Purpose: Quality assurance (QA) for intensity modulated radiotherapy (IMRT) has evolved substantially. In recent years, various ionization chamber or diode detector arrays have become commercially available, allowing pre-treatment absolute dose verification with near real-time results. This has led to a wide uptake of this technology to replace point dose and film dosimetry and to facilitate QA streamlining. However, arrays are limited by their spatial resolution giving rise to concerns about their response to clinically relevant deviations. The common factor in all commercial array systems is the reliance on the gamma index (γ) method to provide the quantitative evaluation of the measured dose distribution against the Treatment Planning System (TPS) calculated dose distribution. The mathematical definition of the gamma index presents computational challenges that can cause a variation in the calculation in different systems. The purpose of this thesis was to evaluate the suitability of detector array systems, combined with their implementation of the gamma index, in the verification and dosimetry audit of advanced IMRT. Method: The response of various commercial detector array systems (Delta4®, ArcCHECK®, and the PTW 2D-Array seven29™ and OCTAVIUS II™ phantom combination, Gafchromic® EBT2 and composite EPID measurements) to simulated deliberate changes in clinical IMRT and VMAT plans was evaluated. The variability of the gamma index calculation in the different systems was also evaluated by comparing against a bespoke Matlab-based gamma index analysis software. A novel methodology for using a commercial detector array in a dosimetry audit of rotational radiotherapy was then developed. Comparison was made between measurements using the detector array and those performed using ionization chambers, alanine and radiochromic film. The methodology was developed as part of the development of a national audit of rotational radiotherapy. Ten cancer centres were asked to create a rotational radiotherapy treatment plan for a three-dimensional treatment-planning-system (3DTPS) test and audited. Phantom measurements using a commercial 2D ionization chamber (IC) array were compared with measurements using 0.125cm3 ion chamber, Gafchromic film and alanine pellets in the same plane. Relative and absolute gamma index (γ) comparisons were made for Gafchromic film and 2D-Array planes respectively. A methodology for prospectively deriving appropriate gamma index acceptance criteria for detector array systems, via simulation of deliberate changes and receiver operator characteristic (ROC) analysis, has been developed. Results: In the event of clinically relevant delivery introduced changes, the detector array systems evaluated are able to detect some of these changes if suitable gamma index passing criteria, such as 2%/2mm, are used. Different computational approaches can produce variability in the calculation of the gamma index between different software implementations. For the same passing criteria, different devices and software combinations exhibit varying levels of agreement with the Matlab predicted gamma index analysis. This work has found that it is suitable to use a detector array in a dosimetry audit of rotational radiotherapy in place of standard systems of dosimetry such as ion chambers, alanine and film. Comparisons between individual detectors within the 2D-Array against the corresponding ion chamber and alanine measurement showed a statistically significant concordance correlation coefficient (ρc>0.998, p<0.001) with mean difference of -1.1%±1.1% and -0.8%±1.1%, respectively, in a high dose PTV. In the γ comparison between the 2D-Array and film it was found that the 2D-Array was more likely to fail in planes where there was a dose discrepancy due to the absolute analysis performed. A follow-up analysis of the library of measured data during the audit found that additional metrics such as the mean gamma index or dose differences over regions of interest can be gleaned from the measured dose distributions. Conclusions: It is important to understand the response and limitations of the gamma index analysis combined with the equipment and software in use. For the same pass-rate criteria, different devices and software combinations exhibit varying levels of agreement with the predicted γ analysis. It has been found that using a commercial detector array for a dosimetry audit of rotational radiotherapy is suitable in place of standard systems of dosimetry. A methodology for being able to prospectively ascertain appropriate gamma index acceptance criteria for the detector array system in use, via simulation of deliberate changes and ROC analysis, has been developed. It has been shown that setting appropriate tolerances can be achieved and should be performed as the methodology takes into account the configuration of the commercial system as well as the software implementation of the gamma index.

Fluorescence lifetime imaging microscopy (FLIM) is a key technique to image cells as, in addition to the advantages of standard fluorescence microscopy, it allows to study the environment and probe interaction in living specimens. Implementing FLIM via Single Photon Counting (SPC) proved to be the most effective technique considering the fluorophores limited photon budget before being irreversibly bleached. This thesis focuses on the development and application of Single Photon Counting techniques to imaging systems and to spectroscopy. Firstly, the BODIPY-C12 molecular rotor was used to determine dyeconcentrations between 3 and 16 μM for living cells and lipid droplets via FLIM and intensity measurements A novel compound, named ET, was tested for the first time on living cells and its possible applications as a molecular rotor discussed. The use of an Electron Bombarded Charge-Coupled Device (EBCCD) camera as a parallel-processing Time to Amplitude Converter device for SPC Imaging with sub-frame exposure time resolution was investigated and, although not implemented, the results supports the proposed method. In order to design a wide field time-correlated single photon counting system, a Complementary Metal-Oxide Semiconductor (CMOS) Fast- Camera was coupled with an 3-stage image intensifier. This proved to be suitable for luminescence lifetime measurements of a Ruthenium complex, with results of 1.7μs comparable with confocal scanning Time-Correlated SPC (TCSPC). Finally, conclusions and future work are discussed.

Supramolecular self-assembly on metallic surfaces is the ideal playground for studying a variety of physical and chemical phenomena. Adsorbed molecules will diffuse and self-organise to form assemblies dictated by their functionalities, while the more or less pronounced metal reactivity will accordingly affect both the supramolecular patterns and the interfacial chemistry. Besides structural aspects, electronic properties are central in determining the energy level alignment at the heterojunction and, thus, the performance of organic-based devices. Notably, charge reorganisation at the metal-organic interface will produce surface dipoles, whose effect is to add electrostatic repulsion to the dispersion-driven supramolecular self-assembly and to change the work function of the surface. Herein, the relation between charge migration (i.e., the creation of surface dipoles) and molecular self-assembly is addressed by studying the behaviour of on-purpose designed molecular units on selected metals. We will show that choosing the substrate on the basis of its work function can selectively allow or inhibit the transfer of charge from the organic material to the electrode. When charge transfer occurs, the growing supramolecular structures exhibit a phase modulation driven by the presence of competing interactions. Moreover, the introduction of reactive moieties in formerly inert tectons will be identified as a suitable strategy for promoting the formation of interfacial dipoles upon surface-mediated chemical reactions. Our work paves the way for a more rational approach to the design of metal-organic systems, as we speculate that charge transfer effects and surface chemistry can be predicted at the stage of molecular design, at variance with the current trial and error approach used in the field of organic electronics. This thesis is based on multiscale theoretical modelling of selected metalmolecule couples and it is the result of a fruitful collaboration with the groups of Prof Davide Bonifazi (Université de Namur) and Prof Giovanni Costantini (University of Warwick).

It is well established that when in close proximity to gold nanoparticles the optical properties of local fluorescent molecules are dramatically altered. When the localised surface plasmon resonance (LSPR), tuned to the fluorophore absorption band is excited a strong optical enhancement is observed near the nanoparticle due to enhancement in the excitation rate. Both the radiative and non-radiative decay rates undergo significant modification, resulting in either quantum efficiency enhancement, or fluorophore quenching, and a corresponding reduction in the fluorescence lifetime. These effects depend on fluorophore and nanoparticle separation the fluorophore quantum efficiency and the alignment of fluorophore excitation and emission wavelength with the LSPR. Fluorescence lifetime imaging microscopy (FLIM) is used to create high-resolution spatial maps of molecular lifetime and intensity values of single gold nanoparticles deposited on a thin fluorescent-doped polymer film, separated by a SiO2 spacer layer. A strong enhancement in emission intensity is observed in the region of a single nanoparticle. The fluorescence lifetime images are described well using two contributions to fluorescence decay; an unmodified term, allowing for the fact that the diffraction limited focus is significantly larger than the nanoparticle, and some average modified term accounting for the reduction in fluorescence lifetime. Large numbers of nanoparticles are interrogated, giving a statistical distribution of intensity enhancement and lifetime reduction, associated with varying nanoparticle size and shape. These nanoparticle populations are measured for a variety of excitation wavelengths, LSPRs, and yes, allowing analysis of the relationship between LSPR and fluorophore excitation and emission wavelength. Additionally dark-field information is collected for individual nanoparticles, allowing a direct comparison between LSPR and modified lifetime in order to investigate a correlation between peak lifetime reduction, and optimal overlap of the fluorophore emission and the location of the LSPR.

Water-in-oil microdroplets are an attractive “tool” in lab-on-a-chip devices, as they offer simple compartmentalisation, constitute tiny reaction chambers and can be used to perform “digital” operations. One of the many benefits they offer is the ability to manipulate droplets by electric fields, which can be implemented on-chip, using electrodes and suitable wiring. Water droplets dispersed in a non-polar oil are manipulated by exploiting the fundamental phenomenon of electrophoretic motion, i.e. motion in response to an external, electric field. There are surprisingly little data regarding the electrophoretic mobility of water droplets dispersed in a non-polar oil and this work aims to elucidate some of the properties of droplet charge from measurements of the electrophoretic mobility of individual water droplets in two different, non-polar oils of similar, physical fluid properties: silicone and paraffin oil. Single droplets of varying pH and ion concentrations were investigated and it was found that the effective initial droplet charge (i.e. the charge a water droplet has before making contact with a biased electrode) is always positive and independent of pH and ion concentration. When the anionic surfactant SDS (Sodium Dodecyl Sulfate) was dispersed in the water phase, the initial droplet charge could be altered from positive to negative at concentrations greater than 1 g/l. However, using cationic surfactant CTAB (Hexadecyltrimethyl Ammonium Bromide) had no impact on droplet surface charge. Once the droplet touches a biased electrode, the droplet charge in increased by a factor of 10 and any surfactant charge effects are overridden. Lastly, complex oil-in-water-in-oil and water-in-oil-in-water-in-oil droplets were created and their electrophoretic mobility was studied. It was found that the inner droplet does not affect electrophoretic motion of the core shell drop, regardless of size and composition, nor does it experience the same (if any) electric field strength the outer water shell is subjected to. This is advantageous in a variety of applications. For example, oil droplets of varying types and sizes could accurately be transported and manipulated at the same speed using monodisperse water shells, which can be either thick or ultrathin. This could also be used for the manipulation of materials that would otherwise be damaged by an electrical field.

Metamaterials are materials whose optical properties can be designed through the accurate engineering of their structure on the subwavelength scale. They have enabled the discovery and study of a variety of interesting new optical properties not normally present in materials found in nature. Furthermore, by designing the local electromagnetic field distributions of such metamaterials, it is possible to engineer not only their linear optical properties but also their nonlinear response, which is fundamental for the development of nonlinear and active nanophotonics for all-optical information processing. In this thesis I will show that plasmonic metamaterials based on metallic nanorod arrays can be designed to have strong third-order nonlinear optical response originating from the nonlinearity of the plasmonic component of the metamaterial, allowing nonlinear processes to be more energy efficient and highly integrated. The nonlinearity will be experimentally determined through the z-scan technique and explained by numerical modeling in both effective medium and fullvectorial simulations. Enhancements of about 50 times for the nonlinear absorption and about 10 times for the nonlinear refraction are observed compared to a smooth metal film. Furthermore, the properties of waveguides comprised of the nanorod metamaterial are studied and the possibility of their integration in conventional Si photonic waveguides is demonstrated. In this context, two all-optical modulators using plasmonic metamaterials are designed, operating in the hyperbolic and epsilon near-zero regimes. Both designs are highly integrated and energy efficient having footprints of 300x440x600 nm3 and 300x180x340 nm3 with an energy consumption of 3.7 pJ/bit and 0.6pJ/bit respectively. The obtained results show great opportunities for nonlinear metamaterials in nanophotonic applications.

This thesis presents an investigation into the morphological features of the Milky Way, the exact structure of which is somewhat of an unknown. We begin with a discussion of the problem at hand, and a review of the literature and methodology associated with determining Galactic structure (Chapter 1). The methodology of the investigation is to use numerical simulations to reproduce the structure of the interstellar medium (ISM) gas under the effect of gravitational forces that represent possible morphologies of the Milky Way, such as spiral arms and inner bars. The ISM is simulated using smoothed particle hydrodynamics (SPH), which has been tailored to ISM scales by the inclusion of cooling, heating and a simple chemical network, discussed in Chapter 2. The Milky Way is first assumed to be grand design in nature, with analytic potentials representing the various arm and bar components. Simulations are then compared to longitude velocity CO emission observations to assess the quality of the reproduction of Galactic morphology. These results are shown in Chapter 3, where best fitting models have a bar pattern speed within 50-60km/s/kpc, an arm pattern speed of approximately 20km/s/kpc, a bar orientation of approximately 45 degrees,and arm pitch angle between 10-15 degrees. While nearly all observed emission features are reproducible, there is no model that reproduces all simultaneously. Using both bar and arm components together we find a better match to the data, but still no perfect reproduction. Models with two arms lack many of the observed features, but models with four arms produce too much local emission in the inner quadrants. Chapter 4 shows more sophisticated synthetic observations, created using a radiative transfer code. Resulting emission features are broadly in keeping with those seen in observations, the strength of which appears a strong function of gas surface density. The analytic potentials are then replaced by a set of discretised mass components that represent the stellar system, which is the subject of Chapter 5. Using a live N-body disc then allows for the dynamic creation of bar and arm features, from which further synthetic observations are produced. Transient arm and bar features are relatively easy to produce, though not necessarily simultaneously. Arm patterns showing two to five arms and some with an effectively flocculent structure are created, with pitch angles around 20 degrees. The pattern speed of which tends to decrease with radius, highlighting that the arms are material rather than wave-like in nature. Best fitting synthetic observations show that a four-armed spiral pattern provides good agreement with observations, more so than that of the fixed potentials, with clear reproduction of nearly all arm features. However, an inner bar appears necessary to remove excess emission seen towards the Galactic centre, which was not present in these models.

Ferrites are a class of magnetic oxides with superior electromagnetic (EM) properties at microwave frequencies when compared to conventional metallic magnetic materials for use in antenna miniturization and radar absorbers. Metamaterials are also a special group of materials, which are known to provide EM responses not found in nature due to subwavelength structuring. In this thesis, a range of ferrite composite materials and metamaterial structures are exploited to develop new methods for controlling permittivity and permeability up to 4 GHz with a view to producing high refractive index materials and to demonstrate broadband impedance matching to free space. The rst section of the thesis uses composites of powdered MnZn ferrite (as the ller) and PTFE (as the matrix), fabricated by a novel cold pressing technique, to produce composites for a range of volume fractions of MnZn ferrite (between 0-80% vol.). The EM properties for all composites were determined as a function of % vol. and the results were found to be in agreement with the Lichtenecker mixing formula. This study is the rst convincing con rmation of the Lichtenecker mixing formula over a broad range of volume fractions (0-80% vol.). The cold pressing method was found to produce composites with reproducible EM properties, and was extended to use aluminium, barium titanate (as llers) and also cellulose as an alternative matrix. Importantly, with regard to the study of cellulose composites, our work is the rst to explore volume fractions of up to 85% and, the rst to con rm the Lichtenecker mixing formula with these materials. The ferrite particle size, as well as the volume fraction of ferrite, impacts the EM response of the composites. Both the permittivity and permeability increase as a function of ferrite particle size; however, the permeability increases at a much faster rate than the permittivity with particle size. It is shown that by controlling the ferrite particle size in conjunction with the volume fraction of ferrite, broadband impedance matching to free space can be realised for tailored values of refractive index. This is the rst study that demonstrates independent control of the permittivity and permeability of ferrite composites by controlling the ferrite particle size. Alternatively, by adding a third component to the two part composite it is demonstrated that broadband impedance matching to free space can also be realised with a refractive index of 16.1 (between 10-50 MHz). This is the rst time, to the authors knowledge, that three part composites have been used to achieve high refractive index materials that are impedance matched to free space. The second section of this thesis takes the concept of metamaterials to structure ferrite composite material with a further view to gain independent control over the permittivity and permeability. By tailoring the EM response of this metamaterial, which is comprised of anisotropic arrays of ferrite cubes, broadband impedance matching to free space is demonstrated. The refractive index over the impedance-matched frequency range is also very high (9.5). The metamaterial also acts as an excellent non-re ecting subwavelength thickness absorber up to 200 MHz. An analytical description of the permittivity and permeability dependence on the metamaterial parameters is developed to predict the EM response of this metamaterial, and of similar systems. In the last part of this thesis, the concept of cubic metamaterials is extended to more complex metallic meta-atoms, where the permittivity and diamagnetic response of the metamaterial are independently tailored to demonstrate how the refractive index can be tuned over a broad frequency range. By understanding the role of individual cube parameters, the diamagnetic response can be controlled between near zero and unity, which greatly alters the refractive index. The results are the rst experimental validation for showing `design' control of the permittivity and permeability of these metamaterials via geometry tuning of the meta-atom design.

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