A variety of scenarios are considered which shed light upon the uses and limitations of classical geometric and topological notions in string theory. The primary focus is on situations in which D-brane or string probes of a given classical space-time see the geometry quite differently than one might naively expect. In particular, situations in which extra dimensions, non-commutative geometries as well as other non-local structures emerge are explored in detail. Further, a preliminary exploration of such issues in Lorentzian space-times with non-trivial causal structures within string theory is initiated.

Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of …

Polycrystals of the intermetallic compound of the Dy{sub 5}(Si{sub x}Ge{sub 1-x}){sub 4} system, where x = 0, 0.25, 0.5, 0.625, 0.675, 0.725, 0.75, 0.775, 0.825, 0.875, and 1, have been prepared by electric-arc-melting on water-cooled copper hearth in an argon atmosphere. A study of phase relationships and crystallography in the pseudobinary system Dy{sub 5}(Si{sub x}Ge{sub 1-x}){sub 4} using X-ray powder diffraction data and optical metallography was completed. It revealed that silicides in the composition range from 0.825 to 1 crystallize in the Gd{sub 5}Si{sub 4}-type crystal structure: germanides in the composition range from 0 to 0.625 crystallize in the Sm{sub 5}Ge{sub 4}-type structure, and alloys with intermediate composition range from 0.675 to 0.775 crystallize in the monoclinic Gd{sub 5}Si{sub 2}Ge{sub 2}-type structure. The -{Delta}S{sub m} values were determined from magnetization measurements for 7 alloys. The alloys with a monoclinic crystal structure which belong to an intermediate phase region have large MCE value, which exceeds those observed in the other two phase regions by 300 to 500%. The nature of the observed magnetic and structural transformations in the Dy{sub 5}(Si{sub x}Ge{sub 1-x}){sub 4} system seems to be similar with those reported for the Gd{sub 5}(Si{sub x}Ge{sub 1-x}){sub 4} system. However, the …

A self stabilized, free standing, z-pinch plasma channel has been proposed to deliver the high intensity heavy ion beam from the end of a driver to the fuel target in a heavy ion inertial fusion power plant. The z-pinch relaxes emittance and energy spread requirements requiring a lower cost driver. A z-pinch transport would reduce the number of beam entry port holes to the target chamber from over a hundred to four as compared to neutralized ballistic focusing thus reducing the driver hardware exposure to neutron flux. Experiments where a double pulse discharge technique is used, z-pinch plasma channels with enhanced stability are achieved. Typical parameters are 7 kV pre-pulse discharge and 30 kV main bank discharge with 50 kA of channel current in a 7 torr background gas atmosphere. This work is an experimental study of these plasma channels examining the relevant physics necessary to understand and model such plasmas. Laser diagnostics measured the dynamical properties of neutrals and plasma. Schlieren and phase contrast techniques probe the pre-pulse gas dynamics and infrared interferometry and faraday effect polarimetry are used on the z-pinch to study its electron density and current distribution. Stability and repeatability of the z-pinch depend on the …

The availability of high power, spectrally and spatially coherent soft x-rays (SXR) would facilitate a wide variety of experiments as this energy region covers the primary resonances of many magnetic and biological materials. Specifically, there are the carbon and oxygen K-edges that are critical for biological imaging in the water window and the L-edges of iron, nickel, and cobalt for which imaging and scattering studies can be performed. A new coherent soft X-ray branchline at the Advanced Light Source has begun operation (beamline 12.0.2). Using the third harmonic from an 8 cm period undulator, this branch delivers coherent soft x-rays with photon energies ranging from 200eV to 1keV. This branchline is composed of two sub-branches one at 14X demagnification and the other 8X demagnification. The former is optimized for use at 500eV and the latter at 800eV. Here the expected power from the third harmonic of this undulator and the beamline design and characterization is presented. The characterization includes measurements on available photon flux as well as a series of double pinhole experiments to determine the coherence factor with respect to transverse distance. The first high quality Airy patterns at SXR wavelengths are created with this new beamline. The operation …

This report provides complete bibliographic citations, abstracts, and keywords for 212 doctoral and master`s theses supported fully or partly by the U.S. Department of Energy`s Environmental Sciences Division (and its predecessors) in the following areas: Atmospheric Sciences; Marine Transport; Terrestrial Transport; Ecosystems Function and Response; Carbon, Climate, and Vegetation; Information; Computer Hardware, Advanced Mathematics, and Model Physics (CHAMMP); Atmospheric Radiation Measurement (ARM); Oceans; National Institute for Global Environmental Change (NIGEC); Unmanned Aerial Vehicles (UAV); Integrated Assessment; Graduate Fellowships for Global Change; and Quantitative Links. Information on the major professor, department, principal investigator, and program area is given for each abstract. Indexes are provided for major professor, university, principal investigator, program area, and keywords. This bibliography is also available in various machine-readable formats (ASCII text file, WordPerfect{reg_sign} files, and PAPYRUS{trademark} files).

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.

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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 …

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.

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 …

The use of high rate anodic dissolution (electrochemical machining) for shaping titanium carbide, zirconium carbide, titanium boride and zirconium boride has been investigated in 2N potassium nitrate and 3N sodium chloride under current densities ranging from 20 to 120 A/cm{sup 2} (corresponding to cutting rates of 0.3 to 1.8 mm/min). The dissolution stoichiometry for all these materials is independent of the current density in the range 20 to 120 A/cm{sup 2}. Both titanium and zirconium appear to dissolve in the +4 state, boron in the +3 state and the weight loss measurements indicate that carbon is oxidized to CO and CO{sub 2}. The current voltage curves permit to establish that, over the entire current density and flow range investigated, dissolution occurs in the transpassive state. The surface roughness obtained on TiC and ZrC is within 3-5 {micro}m and is independent of current density, applied voltage or flow rate.

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 …

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The problem of the bimolecular rate constant, alpha , for the mutual charge neutralization reaction (ion-ion recombination) for ions formed by the vacuum ultraviolet photolysis of nitric oxide is considered. The pressure dependence of alpha over a pressure range of 10 to 600 torr for mixtures of a few hundred microns of NO with He, Ar, Kr, Xe, H/sub 2/, D/sub 2/, and N/sub 2/ was measured. From the low-pressure limit of alpha , the rate constant for charge neutralization in the absence of a third body was found to be k/sub o/ = 2.1 plus or minus 0.4 x 10/sup -7/ cm/sup 3// sec. The high-pressure limit of alpha was estimated to be 2.0 plus or minus 0.5 x 10/sup -6/ cm/sup 3//sec. The third-body efficiencies for promoting the charge-neutralization reaction were measured. The results, relative to He as the third-body gas, are H/sub 2/= 1.4 plus or minus 0.4, D/sub 2/= 1.5 plus or minus 0.4, Ar =3.6 plus or minus 0.8, Kr =4.3 plus or min11.0, N/sub 2/ = 5.2 plus or minus 1.1, and Xe = 6.8 plus or minus 1.5. The average ionic mobility in the gas mixtures is estimated, and the mobilities indicate that …

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An idealized model is postulated embodying the essential features of industrial caustic-chlorine cells with horizontal flowing-mercury cathodes. This model is examined in detail, and relations expressing the local anode potential, cathode potential, and ohmic potential drop in the electrolyte in terms of local current density and other parameters are established. These relations are combined to give a system of equations relating current density at any location along the cell to applied total potential and to operating conditions in the cell upstream of the point in question. Numerical solutions of these equations for several cases of cell operating conditions are carried out on a digital computing machine. The effects of changes in operating parameters upon average current density, individual electrode potentials, and current distribution are evaluated. (auth)

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