The understanding of electrogenic cells and their networks in vitro plays a major role in the development of therapies targeting maladies of the cardiovascular and nervous systems. Continued advancement of this understanding relies on the use of tools which can measure electrical potentials with ever-increasing spatio-temporal resolution and scale. However, present voltage imaging technologies cannot simultaneously achieve sub-cellular resolution while recording over whole-network spatio-temporal scales, which leads to incomplete descriptions of network function and dysfunction. In this thesis, we report on the early stage development of a fundamentally new tool for quantitative voltage imaging which can overcome the physical limitations of the present state of the art. The central goal of the work is to investigate the extent to which charge-state transitions of fluorescent point defects in wide-bandgap semiconducting materials can be exploited to image bio-electrical activity in vitro. Here, we use the nitrogen-vacancy centre in diamond as an experimental platform for exploring this topic. We describe the design, fabrication, and testing of a novel voltage imaging chip technology which relies on optically detecting the charge-state conversion of near-surface nitrogen-vacancy ensembles in response to electrical potentials in solution. These ensembles are localised within nanoscale diamond p-n junctions and embedded within the tips of diamond nanopillars, which we refer to as ‘optrodes’ in analogy with standard electrodes. Through several generations of diamond optrode arrays, voltage sensitivities are increased by more than three orders of magnitude. The work culminates in a device possessing a voltage sensitivity only one order of magnitude less than that of commercial high-density multi-electrode array systems, and we calculate that the sensitivities of future devices can be improved beyond that of state-of-the-art technologies. Concurrent to the development of physical devices, a nonlinear Poisson solver was constructed to study the effects of dopant concentrations and depth distributions, as well as the effects of diamond surface defects, on voltage sensing performance. Informed by this modelling, a new method for precisely tuning the surface chemistry of diamond for optimal charge-state sensing was developed, enabling the fabrication of a device containing high-density nitrogen-vacancy ensembles stabilised entirely in the neutral and positive charge-states. To our knowledge, this is the first ever realisation of high-density nitrogen-vacancy ensembles exclusively comprised of positive and neutrally-charged defects. The thesis concludes with a discussion of known and possible pathways for increasing the performance of future devices. In addition, we highlight some possible directions for fundamental research which may help to further advance this emerging technology. This work establishes the feasibility of using charge-sensitive fluorescent defects in diamond for all-optical imaging of electrical potentials with both high spatial resolution and over large spatial and temporal scales.

Biochemical processes are conducted by interactions of individual molecules that comprise cells. It is the transient physical shape of proteins that dictates their specific functionality. However, imaging individual instances of single molecular structures is one of the notable challenges in structural biology. Presently available protein structure reconstruction techniques, Nuclear Magnetic Resonance (NMR) spectroscopy, X-ray crystallography and cryogenic Electron microscopy (cryo-EM), cannot provide images of individual molecules. Despite their power and their complementary capabilities, said techniques produce only average molecular information. They achieve this by sampling large ensembles of molecules in nearly identical conformational states. As a result, individual instances of a generic, inhomogeneous or unstable atomic structures presently remain beyond reach. We seek to address this problem in a novel way by leveraging quantum technologies. In quantum computing, qubits are usually arranged in grids and coupled to one another in a highly organised manner. However, what if a qubit was coupled to an organic cluster of nuclear spins instead, e.g. that of a single molecule? What can be done with such a system in the context of quantum control and 3D imaging of individual molecular systems? What are its ultimate limits and possibilities? We explore those questions in stages throughout the chapters of this thesis. We begin in Chapter 2 by investigating dipole-dipole interactions present between the nuclear spins in a target molecule, on one side, and between an electron-spin based qubit and each of the nuclear target spins on the other. We consider the Nitrogen Vacancy (NV) centre in diamond as an example of a suitable qubit with an active community interest as a biocompatible nano-magnetometer. Our intention is to lay down foundations that will help us advance from magnetometry to 3D molecular imaging. Our inspiration comes from drawing parallels between the single molecule sensing in the qubit-target system and the clinical Magnetic Resonance Imaging (MRI). An MRI machine directly images a single, specific sample in its native state regardless of its characteristics. That is precisely what we would like to achieve on the molecular level. In Chapter 3, we develop a framework that allows a spin qubit to serve as a platform for 3D atomic imaging of molecules with Angstrom resolution. It uses an electron spin qubit simultaneously as a detector and as a gradient field provider for MRI-style imaging. We develop a theoretical quantum control methodology that allows dipole-dipole decoupling sequences used in solid-state NMR to be interleaved with the gradient field provided by the qubit. In Chapter 4, we propose group-V donors in silicon as a novel qubit platform for bioimaging. Actively researched for quantum computing purposes, such qubits have not been considered in the biological context. A prime example of this class of qubits is the phosphorus donor in silicon (Si:P). We show how its specific set of properties, including long coherence times, large wave function and low operational temperatures can be leveraged for the purposes of atomic level imaging. Finalising the work in Chapter 5, we simulate the imaging process for one transmembrane protein of the influenza virus embedded in a lipid membrane. This demonstration highlights the potential of silicon spin qubits in the future development of in situ single molecule imaging at sub-Angstrom resolution.

Quantum Computing offers the potential to efficiently solve problems for which there are no known, efficient classical solutions such as factoring of semi-prime numbers and simulation of quantum- mechanical systems. This work considers a novel moments-based adaptation of the Variational Quantum Eigensolver (VQE), one of the leading candidates for demonstrating quantum supremacy. The method for improving the estimated ground state energy of a quantum system, obtained using the Variational Quantum Eigensolver, is presented and tested for Heisenberg model systems using IBM’s superconducting quantum devices. The method is based on the application of a Lanczos expansion technique based on the computation of Hamiltonian moments and is found to offer better accuracy than conventional VQE for most cases considered, allowing for a simpler trial state and offsetting the effects of noise.

Advances in theoretical and computational techniques for advancing concepts in nanophotonics along with major development in nanofabrication technologies has enable the realization of nanoscale optical device with unprecedented ability to control light such as plasmonic metasurface. Fabrication of plasmonic devices, however, has long been relying on conventional lithography technique such as electron beam lithography (EBL), focused ion beam (FIB) milling and photolithography (PL). While these lithography techniques have enable construction of sub-wavelengths nanostructures, their reliance on the interaction between charged particles or light beam with polymer resist during pattern writing process require intricate control systems and usually require high operating and maintenance cost. In fact, for FIB and EBL, the writing time can be very slow depending on the pattern area. These approaches, therefore, are unsuitable for industrial scale production thus hindering commercial uptake of metasurfaces. Therefore, there is a need for an alternative low-cost, high-throughput nano-manufacturing approach to overcome the bottleneck in conventional lithography methods. With this motivation in mind, this thesis focused on utilizing the nanoimprint lithography (NIL) technique for fabrication of the designated plasmonic device. NIL uses pattern transfer approach whereby a predefined pattern on a mould is used to replicate the pattern onto another surface. NIL offers scalability and high-throughput large area manufacturing of nanostructures. In this thesis, the versatility and capability of NIL for producing plasmonic device, particularly plasmonic colours, with a potential of scalability is investigated. This includes the investigation of the dynamic flow of the resist during the nanoimprinting process through various process parameters. With this information, it will be shown that NIL is capable of producing multi height, grayscale-like structures through a careful control of the flow of the resist, without relying on control of charged particle or light beams. This novel technique was then utilised as a method to print the plasmonic colouration device, with ability of controlling the hue and saturation of the resulting colours via tuning of the vertical gap size of the structure. Additionally, an investigation of multispectral, polarisation-selective iridescence plasmonic colour will also be shown in this thesis. This was achieved via the elongation of the spatial dimension of plasmonic structure which results in multiple resonances in both visible and infrared region of the spectrum. Such multispectral system will be very useful especially for optical security device. Finally, a novel plasmonic colour designed to preserve the vividness of the resulting colour under unpolarised ambient lighting condition will be demonstrated in this thesis. This involves production of polarization-independent plasmonic structure featuring symmetric cross structures. It will be shown that this device produced excellent colours with preserved hue and vividness, regardless of polarization state of light

X-ray Absorption Spectroscopy (XAS) is the study of quantum interference of the photoelectron emitted upon ionisation of an absorbing atom by an incident x-ray. XAS is one of the most popular techniques of synchrotron science and most modern synchrotrons have several dedicated beamlines for this purpose. The overwhelming majority of research in this field measures secondary fluorescence photons emitted by the sample of interest. This type of measurement suffers from the dominant systematic error of self-absorption of the fluorescence photon which compromises accuracy, analysis and insight. This work presents a novel self-consistent methodology to correct for this systematic error. These results represent an enormous improvement over any previous attempt to correct for this systematic error. This method (and accompanying software package) can be applied to any fluorescence XAS data set leading to a widely-applicable general solution. XAS is an invaluable tool in the interpretation of much organometallic chemical physics including stereochemistry and quantum structure. Ferrocene is arguably the archetypal organometallic. The 1973 Nobel Prize in Chemistry was awarded on the basis of its discovery and for the identification of its extraordinary nanostructure. Subsequently, its nanostructure has been the subject of dozens of experimental investigations using widely-ranging techniques and a continued source of debate for over 6 decades since its discovery. I have successfully investigated the nanostructure of the isolated ferrocene molecule using a novel combination of Fourier Transform Infrared (FTIR) spectra processing techniques. Detailed analysis of experimental data was undertaken using modern Density Functional Theory (DFT) calculations for high-accuracy hypothesis testing. In this way, the most compelling evidence yet of the existence of the ‘eclipsed’ conformer of ferrocene is presented.

The central thread of this thesis describes the testing and commissioning of the optical fibre beam-loss monitor (oBLM) for use at the Australian Synchrotron. The four 125 m long silica fibres that form the sensitive detectors of the oBLM are installed on the Aus- tralian Synchrotron and provide complete baseline coverage of the accelerator, from the electron gun to the end of the storage ring. This configuration provided a range of testing environments in which to characterise the oBLM and investigate potential use cases. The results of these procedures demonstrated that the oBLM was able to objectively discern losses above 200 fC or approximately 10^6 electrons. The timing resolution as averaged from measurements using multiple fibres at several loss locations was determined to be 1.22 +/- 0.19 ns at FWHM across the working range of the fibres. When the oBLM is operated in time of flight mode this corresponds to a spatial resolution of 0.13 +/- 0.02 m, which is smaller than the average component spacing of lattice elements at the Australian Synchrotron and demonstrates that the oBLM is capable of attributing losses to specific errant devices. Potential and productive use cases of the oBLM were then explored and a range of operational techniques were developed, after which the oBLM was integrated into the injection efficiency monitoring and optimisation system. Where it was used, in time of flight mode, to characterise spontaneous losses along the length of the Australian Synchrotron injection and storage ring systems. The diagnostic information it provided from these measurements was employed in the tuning of the injection system and as a consequence the injection efficiency between the linac and booster ring was increased by 60 %. Based on the findings of this thesis an optimised configuration, that best enables the oBLM to address the usage scenarios identified, was created and presented in this thesis.

In modern-day technology, silicon and silicon-based materials play a key role in the production of computing parts, specifically, the transistors within the chips. The exponential densification of transistors has caused the excess heat generated during operation to significantly hamper chip performance. This has led to the rise of hyperbolic language which refers to this problem as the `silicon apocalypse', and the material as `dark silicon', on account of each chip mostly being turned off to limit heating. The focus of this work lies in creating a silicon-based heterostructure with diamond, which has an unparalleled thermal conductivity, to effectively extract and dissipate heat directly from the chip. To realise such a structure, this work explored the usage of single crystal diamond as a substrate for silicon growth. As diamond had been previously grown on silicon carbide with limited coherence, shown in literature by other authors, the work begins by investigating the interface between 3C-SiC and a diamond substrate both experimentally and theoretically. It was found that 3C-SiC could form a coherent interface with diamond across several nanometres and that, through atomistic simulation, it was possible to realise greater regions of coherence. In the fabrication process, which involved heating thermally deposited silicon within an ultra high vacuum chamber, it was discovered that thin film dewetting became a major hurdle for long range coherence. This dewetting phenomenon and the behaviour of silicon on diamond during annealing then became the second major focus of this thesis to better understand how, or if, a coherent interface could be achieved between these two materials. To diminish the possibility of dewetting, which occurs with very thin films, PECVD silicon was chosen as an accessible method to time-efficiently deposit thicker layers. In spite of the benefits of PECVD silicon, crystallisation through annealing did not yield single crystal silicon. Instead, minimal interaction was found below 600C between the diamond substrate and silicon, which exhibited behaviour in line with PECVD silicon on other substrates as reported in the literature. However, at elevated temperatures around 1000C, a novel form of diamond etching was observed. The results gleaned from this work indicated that 3C-SiC/diamond heterostructures with a coherent interface could be produced, and thus, future applications are possible. The formation of a silicon and diamond heterostructure, however, was hampered by thin film dewetting and so further testing is needed to determine whether a coherent interface could be achieved using processing techniques applied in the case of 3C-SiC, but with thicker layers. By utilising a more accessible deposition method, namely PECVD, thicker layers became readily available on diamond substrate. Under thermal treatment, the PECVD silicon was found to crystallise into a polycrystalline layer, and at temperatures exceeding 1000C, even begin etching the diamond substrate. These series of studies bring to light several fundamental details of a silicon and diamond interface that are a prerequisite to the utilisation of diamond substrates in the future, especially with silicon-based materials.

Quantum devices that leverage the manufacturing techniques of silicon-based classical computers make them strong candidates for future quantum computers. However, the demands on device quality are much more stringent given that quantum states can decohere via interactions with their environment. In this thesis, a detailed investigation of ion implantation induced defects generated during device fabrication in a regime relevant to quantum device fabrication is presented. We identify different types of defects in Si using various advanced electrical characterisation techniques. The first experimental technique, electrical conductance, was used for the investigation of the interface state density of both n- and p-type MOS capacitors after ion implantation of various species followed by a rapid thermal anneal. As precise atomic placement is critical for building Si based quantum computers, implantation through the oxide in fully fabricated devices is necessary for some applications. However, implanting through the oxide might affect the quality of the Si/SiO_2 interface which is in close proximity to the region in which manipulation of the qubits take place. Implanting ions in MOS capacitors through the oxide is a model for the damage that might be observed in other fabricated devices. It will be shown that the interface state density only changes significantly after a fuence of 10^13 ions/cm^2 except for Bi in p-type silicon, where significant increase in interface state density was observed after a fuence of 10^11 Bi/cm^2. The second experimental technique, deep level transient spectroscopy, was used to study the defects in the substrate of Si after ion implantation. As Er has the potential of interfacing electrical and optical properties of Si based quantum computers, it is important to know what defects will be present after the implantation because of its large atomic mass. H and Er implantation damages were compared to demonstrate the more complex defect evolution for Er implantation. Although defects were still present after a 400 C anneal, the concentration was reduced by at least one order of magnitude. The last experimental technique, charge pumping, was used on MOSFETs to study the interface state density directly in device structures that can be directly used in, for example, magnetic resonance and quantum sensing applications. Charge pumping has the potential of allowing measurement and manipulation of both electronic and magnetic properties of the interface defects and defects in the MOSFET channel. For such applications it may be necessary to operate the device close to absolute zero temperature. The work presented here represents a first step towards device and technique development with the ultimate aim of pushing measurements to mK temperatures where quantum device operations typically operate.

Establishing a baryogenesis mechanism, a dynamical origin of the baryon asymmetry, remains an open problem in physics. Electroweak baryogenesis is one such mechanism that is often touted for its inherent testability at current and near future experiments. Taking this notion to heart, here we will examine the collider and dark matter phenomenology of three models motivated by electroweak baryogenesis and novel electroweak phase transitions. In chapter 2, we extend the standard model with two real scalar singlets and one vector-like lepton doublet and examine the collider phenomenology, phase transition history, and baryogenesis mechanism. We find that such a model is capable of generating sufficient baryon asymmetry while satisfying electron electric dipole moment and collider phenomenology constraints. In chapter 3, we study the phenomenology of a hypercharge-zero SU(2) triplet scalar whose existence is motivated by two-step electroweak symmetry-breaking models. If the neutral component of the triplet is stable, we find that this model is strongly constrained by disappearing charged track searches and dark matter direct detection experiments. Conversely, if it is unstable, we find that this model is constrained by multilepton collider searches, such that a triplet with a mass less than 230 GeV is almost excluded at 95% confidence. In chapter 4, we examine the collider and dark matter phenomenology of the standard model extended by a hypercharge-zero SU(2) triplet scalar and a gauge singlet scalar. In particular, we study the scenario where both of the new scalars are charged under a single Z2 symmetry. We find that such an extension is capable of generating the observed dark matter density, while also modifying the collider phenomenology such that the lower bound on the mass of the triplet is smaller than in minimal triplet scalar extensions to the standard model.

This thesis focuses on the development of implantable neural interfaces to perform multifunctional neural recording, neural stimulation and biochemical sensing. Neural interfacing devices using penetrating electrodes have emerged as an important tool in both neuroscience research and medical applications. These implantable electrodes enable communication between man-made devices and the nervous system by detecting and/or evoking neuronal activities. Recent years have seen a rapid development of electrodes fabricated using flexible, ultrathin microwires/microfibers. Compared to the arrays fabricated with rigid materials and larger cross sections, these microwires/microfibers have been shown to reduce foreign body response after implantation, with improved signal-to-noise ratio for neural recording and enhanced resolution for neural stimulation. Carbon fibers (CFs) are considered for implant into particular tissue types since they have small size, cause less tissue damage, and are flexible. CF recording electrodes have shown promise as recording electrodes and have the properties necessary to form sensing electrodes. Micron-scale electrodes such as CFs are expected to evoke localized neural responses due to localized electric fields. CFs are traditionally used with fast-scan cyclic voltammetry to study rapid neurotransmitter changes in vivo and in vitro, as they allow real-time detection of catecholamines with high sensitivity and selectivity. However, they possess narrow usable voltage range, which limits their application for neural stimulation. Additionally, surface fouling occurs with certain neurochemicals potentially obstructing further neurotransmitter adsorption onto the electrode surface. Therefore, they need to be coated with other materials to boost their electrochemical properties for neural stimulation. In this thesis, diamond and diamond-like materials, in particular nitrogen doped ultrananocrystalline diamond (NUNCD) hybrid and boron doped carbon nanowall (B-CNW) are considered as coatings for CFs to enhance properties towards neural interface applications. A focus is finding acceptable properties for recording, stimulation and neurochemical sensing. Novel fabrication techniques were developed to deposit the films onto the surface of CFs. Firstly, the surface of CFs was amine-functionalised and covalent bonds were formed with oxygen terminated nanodiamonds. Films were grown on the treated/seeded fibers using plasma-assisted chemical vapor deposition. To fabricate single fiber electrodes, individual fibers were insulated with capillary glass with 100 micrometer of fiber exposed. The physical and chemical properties of NUNCD hybrid and B-CNW were characterized and studied. The results from electrochemical characterization, in conjunction with both in vitro and in vivo assessments, suggest that these electrodes offer a highly functional alternative to conventional electrode materials for both recording and stimulation, yielding safe charge injection capacities up to 25.08 +-12.37 mC/cm2. To test the capability of electrodes for neural stimulation in vitro, explanted wholemount rat retina was used. The electrodes could elicit localized stimulation responses in the explanted retina. These electrodes with micron -scale cross sections have the potential to improve the spatial resolution for stimulation while minimizing axon bundle activation. In vivo and in vitro single-unit recording showed that the electrodes could detect signals with high signal-to-noise ratios up to 8.7. NUNCD hybrid coated CFs were able to electrochemically detect dopamine with high sensitivity and selectivity. Such electrodes are needed for the next generation of miniaturized, closed-loop implants that can self-tune therapies by monitoring both electrophysiological and biochemical biomarkers.

The Epoch of Reionization marks the transitional period of our Universe where the emergent growth of luminous structure begin to ionize the surrounding medium of neutral hydrogen gas. The characterisation of these luminous sources; galaxies or accreting black holes (i.e. quasars) play an important role by tracing sites of early structure formation, thus forms an integral aspect to our overall understanding in galaxy formation and evolution. In this thesis, we investigate the key properties of the rarest, brightest objects that are easily accessible by contemporary means; its large-scale environment and its number density, in the specific context of how stochasticity can affect the measured statistics of these rare objects. In the first part of this thesis, we investigate the impact of luminosity scatter in measurements of galaxy clustering, under the premise that luminosity scatter facilitates the odds for a common halo to contain an over-luminous outlier. We construct a Monte Carlo simulation of mock Hubble Space Telescope field-of-views to collect statistics of visible galaxy neighbours. We find that galaxy luminosity scatter is important in the overall clustering statistics within a field-of-view. However, current observations of weak clustering is consistent with our modeling predictions due to Poisson noise. There is scope in using future clustering measurements as a method to constrain luminosity scatter. The impact of luminosity scatter has a profound impact on the number distribution of luminous objects by broadening the bright end of the luminosity function. We extend the semi-empirical model for the evolution of the galaxy luminosity function by accounting for stochasticity in galaxy luminosities. Our model shows that a non-zero scatter in galaxy luminosities results in a departure from the Schechter function, and the amount of scatter can be constrained by additional large area observations of very bright galaxies. In the second part of the thesis, we extend our analysis of galaxy luminosity stochasticity to quasars. We investigate how quasar luminosity evolves with halo mass under different assumptions of quasar luminosity scatter and quasar duty cycle. We find that quasar luminosity scatter is linked to AGN and star formation feedback in our modeling. With a duty cycle of unity, we find that feedback acts on black holes and galaxies independently. Alternatively, a lower duty cycle favours the interpretation of a common feedback source. We conduct a similar Monte Carlo analysis on the weak clustering around $z\sim6$ quasars. We find that a duty cycle of unity places constraints on galaxy luminosity scatter in order to maintain consistency with observations, while a lower duty cycle does not have any restrictions on galaxy luminosity scatter. The quasar luminosity scatter is not strongly constrained by the field-of-view clustering measurements. Finally, we develop a single parameter semi-empirical model of the evolution for the quasar luminosity function that accounts for quasar luminosity scatter. Our model shows excellent agreement with the $z=3-6$ quasar luminosity functions and is capable of reproducing the $z=0-2$ luminosity functions assuming a small evolution in quasar luminosity scatter. Future measurements of the $z>6$ quasar luminosity function will be essential in validating the robustness of this model.

In this thesis high precision QCD-factorisation tests were performed. The branching ratios B(B → D π ) = (2.67±0.02±0.09)×10 and B(B → D K ) = (2.27±0.06±0.08)×10−4 were measured using (771.58±10.56)×106 B-meson pairs recorded by the Belle experiment. Both values are in tension with the theoretical expectation. The ratio of the branching ratio is measured in a way that allows for the cancellation of the systematic uncertainties arising from the D∗-meson reconstruction; the value of RK/π = B(B → D K )/B(B → D π ) = (8.41±0.24±0.13)×10 was found. Both B(B → D π ) and B(B → D K ) have shown deviations from the prediction, this suggests that the estimation of the Feynman diagrams contributing to the predictions may be inaccurate. The new measured branching ratios were used to perform a high precision QCD factorisation test by measuring ratios with respect to semi-leptonic branching ratios at fixed momentum transfers for different particle species. A deviation for the ratio Γ(B → D h )/dΓ(B → D l ν ̄)/dq of 16% from theoretical predictions was found, suggesting large non-factorisable contributions and/or new physics contributions. Furthermore, SU(3)-symmetry was tested by measuring ratios for pions and kaons of a21(K)/a21(π) = 1.05±0.05 as well as for different particle species. The found value is consistent with unity and therefore no evidence for SU(3)-symmetry breaking effects was found in this test to 5% precision. Thus, for RK/π one can rule out SU(3)- symmetry breaking effects as an explanation for the deviation. Finally, a new vertex fitting algorithm and its implementation for the Belle II software framework was reported. It can improve D∗-meson reconstruction, is com- putationally very efficient and is now the standard vertex fitting tool of the Belle II experiment.