A detailed study was done of the neomycin-B RNA aptamer for determining its selectivity and binding ability to both neomycin– and kanamycin-class aminoglycosides. A novel method to increase drug concentrations in cells for more efficiently killing is described. To test the method, a bacterial model system was adopted and several small RNA molecules interacting with aminoglycosides were cloned downstream of T7 RNA polymerase promoter in an expression vector. Then, the growth analysis of E. coli expressing aptamers was observed for 12-hour period. Our analysis indicated that aptamers helped to increase the intracellular concentration of aminoglycosides thereby increasing their efficacy.

This work presents explorations of the potential energy surface of clusters of atoms and of the interactions between molecules. First, structures of small aluminum clusters are examined and classified as ground states, transition states, or higher-order saddle points. Subsequently, the focus shifts to dispersion-dominated π-π interactions when the potential energy surfaces of benzene, substituted benzene, and pyridine dimers are explored. Because DNA nucleotide bases can be thought of as substituted heterocycles, a natural extension of the substituted benzene and pyridine investigations is to model paired nucleotide bases. Finally, the success of the dispersion studies inspires the development of an extension to the computational method used, which will enable the dispersion energy to be modeled – and the potential energy surface explored – in additional chemical systems. The effective fragment potential (EFP) method is described, as well as various quantum mechanical methods. An ab inito quantum mechanical study of 13-atom aluminum clusters is described. EFP studies of aromatic dimers are reported in which dispersion energy makes a significant contribution to the attraction between monomers. Theory and code development toward a means of computing dispersion energy in mixed ab inito-EFP systems are described.

The MiniBooNE experiment was designed to perform a search for {nu}{sub {mu}} {yields} {nu}{sub e} oscillations in a region of {Delta}m{sup 2} and sin{sup 2} 2{theta} very different from that allowed by standard, three-neutrino oscillations, as determined by solar and atmospheric neutrino experiments. This search was motivated by the LSND experimental observation of an excess of {bar {nu}}{sub e} events in a {bar {nu}}{sub {mu}} beam which was found compatible with two-neutrino oscillations at {Delta}m{sup 2} {approx} 1 eV{sup 2} and sin{sup 2} 2{theta} < 1%. If confirmed, such oscillation signature could be attributed to the existence of a light, mostly-sterile neutrino, containing small admixtures of weak neutrino eigenstates. In addition to a search for {nu}{sub {mu}} {yields} {nu}{sub e} oscillations, MiniBooNE has also performed a search for {bar {nu}}{sub {mu}} {yields} {bar {nu}}{sub e} oscillations, which provides a test of the LSND two-neutrino oscillation interpretation that is independent of CP or CPT violation assumptions. This dissertation presents the MiniBooNE {nu}{sub {mu}} {yields} {nu}{sub e} and {bar {nu}}{sub {mu}} {yields} {bar {nu}}{sub e} analyses and results, with emphasis on the latter. While the neutrino search excludes the two-neutrino oscillation interpretation of LSND at 98% C.L., the antineutrino search shows an …

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The CP violating phase {beta}{sub s}{sup J/{psi}{phi}} is measured in decays of B{sub s}{sup 0} {yields} J/{psi}{phi}. This measurement uses 5.2 fb{sup -1} of data collected in {radical}s = 1.96 TeV p{bar p} collisions at the Fermilab Tevatron with the CDF Run-II detector. CP violation in the B{sub s}{sup 0}-{bar B}{sub s}{sup 0} system is predicted to be very small in the Standard Model. However, several theories beyond the Standard Model allow enhancements to this quantity by heavier, New Physics particles entering second order weak mixing box diagrams. Previous measurements have hinted at a deviation from the Standard Model expectation value for {beta}{sub s}{sup J/{psi}{phi}} with a significance of approximately 2{sigma}. The measurement described in this thesis uses the highest statistics sample available to date in the B{sub s}{sup 0} {yields} J/{psi}{phi} decay channel, where J/{psi} {yields} {mu}{sup +}{mu}{sup -} and {phi} {yields} K{sup +}K{sup -}. Furthermore, it contains several improvements over previous analyses, such as enhanced signal selection, fully calibrated particle ID and flavour tagging, and the inclusion of an additional decay component in the likelihood function. The added decay component considers S-wave states of KK pairs in the B{sub s}{sup 0} {yields} J/{psi} K{sup +}K{sup -} channel. The …

This dissertation describes a variety of studies meant to improve the analytical performance of inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation (LA) ICP-MS. The emission behavior of individual droplets and LA generated particles in an ICP is studied using a high-speed, high frame rate digital camera. Phenomena are observed during the ablation of silicate glass that would cause elemental fractionation during analysis by ICP-MS. Preliminary work for ICP torch developments specifically tailored for the improvement of LA sample introduction are presented. An abnormal scarcity of metal-argon polyatomic ions (MAr{sup +}) is observed during ICP-MS analysis. Evidence shows that MAr{sup +} ions are dissociated by collisions with background gas in a shockwave near the tip of the skimmer cone. Method development towards the improvement of LA-ICP-MS for environmental monitoring is described. A method is developed to trap small particles in a collodion matrix and analyze each particle individually by LA-ICP-MS.

The unique combination of magnetic properties and structural transitions exhibited by many members of the R{sub 5}(Si{sub x}Ge{sub 1-x}){sub 4} family (R = rare earths, 0 ≤ x ≤ 1) presents numerous opportunities for these materials in advanced energy transformation applications. Past research has proven that the crystal structure and magnetic ordering of the R{sub 5(Si{sub x}Ge{sub 1-x}){sub 4} compounds can be altered by temperature, magnetic field, pressure and the Si/Ge ratio. Results of this thesis study on the crystal structure of the Er{sub 5}Si{sub 4} compound have for the first time shown that the application of mechanical forces (i.e. shear stress introduced during the mechanical grinding) can also result in a structural transition from Gd{sub 5}Si{sub 4}-type orthorhombic to Gd{sub 5}Si{sub 2}Ge{sub 2}-type monoclinic. This structural transition is reversible, moving in the opposite direction when the material is subjected to low-temperature annealing at 500 ˚C. Successful future utilization of the R{sub 5}(Si{sub x}Ge{sub 1-x}){sub 4} family in novel devices depends on a fundamental understanding of the structure-property interplay on the nanoscale level, which makes a complete understanding of the microstructure of this family especially important. Past scanning electron microscopy (SEM) observation has shown that nanometer-thin plates exist in every …

This thesis presents the measurement of the charged current quasi-elastic (CCQE) neutrino-nucleon cross section at neutrino energies around 1 GeV. This measurement has two main physical motivations. On one hand, the neutrino-nucleon interactions at few GeV is a region where existing old data are sparse and with low statistics. The current measurement populates low energy regions with higher statistics and precision than previous experiments. On the other hand, the CCQE interaction is the most useful interaction in neutrino oscillation experiments. The CCQE channel is used to measure the initial and final neutrino fluxes in order to determine the neutrino fraction that disappeared. The neutrino oscillation experiments work at low neutrino energies, so precise measurement of CCQE interactions are essential for flux measurements. The main goal of this thesis is to measure the CCQE absolute neutrino cross section from the SciBooNE data. The SciBar Booster Neutrino Experiment (SciBooNE) is a neutrino and anti-neutrino scattering off experiment. The neutrino energy spectrum works at energies around 1 GeV. SciBooNE was running from June 8th 2007 to August 18th 2008. In that period, the experiment collected a total of 2.65 x 10²⁰ protons on target (POT). This thesis has used full data collection in …

MINOS is a long baseline neutrino oscillation experiment, starting with a muon-neutrino beam, for the precise measurement of the atmospheric neutrino oscillation parameters |{Delta}m{sup 2}| and {theta}{sub 23}. The Near Detector measures the neutrino flux and spectra before oscillations. The beam propagates for 735 km to the Far Detector, which measures the depleted spectrum after oscillations. The depletion can be interpreted as {nu}{sub {mu}} {yields} {nu}{sub {tau}} oscillations. Subdominant {nu}{sub {mu}} {yields} {nu}{sub e} oscillations may be allowed if the mixing angle {theta}{sub 13} {ne} 0. The two detectors are functionally identical in order to cancel systematic errors when using the Near Detector data to constrain the Far Detector prediction. A crucial part of the analysis is the relative calibration between the two detectors, which is known at the 2% level. A calibration procedure to remove the time and temperature dependence of the detector response using through-going cosmic muons is presented here. Although the two-detector approach reduces the systematic uncertainties related to the neutrino flux, a cross check on the neutrino parent meson ratios is performed in this thesis. The cross sections of mesons produced in proton-carbon interactions from the NA49 experiment have been measured and the results have been …

High temperature alloys are reviewed, focusing on current superalloys and their coatings. The synthesis, characerization, and oxidation performance of a NiAl–TiB{sub 2} composite are explained. A novel coating process for Mo–Ni–Al alloys for improved oxidation performance is examined. The cyclic oxidation performance of coated and uncoated Mo–Ni–Al alloys is discussed.

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We studied the effects on structural and magnetic phase transitions and the emergence of superconductivity in transition metal substituted BaFe{sub 2}As{sub 2}. We grew four series of Ba(Fe{sub 1-x}TM{sub x}){sub 2}As{sub 2} (TM=Ru, Mn, Co+Cr and Co+Mn) and characterized them by crystallographic, magnetic and transport measurements. We also subjected Ba(Fe{sub 1-x}Cr{sub x}){sub 2}As{sub 2} and Ba(Fe{sub 1-x}Co{sub x}){sub 2}As{sub 2} to heat treatment to explore what changes might be induced.

Modern calculations are becoming an essential, complementary tool to inelastic x-ray scattering studies, where x-rays are scattered inelastically to resolve meV phonons. Calculations of the inelastic structure factor for any value of Q assist in both planning the experiment and analyzing the results. Moreover, differences between the measured data and theoretical calculations help identify important new physics driving the properties of novel correlated systems. We have used such calculations to better and more e#14;ciently measure the phonon dispersion and elastic constants of several iron pnictide superconductors. This dissertation describes calculations and measurements at room temperature in the tetragonal phase of CaFe{sub 2}As{sub 2} and LaFeAsO. In both cases, spin-polarized calculations imposing the antiferromagnetic order present in the low-temperature orthorhombic phase dramatically improves the agreement between theory and experiment. This is discussed in terms of the strong antiferromagnetic correlations that are known to persist in the tetragonal phase. In addition, we discuss a relatively new approach called self-consistent ab initio lattice dynamics (SCAILD), which goes beyond the harmonic approximation to include phonon-phonon interactions and produce a temperature-dependent phonon dispersion. We used this technique to study the HCP to BCC transition in beryllium.

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