The only elements that were made in significant quantity during the Big Bang were hydrogen and helium, and to a lesser extent lithium. Depending on the initial mass of a star, it may eject some or all of the unique, newly formed elements into the interstellar medium. The enriched gas later collapses into new stars, which are able to form heavier elements due to the presence of the new elements. When we observe the abundances in a stellar regions, we are able to glean the astrophysical phenomena that occurred prior to its formation. I compile spectroscopic abundance data from 49 literature sources for 46 elements across 2836 stars in the solar neighborhood, within 150 pc of the Sun, to produce the Hypatia Catalog. I analyze the variability of the spread in abundance measurements reported for the same star by different surveys, the corresponding stellar atmosphere parameters adopted by various abundance determination methods, and the effect of normalizing all abundances to the same solar scale. The resulting abundance ratios [X/Fe] as a function of [Fe/H] are consistent with stellar nucleosynthetic processes and known Galactic thin-disk trends. I analyze the element abundances for 204 known exoplanet host-stars. In general, I find that exoplanet host-stars are not enriched more than the surrounding population of stars, with the exception of iron. I examine the stellar abundances with respect to both stellar and planetary physical properties, such as orbital period, eccentricity, planetary mass, stellar mass, and stellar color. My data confirms that exoplanet hosts are enriched in [Fe/H] but not in the refractory elements, per the self-enrichment theory for stellar composition. Lastly, I apply the Hypatia Catalog to the Catalog of Potentially Habitable Stellar Systems in order to investigate the abundances in the 1224 overlapping stars. By looking at stars similar to the Sun with respect to six bio-essential elements, I created maps that have located two ``habitability windows'' on the sky: (20.6hr, -4.8deg) and (22.6hr, -48.5deg). These windows may be of use in future targeted or beamed searches.

Group III-nitride semiconductors have wide application in optoelectronic devices. Spontaneous and piezoelectric polarization effects have been found to be critical for electric and optical properties of group III-nitrides. In this dissertation, firstly, the crystal orientation dependence of the polarization is calculated and in-plane polarization is revealed. The in-plane polarization is sensitive to the lateral characteristic dimension determined by the microstructure. Specific semi-polar plane growth is suggested for reducing quantum-confined Stark effect. The macroscopic electrostatic field from the polarization discontinuity in the heterostructures is discussed, b ased on that, the band diagram of InGaN/GaN quantum well/barrier and AlGaN/GaN heterojunction is obtained from the self-consistent solution of Schrodinger and Poisson equations. New device design such as triangular quantum well with the quenched polarization field is proposed. Electron holography in the transmission electron microscopy is used to examine the electrostatic potential under polarization effects. The measured potential energy profiles of heterostructure are compared with the band simulation, and evidences of two-dimensional hole gas (2DHG) in a wurtzite AlGaN/ AlN/ GaN superlattice, as well as quasi two-dimensional electron gas (2DEG) in a zinc-blende AlGaN/GaN are found. The large polarization discontinuity of AlN/GaN is the main source of the 2DHG of wurtzite nitrides, while the impurity introduced during the growth of AlGaN layer provides the donor states that to a great extent balance the free electrons in zinc-blende nitrides. It is also found that the quasi-2DEG concentration in zinc-blende AlGaN/GaN is about one order of magnitude lower than the wurtzite AlGaN/GaN, due to the absence of polarization. Finally, the InAlN/GaN lattice-matched epitaxy, which ideally has a zero piezoelectric polarization and strong spontaneous polarization, is experimentally studied. The breakdown in compositional homogeneity is triggered by threading dislocations with a screw component propagating from the GaN underlayer, which tend to open up into V-grooves at a certain thickness of the InxAl1-xN layer. The V-grooves coalesce at 200 nm and are filled with material that exhibits a significant drop in indium content and a broad luminescence peak. The structural breakdown is due to heterogeneous nucleation and growth at the facets of the V-grooves.

he accurate simulation of many-body quantum systems is a challenge for computational physics. Quantum Monte Carlo methods are a class of algorithms that can be used to solve the many-body problem. I study many-body quantum systems with Path Integral Monte Carlo techniques in three related areas of semiconductor physics: (1) the role of correlation in exchange coupling of spins in double quantum dots, (2) the degree of correlation and hyperpolarizability in Stark shifts in InGaAs/GaAs dots, and (3) van der Waals interactions between 1-D metallic quantum wires at finite temperature. The two-site model is one of the simplest quantum problems, yet the quantitative mapping from a three-dimensional model of a quantum double dot to an effective two-site model has many subtleties requiring careful treatment of exchange and correlation. I calculate exchange coupling of a pair of spins in a double dot from the permutations in a bosonic path integral, using Monte Carlo method. I also map this problem to a Hubbard model and find that exchange and correlation renormalizes the model parameters, dramatically decreasing the effective on-site repulsion at larger separations. Next, I investigated the energy, dipole moment, polarizability and hyperpolarizability of excitonic system in InGaAs/GaAs quantum dots of different shapes and successfully give the photoluminescence spectra for different dots with electric fields in both the growth and transverse direction. I also showed that my method can deal with the higher-order hyperpolarizability, which is most relevant for fields directed in the lateral direction of large dots. Finally, I show how van der Waals interactions between two metallic quantum wires change with respect to the distance between them. Comparing the results from quantum Monte Carlo and the random phase approximation, I find similar power law dependance. My results for the calculation in quasi-1D and exact 1D wires include the effect of temperature, which has not previously been studied.

This thesis describes several experiments based on carbon nanotube nanofludic devices and field-effect transistors. The first experiment detected ion and molecule translocation through one single-walled carbon nanotube (SWCNT) that spans a barrier between two fluid reservoirs. The electrical ionic current is measured. Translocation of small single stranded DNA oligomers is marked by large transient increases in current through the tube and confirmed by a PCR (polymerase chain reaction) analysis. Carbon nanotubes simplify the construction of nanopores, permit new types of electrical measurement, and open new avenues for control of DNA translocation. The second experiment constructed devices in which the interior of a single-walled carbon nanotube field-effect transistor (CNT-FET) acts as a nanofluidic channel that connects two fluid reservoirs, permitting measurement of the electronic properties of the SWCNT as it is wetted by an analyte. Wetting of the inside of the SWCNT by water turns the transistor on, while wetting of the outside has little effect. This finding may provide a new method to investigate water behavior at nanoscale. This also opens a new avenue for building sensors in which the SWCNT functions as an electronic detector. This thesis also presents some experiments that related to nanofabrication, such as construction of FET with tin sulfide (SnS) quantum ribbon. This work demonstrates the application of solution processed IV-VI semiconductor nanostructures in nanoscale devices.

Nanofluidic devices in which one single-walled carbon nanotube (SWCNT) spans a barrier between two fluid reservoirs were constructed, enabling direct electrical measurement of the transport of ions and molecules. Ion current through these devices is about 2 orders of magnitude larger than that predicted from the bulk resistivity of the electrolyte. Electroosmosis drives excess current, carried by cations, and is found to be the origin of giant ionic current through SWCNT as shown by building an ionic field-effect transistor with a gate electrode embedded in the fluid barrier. Wetting of inside of the semi-conducting SWCNT by water showed the change of its electronic property, turning the electronic SWCNT field-effect transistor to "on" state. These findings provide a new method to investigate and control the ion and molecule behavior at nanoscale.

Proteins are a fundamental unit in biology. Although proteins have been extensively studied, there is still much to investigate. The mechanism by which proteins fold into their native state, how evolution shapes structural dynamics, and the dynamic mechanisms of many diseases are not well understood. In this thesis, protein folding is explored using a multi-scale modeling method including (i) geometric constraint based simulations that efficiently search for native like topologies and (ii) reservoir replica exchange molecular dynamics, which identify the low free energy structures and refines these structures toward the native conformation. A test set of eight proteins and three ancestral steroid receptor proteins are folded to 2.7Å all-atom RMSD from their experimental crystal structures. Protein evolution and disease associated mutations (DAMs) are most commonly studied by in silico multiple sequence alignment methods. Here, however, the structural dynamics are incorporated to give insight into the evolution of three ancestral proteins and the mechanism of several diseases in human ferritin protein. The differences in conformational dynamics of these evolutionary related, functionally diverged ancestral steroid receptor proteins are investigated by obtaining the most collective motion through essential dynamics. Strikingly, this analysis shows that evolutionary diverged proteins of the same family do not share the same dynamic subspace. Rather, those sharing the same function are simultaneously clustered together and distant from those functionally diverged homologs. This dynamics analysis also identifies 77% of mutations (functional and permissive) necessary to evolve new function. In silico methods for prediction of DAMs rely on differences in evolution rate due to purifying selection and therefore the accuracy of DAM prediction decreases at fast and slow evolvable sites. Here, we investigate structural dynamics through computing the contribution of each residue to the biologically relevant fluctuations and from this define a metric: the dynamic stability index (DSI). Using DSI we study the mechanism for three diseases observed in the human ferritin protein. The T30I and R40G DAMs show a loss of dynamic stability at the C-terminus helix and nearby regulatory loop, agreeing with experimental results implicating the same regulatory loop as a cause in cataracts syndrome.

Molecular dynamics (MD) simulations provide a particularly useful approach to understanding conformational change in biomolecular systems. MD simulations provide an atomistic, physics-based description of the motions accessible to biomolecular systems on the pico- to micro-second timescale, yielding important insight into the free energy of the system, the dynamical stability of contacts and the role of correlated motions in directing the motions of the system. In this thesis, I use molecular dynamics simulations to provide molecular mechanisms that rationalize structural, thermodynamic, and mutation data on the interactions between the lac repressor headpiece and its O1 operator DNA as well as the ERK2 protein kinase. I performed molecular dynamics simulations of the lac repressor headpiece - O1 operator complex at the natural angle as well as at under- and overbent angles to assess the factors that determine the natural DNA bending angle. I find both energetic and entropic factors contribute to recognition of the natural angle. At the natural angle the energy of the system is minimized by optimization of protein-DNA contacts and the entropy of the system is maximized by release of water from the protein-DNA interface and decorrelation of protein motions. To identify the mechanism by which mutations lead to auto-activation of ERK2, I performed a series of molecular dynamics simulations of ERK1/2 in various stages of activation as well as the constitutively active Q103A, I84A, L73P and R65S ERK2 mutants. My simulations indicate the importance of domain closure for auto-activation and activity regulation. My results enable me to predict two loss-of-function mutants of ERK2, G83A and Q64C, that have been confirmed in experiments by collaborators. One of the powerful capabilities of MD simulations in biochemistry is the ability to find low free energy pathways that connect and explain disparate structural data on biomolecular systems. An extention of the targeted molecular dynamics technique using constraints on internal coordinates will be presented and evaluated. The method gives good results for the alanine dipeptide, but breaks down when applied to study conformational changes in GroEL and adenylate kinase.

The research of this dissertation involved quantitative characterization of electrostatic potential and charge distribution of semiconductor nanostructures using off-axis electron holography, as well as other electron microscopy techniques. The investigated nanostructures included Ge quantum dots, Ge/Si core/shell nanowires, and polytype heterostructures in ZnSe nanobelts. Hole densities were calculated for the first two systems, and the spontaneous polarization for wurtzite ZnSe was determined. Epitaxial Ge quantum dots (QDs) embedded in boron-doped silicon were studied. Reconstructed phase images showed extra phase shifts near the base of the QDs, which was attributed to hole accumulation in these regions. The resulting charge density was (0.03±0.003) holes
m3, which corresponded to about 30 holes localized to a pyramidal, 25-nm-wide Ge QD. This value was in reasonable agreement with the average number of holes confined to each Ge dot determined using a capacitance-voltage measurement. Hole accumulation in Ge/Si core/shell nanowires was observed and quantified using off-axis electron holography and other electron microscopy techniques. High-angle annular-dark-field scanning transmission electron microscopy images and electron holograms were obtained from specific nanowires. The intensities of the former were utilized to calculate the projected thicknesses for both the Ge core and the Si shell. The excess phase shifts measured by electron holography across the nanowires indicated the presence of holes inside the Ge cores. The hole density in the core regions was calculated to be (0.4±0.2)
m3 based on a simplified coaxial cylindrical model. Homogeneous zincblende/wurtzite heterostructure junctions in ZnSe nanobelts were studied. The observed electrostatic fields and charge accumulation were attributed to spontaneous polarization present in the wurtzite regions since the contributions from piezoelectric polarization were shown to be insignificant based on geometric phase analysis. The spontaneous polarization for the wurtzite ZnSe was calculated to be psp = -(0.0029±0.00013) C/m2, whereas a first principles' calculation gave psp = -0.0063 C/m2. The atomic arrangements and polarity continuity at the zincblende/wurtzite interface were determined through aberration-corrected high-angle annular-dark-field imaging, which revealed no polarity reversal across the interface. Overall, the successful outcomes of these studies confirmed the capability of off-axis electron holography to provide quantitative electrostatic information for nanostructured materials.