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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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(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)ThesisThis thesis represents an effort to understand the structure of anisotropically strained Bismuth Ferrite (BiFeO3 BFO). This is executed by using anisotropic epitaxy and exploring the structure, magnetism, and electromechanical response in anisotropically strained BFO at various levels of average in-plane strain. This includes in the vicinity of the strain-induced morphotropic phase boundary where large enhancements to the electromechanical performance are identified. Bismuth ferrite (BFO) is a room-temperature magnetoelectric material that is able to easily adapt its crystal structure to accomodate any strain that is applied to it. By utilising high-index crystallographic substrates the effect anisotropic epitaxial strain has been explored using three different substrate materials (SrTiO3, (LaAlO3)0.3(Sr2TaAlO6)0.7 (LSAT), and LaAlO3) each with four orientations. The unit cell parameters of the BFO films behave linearly when weakly compressively strained on SrTiO3, and become more non-linear on LSAT. The strain-driven morphotropic phase boundary in BFO films grown on tilted LaAlO3(310) surfaces is able to stabilise a low-symmetry bridging phase between the well known M_A and M_C symmetries of BFO when deposited on SrTiO3 and LaAlO3 respectively. The anisotropic strain conditions of the substrate miscut force the BFO film to maintain strain along a high-symmetry in-plane direction whilst partially relaxing in the orthogonal low-symmetry in-plane direction. Interferometric displacement sensor (IDS) measurements indicate that the intrinsic piezoresponse of this new phase of BFO is double that of the R'-like version. Moreover we see spectroscopic indications through IDS and band-excitation frequency response measurements that there is a field-induced phase transition occurring under electric field wherein the low-symmetry phase is reversibly interconverted into the tetragonal-like phase creating a giant effective electromechanical response. These observations are fully supported by density functional theory and effective Hamiltonian calculations. When growing thicker films of this soft low-symmetry phase, a rich and detailed phase coexistence between the R', T', and bridging phase arise that is reminiscent of a highly tilted mixed-phase BFO. The topography of these samples also exhibit domain-like periodic stripes that evolve with the crystallography and are intimately linked together. \\ At the end of this thesis a number of neutron scattering experiments are presented on BFO films on YAlO3, LaAlO3, LSAT, and SrTiO3 substrates. Despite calculations and some experimental hints of a C-type antiferromagnetic phase in T'-BFO, there appears to be no evidence of this magnetic phase in BFO//YAO and BFO//LAO. Additionally, a cycloid model has been developed and implemented in order to fit ambiguous cycloidal peaks with a constrained model. This model is applied to two different systems of BFO with the results and interpretations discussed.
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(2023)ThesisHigh-entropy alloys (HEAs) are a new class of metallic materials that contain five or more elements in near-equiatomic compositions and that have received significant research attention in the past decade. The reason for this is that some alloy systems have been reported to crystallise as single-phase materials with face-centred cubic (FCC) crystal structure despite their individual elements often having very different crystal structures. One such example, the CrMnFeCoNi alloy, one of the first HEAs reported by Cantor et al. in 2004, has, furthermore, excellent combinations of mechanical properties such as high strength, excellent ductility, and outstanding fracture toughness at room temperature; interestingly, in contrast to many other materials, these properties improve with decreasing temperature down to liquid nitrogen. The reason for this is the staggered activation of deformation mechanisms such as dislocation glide and nano-scale deformation twinning. While numerous studies have reported the CrMnFeCoNi alloy as well as many other multi-component alloy systems to be chemically homogeneous, little attention has been drawn to the impact of processing history on chemical complexity and as such clustering and ordering phenomena that may impact mechanical performance. In this work, CrMnFeCoNi alloys have been fabricated using different processing routes resulting in a chemically homogeneous and a chemically heterogeneous versions of the material. Using various characterisation methods such as a wavelength-dispersive x-ray spectroscopy-based electron micro-probe analyser (WDXS-EPMA) in combination with energy-dispersive x-ray spectroscopy (EDXS) and atom probe tomography (APT), methods that can be utilised across multiple length scales, element composition as well as spatial distribution of the materials have been investigated. The two materials have furthermore been utilised for an APT parameter study to tailor data acquisition parameter for multi-component alloy systems to obtain high quality atom probe data. Based on the obtained results, a generalised multi-component short-range order (GM-SRO) parameter study was conducted to analyse ordering phenomena in the APT data of the HEAs and compared with medium-entropy alloy subsystems containing 3-4 elements and that can be associated with the HEAs in terms of their mechanical and/or elastic properties. Finally, two non-equiatomic alloys from the chemically distinct regions of the heterogeneous material were fabricated and compared in terms of microstructure development and associated mechanical performance to each other and the equiatomic HEA.
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(2023)ThesisPiezoelectrics are used widely in the microelectronics sectors as sensors, actuators, transducers, capacitors, tunable microwave devices, electrocaloric coolers, etc. The presence of lead in these materials represents an environmental driving force to develop lead-free alternatives. In the present work, the effects of Sn4+ on the solid solubility mechanisms, defect chemistry, phase equilibria, piezoelectric properties, and electrocaloric and energy-storage performances of lead-free (Ba0.85Ca0.15)([Ti0.92 xSnx]Zr0.08)O3 (x = 0.00 0.10) have been examined. The samples were synthesized by solid-state sintering at 1500°C for 12 h in air. The materials were characterized in terms of RT XRD, HT XRD, DSC/TGA, SEM/EDS, XPS, pycnometry, firing shrinkage, Raman, PL, dielectric measurements, and piezoelectric measurements. Despite the widespread assumption of substantial solid solubility, with Sn4+ as a neutral dopant, integration of X-ray photoelectron spectroscopy data and defect equilibria showed that interstitial solid solubility occurred at all Sn4+ doping levels for the three polymorphs obtained, which were orthorhombic Pmm2, tetragonal P4mm, and cubic Pm-3m; simultaneous substitutional solid solubility in tetragonal P4mm was deduced. It also was possible to distinguish the inferred solute distributions as ordered or disordered. The fundamental materials data were interpreted in terms of three solid solubility mechanisms, which were clarified further by the elucidation of four property and performance regions as a function of Sn4+ doping level. The former were separated by two stress-induced phase transformations at x = 0.04 and x = 0.08, which resulted in inflections in the sigmoidal trends in properties and performance as a function of Sn4+ doping level, which were chemical-induced. These trends were directly attributable to the dominant solid solubility mechanism, thus highlighting the importance of knowledge of this factor. While these trends were exemplified by fundamental materials characterization parameters, a higher level of understanding was revealed through the electromechanical characterization, which allowed inference of the order vs disorder of the solid solutions. Integration of these two types of data enabled a comprehensive understanding of the chemical and structural features of these materials and their critical roles in properties and performance. This synthesis also enabled the preparation of a new morphotropic phase diagram, a behavioral phase diagram illustrating the effects of temperature and Sn4+ dopant level on the phase stabilities and invariant points, and a revised BaO-TiO2 equilibrium phase diagram. The present work highlights the importance of the solid solubility mechanism to materials selection, processing, properties, performance, and interpretation of the relevant mechanisms.
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(2023)ThesisComplex borohydrides have the potential to act as solid-state electrolytes for all-solid-state batteries. In this respect, sodium borohydride (NaBH4) is of high interest because it is thermally stable (up to 500 degrees celsius), and it has a high deformability and electrochemical stability against sodium anodes. However, its ionic conductivity at room temperature is extremely low ( ~ 10-10 S cm-1). Accordingly, this thesis aimed at investigating means to create defective NaBH4 structures with the intent to significantly enhance its ionic conductivity. To this aim, several strategies were investigated including the creation of intermediate interfaces, partial anionic substitution, the generation of defects and conducting interfaces through partial hydrolysis. By converting the surface of NaBH4 particles into Na2B12H12 of higher Na+ conductivity, to form NaBH4@Na2B12H12 core-shell structures, the resulting interface was found to lead to an ionic conductivity of 4 × 10-4 S cm-1at 115 degrees celsius, i.e., significantly higher to that of pristine Na2B12H12 (10-7 S cm-1). This demonstrates that it was possible to generate disordered interfaces trough anion mixing. The results suggested that the creation of defects may be more prone to lead to high ionic conductivity. Through partial substitution of BH4- anion by I- in NaBH4, defective NaBH4 structures with varied lattice constants could be created. This anion substitution strategy enhanced the ionic conductivity of NaBH4 doped with NaI to 1.6 × 10-3 S cm-1 at 65 degrees celsius. To further improve upon this, the idea of partial hydrolysis was also investigated with the idea to create both conductivity interfaces and defective NaBH4 structures by exposing NaBH4 to controlled amount of water. The disordered trapped interface located between alpha-NaBH4 and NaB(OH)4 showed fast Na+ dynamics, which led to a Na+ conductivity of 2.6 × 10-3 S cm-1 at 75 degrees celsius. Further addition of poly(ethylene oxide) (PEO) was found to help better control the levels of hydrolysis and the hydrolysed NaBH4-PEO composite electrolyte reached an ionic conductivity of 1.6 × 10-3 S cm-1 at 45 degrees celsius. These results indicate that the controlled formation of defects within NaBH4 is key to the conversion of such hydrides into superionic Na conductors.
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(2023)ThesisLuminescent nanoparticles have shown wide applications ranging from lighting, display, sensors, and biomedical diagnostics and imaging. Among these, fluorescent nanodiamonds (FNDs) containing nitrogen-vacancy (NV) color centers are posed as emerging materials particularly in biomedical and biological imaging applications due to their room-temperature emission, excellent photo- and chemical- stability, high bio-compatibility, and versatile functionalization potentials. The shape variation of nanoparticles has a decisive influence on their fluorescence. However, current relative studies are limited by the lack of reliable statistical analysis of nanoparticle shape and the difficulty of achieving a precise correlation between shape/structure and optical measurements of large numbers of individual nanoparticles. Therefore, new methods are urgently needed to overcome these challenges to assist in nanoparticle synthesis control and fluorescence performance optimization. In this thesis a new correlative TEM and photoluminescence (PL) microscopy (TEMPL) method has been developed that combines the measurements of the optical properties and the materials structure at the exact same particle and sample area, so that accurate correlation can be established to statistically study the FND morphology/structure and PL properties, at the single nanoparticle level. Moreover, machine learning based methods have been developed for categorizing the 2D and 3D shapes of a large number of nanoparticles generated in TEMPL method. This ML-assisted TEMPL method has been applied to understand the PL correlation with the size and shape of FNDs at the single particle level. In this thesis, a strong correlation between particle morphology and NV fluorescence in FND particles has been revealed: thin, flake-like particles produce enhanced fluorescence. The robustness of this trend is proven in FND with different surface oxidation treatments. This finding offers guidance for fluorescence-optimized sensing applications of FND, by controlling the shape of the particles in fabrication. Overall the TEMPL methodology developed in the thesis provides a versatile and general way to study the shape and fluorescence relationship of various nanoparticles and opens up the possibility of correlation methods between other characterisation techniques.
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(2023)ThesisThe self-assembly of proteins into intricate high-order structures can be harnessed for the precise positioning of functional molecules in nanotechnology. The organisation of enzymes on protein scaffolds has been previously shown to enhance enzyme catalytic activity. Additionally, the alignment of metal-binding proteins, known as metalloproteins, on filamentous proteins has been exploited to produce electrically conductive nanowires. The focus of this thesis is on the development of improved biosynthetic strategies for the creation of multifunctional nanomaterials by harnessing the self-assembly of filamentous proteins. Central to the engineering in this thesis is prefoldin, which is a molecular chaperone from archaea with the ability to self-assemble into hetero-hexameric complexes and filamentous structures. Prefoldin proteins exhibits high thermal stability and have engineerable interfaces for bioconjugation of functional proteins. Therefore, the research goal of this thesis was to engineer robust and modular protein scaffolds for the precise position of enzymes and alignment of electrically conductive subunits to create biocatalysis and bioelectronic systems. The first aim of the research was to construct a protein scaffold from a hexameric self-assembling protein and immobilise enzymes on the protein scaffold to examine for enhanced sequential catalytic reactions. The second aim explored the capability of prefoldin filaments to align various metalloproteins in proximity over large distances for electron transfer. Distinct metalloproteins were exploited to create nanowires with various electronic properties for applications in bioelectronic devices. The third aim developed a strategy to localise redox enzymes at either end of the metalloprotein nanowires and potentially demonstrate energy transfer along the nanowire between enzymes undergoing redox reactions. The successful achievement of these aims establishes a biostrategy to use a controllable and modular prefoldin protein scaffold for the fabrication of biocatalysis and bioelectronic devices.
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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.