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(2021)ThesisThe electrochemical water splitting reaction, which consists of hydrogen reduction at the cathode and oxygen evolution (OER) at the anode, is one of the core processes for the utilization of sustainable and green energy sources. However, the sluggish kinetics of the oxygen evolution reaction requires a higher overpotential than the theoretical potential (1.23 V). Engineering a high-performance electrocatalyst is an avenue to improve the reaction kinetics for OER. Bimetallic branched nanoparticles offer substantial benefits for OER electrocatalysts; which include a greatly increased exposed surface area, highly crystalline hcp branches and stable surfaces. This thesis aims to design branched nanoparticles as electrocatalysts for enhanced OER in the following ways: (i) extending the cubic-core hexagonal-branch growth approach for a new bimetallic (Co, Au) system, (ii) leveraging the advantages of the Ru-Pd branched nanoparticles by tuning the surface facets and branch number, and (iii) making branched nanoparticles consisting of a cubic core (Pd) and alloyed branches (RuCo). Chapter one discusses the literature on the oxygen evolution reaction and Co- and Ru-based electrocatalysts for OER as well as the organic solution-phase synthesis method. The limiting factors of Co- and Ru- based catalysts and the strategies for improving their catalytic performance are also summarized. Also outlined is the fundamental understanding for synthesizing metallic nanoparticles using a seed-mediated growth approach in an organic solution phase and controlling the shape and size of the final products. Chapter two describes the synthetic methodology, sample purification, ink preparation for electrochemical measurements and characterization techniques in more detail. Chapter three provides the synthetic approaches and challenges in making Co and Ru branched nanoparticles. Chapter four compares the OER catalytic activity and stability of the Co-Au branched nanoparticles with the Co-Au core-shell and Co3O4 nanoparticles in alkaline media. The improved catalytic performance of the branched nanoparticles can be attributed to the formation of an active and stable oxide layer on the branch surface. Chapter five investigates the effect of branch number, and surface facets on the catalytic properties of the Ru-Pd branched nanoparticles with tunable branch number and surface facets. It is found that tuning surface facets and branch length is essential for enhancing catalytic performance by increasing the exposure of more active sites and improving the accessibility of the catalytic surface to the catalytic reaction. Chapter six explores alloyed branched nanoparticles consisting of a Pd core and RuCo branches and assesses their catalytic activity for OER electrocatalysts. It is demonstrated that Co leaching during catalytic activation in acid solution increases the exposure of highly catalytically active sites on the branch surface resulting in enhanced catalytic activity. Chapter seven concludes the overall results and achievements of this thesis and also discusses future opportunities.
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(2021)ThesisWith a theoretical capacity of 1672 mA h g-1, more than five times higher than any commercially available lithium-ion (Li-ion) cell systems, the lithium-sulfur (Li-S) cell is an attractive candidate for next generation energy storage. Despite this high theoretical capacity, Li-S cells generally suffer from poor capacity retention and working lifetimes that prevent them from mass commercialisation. This is mainly due to current limitations in managing the inherent Li-S redox reactions which involve diffusion and migration of electrochemically active polysulfides. One approach to prevent polysulfide migration is by rational design of the sulfur electrode framework. The aim of this research is to investigate the electrochemical implications of using different frameworks for entrapment of redox active species, mainly designed for the Li-S cell system. The two types of frameworks investigated are: (1) mixed-morphology carbon feeds derived from waste sources wherein the intention is for the carbon to purely act as a structural framework to trap lithium polysulfides, and (2) sulfur-rich copolymers wherein redox active sulfur is covalently bound within the framework. More specifically, the goals involve determining: (1) whether carbon acts purely as a structural framework to trap redox active species during electrochemistry, and (2) whether sulfur-rich copolymers act purely as a sulfur feed. Achieving these goals requires a thorough understanding of what properties in each framework are ideal for the Li-S cell. The main conclusion drawn from this work is that neither of the materials studied behaved as pure structural or covalent frameworks partaking in various side processes. Using specialised techniques such as X-ray powder diffraction, solid-state NMR, and X-ray absorption near-edge structure spectroscopy, the beneficial and parasitic side processes involved in each framework are able to be determined. Overall, a significantly enhanced understanding of the Li S cell chemistry when using these materials is presented in this work.
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(2021)ThesisPhotosynthesis has played a key role in the evolutionary trajectory of life on Earth. The ways in which organisms harvest sunlight have diversified over the billions of years since photosynthesis emerged in the quest for more efficient use of this energy source. The evolutionary origins of some organisms’ light harvesting apparatus, however, have remained elusive as have the causes for stark architectural changes between evolutionarily related organisms. In this thesis, I firstly provide a detailed exploration of published data describing photosynthetic efficiency through the lens of structural biology and quantum mechanics, examining observations from a range of antenna systems. After having built a framework for how an efficient photosynthetic antenna may be constructed, the rest of this thesis explores the evolutionary trajectory of the light harvesting antenna of the cryptophyte algae. Cryptophytes are a clade of secondary endosymbiotic algae which gained their photosynthetic chloroplasts from an engulfed red alga, but produced in an architecturally distinct antenna. Red algae have an antenna comprised of stacked protein rings that form an energetic funnel to the photosynthetic reaction centre which generates chemical energy from photon excitations. Cryptophytes took this energy funnel and dismantled it; complexing one of its component proteins with a peptide of unknown origin (‘cryptophyte alpha’) and packing them at high density within the chloroplast. By examining recently published cryo-electron microscopy maps of red algal antennas, I have discovered the evolutionary ancestor of the unique cryptophyte alpha subunit. Through this discovery, I reveal possible evolutionary events following secondary endosymbiosis leading to the origin of the cryptophyte light harvesting system. Finally, I examine the light harvesting antenna of a particular cryptophyte species, Hemiselmis andersenii, isolating multiple protein components and determining their crystal structures at high resolution. Through this, I discover a more complex antenna than previously thought with multiple protein components and a rich energetic structure. Some of these antenna proteins show previously unrecognised spectral properties and chromophore architecture. This structural data aids in understanding the architectural change between the red algal and cryptophyte light harvesting antennas and further diversification within the cryptophyte clade.
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(2021)ThesisPlanetary waves play a role in a large variety of oceanic and climate dynamics. In particular, Kelvin waves can provide rapid teleconnections from large-scale climate and weather events to remote regions of the globe. Kelvin waves may be partially responsible for linking climatic changes in Southern Ocean winds to increases in subsurface warming around Antarctica that can lead to glacial ice-melt and increases in global sea level rise. Kelvin waves may also link changes in Southern Ocean winds to increases in North Atlantic Deep Water (NADW) formation and an enhancement of the Atlantic Meridional Overturning Circulation (AMOC), which is responsible for circulating a vast amount of the ocean’s heat and nutrient content. However, the exact role of Kelvin waves in these processes is unclear. This thesis aims to further clarify the role that Kelvin waves play in these high-latitude climate processes. First, we use a suite of idealized models in order to better understand the dynamics of barotropic Kelvin waves around Antarctica. We find that super-inertial (high frequency) barotropic Kelvin waves are nearly completely scattered away from the Antarctic coastline due to a combination of coastal geometry and bathymetry. Sub-inertial (low frequency) barotropic Kelvin waves are mostly scattered away from the Antarctic coastline due to bathymetry, however a significant amount of barotropic Kelvin wave energy remains at the Antarctic coastline after one circumnavigation of the continent, enabling a gradual build-up of energy along the coast and the ability to sustain a barotropic Kelvin wave signal around Antarctica over time. Secondly, we perform a diagnostic study using theory and a range of varying resolution model simulations to quantify the amount of subsurface warming along the West Antarctic Peninsula caused by barotropic Kelvin waves via an induced bottom Ekman flow that advects warm Circumpolar Deep Water onto the Antarctic continental shelf. We find that barotropic Kelvin waves can account for a substantial amount of warming within one year, depending on the background temperature gradients and thickness of the bottom Ekman layer. Lastly, we explore the role of Kelvin waves in linking Southern Ocean wind-stress to NADW formation and the AMOC by analysing ensemble simulations from a fully-coupled ocean-sea-ice model at 1/4 degree horizontal resolution (50 vertical levels). We find first mode baroclinic Kelvin waves to propagate along a global coastal and equatorial waveguide from the Southern Ocean forcing region to the North Atlantic, where downwelling waves initiate an enhancement of the AMOC by making surface waters denser.
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(2022)ThesisTime series models are used to model, simulate, and forecast the behaviour of a phenomenon over time based on data recorded over consistent intervals. The digital era has resulted in data being captured and archived in unprecedented amounts, such that vast amounts of information are available for analysis. Feature-rich time-series datasets are one of the data sets that have become available due to the expanding trend of data collection technologies worldwide. With the application of time series analysis to support financial and managerial decision-making, the development and advancement of time series models in the transportation domain are unavoidable. As a result, this thesis redefines time series models for transportation planning use with the following three aims: (1) To combine parametric and bootstrapping techniques within time series models; (2) to develop a time series model capable of modelling both temporal and spatial dependencies in time-series data; and (3) to leverage the hierarchical Bayesian modelling paradigm to accommodate flexible representations of heterogeneity in data. The first main chapter introduces an ensemble of ARIMA models. It compares its performance against conventional ARIMA (a parametric method) and LSTM models (a non-parametric method) for short-term traffic volume prediction. The second main chapter introduces a copula time series model that describes correlations between variables through time and space. Temporal correlations are modelled by an ARMA-GARCH model which enables a modeller to describe heteroscedastic data. The copula model has a flexible correlation structure and is used to model spatial correlations with the ability to model nonlinear, tailed and asymmetric correlations. The third main chapter provides a Bayesian modelling framework to raise awareness about using hierarchical Bayesian approaches for transport time series data. In addition, this chapter presents a Bayesian copula model. The combination of the two models provides a fully Bayesian approach to modelling both temporal and spatial correlations. Compared with frequentist models, the proposed modelling structures can incorporate prior knowledge. In the fourth main chapter, the fully Bayesian model is used to investigate mobility patterns before, during and after the COVID-19 pandemic using social media data. A more focused analysis is conducted on the mobility patterns of Twitter users from different zones and land use types.
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(2022)ThesisSinglet fission is a photo-physical process that generates two triplet excitons from one singlet exciton and can potentially enhance efficiency in photovoltaic systems. The combination of photovoltaics and singlet fission is a novel field for solar energy conversion when there is much interest in renewable, non-destructive, and continuously available energy sources. Singlet fission can also overcome thermalization losses in photovoltaics, which happens in traditional cells when the incident photon energy is higher than the silicon bandgap energy, using a carrier multiplication mechanism. This thesis will design, construct, and characterize photovoltaic devices incorporating singlet fission materials to study singlet fission in practical application. The research focuses on materials characterization, spin dynamics, and electron transfers between acene and the semiconductor layer in Au/TiO2 ballistic cells, and the incorporation of singlet fission layers on silicon-based cell structures. In detail, a set of investigations was developed and summarized by implementing singlet fission materials into a state-of-the-art ballistic photovoltaic device and silicon-based solar cell. The studies demonstrate proof of concept and rationally explain the process. The first part of the thesis investigates thin films of pentacene, TIPS-pentacene, and tetracene via crystallinity, morphology, absorption, and thickness characterization. Additionally, Au and TiO2 layers in Schottky device structures were optimized to achieve the best performance for energy transfer from an applied dye layer (merbromin). The drop-casted dye layer influences the device performance by increasing short-circuit current and open-circuit voltage, demonstrating the ability of charge transfer between the device and the applied film. This device structure provides a test bed for studying charge and energy transfer from singlet fission films. The latter part of the thesis describes several investigations to understand singlet fission in a thin film using this architecture. Magneto-photoconductivity measurements were primarily used to observe the spin dynamics via photoconductivity under an external magnetic field. Control experiments with bare Au/TiO2 devices showed no observable magneto-photoconductivity signal. In contrast, devices with pentacene and tetracene singlet fission layers showed a strong magnetoconductivity effect caused by ballistic electron transfer from the singlet fission layer into the TiO2 n-type semiconductor through an ultra-thin gold layer inserted between the layers. A qualitatively different behavior is seen between the pentacene and tetracene, which reveals that the energy alignment plays a crucial part in the charge transfer between the singlet fission layer and the device. The last section investigates the application of pentacene and tetracene evaporated thin-films as sensitizer layers to a silicon-based solar cell. The optimized Si cell structure with the annealing treatment improved the cell's performance by increasing short-circuit current and open-circuit voltage. The deposition of pentacene and tetracene as sensitizer layers into the device showed some results but posed several challenges that need to be addressed. As the current-voltage and external quantum efficiency measurements were taken, it was observed that material interfaces need to be designed to fully achieve the singlet fission of the acene layer into the Si devices.
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(2021)ThesisPiezoelectric single crystals provide a large electro-mechanical response that is desired for sensor and actuator applications. However, the complexity and cost of single crystal growth inhibits their widespread use. Alternatively, polycrystalline piezoelectrics can be easily fabricated at low cost. Due to the anisotropic piezoelectric response, the electro-mechanical response of polycrystals is largely limited by the elastic coupling of randomly aligned grains. Microstructural engineering via crystallographic texturing of polycrystalline ceramics offers an alternative method that both enhances the electro-mechanical response while maintaining an economical fabrication process. There is currently limited understanding on how the changes in the microstructure from the texturing process, such as the addition of heterogenous templates and changes in grain orientation distribution, impacts the electro-mechanical response mechanisms. Understanding the structural and electro-mechanical mechanism that enhances the piezoelectric response will benefit sensor and actuator applications such as sonar systems and medical imaging instruments. In this thesis, a range of techniques were used to study the microstructural changes and the strain mechanisms from crystallographic texturing, and its impact on the electro-mechanical response. The local response of electro-mechanical phase-change ceramics was investigated by theoretical calculations to see how texturing changed the strain heterogeneity at the grain-scale. Textured ceramics of Pb(Mg1/3Nb2/3)O3− x%PbTiO3 (PMN-PT) were fabricated by tape casting and templated grain growth, using BaTiO3 platelet templates. The structure of these textured ceramics was characterised using synchrotron x-ray diffraction to gain a more comprehensive understanding on the texture that develops. In situ electric-field dependent diffraction measurements were then used to study how texture affects the electro-mechanical response mechanism. And lastly, the piezoelectric non-linearity and response stability over time was analysed in the direct piezoelectric response mode. Changes in electric-field-induced phase transformation local strain response in polycrystalline piezoelectrics of varying grain orientation distribution was studied through theoretical calculations. The March-Dollase function was used to generate texture distributions in a model polycrystal, and strains associated with phase transitions from pseudo-cubic to tetragonal, rhombohedral and orthorhombic symmetries were calculated. In the tetragonal system, the overall strain response was improved by 60% with crystallographic texture, at very strong texture (of March Dollase distribution r = 0.05); and the local strain heterogeneity was similar to the random system. However, moderate increases in texture had a negative impact on the strain heterogeneity. In crystallographic symmetries with higher numbers of possible polarization (and thus spontaneous strain) directions, the magnitude of the strain response increased, and the heterogeneity of the system decreased. Using high energy x-ray diffraction and in situ electric-field dependent measurements, the microstructural modifications due to crystallographic texturing and the resulting electro-mechanical response mechanisms were investigated. Structural analysis of textured ceramics, by calculating the orientation distribution function (ODF), showed that sheet-like texture developed in the piezoelectric. Texture characterisation, by calculating the ODF, was able to provide a more comprehensive quantification of texture than the Lotgering factor, where multiple samples with a 95% Lotgering factor showed different ODFs and maximum Multiples of Random Distribution (MRD) values of 12.8 and 16.54. In addition to the crystallographic texture observed in the diffraction pattern, a ferroelastic texture was also seen. Termed the ‘self-poling effect’, this unique structural distortion reduced the remanent strain of the textured piezoelectric to 0.13% after poling to 2 kV/mm, while the random (untextured) ceramic produced a remanent strain of 0.18% after poling to 2 kV/mm. On a subsequent unipolar strain cycle, however, the textured ceramic achieved a larger response of 0.16% compared to 0.096% of random ceramic. A new strain mechanism model was proposed to explain the relationship between the self-poling effect and the observed strain behaviour. Finally, the direct piezoelectric response in textured ceramics was measured to understand the piezoelectric non-linearity and response stability under application-like conditions. By applying a static offset and dynamic sinusoidal compressive loading, the d33 and d32 response were measured. The piezoelectric non-linear behaviour increased with crystallographic texturing. In particular, the piezoelectric property in the d33 mode, deteriorated faster and was more unstable, losing around 60% of its original d33 value once the offset load was released. On the other hand, the d32 response of texture ceramics was able to recover 90% of its original response after loading. Furthermore, the stability of the piezoelectric response in textured piezoelectric was observed to be compositionally dependent, where the d32 response decayed over time faster in PMN-31PT than in PMN-32PT. The results from this thesis shows that crystallographic texturing alters the local strain environment, affecting the electro-mechanical response mechanisms, both enhancing the response but also potentially degrading the expected lifetime and performance of these ceramics. Further work in understanding the microstructural interaction with the electro-mechanical response will help to optimise texture fabrication of piezoelectric materials for industrial applicability.
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(2023)ThesisPluripotent stem cell-derived cardiomyocytes (hPSC–CM) have great importance for predicting safety parameters for pharmaceutical compounds and models of healthy versus disease states of the human heart. In recent years, there has been an insistence that all new pharmaceutical products are tested on in vitro models for potential proarrhythmic effects and the increased demand for improved biomimetic hPSC-CM in pharmaceutical safety assays such as the Comprehensive in vitro Proarrhythmic Assay (CiPA). In addition, hPSC-CM are being utilised in cell therapies to treat and reverse the effects of ischaemic heart disease, offering potential cures for cardiovascular diseases instead of treatments for delaying progressive heart failure. In the first part of this thesis, I will examine how purified extracellular matrix proteins (ECMPs) can influence pluripotent stem cell (PSC) behaviour and how we may use this to precondition cardiac progenitor lineage specifications. I use array-based techniques to investigate how protein combinations affect proliferation, pluripotency, germ layer, and cardiac progenitors. This method allows us to visualise how individual proteins can affect cells' behaviour in a larger array whilst highlighting how specific combinations can precondition pluripotent cells towards a cardiomyocyte lineage. This combinatorial approach led to the identification of several unique matrices that promote differentiation, which will aid efforts at producing therapeutically useful cell types with greater efficiency. In the second part of this thesis, I demonstrate a novel bioreactor that attenuates a magnetic field to dynamically modulate the stiffness of magnetoactive hydrogel to look at how biomimetic dynamic stiffening of a substrate can influence cardiomyocyte lineage specification. We investigate how biomimetic in vivo mechanics may influence cell fate by following the expression profiles of cells in different dynamic environments. Non-invasive electromagnetic signals affect substrate stiffness when combined with magnetic particles and magnetic fibres and how this can help direct cell orientation and accompanying lineage specification Finally, I investigate how variability in cell phenotypes and expression patterns are influenced by biomimetic cues and how these variabilities could be utilised in future safety assessment protocols and cell therapy treatments for cardiovascular disease.
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(2023)ThesisDistinct localisation of macromolecular structures relative to cell shape is a common feature across the domains of life. One mechanism for achieving spatiotemporal intracellular organisation is the Turing reaction-diffusion system (e.g. Min system in the bacterium Escherichia coli controlling in cell division). In this thesis, I explore potential Turing systems in archaea and eukaryotes as well as the effects of subdiffusion. Recently, a MinD homologue, MinD4, in the archaeon Haloferax volcanii was found to form a dynamic spatiotemporal pattern that is distinct from E. coli in its localisation and function. I investigate all four archaeal Min paralogue systems in H. volcanii by identifying four putative MinD activator proteins based on their genomic location and show that they alter motility but do not control MinD4 patterning. Additionally, one of these proteins shows remarkably fast dynamic motion with speeds comparable to eukaryotic molecular motors, while its function appears to be to control motility via interaction with the archaellum. In metazoa, neurons are highly specialised cells whose functions rely on the proper segregation of proteins to the axonal and somatodendritic compartments. These compartments are bounded by a structure called the axon initial segment (AIS) which is precisely positioned in the proximal axonal region during early neuronal development. How neurons control these self-organised localisations is poorly understood. Using a top-down analysis of developing neurons in vitro, I show that the AIS lies at the nodal plane of the first non-homogeneous spatial harmonic of the neuron shape while a key axonal protein, Tau, is distributed with a concentration that matches the same harmonic. These results are consistent with an underlying Turing patterning system which remains to be identified. The complex intracellular environment often gives rise to the subdiffusive dynamics of molecules that may affect patterning. To simulate the subdiffusive transport of biopolymers, I develop a stochastic simulation algorithm based on the continuous time random walk framework, which is then applied to a model of a dimeric molecular motor. This provides insight into the effects of subdiffusion on motor dynamics, where subdiffusion reduces motor speed while increasing the stall force. Overall, this thesis makes progress towards understanding intracellular patterning systems in different organisms, across the domains of life.
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(2022)ThesisSponges can harbour diverse communities of microbial symbionts, collectively referred to as a holobiont. Sponge symbionts play important ecological and mutualistic roles, including cycling of carbon, nitrogen, and sulfur; provisioning the host with essential compounds; and producing bioactive metabolites that confer fitness advantages to the holobiont. Recent metagenomics and bioinformatics advances facilitate genomic reconstruction and metabolic characterisation of uncultured prokaryotic species. Leveraging these tools, I reconstructed 75 metagenome-assembled genomes (MAGs) that represent 21 novel sponge-associated species: ten Gammaproteobacteria, six Acidimicrobiia, and five Acidobacteriota. The gammaproteobacterial species were metabolically diverse, likely representing adaptations to diverse habitats associated with different sponge species. Two species from the Candidatus genus Azotimanducus comprised almost identical patterns of organoheterotrophy that likely enabled them to colonize the same sponge host, but differed in other features that likely allowed for niche partitioning and cohabitation. Unlike the sponge-associated Gammaproteobacteria, the Acidimicrobiia shared very similar genomic features. Of particular interest, sponge-associated Acidimicrobiia were predicted to produce bioactive compounds that may modulate host signalling pathways, suggesting a potential role in host health. The sponge-associated Acidobacteriota likely predominantly formed symbiosis with their hosts prior to the phylogenetic split between sponges and corals. All five acidobacteriotal species shared similar patterns of organoheterotrophy, likely allowing for scavenging organic substrates from the host environment. Another feature that was specifically enriched in the novel sponge-associated Acidobacteriota was their capacity to produce diverse B-vitamins, with Candidatus Versatilivorator vitaminiformans comprising the genetic capacity to produce all of them. All 21 novel species also comprised unique respiratory, degradation, biosynthetic, and defensive features that likely mediate their interactions with the corresponding hosts. Features shared by the majority of the species were also identified. Altogether, the comprehensive genomic characterisation of sponge symbionts in this thesis has uncovered unique and shared features, highlighting the importance of extensive surveys into uncultured sponge symbiont diversity and function.