger chromosome. The findings from this study give insight into the basic nature of chromosome territory patterns in bird species with highly rearranged karyotypes. Overall, results presented in this thesis provide significant insight into genome organization and evolution in the Falco genus, revealing previously undetected levels of chromosomal synteny between three species important to the UAE. Results generated here have also made a significant contribution to the chromosome-level genome assembly of the Saker falcon, providing tools for further study of avian species both within and beyond the falcon group.

Scientific developments have enabled glasses to fulfil an array of applications, from windows to bioactive glasses in regenerative medicine. To further exploit the capability of this versatile material, it is imperative that their structure is understood. In this thesis, the structure of three glass systems containing halides as anions were investigated. The first of these was the intermediate glass former ZnCl2 which was modelled computationally using classical molecular dynamics (MD). The addition of the adiabatic core-shell model was able to account for anion polarisability. This enabled the first fully tetrahedral model of ZnCl2 glass to be attained. While 86% of the ZnCl4 tetrahedral units were corner-sharing, 14% were found to be edge-sharing. The calculated total neutron and x-ray structure factors closely replicated those obtained experimentally in other works. The intermediate glass former ZnCl2 was later compared to the strong glass former SiO2. The main contribution in the first sharp diffraction peaks came from the cation-anion contribution, rather than the cation-cation contribution as previously reported. Next to be investigated was a CaO-SiO2-CaCl2 glass series. This was to help elucidate the structure of more complex CaO-SiO2-P2O5-CaCl2 chlorine-containing bioactive glass compositions. A glass series was synthesised by collaborators, and compositional analysis in this work revealed that chlorine losses via chlorine volatilisation occurred as HCl. The glass series was studied experimentally using neutron diffraction (ND) and x-ray absorption spectroscopy (XAS) at the Ca and Cl K-edge. By probing the calcium environment using ND and XAS, generally good agreement between the Ca-O and Ca-Cl coordination numbers was achieved. The total correlation functions from neutron diffraction did not exhibit a noticeable contribution around 2.1Å which would have been expected for Si-Cl bonding. Computational modelling was performed using MD with the addition of the adiabatic core-shell model. No Si-Cl bonding was observed, and the calculated total neutron structure factors closely resembled those obtained experimentally. The glass models were found to become phase separated with increasing CaCl2 content to form a biphasic system of calcium silicate and calcium chloride phases. Interestingly, there was a tendency towards phase separation even in glass models containing small amounts of CaCl2. The remaining glass system, CaO-SiO2-CaF2, was studied to help elucidate the structure of more complex CaO-SiO2-P2O5-CaF2 fluorine-containing bioactive glasses. Following the synthesis of the CaO-SiO2-CaF2 glass series, compositional analysis revealed that fluorine losses due to fluorine volatilisation occurred as HF. The calcium environment of the glasses was probed using ND and XAS at the Ca K-edge. Distinguishing the overlapping Ca-F and Ca-O paths around 2.3Å and 2.4Å respectively was challenging. The glass series was modelled computationally using MD with the addition of the adiabatic core-shell model. The calculated total neutron structure factors closely replicated those from experiment. The glass models also revealed that while fluorine ions overwhelmingly bond with calcium ions, small amounts of Si-F bonding are observed which conceivably cannot be resolved experimentally.

The classical T-Tauri star HH30 in Taurus-Auriga exhibits a well-collimated plume of hot, optically-emitting atomic and partially ionised Hydrogen, and also a colder, dense, wide-angle molecular Hydrogen ouflow. Observations suggest HH30 is a binary system system, surrounded by a circumbinary accretion disc. We investigated the propagation and interaction of dual atomic and molecular outflows from HH30, using a series of numerical simulations with parameters informed by observational campaigns. These 3-dimensional models were computed using the established Eulerian astrophysics code ZEUS-MP, with in-house modifications and an enhanced chemistry and cooling module. These simulations assumed off-domain launch and tracked the evolution of the jets over spatial scale of ~ 100 AU, and with a timescale ~ 100 - 200 years. The propagation in this region is of special interest, as this is where the greatest difference between the two scenarios is likely to emerge. Our work here differs from "classical" simulations of jet propagation by virtue of one or both outflow sources moving in an orbit. Two competing scenarios were investigated, in which the morphology of the light-year scale outflow from HH30 is explained by different kinds of motion of the atomic outflow source, and in which the launch site of the molecular outflow differs. In both cases a velocity-pulsed atomic jet emerges from the more massive binary object. In the Orbital scenario, the orbital motion of the primary explains the morphology seen at large scale, while the molecular flow is launched from the secondary partner; in the Precessional scenario, precession of the primary dominates the morphology, while launch of the molecular flow is from the inner edge of the circumbinary disc. The binary orbit and inner depletion zone of the circumbinary disc differs between the scenarios, with the Precessional scenario having a much smaller orbit and correspondingly reduced inner depletion zone. Clearly identifiable structural differences emerge between the simulated models. We compared the effects of the two different kinds of perturbing molecular outflow on the faster atomic jet; position, velocity, line mass per unit length, temperature and other variables, as a function of distance x (AU) from the binary source. Linear and quadratic fit functions were determined to facilitate comparison with observation. These quantify the expected behaviours of the atomic jet in the presence of the two different kinds of molecular flow. Where the fit function domains overlap direct comparisons may be drawn; where 26 < x < 42 AU, the average velocity as a function of distance is Vx(x) = (1.39×10^−1 ±2.15×10^−3)x + (246.82±1.29) km s^−1 in the Precessional model, while in the Orbital model we find Vx(x) = (−3.26 ± 0.26)x + (269.57 ± 6.75) km s^−1. In the region 10 < x < 60 AU, the Precessional model has temperature dependence T(x) = (64.53 ± 12.54)x + (3535 ± 330) K. Whilst in the same region of the Orbital model, T(x) = (401.99 ± 333.19)x + (4258.4 ± 1340.3) K. Synthetic Mass-Velocity Spectra have been generated for our models, to investigate distinguishing features of these spectra in the presence of the two different types of molecular outflow. The shallow-angle spectra matching the aspect angle of HH30 itself are examined and the link between outflow scenario and time variability discussed. Spectra from the same dual outflow systems observed at different aspect angles to the sky plane are given, to provide a means to confirm these senarios in other HH30-like T-Tauri stars. Using code written in-house to calculate emission using rate coefficients for photon production, we generated synthetic observations; spatially resolved images, velocity channel maps and position-velocity diagrams. The morphology of the synthetic images from the two scenarios when compared to HST R-band imaging of HH30 suggests that the Orbital case is unlikely, whilst the Precessional case is supported.

The results of artificial modification experiments in which the electron temperature and density of the high latitude ionosphere are intentionally altered by means of high power, HF radio waves are presented. The modified F-region was probed by means of low power diagnostic radio signals. The measurement of the amplitude and spectral content of the diagnostic signals yield information on the spatial development of both large scale, isotropic structures and small scale, strongly field aligned irregularities (FAI&apos;s), induced in the ionospheric plasma by the high power (heating) waves. In addition to this, the temporal development has been investigated for the first time. Observation of the ionospherically reflected heating wave provides new insight into the heater wave self-depletion processes and the growth and saturation mechanisms of the FAI&apos;s. The experimental observations indicate that anomalous absorption of electromagnetic waves, due to scattering from small scale FAI&apos;s plays an important role in the ionospheric modification processes at high latitudes. The scale lengths of the irregularities, along and across the magnetic field, have been deduced from several different experiments. These include the measurement of anomalous absorption of an O-mode diagnostic signal, the first investigation of the spectral indices derived from the power law spectra of X mode diagnostic signals, measurement of the ionospheric drift velocity and the first ever co-ordinated EISCAT-heater studies. In the latter case, the EISCAT VHF/UHF radar facility provided an additional diagnostic tool to measure the electron temperature, (Te), enhancement during periods of heating. Derivation of the relaxation time (rate constant) of the observed Te enhancement provides an estimate of the rate of diffusion of plasma across the magnetic field. Many of the features reported were observed for the first time and provided considerable insight into the plasma physics of the heating process.

This thesis presents results from the NONCENTRIC experiment, conducted by the University of Leicester, in which five trans-auroral and polar cap HF propagation paths were monitored during two one-month campaigns. Signal strength, noise level, Doppler spreading and signal recognition were determined each hour on fourteen frequencies in the range 3 to 23 MHz. The diurnal variations in signal recognition and signal strength are consistent with the ionospheric changes produced by solar illumination. This behaviour is modified by processes occurring within the auroral zone and polar cap during disturbed geomagnetic conditions. Electron densities within the auroral ionosphere increase as a consequence of particle precipitation during disturbed conditions. Auroral enhancement of the D region attenuates signals on trans-auroral paths. This occurs in bursts with durations of tens of minutes, simultaneous with the occurrence of substorms. The magnitude of the absorption can be correlated with changes in the geomagnetic field at geosynchronous orbit. In contrast, enhanced electron densities within the auroral zone E and F regions increase the maximum frequency of propagation, especially at night, thus extending the propagation bandwidth. Within the winter polar cap ionosphere, sporadic high frequency propagation becomes possible from ionization patches convected from the dayside ionosphere. Prolonged periods of geomagnetic disturbance result in global changes in F region electron density, known as ionospheric storms. Four storms studied produce a decrease in the maximum usable frequency, a degradation of propagation reliability and, within the polar cap, an increase in the lowest usable frequency. Such periods of propagation degradation typically have a duration of five days, even during mild storm conditions. This comprehensive study of high latitude HF propagation has produced an improved understanding of the changes in the electron density of the polar ionosphere during both quiet and geomagnetically disturbed conditions.

The term hypervelocity refers to something that is travelling at speeds in excess of a few km/s. Impacts within the Solar System generally occur at these speeds, hence they are referred to as Hypervelocity Impacts. Typical impact speeds in the Solar System depends on their location. Within the main asteroid belt, the average impact speed is generally considered to be 5 km/s. Moving to impacts on Earth, the Moon and Mars, an asteroid average impact speed is approximately 22, 19 and 9 km/s respectively. Move to the outer Solar System and the average impact speed on Pluto is thought to be approximately 2 km/s Generally, research into hypervelocity impacts looks into cratering and the ejecta from these craters. However, the fate of the projectile is relatively neglected. Hence, this topic was explored in this thesis. To achieve this, experiments were performed using the University of Kent's two-stage light gas gun. Along with a mechanical effect on the projectile material, the propagating shock wave can cause effects on the molecular structure. This can be investigated using Raman Spectroscopy, which is an inelastic scattering effect resulting from the laser light interaction with the molecules of the sample. By comparing a before and after spectrum of an impacted material, it is possible to determine the effects of shock pressure. An important biomarker is carbon. The Raman spectra of carbon often contain a D (disorder) and G (graphite/order) band. The amplitude and area ratios of these two bands denote the structural organisation of the carbon-bearing materials. Impacting these materials can affect the Raman spectra. Changes in the spectra can reflect the effect shock pressures have had on the molecular structure of the material. Firstly, the mechanical effect of a hypervelocity impact was investigated for basalt and shale. The materials were filed into 1.5 mm cubes. These cubes were then fired into water at speeds up to 6.13 km/s (peak shock pressure of 30.9 GPa). The water was then filtered through a 0.1 um filter membrane and a scanning electron microscope used to image the entire filter paper. ImageJ was then used to analyse the fragments. From this, information on the morphology, cumulative fragment size distribution, survival percentage and the energy density at the catastrophic disruption threshold are obtained. Catastrophic disruption is where the shock wave of an impact is sufficiently intense that the largest fragment is equal to or less than 50% of the original mass of the body (exactly 50% is the threshold limit). Over 400,000 fragments were measured per shot, providing fragment sizes down to 10^-3 of the original projectile size. When excluding the partially disrupted projectiles (impacts not sufficient enough to surpass the catastrophic disruption threshold limit), the average semi-minor to semi-major axis ratio (b/a) for basalt and shale were 0.58 +/- 0.16 and 0.59 +/- 0.14 respectively. This suggests that the difference in morphology does not have an effect on this ratio at higher impact speeds. From the results an estimate of percentage survival at Pluto, the Moon, in the asteroid belt and on Mars is 76 +/- 11 %, 39 +/- 8 %, 17 +/- 5 % and 10 +/- 4 % respectively. It was found that for basalt and shale the catastrophic disruption energy density was (24.0 +/- 2.1) x 10^4 and (9.4 +/- 5.0) x 10^4 J/kg respectively. The work then moved on to investigating the effect of the shock upon the fragments of the projectile. An additional material (graphite) was used with basalt and shale. The materials were shot using the same method used to investigate the mechanical effect of the hypervelocity impact. Pre-shot the projectile was mapped using a 532 nm laser in a Raman spectrometer. These spectra were then compared to the spectra of 40 separate randomly chosen fragments in each shot. From this, it is possible to determine the shock pressure effects of the impact. Although no trends were identified positive shifts were observed for the D band peak position for basalt and shale, the G band peak position of basalt experienced a positive shift while graphite experienced both a positive and negative shift. Additionally, the G band width for basalt and shale experienced an absolute narrowing of 12.2% and 8.1% respectively, while graphite exhibited an absolute broadening of 17.6%. Overall, all the materials displayed an increased structural disorder after impact, as suggested by plotting the Raman spectra R1 and R2 values. These are ratios of the D and G band amplitudes (R1) and the bands' areas (R2). Furthermore, it was found from this work that there is a possibility of misinterpreting a sample when attempting to determine whether it is biotic carbon if from a shocked environment. The samples were also subjected to static pressure up to a maximum pressure of 3.59 GPa using a diamond anvil cell, and heating/cooling (temperature range 173 to 773 K) using a Linkam temperature stage. This was done in order to ascertain the effects of flash heating upon Raman spectra during hypervelocity impacts. It was found that the effects of temperature are mostly opposite to the effect of shock and static pressure on a carbon Raman spectrum. Increasing static pressure led to the G band peak position for shale and graphite shifting a total of 19.2 and 15.0 cm^-1, at 3.48 and 3.23 GPa respectively. In contrast, for shale and graphite the D and G band peak position were shifted to lower wavenumbers at high temperature (>300 K), and to higher wavenumbers at low temperature (< 300 K). Finally, the capture effect upon olivine as a constituent of a mineral assemblage was also investigated. These capture effects are shock pressures ≤300 MPa (Trigo-Rodriguez et al. 2008) and heating to over 1,000 °C for a brief period of a microsecond (Naguchi et al. 2007, Leroux 2012, see). Ground carbonaceous chondrite (CR2) was red at approximately 6.1 km s⁻¹ (Stardust collection speeds) into aerogel in order to investigate the capture effects. Three examples of shifted olivine spectra were observed. An estimate of the shift for the peaks P1 and P2 (the main two peaks seen in olivine spectra) for the three spectra are 1.21, 1.56 and 1.48 cm⁻¹ and 1.81, 3.40 and 3.21 cm⁻¹, both to lower wavenumbers, respectively. The capture effects exhibited by olivine when contained within a mineral assemblage were found to be less than those when the olivine was a single grain. In summary, the work in this thesis was undertaken in order to understand the hypervelocity impact effects upon the projectile. This is reasonably straight forward for the mechanical effects, however, the shock effects upon the carbon Raman bands were more complex. The most significant is the natural variation in the raw sample spectra. Despite this, it is possible to observe the effects of shock pressure upon the carbon D and G bands.

Near-Earth asteroids are the small rocky bodies orbiting the Sun in the vicinity of Earth's orbit. They are remnants of the planetesimals formed in the young Solar System, which repeatedly collided and underwent disruption. They form loosely-bound aggregates dubbed 'rubble piles'. Their dynamical and physical evolution is expected to be affected by a nongravitational torque called the YORP effect. The YORP effect is a torque due to the anisotropic emission of thermal photons on minor bodies in the Solar System. For small asteroids the radiation recoil torques can systematically modify rotational rates or shift spin axis orientations (Rubincam, 2000). The effect is crucial to understanding the dynamical and physical evolution of near-Earth asteroids, like the alignment of spin-axes (Slivan, 2002), the peculiar spin-top shapes observed for a few targets (Ostro et al., 2006; Scheeres et al., 2006), or rotational fission and evolution of asteroid binaries (Walsh et al., 2008; Pravec et al., 2010; Jacobson and Scheeres, 2011; Jacobson et al., 2016). The first direct detection of the asteroidal YORP effect on asteroid (54509) 2000 PH5 was possible thanks to the combination of radar and photometric lightcurve observations (Lowry et al., 2007; Taylor et al., 2007). Since then, YORP spin-up has also been detected on several other asteroids. However, the sample is still very small, and further observational data is needed to refine the YORP theories. The asteroids (1917) Cuyo and (85990) 1999 JV6, discussed here, were selected from a sample of nearly 40 YORP-detection candidates that were monitored photometrically, and in infra-red, through an ESO Large Programme (ESO LP) led by S. C. Lowry at the ESO New Technology Telescope and Very Large Telescope telescopes, and at other facilities with associated programmes. The ESO LP has been used to acquire photometric lightcurves of the asteroid (1917) Cuyo spanning the period between 2010 and 2013, which, combined with the 1989-2008 archive lightcurves, should provide a large enough time-base to constrain a possible YORP strength. However, the distribution of observations in time results in effectively having observations from just two epochs. This produces potential YORP values in the range of −0.7 × 10−8 rad/d² (radians per day squared) and 1.5 × 10−8 rad/d². The rotation pole of the object is most likely located at l = 46°, b = -62°. The sidereal period was refined relative to earlier lightcurve estimates, to be (2.6897642 ± 0.0000035) h (hours). The shape of the object suggests the presence of an 'equatorial bulge', typical for an evolved system close to shedding mass due to fast rotation. For asteroid (85990) 1999 JV6, the data in the ESO LP span the period between 2007 and 2016. Additionally, the author has secured radar spectra and imaging observations with Arecibo and Goldstone planetary radars. Having radar observations permitted additional constraints on the shape and spin-state, but YORP spin-up was not detected. The asteroid is shown to have a bi-lobed shape, likely a result of two ellipsoidal components collapsing onto each other. The smaller lobe is close to spherical and has diameters (345 ± 9) m, (281 ± 8) m and (291 ± 9)m, and the larger is more elongated, with (580 ± 10) m, (322 ± 5) m and (332 ± 7) m. The rotation pole resides at negative latitudes in a circle of a 10° radius, close to the southern pole of the celestial sphere. The refined sidereal rotation period is (6.536787 ± 0.000006) h. No YORP-induced change in period was detected using the phase offset measurement using the radar model, however the global lightcurve-only analysis shows the object could be experiencing a spin-up of up to 7 × 10−8 rad/d². The shapes and spin-states developed here were used in further studies, beyond the scope of this thesis. Combined with the infra red observations the outcome of this work was used for thermophysical analysis by ESO LP collaborator B. Rozitis to constrain physical properties of both targets. The shape and rotation state of (1917) Cuyo can be used to investigate cohesive forces as a way to explain why some targets survive rotation rates faster than the fission limit. The detection of non-gravitational acceleration in the orbital motion of the asteroid (85990) 1999 JV6 combined with thermophysical modelling suggest a low, cometary-like density. The shape modelling and spin-state analysis tools were also applied to a Jupiter family comet, and the Rosetta mission target, 67P/Churyumov Gerasimenko. The author contributed to the confirmation of the seminal measurement of spin-rate change between previous perihelion approach and the arrival of Rosetta (Mottola et al., 2014, incl. A. Rożek). The detected 20 min decrease in the sidereal period, from ≈12.7 h to ≈12.4 h, was later linked to cometary activity (Keller et al., 2015b; Bertaux, 2015). Tools were also developed to assess the mean insolation of the comet’s surface, useful in calculations of nucleus dust production rates (Guilbert-Lepoutre et al., 2014, incl. A. Rożek), establish jet-activity source regions on the surface of the nucleus (Lara et al., 2015; Lin et al., 2015, 2016, incl. A. Rożek), and calibrate ground-based photometry using the spacecraft shape model (Snodgrass et al., 2016, incl. A. Rożek).

Cryptosporidium parvum is among the most common parasites in the known world and represents one of the leading causes of death among the immunocompromised. As an apicomplexan, C. parvum has many similarities to other globally important parasites such as Plasmodium falciparum and Toxoplasma gondii. Among these similarities are a complex life cycle and the ability to invade host cells. However, unlike most other apicomplexans, the cryptosporidia appear to have lost their namesake organelle, the apicoplast, and drastically reduced the size of their genome. For decades this caused issues in classifying the cryptosporidia. This has been potentially resolved, however, by recent phylogenetic studies that revealed a strong relationship between the cryptosporidia and the gregarines. The gregarines were parasites exclusively of invertebrates, until the reclassification to include the cryptosporidia. Though research into apicomplexan evolution and biology is still a nascent field, even less is known about the invertebrate portion. This is largely due to the lack of molecular tools and culturing techniques that are required to explore any organism beyond basic phylogenetics, in addition to their medical irrelevance prior to the inclusion of Cryptosporidium. Therefore, C. parvum represents a potential model organism for the gregarines and the evolutionary adaptations of apicomplexans from invertebrate to vertebrate hosts. It was the purpose of this thesis, therefore, to establish the tools and methodologies that would be required to begin developing C. parvum as such. To achieve this, first I successfully developed the world's first long-term culturing system of C. parvum, capable of maintain a live parasite culture for 60 days. Additionally, I developed novel methods of detecting and characterising the infection, including NMR based characterisation of infection metabolomes which also revealed a potentially more involved role for Taurine in the pathology of the infection. Furthermore, to demonstrate the power and applicability of this new system I produced the first experimental evidence for a functional ISC system within C. parvum. This also adds to a now growing list of non-canonical mitochondria containing organisms that still maintain an active mitochondrial Fe/S cluster biosynthetic pathway. In conclusion, this thesis represents a large step forward for both the C. parvum and gregarine fields and establishes many of the necessary techniques required for a new push in understanding these apicomplexans and their organelles.

Gold nanoparticles are particularly attractive agents in medical imaging and laser therapy due to their unique optical properties. This study seeks to propose and analyse solutions aimed at imaging the distribution of gold nanoparticles in scattering media and biological tissue using a photothermal modulation technique combined with phase sensitive Optical Coherence Tomography (OCT). In this thesis, a spectrometer based phase sensitive OCT system and a swept source based phase sensitive OCT system are developed separately to fulfil this goal. In each OCT system, a Ti:Sa laser beam is coaxially combined with the OCT probing beam. The photothermal detection of gold nano-rods in multiple layer of the sample is completed by fixing the combined beam on a single lateral position on the sample and modulating the frequency of the Ti:Sa beam to the sample. The photothermal imaging of gold nano-rods in multiple layers of the sample is achieved by raster scanning the combined beams over the sample, modulating the Ti:Sa beam to the sample and then generating high contrast en-face images displaying the phase values retrieved from the OCT signal. Using the recently developed Complex Master/Slave interferometry technique, en-face images can be acquired in real time. In this thesis, application of this technique to a swept source based OCT system is presented. A system is specifically developed to produce en-face phase images of multiple layers of the studied sample. By doing this, the phase sensitive function of the Complex Master/Slave interferometry technique is demonstrated for the first time.

Advancement in science and technology has profoundly depended on new types of glass innovation. The glasses that were studied in this project are binary barium silicate glasses, binary barium fluorozirconate glasses, ZBLAN glasses and 〖Eu〗^(3+) doped ZBLAN glass (the ZBLAN glasses are based on binary barium fluorozirconate glass). The high atomic number of barium in the barium silicate glasses provides high mass and high electron density providing its applications for heat and X-ray shielding. The phenomena such as phase separation in the barium silicate glass will affect its properties of durability and electrical conductivity. On the other hand, ZBLAN glasses have a broad infrared optical transmission window due to the weaker bonding/interaction of F^- ions. Due to the presence of lanthanum in the composition ZBLAN glass can be easily doped with rare-earth ions such as 〖Eu〗^(3+) giving it many optical applications such as optical amplifier and fibre lasers. Hence, it's essential to study the structure of these glasses to understand their properties for applications. This thesis used the classical molecular dynamics modelling technique to study the static atomic structure of glass. Generally, fluoride glasses can be formed by totally replacing oxygen atoms in oxide glasses by fluorine atoms. The oxide silicate glasses are common glasses that follow the Zachriasen rules of glass formation but the fluorozirconate glasses do not and lack fixed structural units. The structure analysis was performed at short-range order (e.g. coordination number, bond length and bond angle), medium-range order (e.g. network connectivity) and long- range order (e.g. phase separation). The related crystals were also simulated in similar conditions to the glasses to compare their atomic structure. Normally at short-range order glass structure is similar to its related crystal but the differences between them starts from the position and number of next nearest neighbours and increases thereafter. Additionally, the new methods such as rotational invariants and grid analysis were used to scrutinise structural units and phase separation respectively. The model of barium silicate glass shows good agreement with experimental diffraction data. The typical bond length and coordination number for Ba were 2.97 Å and approximately 7 respectively. The model did not show any phase separation at low Ba content and hence for further investigation very large models of alkaline earth silicate glasses were studied to see how Ba, Ca and Mg are distributed in the glass. The grid analysis was used to see the distributions which show homogeneity for Ba and Ca and inhomogeneity for Mg cation. The structural units of fluorozirconate glasses were carefully studied as they do not follow the Zachriasen glass model. The coordination number for Zr was mixture of 7 and 8. The rotational invariant analysis shows that the structural units of ZrF_n polyhedra for coordination number 7 and 8 were similar to Augmented Triangular Prism and Biaugmented Triangular Prism respectively. However, rotational invariant values for BaF_n polyhedra tend more towards random. The large complex model of 〖Eu〗^(3+) doped ZBLAN glass was made as it is studied for optical applications. The initial analysis was to observe whether Zr and Ba has similar structural roles as in binary fluorozirconate glass system which they do. Considering the extra elements in ZBLAN glass, Al behaves like a network former and has octahedra structural units whereas La and Na behave like modifiers. In the glass Eu was uniformly distributed with predominantly coordination number of 8 and does not have well defined structural units.