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Organisms have evolved a remarkable ability to mineralize complex skeletons and functional biomaterials. These structures are nucleated and grown in close associaiton with macromolecular assemblages of proteins and polysaccharides that are implicated in regulating all stagees of mineralization. Because of this intimate association of organic with inorgaic components, many studies have investigated the effects of particular organic species on mineral morphology, phase, and growth rate. However, the diversity and species-specific nature of the organic assemblages associated with biominerals across a wide variety of taxa, has limited our understanding of how organisms use biomolecules to regulate skeletal formation. It is clear that a mechanistic picture of biomolecular controls on mineralization requires molecular-level investigations of the interplay between organic and inorganic components at all stages of crystallizaiton. This dissertation presents the findings from theoretical and experimental studies of the physical mechanisms that underlie biomolecule controls on mineral formation. Molecular dynamics simulations probe the effects of acidic molecules on the hydration of alkaline earth cations. After first calculating baseline hydration properties for magnesium, calcium, strontium, and barium, I determine the effects of carboxylate-containing molecules on cation hydration state as well as the kinetics and thermodynamics of water exchange. Experimental work utilizes self-assembled monolayers as proxies for matrix macromolecules in order to understand their effects on CaCO3 nucleation kinetics and thermodynamics. Estimates of nucleation rates and barriers are made from optical microscopy data and correlated with measurements of crystal – substrate rupture force from dynamic force microscopy. These investigations show that an important function of biomolecules in directing mineralization lies in their ability to modulate cation hydration. Both chemical functionality and molecular conformation are influential in regulating the kinetics and thermodynamics of mineral nucleation, and these effects may be predicted by the strength of interaction between organic and inorganic components. These findings contribute to a mechanistic understanding of how organic matrices act to regulate biomineral formation. They demonstrate a plausible physical basis for how carboxyl-rich biomolecules accelerate the kinetics of biomineral growth and suggest roles for organic species in the nucleation and pre-nucleation stages of mineralization. / Ph. D.

Molecular cell biology has been an intensively studied interdisciplinary field with the rapid development of experimental techniques and fast upgrade of computational hardware and numerical tools. Recent technological developments have led to single-cell experiments which allow us to probe the role of stochasticity in cellular processes. Stochastic modeling of the corresponding processes is thus an essential ingredient for the understanding and interpretation of cellular systems of interest. In this thesis, we explore several nucleation-based stochastic cellular processes, i.e. Min protein oscillation in Escherichia coli, pausing phenomena in DNA transcription, and single-molecule enzyme kinetics. We focus on the key experimental results and build up stochastic models accordingly to provide quantitative insights to the underlying physical mechanisms for the corresponding biological processes. We utilize specific mathematical methods and computational algorithms to gain a better understanding and make predictions for further experimental explorations in the relevant fields. / Ph. D.

Microstructural data on the orientation and distribution of minerals can be utilized to better understand the processes controlling mineral crystallization during metamorphism and the extent to which equilibrium versus kinetic factors control the evolution of metamorphic rocks. Four studies in this dissertation address this, finding that: i) garnet crystals crystallize via epitaxial nucleation in which garnet crystallizes by templating on the crystal structure of muscovite; ii) the distribution of grain boundary void space at quartz-quartz and garnet-quartz grain boundaries is a function of the orientation of quartz crystals on either side of the grain boundary. There are more voids, and in some cases larger voids, at grain boundaries in which the a-axis of a neighboring quartz grain is perpendicular to the grain boundary than any other orientation; iii) the chemical potentials of garnet-forming components evolve differently in samples in which garnet growth either significantly or minimally overstepped equilibrium garnet-forming reactions; iv) the southwestern Meguma Terrane, Nova Scotia, experienced peak metamorphic conditions of ~630ºC and 4.0 kbar, likely resulting from regional metamorphism during the Neoacadian orogeny. A case study on the mechanisms controlling garnet crystallization in one Nova Scotian sample reveals that the rate limiting step of garnet crystallization was probably the diffusional transport of Al through the intergranular matrix. Taken together, this work has implications for understanding: i) the properties of grain boundaries in metamorphic rocks and ii) the extent to which equilibrium versus kinetic factors impact metamorphic petrogenesis. / Doctor of Philosophy / A fundamental question in the development of metamorphic rocks, or rocks that form due to changes in pressure and temperature conditions deep in the Earth's mountain belts, is: what controls the crystallization of new minerals? While pressure, temperature, and bulk composition likely play a major role in this, it is also possible that the distribution of reactant minerals and the transport of elements through the rock may also play a role in mineral crystallization. This dissertation explores several projects related to this broad topic. In one example, garnet, an important metamorphic mineral, was found to crystallize by utilizing the atomic structure of another mineral in the rock. This creates a favorable pathway for the crystallization of garnet, which preferentially grows on this 'parent' mineral. Further, the distribution of porosity, or void space, at the interfaces between mineral grains in metamorphic rocks is found to be controlled by the orientation of those minerals. This porosity likely formed when the rocks were exhumed from deep in the Earth towards its surface. Metamorphic rocks can also tell the story of continental plates colliding millions of years ago. In an example from the formation of the Appalachian Mountains ~400 million years ago, a combination of collisional tectonic forces and the heat from magmas in the shallow crust resulted in metamorphic rock, which make up much of southern Nova Scotia today. This work has important implications for understanding: i) porosity in metamorphic rocks and ii) how minerals crystallize during metamorphism.

Electrical properties of Si- and Mg-doped InAs epitaxial layers grown by MOCVD were studied by performing magneto-transport measurements at different temperatures, from 300 K down to 1.2 K. The longitudinal magnetoresistance and Hall effect indicate a three-band system existing in n-type (p-type) InAs, which consists of the surface accumulation (inversion) layer, the bulk electron (hole) layer, and the nucleation layer. Therefore, a classical parabolic background in magnetoresistance due to multi-carrier occurs at low fields. With the magnetic field being further applied, a linear magnetoresistance caused by inhomogeneities is revealed. At liquid helium temperature, the Shubnikov-de Haas magneto-oscillations are also observed. These transport characterizations provide a means of analyzing the band structure at the InAs surface. In a set of n-type InAs epilayers with Si doped at different levels, the bulk electron density increases as the doping level increases. The increased ionized impurities lead to lower electron mobilities due to more Coulomb scatterings. For all the n-type InAs films, except the two active layers (surface and the bulk), the nucleation layer contributes to the film conductivity as well with an electron density of ~ 5 x 10¹⁷ cm⁻³ and a mobility of ~ 2000 cm²}/Vs. In a cooldown process, the electron density of each layer slightly and monotonically decreases whereas the mobility experiences a maximum from the competition between phonon scatterings and Coulomb scatterings. The phonon scattering overwhelms the Coulomb scatting at high temperatures, but declines as temperature decreases, thus the mobility increases. Around 100 K, the temperature-independent ionized impurity scattering becomes comparable with and starts exceeding the phonon scattering, as temperature further lowered, the screening effect of the Coulomb scattering is weakened because of the decreased carrier densities. As a result, the mobility starts dropping. The maximum mobility corresponds to a minimum resistance, which explains the non-trivial temperature dependence of the resistance in the cooldown history. For the p-type InAs film, the doping with Mg in the course of MOCVD growth allows us to obtain a large hole density and a low mobility at 300 K. At low temperatures, holes are frozen out, and a strong negative magnetoresistance with a dip at 0 field are observed, which is the antilocalization signal from accumulation electrons. This is a strong technique to probe the surface quantum states and derive the phase coherence length and the spin flip length of surface electrons. / Master of Science

Aquatic environments contain a great diversity of microorganisms, some of which may be aerosolized and transported long distances through the atmosphere. The bacterium Pseudomonas syringae can be found in aquatic environments and in the atmosphere and may express an ice nucleation protein (bacteria expressing the protein are Ice+ and bacteria not expressing the protein are Ice-). Ice+ bacteria may be involved in cloud formation and precipitation processes due to their ability to freeze water at warmer temperatures. Freshwater aerosolization processes are not well understood, particularly the role the Ice+ phenotype may play. Water samples were collected from Claytor Lake, Virginia, USA and screened for Ice+ P. syringae. Results indicated that between 6% and 15% of Pseudomonas colonies assayed were Ice+. Preliminary phylogenetic analysis of cts (citrate synthase) sequences from strains of P. syringae showed a surprising diversity of phylogenetic subgroups present in the lake. A Collison nebulizer was used to aerosolize an Ice+ and an Ice- strain of P. syringae under artificial laboratory conditions. The aerosolization of P. syringae was not influenced by water temperature between 5° and 30°C. In general, the culturability (viability) of P. syringae in aerosols increased with temperature between 5 and 30°C. The Ice+ strain was aerosolized in greater numbers than the Ice- strain at all temperatures studied, suggesting a possible connection between the Ice+ phenotype and aerosol production. A quantitative empirical assessment of aerosolized droplets was generated using a laboratory flume and high-speed video. Droplet diameter and initial velocity upon leaving the water surface were examined at four wind speeds (3.5, 4.0, 4.5, and 5.0 m/s), and the results showed that droplet diameter and velocity had a gamma distribution and droplet mass flux increased exponentially with wind speed. An estimate of the potential amount of bacteria capable of aerosolizing was made for each wind speed. An interdisciplinary unit for advanced high school students has been developed presenting biological aerosolization and ice nucleation. This interdisciplinary work combines modeling and experimental approaches across biology and engineering interfaces, with the goal of increasing our understanding of microbial aerosols from aquatic environments that may impact our planet's water cycle. / Ph. D.

Investigations of polarization switching over broad time and electric field domains, in various modified Pb-based perovskite ferroelectrics, were systematically performed by ferroelectric switching current transient and bipolar drive P-E responses. Studies were performed from E«Ec to E»Ec, where Ec is the coercive field These investigations have shown the presence of broad relaxation time distributions for the switching process, which can extend over several decades in order of magnitude in time, and where the distribution is strongly dependent on the applied electric field. By performing the study of domain dynamics and polarization switching over extremely broad time domains (10⁻⁸ t < 10² sec), more complete information has been obtained that allows for development of a better mechanistic understanding. Prior polarization kinetics studies have focused on relatively narrow time ranges, and were fit to the Avarami equation, which contains a single relaxation time. However, our broad band width polarization dynamics and frequency relaxation studies have been fit to multiple stretched exponential functions extending over decades of order of magnitude in the time domain. Stretched exponential functions for domain nuclei formation, and for domain variant growth have been found. For example, [001]c, [110]c, and [111]c oriented PZN-4.5%PT crystals, nucleation was found to be a volume process (n=3) rather than just a domain wall restricted process. Consequently, nucleation is heterogeneous. And, growth of a domain variant with reversed polarization was found to be a boundary process (n=2), involving diffuse or rough domain walls. We have extended these studies to various types of ferroelectrics including hard, soft and relaxor types. / Master of Science

Molecular dynamics simulations are use to study the energetics and deformation response of random grain boundaries in polycrystalline Nickel. Computer generated samples of defect-free Ni were created, plastically deformed, and examined as a baseline understanding to the underlying mechanisms of deformation and intergranular fracture in FCC metals. Two types of samples were utilized: a sample with columnar grains consisting of pure <110> tilt boundaries and a thin-film sample with 3D grain orientations modeled after an experimental sample of austenitic steel. The structure and energies of these random boundaries under stress and temperature was analyzed. Heterogeneous displacement maps were made for a side-by-side comparison of the dislocation activity and interactions with the grain boundaries. The dislocation behavior was found to be consistent between the two digital sample types and further comparison with experimental samples was made. The intergranular cracking behavior was also studied and various factors were examined to generate general trends. Crack initiation was observed to typically occur in random high-angle boundaries close to a triple junction where the cracks have high angles with respect to the tensile loading direction. The cracking results from the simulations agree well with current preliminary results of experimentally deformed austenitic steel samples. Furthermore, the behavior and failure of the thin-film sample is compared with its corresponding experimental sample. / Master of Science