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(2021) Webb, DavidThesisPlanetary 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.
(2023) Ireland, JakeThesisPluripotent 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.
(2023) Al Taief, KarrarThesisSelf-assembled short peptide hydrogels based on natural proteins have been designed to mimic natural environment of extracellular matrix (ECM) in tissue. Yet this class of hydrogels solely lacks the ability to represent the entire complexity of the ECM. To address this problem, requires novel design of synthetic materials incorporating natural biopolymers. In this work, library of peptides based on protein motifs were designed that form self-assembled hydrogel. Animal source or human source biopolymers were then mixed with these peptides to fabricate dual-functional hybrid hydrogels. The incorporation of biopolymers at a concentration much lower than the peptide concentration, drastically enhanced the mechanical property of these hybrid systems. Both animal and human biopolymers are commercially available at high cost, however, incorporating minimum concentrations of both into this novel hybrid hydrogel will reduce the need for the biopolymer in a cost-effective manner. Additionally, these hybrid hydrogel systems are readily tuned by designing or re-arranging the target peptides sequences to fulfil the required applications of these hydrogels. Another peptide carrying cell-adhesion epitope, was designed based on a key binding motif for skin cells. The peptide self-assembled into self-supporting hydrogel. While biological compatibility of this gelator with skin cells was suboptimal over a long period of time, on the other hand, in 2D cultures of human Mesenchymal Stem Cells (hMSCs) no adverse reactions were noted and the hMSCs were shown to spread over a 7 days period on top of the hydrogel formed. Remarkably, exposure of this peptide to light triggered dynamic assembly. This photo-induced modulation of peptide assembly could be harvested for future therapeutic applications.
(2023) Pappas, BillyThesisDevices which exploit the quantum properties of materials are widespread, with information processors and sensors showing significant recent progress. Organic materials offer interesting opportunities for quantum technologies owing to their engineerable spin properties, with spintronic operation and magnetic field sensing demonstrated in research grade devices, as well as proven compatibility with large scale fabrication techniques. Yet several important challenges remain as we move toward scaling these proof-of-principle quantum devices to larger integrated logic systems or spatially smaller sensing elements – particularly those associated with the variation of spin properties both within and between devices. In this thesis, we explore three aspects influencing the homogeneity of spin interactions experienced by excitations in their local molecular environments – spatial, temporal and energetic variations. The resolution of these variations is realised through magneto-optical spin spectroscopy, whereby the modulation of optoelectronic processes in organic light-emitting diodes are imaged under the application of external magnetic fields. Using this technique, we map the spatiotemporal and energetic distributions of important spin quantum properties common to many molecular compounds, the results of which highlight the challenges of miniaturising and integrating these technologies for sensing and logic-based applications. In addition to characterising the variability of hyperfine interactions across the microscopic molecular landscape, we observe the spatial correlation of this property for lengths up to 7 micrometres in both a polymer and small molecule material, and dynamic at room temperature. The energy dependence of exchange interaction strengths were also resolved in thermally activated delayed fluorescence materials, with variabilities exceeding 50% and which should be accounted for in future design rules of high performance fluorescent molecules. Our investigations into the variation and correlation of spin interactions in space, time and energy provide important characterisations of the spin properties possessed by molecular materials for use in quantum devices. The miniaturisation, integration and scaling of technologies employing these materials will have to contend with this variation.
(2023) Lam, NgaThesisThe 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.