School of Physics - Theses
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ItemBelle II Silicon Vertex Detector and a measurement of B → D**lν decays at Belle( 2021)The Belle II Silicon Vertex Detector (SVD) is a silicon strip detector designed to possess a high irradiation tolerance and short shaping time, making the detector suitable for operation at the high luminosity SuperKEKB collider. In this thesis, the construction of the inner most layer of the detector ''Layer-3'' and subsequent electrical characterisation of the devices are described. Each of the 11 Layer-3 ladders produced were of a high electrical quality, with a strip failure rate of less than 0.2%, demonstrating each of the ladders to be a suitable candidate for installation into the Belle II detector. In the early stages of the detector commissioning phase, numerous high occupancy regions were discovered on the origami sensors. This problem was identified to be caused by crosstalk between control lines on the pitch adapters and the electrodes of the sensor beneath. An algorithm was developed to identify events in which these clusters were present, such that further studies into the affect of the crosstalk clusters could be performed. In particular, the impact on the track finding performance was studied in the search of an offline software approach to mitigating the crosstalk clusters. It was found that the signal-to-noise Ratio (SNR) of the crosstalk clusters were distinct from clusters deposited by signal tracks and an SNR cut based approach demonstrated an improvement to the tracking computation time of order 10%, and a slight improvement to the track parameter resolution. The hit occupancy in the SVD is expected to continually increase as the instantaneous luminosity of SuperKEKB increases over the course of the experiment. As a means of reducing the exponentially growing number of 2D hit candidates which are supplied to the track finding software, detector information was utilised to filter background events. Through exploiting cluster charge, cluster time, and cluster size correlations between each side of the strip detector, a quality index was assigned to each of the reconstructed 2D hits. The quality index of the 2D hits was included in the track candidate multivariate classifier (MVC), having the second highest impact of all the included variables. Through inclusion as a feature of the MVC, the purity of the global track quality ranking was improved. Additionally, a measurement of the semi-inclusive $B\rightarrow D^{**}\ell\nu$ rates, (where $\ell$ denotes either an electron or a muon) were obtained from the entire 711 $fb^{-1}$ Belle data-set. $B\rightarrow D^{**}\ell\nu$ decays are of particular interest due to the uncertainty in the branching fractions calculated by previous measurements. A more precise measurement is of importance for the difference between the inclusive charmed semileptonic decay rate and the sum of the exclusive charmed semileptonic decays (the ``gap problem'') and for improving the precision of future measurements of $\mathcal{R}(D)$ and $\mathcal{R}(D^{*})$, where new physics may be observed. The tag-side $B$ meson is fully reconstructed in a hadronic decay mode with the latest \ac{BDT} tagging algorithm. The measured branching fractions are $\mathcal{B}(B^{+}\rightarrow D^{-}\pi^{+}\ell^{+}\nu) = (0.396 \pm 0.014 \pm 0.020)\% $, $\mathcal{B}(B^{+}\rightarrow D^{*-}\pi^{+}\ell^{+}\nu) = (0.509 \pm 0.019 \pm 0.030)\%$, $ \mathcal{B}(B^{0}\rightarrow \bar{D}^{0}\pi^{-}\ell^{+}\nu) = (0.364 \pm 0.020 \pm 0.020)\%$, $\mathcal{B}(B^{0}\rightarrow \bar{D}^{*0}\pi^{-}\ell^{+}\nu) = (0.589 \pm 0.030 \pm 0.040)$. Each of which are in agreement with current world averages, apart from $\mathcal{B}(B^{+}\rightarrow D^{*-}\pi^{+}\ell^{+}\nu)$, which falls below the world average by 1.8$\sigma$. Each of these measurements offer a higher precision than previous results.
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ItemReal-time Detection and Identification of Pathogens and Pollutants through Optical Imaging( 2021)The rapid and accurate detection and identification of pathogens and pollutants are crucial to prevent problems related to health and safety. Optical imaging offers the opportunity to timely detect and identify those micro and nano-objects on-site. In this study, we investigated the potential of confocal microscopic imaging for label-free, real-time, and non-invasive detection and identification of harmful pathogens and toxic pollutants by exploiting their intrinsic fluorescence features - emission spectra and fluorescence lifetime. All materials have the natural capability to fluoresce due to the presence of endogenous fluorophores. These endogenous fluorophores show characteristic excitation-emission spectra and fluorescence lifetime, which makes them attractive endogenous probes. Intrinsic fluorescence-based methods are advantageous compared to extrinsic fluorescence-based methods due to minimal sample handling, no chemical processing or modification, and acquisition of results in a few minutes after sample preparation. Chapter 1 is a general introduction to the field of fluorescence and provides a comprehensive literature review that leads to the research question and motivation behind current research work. Chapter 2 describes the fluorescence techniques and methodology employed in this thesis. Chapter 3 investigates the intrinsic fluorescence properties of three polyaromatic hydrocarbons (PAHs), namely, pyrene, phenanthrene, and naphthalene, using confocal microscopy. PAHs are toxic and carcinogenic and are considered primary pollutants. In this work, we exploit the intrinsic fluorescence of PAHs for their detection and measure the emission spectra of PAHs for their identification in the soil samples. Then, through the application of ImageJ software, we perform quantification analysis of PAHs in the soil samples. Chapter 4 studies the intrinsic fluorescence characteristics, i.e., emission spectra and fluorescence lifetime of nematode genus and species, for their rapid detection and identification. In this study, we observe that these pathogens contain various intracellular biochemicals that act as endogenous fluorophores that assist in their rapid and on-site detection and identification using confocal microscopy. We also demonstrate that these eggs can be detected and identified in the sludge samples. Then, using Raman vibration spectroscopy, we find the origin of fluorescence in these nematode eggs. This work, for the first time, demonstrates real-time detection and identification of eggs of sub-species of nematodes, i.e., Ascaris suum and Ascaris lumbricoides using their intrinsic fluorescence properties. Currently, rapid detection and identification of Gram-positive, Gram-negative, and multi-drug resistant strains of bacteria are crucial to control infections and prescribe an appropriate antibiotic to an infected patient. To address this, in Chapter 5, we report on the evaluation of confocal microscopy for the identification of clinically important and multi-drug resistant (MDR) bacteria in real time, using their intrinsic fluorescence features, i.e., emission spectra and fluorescence lifetime. We observe that difference in emission spectra and fluorescence lifetimes can be used as a fingerprint for identification of 12 bacterial species and MDR strains in real-time. Further, dilution experiments demonstrate that using intrinsic fluorescence bacteria can be detected and identified at sepsis concentration. The research on bacterial biofilm dynamics has not been extensively explored; hence, understanding of bacterial biofilms dynamics is still in infancy. Chapter 6 explores the bacterial biofilms dynamics by exploiting their intrinsic fluorescence properties. We measure the fluorescence lifetime and emission spectra of four clinically important bacterial biofilms at different stages of their growth. In addition, we also explore the origin of bright red fluorescence in these bacterial biofilms by measuring the fluorescence lifetime of the biofilm components. Chapter 7 concludes the major contributions of the research described in this thesis and discusses potentially useful future applications.
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ItemDense matter and magnetic fields in neutron stars( 2021)The life cycle of main sequence stars with masses in the range 8 - 25 solar masses ends in a supernova explosion, whose remnant is a dense compact object called neutron star. The huge gravitational field of neutron stars, counterbalanced by the pressure of strongly degenerate matter, combined with intense magnetic fields offer the opportunity to probe matter in extreme conditions, far beyond the reach of contemporary laboratory experiments. The wealth of observations of neutron stars gradually reveals more facets of their nature, although much is yet to be discovered. The aim of this work is to study the interplay of two ingredients of neutron star physics: dense matter and magnetic fields. The properties of ultra-dense matter can be inferred from the thermal radiation emitted by isolated neutron stars and magnetars. Detailed models of the atmosphere, surface, crust and core are required to determine how information about dense matter in the core is filtered out by the outer layers. Often, several key quantities that determine the thermal luminosity are unknown, such as the mass and radius, or the chemical composition and magnetic field configuration. The ionization state and emission model adopted for the stellar atmosphere and the chemical composition of the outer envelope (i.e. a layer with a typical thickness of ~ 100 m) affect the thermal radiation produced at the surface. Strong magnetic fields modify the heat transport in the atmosphere and in the crust and can decay, producing high Joule heating rates, complicating the interpretation of thermal luminosity observations in terms of the internal chemical composition and the neutrino emission processes active in the deeper regions of the core. Chapters 2 and 3 study the thermal radiation produced by neutron stars with cores hosting unconventional particles such as hyperons by performing state-of-the-art magneto-thermal evolution simulations. The influence of the magnetic field on the thermal evolution is examined for several plausible initial magnetic field configurations, and the thermal luminosity is compared with the data of thermally emitting, isolated neutron stars and magnetars. It is found that (i) internal heating is required by stars with and without hyperon cores, regardless of the composition of the outer envelope, if direct Urca processes activate in stars with masses ~ 1 solar mass and neutrons are superfluid in a large fraction of the core; and (ii) the thermal power produced by the dissipation of crustal electric currents sustaining the magnetic field can hide the effect of fast cooling processes related to the appearance of hyperons in the core, making hard to infer the chemical composition of neutron stars from thermal luminosity data. Although the intense magnetic field of neutron stars plays a central role in their phenomenology, the internal field is poorly known, and often one relies on simplistic magnetic topologies. Additionally, neutron stars may have internal velocity fields generated by differential rotation that affect the magnetic field configuration. One important question is whether in such conditions the magnetic field can force the fluid to rotate uniformly with the solid crust, or whether the fluid can be in a state of differential rotation on long, viscous time-scales. Due to computational limitations, performing detailed magneto-thermal simulations with the addition of evolving internal velocity fields of several fluid components is a nontrivial task. However, one can gain some insight into the magnetic configuration in the presence of internal flows by modeling the star as a spherical shell containing a single, idealized and electrically conducting fluid. In Chapter 4 we study the implications of internal fluid flows on the magnetic field configuration by applying a constant rotational shear between the inner and outer boundaries. It is found that differential rotation tangles the magnetic field lines and produces small-scale toroidal flux tubes containing bundles of closed toroidal field lines in proximity of the magnetic equator. In these toroidal flux tubes, the fluid velocity is set by viscosity rather than by the magnetic field, allowing differential rotation in neutron star interiors to persist on long, viscous time-scales. Hyperons are not the only unconventional particles that may appear in neutron star cores. Typical densities in massive stars may be sufficiently high for quarks to deconfine, and crystalline phases arising from inhomogeneous condensation of quarks may form. In Chapter 5 we develop an analytic approximation for the free energy of deconfined quark matter and study its ground state in the presence of strong magnetic fields and at high temperatures, which may be characteristic of neutron star binary mergers. It is shown that the magnetic field and temperature compete in enlarging and reducing respectively the region of the phase diagram where inhomogeneous phases of quark matter are favored, which correspond to the regions where the neutrino emissivity of quark matter increases due to the activation of direct Urca processes.
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ItemEntanglement in superconducting quantum devices and improving quantum circuit compilation( 2021)Quantum computing has the potential to solve many computational problems more efficiently than classical computing. It is expected to expand our ability to simulate and solve difficult and classically intractable problems in many fields of research and industry. However we are currently in the noisy intermediate-scale quantum (NISQ) era of quantum computing where devices are relatively small and suffer significant levels of noise. In this thesis we report on experiments on IBM Quantum devices, which are among the most advanced quantum devices in the world, to assess the growing capabilities of quantum computing. We focus on the ability to prepare and detect sizeable multi-qubit entangled states, which is a critical milestone for quantum physical platforms. In our first set of experiments, graph states of 20, 53 and 65 qubits are prepared on IBM Quantum devices and are shown to be fully bipartite entangled. Before these experiments, the largest cluster of qubits shown to be bipartite entangled on a gate-based quantum computer was 16 qubits. In another experiment, a Greenberger-Horne-Zeilinger (GHZ) state is prepared over all 27 qubits of the ibmq_montreal device and is demonstrated to exhibit the stronger genuine multipartite entanglement (GME), the largest state shown to exhibit GME to date. These results highlight the positive advancement of quantum computing technology towards the physical realisation of sizeable and complex quantum algorithms. Physical quantum devices usually have limited connectivity. So they typically have coupling maps that specify which pairs of qubits support direct application of two-qubit gates. Mapping quantum circuits to physical devices requires qubit states on the device to move to target qubits via a sequence of SWAP gates to satisfy two-qubit gate coupling map requirements. One approach to finding optimised SWAP schedules involves solving a problem called multi-qubit pathfinding (MQP). We introduce an algorithm that finds optimal solutions to this problem. It primarily minimises the total SWAP gate circuit depth and secondarily minimises the accumulated gate errors. The algorithm is benchmarked on a variety of quantum hardware layouts. The run time appears comparable to current state-of-the-art algorithms while additionally optimising with respect to accumulated gate error and the algorithm is flexible with respect to variations on the problem. Large scale complex quantum algorithms will require robust error-correcting protocols performed over encoded logical qubits. Only a small set of gates can be applied transversally to encoded quantum states, and only a subset of unitary gates can be fault-tolerantly applied via resource-expensive distillation procedures. Together, these gates can be multiplied in sequence to generate any unitary gate to arbitrary precision, where sequences are found using a gate synthesis procedure. We assign resource costs to various base gates and perform cost-optimal single-qubit gate synthesis with the standard Clifford+T base gate set along with additional gates from the Clifford hierarchy. We show that by including higher orders of the Clifford hierarchy, cost savings of over 50% could potentially be achieved. This suggests that adapting current synthesis algorithms to support higher order Clifford hierarchy base gates and individually assigned resource costs could provide substantial benefits.
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ItemOxygen Terminated Nanodiamond Photoelectrodes for Neuromodulation( 2021)Neuromodulation is used for the treatment of a number of neural impairments that hinder cell activation and proper information transfer. The treatment of psychiatric disorders, Alzheimer’s and Parkinson’s disease, motor function disorders, blindness due to retinal degeneration, dystonia, and epilepsy are some of the examples of clinical applications of neuromodulation. Beyond the widely used approach of using wired electrodes for neuromodulation, various methods have been explored. One of them is to use light to wirelessly control neural networks. When used within safe intensity limits, light can stimulate or modulate the function of neurons. Among the wide variety of optical neuromodulation and stimulation methods is the use of photosensitive thin films or particles as transducers to convert the incident light into electrical signals. It has been claimed that this method can be less invasive than electrically driven stimulation and has the added benefit of scalability in both stimulation location and resolution. Moreover, compared with the optogenetic neuromodulation technique, photoactive surfaces have the capability to eliminate the need for genetic modification to introduce photosensitive proteins to the target neural tissues and possible adverse immune system responses. In this technique, photo-excited charge carriers in an electrode are used to stimulate neural tissue. Various materials have been used for this purpose such as conductive polymers, photoconductive silicon, and semiconducting quantum dots, but many of these materials are not ideal because they lack sufficient biostability and are in some cases toxic. Diamond-based materials are excellent candidates owing to their high corrosion resistance, good biocompatibility, and excellent charge injection properties and recent publications demonstrate their electrical response to illumination. A key feature of diamond-based materials is the ability to control their properties by controlling their surface termination. Surface modification is used to alter nanodiamond properties such as chemical affinity, and electrical and optical properties. In particular, the transfer of photoexcited electrons from the conduction band of the nanodiamond to the adlayer at the nanodiamond surface depends on the surface termination of this material. By tuning these surface properties, a diamond can be an effective photocathode for neural stimulation/modulation. Earlier works have demonstrated that oxygen terminated diamond displays a charge-balanced capacitive charge transfer when it is illuminated in saline solution. In capacitive charge transfer, no photoexcited electrons are transferred across the interface and the diamond/electrolyte adlayer can be modelled as a simple electrical capacitor. On the other hand, hydrogen-terminated diamond exhibits Faradic charge transfer, which may be due to the transfer of photoexcited electrons to the adlayer because of the negative electron affinity of the hydrogen-terminated surface. This suggests that the properties of oxygen terminated diamond are more favourable for neural stimulation/modulation. The capacitive charge transfer mechanism is known to minimize both electrode damage and cell degradation which should be avoided in neural stimulation. This thesis starts by examining the properties of oxygen terminated detonation nanodiamond (O-DND) particles with the size of 20 nm to 170 nm. Earlier works have demonstrated that such particles can be incorporated into living cells. When coupled with the high surface area to volume ratio for nanoparticles, this system is potentially attractive for optically induced cell stimulation/modulation. Whilst the presence of a photogenerated charge accumulation layer on oxygen-terminated diamond films has been demonstrated, this has not been experimentally observed in O-DND particles. In this project, furnace annealing is used to oxygen terminate DND powder and to investigate the effect of light on O-DND particles’ surface charge in an aqueous solution. During these experiments, two new techniques are developed. In the 1st method, the electric double layer around the nanoparticles is probed whilst suspended in saline solution and without the need for any electrical connection to the nanoparticles. To do this a 4-electrode electrochemical impedance spectroscopy technique is used to measure the complex impedance of the O-DND nanoparticles suspended in the saline solution as a function of frequency. This technique shows good sensitivity to the surface termination of DND and using this technique, the capacitance and resistance of the particles suspended in the saline solution were extracted. Building on this method, the effect of light on the EDL of the nanoparticles is investigated. Whilst the capacitance and resistance of particles in saline solution is measured, the changes in particle capacitance and resistance due to light illumination are too small to be measured within the standard error range. In the 2nd method, the zeta potential of particles in a solution is measured using the laser doppler electrophoresis technique. The zeta potential directly relates to the surface charge of the nanoparticles, and by measuring it, the light-induced changes in the surface charges may be observed. Here a conventional Zetasizer is modified to allow measurement of the zeta potential while the samples are illuminated with an optical fibre. Using this technique, the changes in surface charge is characterized as a function of different surface terminations, but no changes in the zeta potential under illumination are detected within the sensitivity of the technique. Possible reasons for the lack of observable changes in zeta potential under illumination are discussed. In the 2nd part, this work is focused on the photoresponse of nitrogen-doped ultrananocrystalline diamond, under the assumption that the defect levels created by the nitrogen doping contribute to a photoresponse at longer wavelengths (around 800 nm) which makes it a favourable material for photostimulation. The same surface termination is employed for the nitrogen-doped ultrananocrystalline diamond (N-UNCD) films to evaluate oxygen terminated N-UNCD as a biocompatible photoactive surface for neural stimulation. The oxygen annealing time is optimized to gain the maximum electrochemical capacitance for photoelectrodes, and the electrochemical properties of samples are investigated. Moreover, the electrochemical capacitance of N-UNCD samples oxygen terminated with different techniques is measured and compared with the oxygen annealed sample. The oxygen annealed sample exhibits the greatest electrochemical capacitance and can be optimized to reach a value of about 30 mF cm-2, 6 times higher than other techniques used in this thesis and also previously reported Pt electrodes and comparable to sputtering iridium oxide electrodes. This enhancement is suggested to be due to a combination of factors, including oxygen surface functionalities, graphitic grain boundary etching, and the removal of trans-polyacetylene (TPA) and hydrogen from the sub-surface layer during the oxygen annealing process. N-UNCD exhibits a photoresponse at longer wavelengths, hence it is possible to employ Near-infrared (NIR) light for photoexcitation. NIR light has a higher penetration depth and less phototoxicity than the lower wavelength which makes N-UNCD a favourable material for in vivo photostimulation. The oxygen annealed N-UNCD, which displays a very high surface capacitance, is evaluated in terms of its photoresponse to NIR light. Under optimal conditions, a capacitive photocurrent of 3.7 uA/W is achieved, higher than previously reported photocurrent values of optically driven N-UNCD electrodes. This translates to an approximate 200 times increase in the photocurrent compared with the as-grown sample. Surface sensitive spectroscopy techniques reveal that these orders of magnitude enhancement in photocurrent are due to the formation of a diamond-rich capping layer as the result of preferential etching of graphite at the grain boundaries. It has been suggested that the surface treatments in reactive oxygen resulted in changes in the surface functional groups, which modulate the surface Fermi level. These results hold significance for applications of oxygen terminated N-UNCD photoelectrodes for neuromodulation applications. For neuromodulation, the surface of the electrode must support neuronal growth as well as had perfect biostability. The stability test results show that oxygen annealed N-UNCD photoelectrodes have remarkable stability when stimulated over many cycles in saline. Moreover, the surface of oxygen annealed N-UNCD displays significant biocompatibility and encourages neuron growth without the necessity of promoters, indicating that it is highly biocompatible. When studying the neuronal growth on oxygen annealed N-UNCD surfaces, light stimulation is found to greatly enhance neuronal growth, with better survival rates and improved neurite outgrowth. As the light illumination does not show a significant impact on the control samples, the improved neuronal growth on oxygen annealed N-UNCD films is tentatively concluded to be due to their photoelectric responses. This is the first evidence that implies the potential for using the photoresponse from oxygen terminated N-UNCD to improve neuronal growth. These results suggest that light could be used to direct the growth of specific neural networks. Possibly in the future oxygen terminated N-UNCD photoelectrodes could find applications for neural network regeneration and nervous system repair.
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ItemMeasuring the Epoch of Reionization Signal with Murchison Widefield Array( 2021)With the emergence of the first stars and galaxies at ~100 million years, the Dark Ages ended. The ultraviolet radiation from the first structures started to reionize the surrounding neutral hydrogen, creating ionized bubbles. Gradually the bubbles grew and merged until the intergalactic medium was completely ionized. This transition was a critical phase in the evolution of the Universe, called the Epoch of Reionization (EoR), spanning the redshift range of z ~10-6. Understanding the critical physics happening in this epoch answers many questions about the structure formation and evolution of the Universe. The observation of the neutral hydrogen 21-cm signal is an excellent probe for tracing the ionization process and studying the underlying physics happening therein. Technically, the EoR experiments utilise radio interferometry which provides the required sensitivity and resolution in the frequency range of interest. The sensitivity of current instruments allows us to statistically measure the power spectrum of the EoR signal, while the next generation of instruments is under development with the ultimate goal of direct imaging of EoR. This work measures the EoR signal at a redshift range of z~6-7 with Murchison Widefield Array (MWA), a radio interferometer located in Western Australia. However, detection of the EoR signal is a challenging procedure due to the low amplitude of the signal (~10mK), bright foregrounds (up to 4-5 order of magnitude brighter than signal), ionospheric distortions, Radio Frequency Interference and instrumental effects. An integration time of ~1500 hours MWA EoR data can potentially detect the EoR signal with an S/N of 14 [1]. However, signal detection is currently limited by the aforementioned systematics. They contribute to the power exceeding the thermal noise level. Therefore, detection of the signal requires the development of different strategies to overcome these challenges. This thesis analyzes the EoR data from MWA while developing, improving and providing insight into systematic mitigation approaches to obtain a more precise measurement. The MWA EoR observing program is targeted on three different EoR fields: EoR0, EoR1 and EoR2. In this work, we measure the signal from two fields. First, we calibrate the EoR data from the EoR0 field and develop a data quality metric for refining the data. As a result, the first deep measurements of power spectrum with MWA, using the RTS+CHIPS pipeline, with ~32hr integration is obtained. The lowest upper limit is Delta^2 <= 2.5x10^4 mK^2 at k=0.14 (hMpc)^-1 and z=6.5 which is consistent with previous results from other instruments. Next, we explore some strategies to mitigate the foreground contamination which is a major obstacle in detection of the EoR signal. We modelled the Galactic Diffuse Synchrotron Emission, the dominant foreground at the redshift of interest, over the MWA field. However, since the MWA is a wide field experiment, it requires a full sky model. Therefore, we explored another strategy, i.e. developing a weighting scheme for baselines based on the severity of their contamination. Another accomplishment in this thesis is the analysis of EoR data from the MWA EoR1 field which has a different foreground containing the bright radio galaxy of Fornax-A with a total flux density of ~500Jy at 189 MHz. A precise model of Fornax-A is essential for effective foreground removal. Using the imaging capability of the analysis pipeline and available shapelet fitting tools, the model of Fornax-A in our sky catalogue is improved. While improving our analysis algorithm, we made an effort to mitigate contamination in our measurements by detecting systematic signatures in the data and excluding them. We explored various features in the data, hunting for the source of systematic signatures. We also recognised the visibility noise RMS as a metric to distinguish the more contaminated data within a refined dataset. Eventually, we obtained the upper limits on the EoR signal power spectrum from the MWA EoR1 field at three redshift bands centered at 6.5, 6.8 and 7.1 with the lowest at z=6.5 of Delta^2 <= (73.78 mK)^2 at k=0.13 h Mpc^-1, from ~14 hr data integration. Although it contains a shorter integration time relative to the previous EoR1 analysis[2] (~19 hr), the limits are lower (~1.26 times), thanks to the improvements in the analysis algorithms, foreground modelling and data refinement strategies. We also compared the analysis results from EoR0 and EoR1 fields. It is shown that, due to the improvements achieved in this work, EoR1 can potentially lead to lower limits (at least on large scales) which warrants analyzing longer integrations from this field. In the final chapter, suggestions for further systematic mitigation and obtaining lower limits are provided.
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ItemSimulating the Epoch of Reionisation( 2021)The first stars and quasars to form in our universe drove a universal phase transition known as epoch of reionisation, where the diffuse hydrogen gas between galaxies was ionised. The epoch of reionisation is the last period in the history of our universe to be studied in detail, and requires detailed theoretical models in order to interpret our observations. Cosmological simulations provide a way to create detailed approximations of physical processes on large scales that are impossible to solve analytically. This allows us to draw connections between the physical parameters we wish to know, and the observable data we measure. In this thesis, we use different types of cosmological simulations to study the epoch of reionisation. We use the semi-analytic galaxy evolution model Meraxes to place constraints on the epoch using measurements of the intergalactic medium temperature. We use the hydrodynamic simulation Bluetides to make predictions for a future observational strategy where radio images of bright galaxies are stacked together to measure their average signal. Finally, we make enhancements to a hydrodynamic simulation code, MP-Gadget intended for use in the Asterix simulation to improve its calculation of the epoch of reionisation topology.
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ItemNo Preview AvailableStructure of Zinc and Metal Binding Sites in N-truncated Cu Amyloid-beta from X-ray Absorption Fine Structure( 2021)X-ray absorption spectroscopy (XAS) is an advanced technique to explore structural information of many types of materials due to its sensitivity and adaptability. Quantum interference of the incoming and outgoing photoelectrons of an absorbing atom reveals the local environment of the absorbing atom and hence a number of fundamental parameters of the material. However, detection of high accuracy data and propagation of experimental uncertainties is limited due to lack of technology. This thesis implemented high accuracy techniques such as the X-ray extended range technique (XERT) and the Hybrid technique to collect high accuracy absorption and fluorescence measurements at ambient temperatures. Protocols of these techniques dictate that systematic errors are investigated over an extended range of experimental parameter space, resulting in better analysis of the mass attenuation coefficients and X-ray absorption fine structure (XAFS) across the K-edge. These techniques can be used to investigate significant systematic errors such as dark currents, blank normalization, harmonics, scattering effects, thickness effect, energy bandwidth, roughness and energy calibration and correct them for precise extended X-ray absorption fine structure (EXAFS) analysis of zinc. The first XERT-like experiment at the Australian Synchrotron was successfully implemented on the XAS beamline to collect high accurate X-ray mass attenuation coefficients across an energy range including the zinc K-absorption edge and XAFS of zinc. Dark current correction was quantified and reached up to 57% for thicker foils and was also significant for thin sample foils. Blank measurements normalized attenuation measurements and scaled thin foil attenuation by 60-500% and even corrected thicker foil attenuation by up to 90%. Discrepancies between different thick foils of up to 20% is corrected using the full-foil mapping technique. The energy was calibrated using standard reference foils. Fluorescence scattering was significant for these measurements and explored carefully. A method base on the different aperture combination was introduced to investigate fluorescence radiation. In this current work, fluorescence radiation has a large impact on the attenuation measurements of thicker sample foils. The correction is energy and sample thickness dependent and therefore significantly affected on the oscillations in the near-edge region. The occurrence of background fluorescence scattering from an unidentified background object in the upstream beamline was observed and corrected for zinc measurements. The correction of fluorescence radiation changes the attenuation of measurements by up to 15.5% and reduced the standard error from the dispersion and the variance by up to 50.0% for thickest sample foil. These results produce the most accurate mass attenuation measurements of zinc from 34.77 to 323.76 (cm2g-1) over the energy range from 8.51 keV to 11.59 keV. The absolute experimental uncertainties were propagated based on systematics and range from 0.023% to 0.036%. These high accuracy studies enable rigorous investigations of discrepancies between theory and experiment and precise structural investigations. The experimentally obtained mass attenuation coefficients deviate by abut 50% from the theoretically tabulated vales near the zinc K-edge. This strongly implies the improvements in theoretical tabulations of the mass attenuation coefficients. The high accuracy data for zinc led to the ability to derive the imaginary component of the atomic form factors and a novel investigation of edge factor and edge ratio of zinc. The XAFS analysis yielded bond lengths and nanostructure of zinc with uncertainties from 0.003 angstrom to 0.008 angstrom. This is superior to many crystallographic analyses of spacing from lattice structure, and is sufficient to investigate and determine thermal parameters with an accuracy of 5%. Our high accuracy data provide great insights into local dynamic motion that is impossible to observe through conventional crystallography. These results can be used for explicit explorations of solid-state effects including inelastic mean free paths, inelastic and elastic scattering cross-section. XAS is an ideal, element selecting tool to investigate many biological samples such as organometals and metal peptides as it provides high resolution structural information and is suitable for sensitive samples. N-truncated Cu:Amyloid-beta (Cu:Abeta) peptide complex contributes to oxidative stress and neurotoxicity in Alzheimer's patient's brains. Redox properties of Cu metal in different Amyloid-beta peptide sequences are inconsistent. Our novel X-ray absorption spectroscopy spectro-electrochemical technique (XAS-SEC) allows an understanding of redox characteristics of Cu ion in different Cu:Abeta peptide sequences and the structural information such as bond lengths and thermal parameters of Cu metal binding sites under near physiological conditions. We determined the geometry of binding sites for the key Cu binding in Abeta4-9/12/16 and the ability of these peptides to perform redox cycle in a manner that might produce toxicity in human brains. We propagated experimental uncertainties due to systematics errors and incorporated in EXAFS analysis for determining precise structural parameters with reliable uncertainties. Our low temperature XAS measurements reveal that Cu(II) is bound to the first amino acids, in the high-affinity amino-terminal copper nickel (ATCUN) binding motif, with an oxygen in a tetragonal pyramid geometry in the Abeta4-9/12/16 peptides. Room temperature XAS-SEC measurements implies metal reduction in Abeta4-16 peptide. Robust investigations of EXAFS provide structural details of Cu(I) binding with bis-His motif and a water oxygen in quasi tetrahedral geometry. Oxidized XAS measurements of Abeta4-12/16 reveal that both Cu(II) and Cu(III) are accommodated in ATCUN-like binding site. A new protocol was developed using EXAFS data analysis for monitoring radiation damage.
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ItemWeak Coupling Renormalization Group Approach to Unconventional Superconductivity in 2D Lattice Systems( 2021)Unconventional superconductivity has experienced tremendous growth in research interest and activity ever since the discovery of high-Tc superconductors. The variety and rich phenomenology of superconducting phases are promising for future device applications and technological advancement. Topological superconductivity constitutes another class of unconventional superconductors which are sought after for their applications as a material platform for fault-tolerant quantum computing. Until now, however, only a handful of candidate materials are known, and the lack of understanding of what exactly drives those phases represents a major challenge. There is no "recipe" yet for how to systematically search for topological superconductors. Similarly, there is no widely accepted theory that explains the microscopic mechanisms behind unconventional superconductors in general. The presented work extends the weak coupling renormalization group method, which we employ to provide a systematic study of unconventional superconductivity in two dimensional lattice systems. One of the major goals is to find out which of the possible "ingredients" - lattice symmetries, longer-range effects, multi-orbital effects, topology of the non-interacting system, and spin-orbit interactions - can promote the formation of topological superconducting states. We apply our method to paradigmatic lattice models and use our results for benchmarking. We then study an application to real materials: a monolayer of tin adatoms on a silicon substrate and a comparison of the LNO/LAO heterostructure with a barium copper oxide superconductor. After that, we continue with an investigation of the effect of Rashba-spin orbit coupling, which breaks inversion symmetry and thus causes mixing of spin-singlet and spin-triplet states, and a study on the effect of different topologies of the non-interacting system on the superconducting state. One of the overarching conclusions is that strong longer-range effects, like longer-ranged hopping and nearest-neighbor interactions, tend to benefit topological superconductivity. Furthermore, lattices with hexagonal symmetry seem to be especially beneficial for topological superconducting states with (relatively) high critical temperature.
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ItemQuantum dynamics of atoms in intense laser fields( 2021)Intense laser-atom interactions are of research interest primarily due to their potential as a table-top source of coherent short-wavelength radiation. The production of this radiation, known as High Harmonic Generation (HHG), is driven by the electric field of the laser and depends on electron motion at timescales significantly shorter than the oscillation period of the field. The response of an atom is highly-nonlinear and can be modelled accurately only by the numerical solution Time-Dependent Schrodinger Equation (TDSE), a procedure which is computationally expensive. Such modelling is essential for the fine tuning or optimisation of these light sources. In this thesis, a novel method of performing TDSE integration is presented, based on the Stabilised Bi-Conjugate Gradient method (BiCG-STAB). This is an iterative procedure which allows substantial flexibility in the representation of the atomic wavefunction and the Hamiltonian operator. A requirement of this method is that the equations are suitably preconditioned to ensure smooth convergence of the algorithm. It is shown that the ability of this method to incorporate higher-order representations of the spatial and temporal derivatives with minimal cost is particularly advantageous. This method is shown to be faster than established methods, most notably in the computationally difficult cases of high laser intensity and long wavelength, or when the demands of accuracy are high. Using this method, the dynamics of atoms in intense laser fields are studied in a variety of contexts. The photoelectron spectra produced in interactions with atomic hydrogen are investigated in great detail as a function of laser pulse parameters. This is highly relevant to the use of photoelectron spectra as a calibration standard for laser systems. HHG in two colour fields is also investigated in two projects: the first of these examines selection rules of harmonic emission from two femtosecond pulses of incommensurate frequencies; the second project assesses the viability of enhancement of attosecond pulse generation through the introduction of a third harmonic field with a tunable phase. It is found that the production of relevant harmonics can be enhanced when the third harmonic is adjusted to boost ionisation at favourable parts of the cycle. Finally, a means of visualising and interpreting the output of TDSE simulations is investigated through the use of the Wigner quasi-probability distribution. This provides a phase space depiction of the evolution of atoms in strong laser fields that allows for direct comparison to semiclassical models. This builds upon previous applications of Wigner methods to strong field interactions by application to three-dimensional wavefunctions.