Conformational changes in biomolecules often take place on longer timescales than are easily accessible with unbiased molecular dynamics simulations, necessitating the use of enhanced sampling techniques, such as adaptive umbrella sampling. In this technique, the conformational free energy is calculated in terms of a designated set of reaction coordinates. At the same time, estimates of this free energy are subtracted from the potential energy in order to remove free energy barriers and cause conformational changes to take place more rapidly. This dissertation presents applications of adaptive umbrella sampling to a variety of biomolecular systems. The first study investigated the effects of glycosylation in GalNAc2-MM1, an analog of glycosylated macrophage activating factor. It was found that glycosylation destabilizes the protein by increasing the solvent exposure of hydrophobic residues. The second study examined the role of bound calcium ions in promoting the isomerization of a cis peptide bond in the collagen-binding domain of Clostridium histolyticum collagenase. This study determined that the bound calcium ions reduced the barrier to the isomerization of this peptide bond as well as stabilizing the cis conformation thermodynamically, and identified some of the reasons for this. The third study represents the application of GAMUS (Gaussian mixture adaptive umbrella sampling) to on the conformational dynamics of the fluorescent dye Cy3 attached to the 5' end of DNA, and made predictions concerning the affinity of Cy3 for different base pairs, which were subsequently verified experimentally. Finally, the adaptive umbrella sampling method is extended to make use of the roll angle between adjacent base pairs as a reaction coordinate in order to examine the bending both of free DNA and of DNA bound to the archaeal protein Sac7d. It is found that when DNA bends significantly, cations from the surrounding solution congregate on the concave side, which increases the flexibility of the DNA by screening the repulsion between phosphate backbones. The flexibility of DNA on short length scales is compared to the worm-like chain model, and the contribution of cooperativity in DNA bending to protein-DNA binding is assessed.

Silicon nanowires were grown epitaxially on Si (100) and (111) surfaces using the Vapor-Liquid-Solid (VLS) mechanism under both thermal and plasma enhanced growth conditions. Nanowire morphology was investigated as a function of temperature, time, disilane partial pressure and substrate preparation. Silicon nanowires synthesized in low temperature plasma typically curved compared to the linear nanowires grown under simple thermal conditions. The nanowires tended bend more with increasing disilane partial gas pressure up to 25 x10-3 mTorr. The nanowire curvature measured geometrically is correlated with the shift of the main silicon peak obtained in Raman spectroscopy. A mechanistic hypothesis was proposed to explain the bending during plasma activated growth. Additional driving forces related to electrostatic and Van der Waals forces were also discussed. Deduced from a systematic variation of a three-step experimental protocol, the mechanism for bending was associated with asymmetric deposition rate along the outer and inner wall of nanowire. The conditions leading to nanowire branching were also examined using a two-step growth process. Branching morphologies were examined as a function of plasma powers between 1.5 W and 3.5 W. Post-annealing thermal and plasma-assisted treatments in hydrogen were compared to understand the influences in the absence of an external silicon source (otherwise supplied by disilane). Longer and thicker nanowires were associated with longer annealing times due to an Ostwald-like ripening effect. The roles of surface diffusion, gas diffusion, etching and deposition rates were examined.

Ge1-ySny alloys represent a new class of photonic materials for integrated optoelectronics on Si. In this work, the electrical and optical properties of Ge1-ySny alloy films grown on Si, with concentrations in the range 0 ≤ y ≤ 0.04, are studied via a variety of methods. The first microelectronic devices from GeSn films were fabricated using newly developed CMOS-compatible protocols, and the devices were characterized with respect to their electrical properties and optical response. The detectors were found to have a detection range that extends into the near-IR, and the detection edge is found to shift to longer wavelengths with increasing Sn content, mainly due to the compositional dependence of the direct band gap E0. With only 2 % Sn, all of the telecommunication bands are covered by a single detector. Room temperature photoluminescence was observed from GeSn films with Sn content up to 4 %. The peak wavelength of the emission was found to shift to lower energies with increasing Sn content, corresponding to the decrease in the direct band gap E0 of the material. An additional peak in the spectrum was assigned to the indirect band gap. The separation between the direct and indirect peaks was found to decrease with increasing Sn concentration, as expected. Electroluminescence was also observed from Ge/Si and Ge0.98Sn0.02 photodiodes under forward bias, and the luminescence spectra were found to match well with the observed photoluminescence spectra. A theoretical expression was developed for the luminescence due to the direct band gap and fit to the data.

Nuclear proliferation concerns have resulted in a desire for radiation detectors with superior energy resolution. In this dissertation a Monte Carlo code is developed for calculating energy resolution in gamma-ray detector materials. The effects of basic material properties such as the bandgap and plasmon resonance energy are studied using a model for inelastic electron scattering based on electron energy-loss spectra. From a simplified "toy model" for a generic material, energy resolution is found to oscillate as the plasmon resonance energy is increased, and energy resolution can also depend on the valence band width. By incorporating the model developed here as an extension of the radiation transport code Penelope, photon processes are also included. The enhanced version of Penelope is used to calculate the Fano factor and average electron-hole pair energy in semiconductors silicon, gallium arsenide, zinc telluride, and scintillators cerium fluoride and lutetium oxyorthosilicate (LSO). If the effects of the valence band density-of-states and phonon scattering are removed, the calculated energy-resolution for these materials is fairly close to that for a toy model with a uniform electron energy-loss probability density function. This implies that the details of the electron cascade may in some cases have only a marginal effect on energy resolution.