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Methane (CH4), the cleanest burning fossil fuel, has the potential to solve the energy crisis owing to the growing population and geopolitical tensions. Whilst highly calorific, realising its potential requires efficient storage solutions, which are safe and less energy-intensive during production and transportation. On the other hand, carbon dioxide (CO2), the by-product of human activities, exacerbates global heating driving climate change. CH4 is abundant in natural systems, in the form of gas hydrate and trapped gas within geological formations. The primary aim of this project was to learn how Nature could store such a large quantity of CH4 and how we can potentially extract and replace the in-place CH4 with atmospheric CO2, thereby reducing greenhouse gas emissions. We studied this question by applying molecular dynamics (MD) and Monte Carlo (MC) simulation techniques. Such techniques allow us to understand the behaviour of confined fluids, i.e., within the micropores of silica and kerogen matrices. Our simulations showed that CH4 hydrate in confinement could form under milder conditions than required, deviating from the typical methane-water phase diagram, complementing experimental observations. This research can contribute to artificial gas hydrate production via porous materials for gas storage. Besides that, the creation of 3D kerogen models via simulated annealing has enabled us to understand how maturity level affects the structural heterogeneity of the matrices and, ultimately CH4 diffusion. Immature and overmature kerogen types were identified to having fast CH4 diffusion. Subsequently, our proof-of-concept study demonstrated the feasibility of recovering CH4 via supercritical CO2 injection into kerogens. Insights from our study also explained why full recovery of CH4 is impossible. A pseudo-second-order rate law can predict the kinetics of such a process and the replacement quantity. A higher CO2 input required than the CH4 recovered highlights the possibility of achieving a net-zero future via geological CO2 sequestration.

This thesis explores the formation and operation of shrimp economies that bring together multiple species and their ecological conditions of production through capitalist and more-than-capitalist relations in contexts of agrarian, technical, and environmental changes. It focuses on the Mekong Delta in Vietnam, where due to climate change and salinity intrusion, farmers and companies are shifting from growing rice to breeding shrimp in an effort to adapt to climate change and help alleviate poverty. These strategies of adaptation and livelihood, however, also have effects on delta ecologies and economies. The research draws these dynamics together at the intersection of water and society, or hydro-social life, to examine different sites amid the history of water management in the Mekong Delta. Multi-species and multi-sited ethnography were conducted, following shrimp through the hatchery, the shrimp farm, and the laboratory within and beyond the Mekong Delta. This research argues that shrimp economies, as a form of bioeconomy, are formed and constructed by organising hydro-social lives across three sites: (1) shrimp reproduction in the hatchery, (2) shrimp growth on the farm, and (3) scientific research in the laboratory. Hydro-social lives assemble and reassemble water-shrimp-human-environment relations to create the material basis of shrimp production. Meanwhile, hydro-social lives involve both capitalist and more-than-capitalist relations, which drive significant agrarian, technical, and environmental changes to farmers and capitalists within and beyond the Mekong Delta. This study makes three original contributions. First, it extends work in political economy and political ecology on the socio-natural organisation of commodity production by analysing the materiality of shrimp production, and capitalist and more-than-capitalist relations in bioeconomies. Second, it contributes to water research by examining how water-shrimp-human-environment relations are integral to the production of aquatic animals. Third, it unfolds hydro-social life in the hatchery, the delta, and the laboratory to examine these complex and dynamic relations in different environments, contributing to delta studies and STS.

The current study examines the interfacial behaviour and foaming potential of poly(vinylpyrrolidone) (PVP, 40 kDa)-silica composite nanoparticles. Individually, the two components, PVP and hydrophilic silica nanoparticles, exhibit very little foaming potential. In contrast, combining the two components to form silica-PVP core-shell nanocomposites via polymer physisorption leads to good ‘foamability’ and long-term foam stability. Optical reflectivity (OR) measurements showed that the adsorption of PVP on silica can be regarded as irreversible with the saturated polymer surface excess around 1 mg/m2, in good agreement with the thermogravimetric analysis (TGA) data. The adsorbed 40 kDa PVP film is highly hydrated (contained water 40-55 wt%), behaving as a steric barrier, which helps to keep the particles apart. Addition of an electrolyte (Na2SO4) was shown to have a marked effect on the foam stability. By varying Na2SO4 concentration between 0 and 0.55 M, three regions of foam stability were observed: rapid foam collapse (≤ 0.01 M), delayed foam collapse at 0.1 M, and long-term stability (~ 10 days) at 0.55 M. The observed transitions in foam stability were better understood by studying the microstructure and rheological properties of the particle-laden interfaces using different techniques such as Langmuir trough, Interfacial Shear Rheometer (ISR400), Brewster angle microscopy (BAM) and cryo scanning electron microscope (cryo-SEM). Meanwhile, the 2D structure of particle-laden interfaces surrounding an air bubble and deposited at a planar interface were correlated using cryo-SEM and BAM images to elucidate the interfacial shear rheology of particle-stabilized bubbles and its relation to foam stability. For rapidly collapsing foams, the interfaces were characterized as being “liquid-like”. By contrast, the enhanced foam stability at 0.1 M and 0.55 M Na2SO4 was attributed to the formation of solid-like (pseudo solid-like for the 0.1 M particle layer) interfacial particle layers surrounding bubbles, at a compression state in the region of the liquid to solid (L-S) phase transition. The increased interfacial rigidity was attributed to adhesion between interpenetrating polymer layers. For the most stable foam (prepared in 0.55 M Na2SO4), particles strongly aggregated at the interface into a connected particle network, forming a strongly elastic interfacial layer. Hence, bubble-bubble coalescence was found to be significantly retarded by the aggregation of nanocomposite particles at 0.55 M, with the long term destabilization resulting from bubble coarsening. For rapidly destabilizing foams, however, the contribution from bubble-bubble coalescence was shown to be more significant. Further investigations need to be carried out to prevent bubble coarsening.

The transfer of mitochondria, whether through natural or artificial pathways, has been experimentally validated across various cell lines, demonstrating potential benefits for host cells experiencing mitochondrial dysfunction. However, conflicting reports suggest that our understanding of the outcomes of mitochondria transfer in host cells remains incomplete. This dissertation aims to delve into the concept of mitochondria transfer and examine its effects on metabolism, viability, and oxidative stress in breast cancer host cells. The novelty of this dissertation lies in the utilization of fluorescence lifetime imaging to analyze the metabolic profiles of individual mitochondria. Through the combination of fluorescence labeling and NADH lifetime imaging, we have discovered that newly formed mitochondria in breast cancer host cells exhibit an increase in the bound fraction of NADH, indicating a reliance on Oxidative Phosphorylation (OXPHOS). While the enhancement of OXPHOS leads to heightened respiration and proliferation, the accumulation of reactive oxygen species (ROS) levels surpasses the tolerance threshold of breast cancer cells towards oxidative stress, resulting in elevated drug sensitivity when exposed to anticancer drugs. The significance of this dissertation resides in its multifaceted approach, shedding light on the impact of mitochondria transfer and establishing new methodologies for future research endeavors.

Effective use of renewable energy resources has been regarded as the most promising solution to climate emergency and energy crisis. However, the fluctuating and intermittent nature of renewable resources causes stability issues in the electric grid. High-capacity electrical energy storage is essential to stabilize the electric power supply using renewable resources. Among various types of energy storage systems, organic redox flow battery (ORFB) has attracted attentions due to their high stability, flexibility, low cost, and environmental compatibility, but the performance of the ORFB still needs a significant improvement due to their low energy or current density. Specifically, even though the efficiency of the electrode, where the redox reactions occur, is critical to the ORFB performance, the disordered structures of widely used carbon-based electrodes hinder the convective flux of electrolytes. This makes the ion transport through the electrodes very restricted, which is a major challenge in ORFB. To overcome the major challenge while enhancing or maintaining other electrode properties, directional graphene aerogel (DGA) was proposed as an electrode material, and the DGA synthesis and ion transport for its electrode application are discussed here. As DGAs are synthesized by freeze casting, the control of water-ice phase change and the effect of graphene-water interaction on freezing and structuring are important to develop the DGA synthesis. Also, understanding of ion transport through graphene channels with convective flux should be enhanced for the design of effective DGA electrodes. Multiscale simulations employing molecular dynamics and finite volume methods were conducted to investigate the propagation and shape of the water-ice interface under various freezing conditions (e.g., temperature, crystal orientation, container geometry, etc.) and the ion electric mobility with convective flux under different graphene-surface interactions and channel conditions. Through this research, I identified 1) various ice propagation control methods and structuring mechanisms during the freezing, 2) the roles of the Rayleigh-Bénard convection on the propagation and shape of the water-ice interface, and 3) the effects of surface interaction on the ion mobility in graphene nanochannels under the coupling of field- and pressure-driven transport. This research explores new possibilities to enhance the ion transport of DGA electrodes for ORFB.

In order to enable detailed biological studies with the naturally occurring enantiomer and test the feasibility of our synthetic route, a large scale synthesis towards (–)-muironolide A was carried out. A series of optimizations on the synthesis of different fragments were achieved, including the diene amine and chlorocyclopropyl ketide. A newly designed chiral terpyridine was tested as a ligand in the key intramolecular Diels-Alder reaction.In another research area of mine, chiral lithium amides derived from C2-symmetric tetraamines, acting as non-covalent chiral auxiliaries, provide a pathway to generate tetrasubstituted and quaternary carbon centers directly through the -functionalization of carboxylic acids. All chiral amines can be easily recovered by acid-base extraction with no loss of enantiomeric purity. Crystallographic, spectroscopic and computational studies elucidated the structure of an enediolate-lithium amide mixed aggregate as the origin of stereoselectivity. Using a similar aggregation process, the alkylation of ,-unsaturated carboxylic acid was also achieved with both high enantio- and regioselectivity. This method was attempted as a key step to establish the chirality in the concise synthesis of (–)-morphine, and resulted in a competing conjugate addition of dienoic acid in the presence of an activated alkyl halide. Inspired by the competition reaction, a method of enantioselective Michael-initiated ring closure was developed. Carbocyclic compounds can be synthesized in good to excellent stereoselectivities, providing a streamlined approach to the construction of densely functionalized cycloalkanes.

Ultrasound is a type of mechanical energies that have been widely employed in clinical diagnosis and therapeutic use. The overall goal of this dissertation is to further develop ultrasound-based imaging modality in assisting cancer diagnosis and explore the transcranial focused ultrasound (tFUS) in brain stimulation. In this dissertation, I firstly summarize my research on detecting cancer by harnessing a passive-mode ultrasound generated by magnetoacoustics. Probing the electrical conductivity of in vivo tissues, a high-frequency magnetoacoustic tomography with magnetic induction (hfMAT-MI) imaging system has been developed for cancer imaging with 1-mm spatial resolution. With the aid of magnetic nanoparticles (MNPs), the magnetoacoustic tomography is further enhanced in the imaging contrast and thus used to reconstruct the in vivo biodistribution of MNPs noninvasively. By reversing the imaging model, I secondly introduce my studies of transmitting active-mode pulsed ultrasound in a transcranial way and electrically sensing global and local brain responses to the deposited low-intensity ultrasound energy. In this second research topic, non-invasive electroencephalography (EEG)-based source imaging (ESI) is used to map the whole brain dynamics, which allows to better understand the effects of tFUS stimulation with high spatiotemporal resolutions. Furthermore, towards a mechanistic investigation, intracranial electrophysiological recordings from in vivo brains receiving low-intensity tFUS uncover an intrinsic cell-type specificity of neurons in responding to levels of ultrasound pulse repetition frequencies. Potential confounding factors, i.e. auditory side effects and somatosensation are also studied to thus identify the direct neuronal effects induced by the tFUS in vivo.

In this thesis, we aim to develop robust multi-level micromechanical constitutive models for human bone tissues. First, the hierarchical microstructure of human bones is considered, and a multi-scale micromechanical homogenization scheme is proposed in Chapter 3. The proposed framework predicts that the pattern of mineralization and the shape of the mineral crystals serve to improve the mechanical function of collagen fibrils along the longitudinal axis. The numerical results in comparison to the experimental data from nanoindentation tests reflect a predictive precision and demonstrate the capability of the current micromechanical model to simulate the key behavior at this scale. The effects of collagen fibril orientations upon the elastic properties of bone lamellae or lamellar units are studied in the following chapter. The homogenized anisotropic elastic properties of bone lamellae or lamellar units are estimated using an innovative method: multiscale homogenized model of ultrastructure combined with a micromechanical framework of layered composite for lamellar units and fibril orientation patterns observed in the experiments. Five fibril orientation patterns are compared in this study - the orthogonal and twisted plywood pattern, the five sublayer pattern, an X-ray diffraction-based pattern, and a microscopy observed pattern. The model results show the deviation of fibrillar orientation from the anatomical axis (osteon axis) and demonstrate that the elastic mechanical behaviors of bone lamellae vary with different fibril orientation patterns. The proposed method opens new possibilities in the exploitation of fibrillar orientation data and provides a better understanding of the mechanical properties of bone lamellae. The effects of accumulation of diffuse damage in human bone upon the material properties of lamellae are investigated in Chapter 5. A three-parameter formulation is adopted to characterize the evolution of density of microcracks. An effective elastic micromechanical damage formulation for bone with evolutionary matrix cracking is then proposed based on Ju and Tseng's micromechanical damage formulation. It is demonstrated that microdamage exists in bone in vivo, accumulates with age and contributes to the degradation of bone's material properties. In Chapter 6, on the basis of constant-shear model, the rising R-curve behavior of human cortical bone at the lamella level is studied with the framework of linear-elastic fracture mechanics combined with multi-scale effective elastic micromechanical model for lamella. By taking advantage of cumulative probability function or Weibull distribution, the effect of collagen fiber breakage is simulated. The distribution and evolution of fiber bridging stress, crack mouth opening, and stress intensity factor then are analyzed by considering the probable fiber breakage. Crack bridging by collagen fibrils in toughening cortical bone was first time investigated systematically. A three-dimensional structural model composed of two different unit cells, which have distinct mechanical behavior in the vertical direction, with doubly tapered struts for human vertebral cancellous bone is proposed in Chapter 7. The ensemble-volume and orientation averaging procedures are employed to derive the equations. The effects of age-related changes in vertebral cancellous bone on effective stiffness and collapse stress in both horizontal and vertical directions are studied. The predicted mechanical behaviors of human vertebral cancellous bone are generally consistent with experimental observations in the literatures.

A QTL (Quantitative Trait Locus) is chromosomal location of a gene controlling a specific phenotypic characteristic (trait). This trait might be governed by two or more genes and may be affected by environmental interaction. The USA soybean seed composition, when averaged over years and states, is 18.7% oil and 35.3% protein. Soybean seed provides cooking oil for humans and protein for livestock. Concurrent genetic improvement of seed protein (pro) and oil content has been difficult to achieve due to the negative genetic correlation of the two traits. This negative correlation could be due to a pair of tightly linked protein and oil QTLs, whose individual alleles are linkage-paired to give rise to high pro - low oil or low pro – high oil, phenotypes, OR it could be due to just one pleiotropic QTL, whose two alleles have inverse effects on both oil and protein. This thesis objective is to find oil QTLs with minimal effect on protein. Three F2 populations were developed by mating of two high oil lines with each other and with Williams 82, a current high-yield cultivar. About 500 individual F2 plants in each population produced F2.3 seed progenies and then F2.4 seed progenies that were phenotyped for seed protein and oil content. Selective genotyping was used to genotype F2 plant progenitors of only the highest and the lowest seed oil deciles of F2.4 seed progenies. A 1536 SNP locus assay chip was used for genotyping. In the three mapping populations, eight seed oil QTLs with LOD scores greater than 3.0 were detected and mapped on seven linkage groups using R/qtl software. Six statistically significant seed oil QTLs on LG-C2 (Chr6), LG-M (Chr7), LG-B1 (Chr11), LG-F (Chr13), LG-E (Chr15), and LG-L (Chr19) were detected using genome-wide permutation tests (α = 0.05). Of the seed oil QTLs detected in this study, only the seed oil QTLs on LG-F (Chr13) have no significant impact on seed protein content. For improving the seed oil content in high yielding soybean cultivars, S17276 allele (Chr13) from the parental line RMLPC1-311-128-128 may be useful to soybean breeders to improve soybean seed oil content without effecting on seed protein content. Advisor: James E. Specht

The rigorous developments of GIS over the past decades have enabled application developers to create powerful systems that are used to facilitate the management of spatial data. Unfortunately, each one of these systems is specific to a local service, with little or no interconnection with services in other locales. This makes it virtually impossible to perform dynamic and interactive GIS operations across multiple locales which have similar or dissimilar system configurations. The Spatial Data Transfer Standard (SDTS) resolved the problems partially by offering excellent conceptual and logical abstraction model for data exchange. Recent advancements of the Internet enlightened the GIS community as to the realization of an ideal concept of information interchange. A suite of new technologies that embraces Extensible Markup Language (XML), Scalable Vector Graphics (SVG), Portable Network Graphics (PNG) and Java creates a powerful and new perspective that can be applied to all phases of online GIS system development. The online GIS is a Web-based approach to integrating diverse spatial data sources for GIS applications. To address the spatial data integration options and implications related to the Web-based approach the investigation was undertaken in 5 phases: (1) Determine the mapping requirements of graphic and non-graphic spatial data for online GIS application; (2) Analyze the requirements of spatial data integration for online environments; (3) Investigate a suitable method for integrating different formats of spatial data; (4) Study the feasibility and applicability of setting up the online GIS; and (5) Develop a prototype for online sharing of teaching resources. Resulting from the critical review on current Internet technology, a conceptual framework for spatial data integration was proposed. This framework was based on the emerging Internet technology on XML, SVG, PNG, and Java. It was comprised of four loosely coupled modules, namely, Application Interface, Presentation, Integrator, and Data module. This loosely coupled framework provides an environment that will be independent of the underlying GIS data structure and makes it easy to change or update the system as a new task or knowledge is acquired. A feasibility study was conducted to test the applicability for the proposed conceptual framework. A detailed user requirements and system specification was thus devised from the feasibility study. These user requirements and system specification provided some guidelines for online GIS application development. They were expressed specifically in terms of six aspects: (1) User; (2) Teaching resources management; (3) Data; (4) Cartography; (5) Functions; and (6) Software development configuration. A prototype system based on some of the devised system specifications was developed. In the prototype software design, the architecture of a Three-Tier Client-Server computing model was adopted. Due to the inadequacy of native support for SVG and PNG in all currently available Web browsers, the prototype was thus implemented in HTML, Java and vendor specific vector format. The prototype demonstrated how teaching resources from a variety of sources and format (including map data and non-map resources) were integrated and shared. The implementation of the prototype revealed that the Web is still an ideal medium for providing wider accessibility of geographical information to a larger number of users through a corporate intranet or the Internet cost-effectively. The investigation concluded that current WWW technology is limited in its capability for spatial data integration and delivering online functionality. However, developing of XML-based GIS data model and graphic standards SVG and PNG for structuring and transferring spatial data on the Internet appear to be providing solutions to the current limitations. It is believed that the ideal world where everyone retrieving spatial information contextually through a Web browser disregarding the information format and location will eventually become true.