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(2014)ThesisIn this thesis we present single-shot spin readout of precision placed phosphorus donors in silicon. The spin states of an electron bound to phosphorus donors in silicon make promising building blocks for the realisation of a solid state quantum computer due to their remarkably long coherence and relaxation times. Recent progress in scanning tunnelling microscope (STM) lithography has made it possible to place these donors with atomic accuracy, opening the way to individual qubit control and hence scalability. We present spin readout from two different STM-patterned devices where the electron spin qubit is hosted by either a cluster of about four phosphorus donors or a single phosphorus donor and tunnel-coupled to an atomically planar single electron transistor (SET). We demonstrate high fidelity (approx. 90%) single shot spin readout of the cluster qubit via spin-to-charge conversion and show long spin life times of T1 = 1.3 s (B=1.5 T) despite the multi-donor, multi-electron character of the spin qubit. For the single P donor we extrapolate a slightly larger T1 of approx. 6 s at B=1.5 T, consistent with previous measurements of single donor spin life times. Using atomistic tight-binding calculations, we confirm the dependency of the relaxation rate on both donor and electron numbers, where we show that multi-donor single-electron systems provide the highest T1. We also demonstrate the concept of using the single donor as a spectrometer to analyse the energy level structure of the SET island. Finally, the successful spin readout of the cluster qubit with long measured T1 provides an opportunity to use cluster qubits in conjunction with single donor qubits to achieve qubit addressability by a global microwave field with very low error rates. We show by atomistic tight binding modelling, that the electron spin resonance (ESR) frequency of a double donor qubit can be separated by up to 350 MHz from the ESR frequency of a single donor qubit due to the difference in the hyperfine coupling, allowing qubit rotations with error rates as low as approx. 10^(-5). Together, these results advance STM device fabrication technology towards the realisation of scalable donor based qubit architectures in silicon.
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(2015)ThesisColour is one of nature’s most remarkable signal features, and plays crucial roles in numerous biological interactions. This thesis uses modern comparative methods to quantify trends in colouration across macroecological gradients. To advance the study of biogeographical patterns in colour, I needed to establish the best methodological approach for quantitative cross-taxa analyses. Analysis of bird and flower colours revealed that to quantify a species’ colour to within 5% of the true mean, only one sample is really necessary. Brightness is more variable, requiring four samples to achieve this precision. The idea that species in tropical regions are more colourful than those at higher latitudes has endured for more than a century. I provide the first taxonomically and spatially broad, quantitative test of the colourful tropics hypothesis. I measured the colours of 570 bird species, 424 butterfly species and flowers of 339 Angiosperm species using reflectance spectrometry and wave-band limited photography. I calculated colour brightness, saturation, diversity, hue disparity and maximum contrast for each species. Phylogenetic and cross-species analyses showed that birds, butterflies and flowers in tropical regions are not on average more colourful than species in higher latitudes, and formally reject the long-standing hypothesis. Next, I determined which biotic and abiotic factors were most influential in shaping macroecological patterns in colouration, and evaluated the generality of several current hypotheses regarding environmental drivers of colour. Relationships between flower colouration and environmental variables were often opposite to those of bird and butterfly colours. For example, birds and butterflies tend to be less colour-saturated under high solar radiation, while flowers tend to be more colour-saturated. Macroecological gradients in flower colour were best predicted by rainfall and the diversity of plants and of pollinating insects, while bird and butterfly colours were best predicted by bird diversity, solar radiation and temperature. Birds, butterflies and flowers show similar latitudinal gradients in colour, but these are driven by different environmental variables. My thesis substantially advances comparative analysis of colouration. As well as finally quantifying the latitudinal gradients in colour, this research will inform future study design, and enable development of novel hypotheses in colour ecology and evolution.
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(2015)ThesisMiniaturisation of electronic devices has driven development of high speed, high density processors and memory elements. This process has required extensive optimisation of semiconductor materials and interfaces as the random nature of doping increasingly affects device performance and the influence of non-ideal surfaces and interfaces need to be counteracted. As Moore's law for silicon may soon reach its limit, there is a desire to harness electrically efficient III-V semiconductor materials in an economically viable way. There is also a desire to utilise new functionalities brought by quantum mechanics, thermoelectrics and organic materials. This thesis explores the role of p-type AlGaAs/GaAs heterostructures, self-assembled semiconductor nanowires and organic polymer electrolytes in this broad research programme. My research investigated the impact of background potentials generated by doping and surface states for quantum devices. I developed new wrap-gating techniques for InAs semiconductor nanowires towards economically viable arrays of III-V transistors on silicon substrates. This involved both conventional metal/oxide wrap-gates as well as nanoscale patterning of polymer electrolyte films to both improve the compatibility of organics with nanostructures and seek new functionalities for nanowire transistors. I then used polymer electrolytes to both act as an external dopant, and set the background potential for nanowire thermoelectrics. I also developed proof-of-principle complementary n- and p-type proton-to-electron transducers. Throughout, I highlight the importance of dopants and surfaces. I show how these non-ideal aspects of semiconductor devices affect performance and attempt to find solutions where possible by, e.g., using sulfur-based surface passivation solutions or polymer electrolytes as an external dopant. Using these examples I illustrate that the drive to develop new technologies leads to new physics on both ends. Imperfections in research devices lead to new understanding of material physics, and once these are overcome, the new functionalities embodied by the devices can be used to study new aspects of nature.
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(2013)ThesisPulverized coal injection (PCI) technology is widely used in ironmaking blast furnaces due to its various benefits. Therefore it is natural to seek further improvements to maximise its benefits. An extensive study has discovered that PCI technology can be further improved by co-firing coal with coal blends, charcoal and other injectants. Effects of these injectants have been experimentally studied to reveal the complex in-furnace physicochemical phenomenon. However these studies are insufficient in describing the key governing phenomena. Hence numerical studies is preferred to overcome the limitations. In the first half of this thesis, the combustion behaviours of coal blends and charcoal are investigated in a pilot-scale test-rig using a three-dimensional computational fluid dynamics (3D CFD) model. The results show that the combustion efficiency of ternary blends is higher than binary blends by 4-8% for the same fraction of highest volatile coal due to the higher synergistic effect. The combustion efficiency of charcoal is found to be higher than coal by 10% for the same volatile matter content and sizing due to the faster char combustion. A raceway is a cavity formed from the injection of a high speed jet into the packed coke bed. Blast furnace operation is heavily dependent on the supply of heat and gas from the raceway to the surrounding coke bed for the smelting purpose. Therefore when the PCI is used, the combustion of coal inside the raceway is important for determining the heat and gas distributions. The majority of past studies have focused on the effect of PCI technology on the raceway formations. Therefore in the latter half of this thesis, the effects of raceway shape and size on the PCI performances are investigated. The PCI in the raceway is simulated in a full-scale 3D CFD model. The results indicate that the combustion efficiency of coal can be improved with an enlarged recirculation zone and/or shortened jet and their extension. Increasing the raceway size is also found to improve the combustion efficiency as the particle travelling time is extended. The findings in this thesis are helpful to understand and optimize PCI operations in practice.
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(2012)ThesisNext generation sequencing (NGS) is defined by parallel sequencing of short DNA fragments, or ‘reads’. In ‘deep sequencing’ studies, aligned NGS reads are treated as a population sample, with genetic variation in individual reads being meaningful. Deep sequencing has revolutionised the study of microbial evolution. However, distinguishing single nucleotide variants (SNVs) from sequencing errors remains challenging. In this thesis, I first show the power of deep sequencing in a hepatitis C virus (HCV) study. Using published methods and manual analysis, SNVs with frequencies down to 0.1% were detected. Phylogenetic analysis indicated early HCV evolution is driven by two bottlenecks, associated with transmission and immune response respectively. The HCV study's SNV calling methods are then developed and improved, by introducing a statistical test of strand bias (to remove systematic errors) combined with probabilistic read clustering (to remove random errors). The validity of this method is supported through formal statistical argument and analysis of control HCV and HIV data. While control data is an invaluable tool for assessing SNV calling, it is not always available. To overcome this limitation, I implemented the software GemSIM. GemSIM creates and uses empirically derived, sequence context based error models to emulate individual sequencing runs. Analysis of models from Illumina and Roche-454 data showed that error profiles vary even between different runs of the same technology, affecting SNV calling accuracy. Finally, I performed a pioneering application of deep sequencing to bacteria. Using matched samples, variants with frequencies down to 0.5% were detected in biofilms from Pseudomonas aeruginosa 18A (a clinical isolate) and PA01 (a lab strain). Biofilm microevolution was reproducible within a strain: PA01 biofilms featured rapid evolution and growth of PA01’s phage Pf4, with strong selection for c repressor mutants; while 18A biofilms featured selection of specific variants within the bacterial genome. Comparison with a Phaeobacter gallaciensis biofilm indicated that in general, adaptation within biofilms is typified by selection for a small number of non-synonymous variants within key genes involved in biofilm and competition related pathways. In conclusion, through careful analysis, experimental design, and the use of controls, sequence errors may be overcome, allowing deep sequencing to reveal the molecular evolution of microbes in unprecedented detail.
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(2013)ThesisDiscoveries of aerobic coal degrading microorganisms have led to their utilisation in various biotechnological coal processes. One promising application of these microbes is the acceleration of coal to methane, which provides an avenue for more sustainable coal usage. However, despite the various findings of coal degraders and related mechanisms, a key aspect in coal degradation, which is cell attachment and colonisation, has been largely neglected. This study is among the first to describe in detail microbial cell attachment and colonisation on coal. Using coal-degrading bacteria and fungi, the initial cell attachment and biofilm formation on coal were investigated across different coal types and conditions. Physico-chemical analyses based on contact angle measurements revealed that hydrophobicity, surface free energy and adhesion thermodynamics, as well as secondary biological and environmental factors, played a crucial role in governing the first form of cell interaction with coal. Direct observation and electron microscopy highlighted different colonisation mechanisms on coal based on cell morphology, surface topography and environmental conditions. Correlations were found between colonisation and degradation of coal, which stressed the importance of cell attachment in coal degradation, although exceptions were present. Another interest of this study was to isolate native coal-degrading fungi for potential field applications. Through multiple coal degradation screenings, Fusarium oxysporum G9o was discovered as a promising bituminous coal-degrading fungus. The isolate showed softening of raw bituminous coal, and infrared analyses revealed oxidation and cleaving mechanisms of coal components. Further, the colonisation of coal by soil communities was monitored through microbial community analyses using Terminal- Restriction Fragment Length Polymorphism (T-RFLP) and pyrosequencing analyses. Unique communities from soil were identified as dominant colonisers on coal, which have not been previously revealed through conventional cultural techniques. Overall, the findings in this study provide valuable insights into the mechanisms of cell attachment and colonisation on coal. This serves as a foundation for a new research area in coal microbiology, which will increase our currently limited understanding on coal-cell interactions.
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(2013)ThesisTiH2 powder has been trialled as an alternative to Ti-powder to fabricate titanium-based products. To enhance the utilization of TiH2 powder, further understanding of the dehydrogenation mechanism of TiH2, the effect of hydrogen on dehydrogenated and equal channel angular pressed (ECAP) samples and on the fabrication of titanium matrix composites (TMC) is critical. This research work analysed the phase transformation steps of TiH2 to Ti using high-temperature X-Ray Diffraction with the dehydrogenation step occurring under both isothermal and non-isothermal conditions. Crystallographic data was obtained through Rietveld analysis. Results showed that, with increasing temperature expansion occurred, which was negated by the phase transformations due to dehydrogenation. The sequence of TiH2 phase transformations were: delta−>delta’−>beta−>beta’−>alpha−>alpha’-phase. Further confirmation of the mechanistic steps was obtained through thermogravimetric analysis, transmission electron microscopy and selected area electron diffraction studies. The dehydrogenation reaction of compacted TiH2 powder was investigated in terms of four parameters, namely, heating rates, compaction pressures, temperatures and times, in order to optimize the dehydrogenation process. The hydrogen loss and bulk density decreased with increasing heating rate while the density and hardness improved with the increasing in temperature and time. TMCs were fabricated using TiH2 powder containing SiC or TiB2 as the reinforcement. In samples with SiC, when the sintering temperature was increased, the density, hardness and the reaction layer (TixSiyCz layer) were found to increase. However, the density and hardness decreased when TiB2 powder content increased. Hardness values were affected by the H2 content in the matrix and the reinforcement. Back-pressure ECAP on sintered TiH2 samples was carried out at 590°C using route C, where the sample is rotated 180° with focus on the hydrogen effect. Density of the ECAP samples reduced when the hydrogen content was increased. The presence of hydrogen improved the hardness and tensile strength, but the ductility was lowered. Dehydrogenation is very crucial step for TiH2 powder because of the phase transition from delta−>beta−>alpha-titanium, which is a critical step in the fabrication of TMC and titanium alloys from TiH2 powder.
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(2017)ThesisSpintronics (“spin transport electronics” or “spin electronics”) is an emerging technology where information is encoded in spin rather than charge. With a view to incorporate spin in semiconductor physics, strongly spin-orbit coupled systems such as semiconductor holes have generated burgeoning interest. Motivated by the recent progress in achieving all-electrical spin control in hole systems, this thesis seeks to further the understanding of spin-orbit interactions in low-dimensional semiconductor hole systems. In particular, we consider various inversion-asymmetric two- (2D) and one-dimensional (1D) hole systems where the energy levels are split by the spin-orbit interaction. Firstly, we consider 2D holes in single heterojunctions. We combine the variational method, perturbation theory, and theory of invariants to derive an analytical expression for the spin-orbit interaction terms. The spin splitting is calculated as a function of hole density and dopant type. We demonstrate the semianalytical approach is readily generalizable to various materials, and show results for common semiconductors GaAs, Ge, InSb, InAs, and Si. The analytical results yield the correct trend that the strength of spin-orbit interaction increases with density and molecular weight. Furthermore, we find that in zincblende materials with a finite Dresselhaus spin-orbit interaction, the Rashba spin-orbit interaction is still the dominant contribution to the spin splitting. Secondly, we experimentally demonstrate electrical control of Rashba and in-plane Zeeman spin splittings of 2D holes in a (100) top- and back-gated GaAs quantum (QW). We show that the in-plane Zeeman splitting increases faster with the in-plane magnetic field at high densities. We also find that both Rashba and in-plane Zeeman splitting are suppressed when the QW is asymmetric, consistent with the fact that the heavy-light hole splitting increases with QW asymmetry. These findings reflect the nature of the J = 3/2 spin quantization axis of heavy holes. Finally, we investigate spin to charge conversion in one-dimensional GaAs holes. In a mesoscopic structure with a strong spin-orbit coupling, spin accumulation can be generated from a charge current. In this chapter, we exploit the energy-dependent transmission through a quantum point contact (QPC) to detect conversion between spin and charge currents in both linear and non-linear régimes.