Applications augmented with adaptive capabilities are becoming common in parallel computing environments. For large-scale scientific applications, dynamic adjustments to a computationally-intensive part may lead to a large pay-off in facilitating efficient execution of the entire application while aiming at avoiding resource contention. Application-specific knowledge, often best revealed during the run-time, is required to initiate and time these adjustments. In particular, General Atomic and Molecular Electronic Structure System (GAMESS) is a program for ab initio quantum chemistry that places significant demands on the high-performance computing platforms. Certain electronic structure calculations are characterized by high consumption of a particular resource, such as CPU, main memory, or disk I/O. This may lead to resource contention among concurrent GAMESS jobs and other programs in the dynamically changing environment. Thus, it is desirable to improve GAMESS calculations by means of dynamic adaptations. In this thesis, we show how an application- or algorithm-specific knowledge may play a significant role in achieving this goal. The choice of implementation is facilitated by a module-driven middleware easily integrated with GAMESS that assesses resource consumption and invokes GAMESS adaptations to the system environment. We show that the throughput of GAMESS jobs may be improved greatly as a result of such …

This thesis presents a search for physics beyond the standard model of elementary particles in events containing three or more charged leptons in the final state. The search is based on an R-parity violating supersymmetric model that assumes supersymmetric particles are pair produced at hadron colliders and the R-parity violating coupling is small enough so that these particles ''cascade'' decay into the lightest supersymmetric particle. The lightest supersymmetric particle may only decay into two charged leptons (electrons or muons) plus a neutrino through a lepton number violating interaction. Proton-antiproton collision events produced with {radical} s= 1.96 TeV are collected between March 2002 and August 2004 with an integrated luminosity of 346 pb{sup -1}. R-parity violating supersymmetry is sought for in two data samples, one with exactly three leptons and one with four or more leptons. The trilepton sample has a modest background primarily from Drell-Yan events where an additional lepton is a result of photon conversions or jet misidentification while the four or more lepton sample has an extremely low background. In the three lepton samples 6 events are observed while in the four or more lepton sample zero events are observed. These results are consistent with the standard model …

Our explorations of rare-earth, transition metal intermetallics have resulted in the synthesis and characterization, and electronic structure investigation, as well as understanding the structure-bonding-property relationships. Our work has presented the following results: (1) Understanding the relationship between compositions and properties in LaFe{sub 13-x}Si{sub x} system: A detailed structural and theoretical investigation provided the understanding of the role of a third element on stabilizing the structure and controlling the transformation of cubic NaZn{sub 13}-type structures to the tetragonal derivative, as well as the relationship between the structures and properties. (2) Synthesis of new ternary rare-earth iron silicides RE{sub 2-x}Fe{sub 4}Si{sub 14-y} and proposed superstructure: This compound offers complex structural challenges such as fractional occupancies and their ordering in superstructure. (3) Electronic structure calculation of FeSi{sub 2}: This shows that the metal-semiconductor phase transition depends on the structure. The mechanism of band gap opening is described in terms of bonding and structural distortion. This result shows that the electronic structure calculations are an essential tool for understanding the relationship between structure and chemical bonding in these compounds. (4) Synthesis of new ternary rare-earth Zinc aluminides Tb{sub 3}Zn{sub 3.6}Al{sub 7.4}: Partially ordered structure of Tb{sub 3}Zn{sub 3.6}Al{sub 7.4} compound provides new insights into …

A measurement is presented of the inclusive jet cross section using the Midpoint jet clustering algorithm in five different rapidity regions. This is the first analysis which measures the inclusive jet cross section using the Midpoint algorithm in the forward region of the detector. The measurement is based on more than 1 fb{sup -1} of integrated luminosity of Run II data taken by the CDF experiment at the Fermi National Accelerator Laboratory. The results are consistent with the predictions of perturbative quantum chromodynamics.

Leptoquarks are exotic particles that have color, electric charge, and lepton number and appear in extended gauge theories and composite models. Current theory suggests that leptoquarks would come in three different generations corresponding to the three quark and lepton generations. We are searching for charge 1/3 third generation leptoquarks produced in p{bar p} collisions at {radical}s = 1.96 TeV using data collected by the D0 detector. Such leptoquarks would decay into either a tau-neutrino plus a b-quark or, if heavy enough, to a tau-lepton plus a t-quark. We present preliminary results on an analysis where both leptoquarks decay into neutrinos giving a final state with missing energy and two b-quarks using 367 pb{sup -1} of Run II D0 data taken between August 2002 and September 2004. We place upper limits on {sigma}(p{bar p} {yields} LQ{ovr LQ})B{sup 2} as a function of the leptoquark mass M{sub LQ}. Assuming B = 1, we exclude at the 95% confidence level third generation leptoquarks with M{sub LQ} < 197 GeV/c{sup 2}.

Fluidized beds (FB) reactors are widely used in the polymerization industry due to their superior heat- and mass-transfer characteristics. Nevertheless, problems associated with local overheating of polymer particles and excessive agglomeration leading to FB reactors defluidization still persist and limit the range of operating temperatures that can be safely achieved in plant-scale reactors. Many people have been worked on the modeling of FB polymerization reactors, and quite a few models are available in the open literature, such as the well-mixed model developed by McAuley, Talbot, and Harris (1994), the constant bubble size model (Choi and Ray, 1985) and the heterogeneous three phase model (Fernandes and Lona, 2002). Most these research works focus on the kinetic aspects, but from industrial viewpoint, the behavior of FB reactors should be modeled by considering the particle and fluid dynamics in the reactor. Computational fluid dynamics (CFD) is a powerful tool for understanding the effect of fluid dynamics on chemical reactor performance. For single-phase flows, CFD models for turbulent reacting flows are now well understood and routinely applied to investigate complex flows with detailed chemistry. For multiphase flows, the state-of-the-art in CFD models is changing rapidly and it is now possible to predict reasonably well …

In an effort to mimic the growth of natural bone, self-assembling, micelle and gel-forming copolymers were used as a template for calcium phosphate precipitation. Because of the cationic characteristics imparted by PDEAEM end group additions to commercially available Pluronic{reg_sign} Fl27, a direct ionic attraction mechanism was utilized and a polymer-brushite nanocomposite spheres were produced. Brushite coated spherical micelles with diameters of {approx}40 nm, and agglomerates of these particles (on the order of 0.5 {mu}m) were obtained. Thickness and durability of the calcium phosphate coating, and the extent of agglomeration were studied. The coating has been shown to be robust enough to retain its integrity even below polymer critical micelle concentration and/or temperature. Calcium phosphate-polymer gel nanocomposites were also prepared. Gel samples appeared as a single phase network of agglomerated spherical micelles, and had a final calcium phosphate concentration of up to 15 wt%. Analysis with x-ray diffraction and NMR indicated a disordered brushite phase with the phosphate groups linking inorganic phase to the polymer.

MiniBooNE seeks to corroborate or refute the unconfirmed oscillation result from the LSND experiment. If correct, the result implies that a new kind of massive neutrino, with no weak interactions, participates in neutrino oscillations. MiniBooNE searches for {nu}{sub {mu}} {yields} {nu}{sub e} oscillations with the Fermi National Accelerator Laboratory 8 GeV beam line, which produces a {nu}{sub {mu}} beam with an average energy of {approx} 0.8 GeV and an intrinsic {nu}{sub e} content of 0.4%. The neutrino detector is a 6.1 m radius sphere filled with CH{sub 2}, viewed by 1540 photo-multiplier tubes, and located 541 m downstream from the source. This work focuses on the estimation of systematic errors associated with the neutrino flux and neutrino interaction cross section predictions, and in particular, on constraining these uncertainties using in-situ MiniBooNE {nu}{sub {mu}} charged current quasielastic (CCQE) scattering data. A data set with {approx} 100,000 events is identified, with 91% CCQE purity. This data set is used to measure several parameters of the CCQE cross section: the axial mass, the Fermi momentum, the binding energy, and the functional dependence of the axial form factor on four-momentum transfer squared. Constraints on the {nu}{sub {mu}} and {nu}{sub e} fluxes are derived using …

In recent years, semiconductor nanocrystal quantum dots havegarnered the spotlight as an important new class of biological labelingtool. Withoptical properties superior to conventional organicfluorophores from many aspects, such as high photostability andmultiplexing capability, quantum dots have been applied in a variety ofadvanced imaging applications. This dissertation research goes along withlarge amount of research efforts in this field, while focusing on thedesign and development of new nanoprobes from semiconductor nanocrystalsthat are aimed for useful imaging or sensing applications not possiblewith quantum dots alone. Specifically speaking, two strategies have beenapplied. In one, we have taken advantage of the increasing capability ofmanipulating the shape of semiconductor nanocrystals by developingsemiconductor quantum rods as fluorescent biological labels. In theother, we have assembled quantum dots and gold nanocrystals into discretenanostructures using DNA. The background information and synthesis,surface manipulation, property characterization and applications of thesenew nanoprobes in a few biological experiments are detailed in thedissertation.

Electroanalytical chemistry is often utilized in chemical analysis and Fundamental studies. Important advances have been made in these areas since the advent of chemically modified electrodes: the coating of an electrode with a chemical film in order to impart desirable, and ideally, predictable properties. These procedures enable the exploitation of unique reactivity patterns. This dissertation presents studies that investigate novel reaction mechanisms at self-assembled monolayers on gold. In particular, a unique electrochemical current amplification scheme is detailed that relies on a selective electrode to enable a reactivity pattern that results in regeneration of the analyte (redox recycling). This regenerating reaction can occur up to 250 times for each analyte molecule, leading to a notable enhancement in the observed current. The requirements of electrode selectivity and the resulting amplification and detection limit improvements are described with respect to the heterogeneous and homogeneous electron transfer rates that characterize the system. These studies revealed that the heterogeneous electrolysis of the analyte should ideally be electrochemically reversible, while that for the regenerating agent should be held to a low level. Moreover, the homogeneous reaction that recycles the analyte should occur at a rapid rate. The physical selectivity mechanism is also detailed with respect to …

Immunoassays have been utilized for the detection of biological analytes for several decades. Many formats and detection strategies have been explored, each having unique advantages and disadvantages. More recently, surface-enhanced Raman scattering (SERS) has been introduced as a readout method for immunoassays, and has shown great potential to meet many key analytical figures of merit. This technology is in its infancy and this dissertation explores the diversity of this method as well as the mechanism responsible for surface enhancement. Approaches to reduce assay times are also investigated. Implementing the knowledge gained from these studies will lead to a more sensitive immunoassay requiring less time than its predecessors. This dissertation is organized into six sections. The first section includes a literature review of the previous work that led to this dissertation. A general overview of the different approaches to immunoassays is given, outlining the strengths and weaknesses of each. Included is a detailed review of binding kinetics, which is central for decreasing assay times. Next, the theoretical underpinnings of SERS is reviewed at its current level of understanding. Past work has argued that surface plasmon resonance (SPR) of the enhancing substrate influences the SERS signal; therefore, the SPR of the extrinsic …

The MINOS Far Detector is a 5400 ton iron calorimeter located at the Soudan state park in Soudan Minnesota. The MINOS far detector can observe atmospheric neutrinos and separate charge current {nu}{sub {mu}} and {bar {nu}}{sub {mu}} interactions by using a 1.4 T magnetic field to identify the charge of the produced muon. The CPT theorem requires that neutrinos and anti-neutrinos oscillate in the same way. In a fiducial exposure of 5.0 kilo-ton years a total of 41 candidate neutrino events are observed with an expectation of 53.1 {+-} 7.6(system.) {+-} 7.2(stat.) unoscillated events or 31.6 {+-} 4.7(system.) {+-} 5.6(stat.) events with {Delta}m{sup 2} = 2.4 x 10{sup -3} eV{sup 2}, sin{sup 2}(2{theta}) = 1.0 as oscillation parameters. These include 28 events which can have there charge identified with high confidence. These 28 events consist of 18 events consistent with being produced by {nu}{sub {mu}} and 10 events being consistent with being produced by {bar {nu}}{sub {mu}}. No evidence of CPT violation is observed.

Slant-path buildup factors for photons between 1 keV and 10 MeV for nine radiation shielding materials (air, aluminum, concrete, iron, lead, leaded glass, polyethylene, stainless steel, and water) are calculated with the most recent cross-section data available using Monte Carlo and discrete ordinates methods. Discrete ordinates calculations use a 244-group energy structure that is based on previous research at Los Alamos National Laboratory (LANL), but extended with the results of this thesis, and its focused studies on low-energy photon transport and the effects of group widths in multigroup calculations. Buildup factor calculations in discrete ordinates benefit from coupled photon/electron cross sections to account for secondary photon effects. Also, ambient dose equivalent (herein referred to as dose) buildup factors were analyzed at lower energies where corresponding response functions do not exist in literature. The results of these studies are directly applicable to radiation safety at LANL, where the dose modeling tool Pandemonium is used to estimate worker dose in plutonium handling facilities. Buildup factors determined in this thesis will be used to enhance the code's modeling capabilities, but should be of interest to the radiation shielding community.

Eddy current nondestructive evaluation (NDE) is usually carried out by exciting a time harmonic field using an inductive probe. However, a viable alternative is to use transient eddy current NDE in which a current pulse in a driver coil produces a transient .eld in a conductor that decays at a rate dependent on the conductivity and the permeability of the material and the coil configuration. By using transient eddy current, it is possible to estimate the properties of the conductive medium and to locate and size potential .aws from the measured probe response. The fundamental study described in this dissertation seeks to establish a theoretical understanding of the transient eddy current NDE. Compared with the Fourier transform method, the derived analytical formulations are more convenient when the transient eddy current response within a narrow time range is evaluated. The theoretical analysis provides a valuable tool to study the effect of layer thickness, location of defect, crack opening as well as the optimization of probe design. Analytical expressions have been developed to evaluate the transient response due to eddy currents in a conductive plate based on two asymptotic series. One series converges rapidly for a short time regime and the other …

Organic chemistry has served as a solid foundation for interdisciplinary research areas, such as molecular biology and medicinal chemistry. An understanding of the biological activities and structural elucidations of natural products can lead to the development of clinically valuable therapeutic options. The advancements of modern synthetic methodologies allow for more elaborate and concise natural product syntheses. The theme of this study centers on the synthesis of natural products with particularly challenging structures and interesting biological activities. The synthetic expertise developed here will be applicable to analog syntheses and to other research problems.

We present results of a search for the anomalous production of events containing a high-transverse momentum charged lepton ({ell}, either e or {mu}) and photon ({gamma}), accompanied by missing transverse energy (E{sub T}), and/or additional leptons and photons, and jets (X). We use the same kinematic selection criteria as in a previous CDF search, but with a substantially larger data set, 305 pb{sup -1}, a p{bar p} collision energy of 1.96 TeV, and the upgraded CDF II detector. We find 42 {ell}{gamma}E{sub T} events versus a standard model expectation of 37.3 {+-} 5.4 events. The level of excess observed in Run I, 16 events with an expectation of 7.6 {+-} 0.7 events (corresponding to a 2.7 {sigma} effect), is not supported by the new data. In the signature of {ell}{ell}{gamma} + X we observe 31 events versus an expectation of 23.0 {+-} 2.7 events. In this sample we find no events with an extra photon or E{sub T} and so find no events like the one ee{gamma}{gamma} E{sub T} event observed in Run I.

Direct imaging of extrasolar planets is an important, but challenging, next step in planetary science. Most planets identified to date have been detected indirectly--not by emitted or reflected light but through the effect of the planet on the parent star. For example, radial velocity techniques measure the doppler shift in the spectrum of the star produced by the presence of a planet. Indirect techniques only probe about 15% of the orbital parameter space of our solar system. Direct methods would probe new parameter space, and the detected light can be analyzed spectroscopically, providing new information about detected planets. High contrast adaptive optics systems, also known as Extreme Adaptive Optics (ExAO), will require contrasts of between 10{sup -6} and 10{sup -7} at angles of 4-24 {lambda}/D on an 8-m class telescope to image young Jupiter-like planets still warm with the heat of formation. Contrast is defined as the intensity ratio of the dark wings of the image, where a planet might be, to the bright core of the star. Such instruments will be technically challenging, requiring high order adaptive optics with > 2000 actuators and improved diffraction suppression. Contrast is ultimately limited by residual static wavefront errors, so an extrasolar planet …

Leptoquarks (LQ) are particles with both color and lepton number predicted in some gauge theories and composite models. Current theory suggests that leptoquarks would come in three different generations. We report on a search for charge 1/3 third generation leptoquarks produced in p{bar p} collisions at {radical}s = 1.96 TeV using data collected by the D0 detector at Fermilab. Such leptoquarks would decay into a tau-neutrino plus a b-quark with branching fraction B. We present preliminary results on an analysis where both leptoquarks decay into neutrinos giving a final state with missing energy and two b-jets. Using 425(recorded) pb{sup -1} of data, we place limits on {sigma}(p{bar p} {yields} LQ{ovr LQ})B{sup 2} as a function of the leptoquark mass. Assuming B = 1, we excluded at the 95% confidence level scalar third generation leptoquarks with M{sub LQ} < 219 GeV.

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Superaustenitic stainless steels constitute a group of Fe-based alloys that are compositionally balanced to have a purely austenitic matrix and exhibit favorable pitting and crevice corrosion resistant properties and mechanical strength. However, intermetallic precipitates such as sigma and Laves can form during casting or exposure to high-temperature processing, which degrade the corrosion and mechanical properties of the material. The goal of this study was to accurately characterize the solid-solid phase transformations seen in cast superaustenitic stainless steels. Heat treatments were performed to understand the time and temperature ranges for intermetallic phase formations in alloys CN3MN and CK3MCuN. Microstructures were characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and energy and wavelength dispersive spectroscopy (EDS, WDS). The equilibrium microstructures, composed primarily of sigma and Laves within purely austenitic matrices, showed slow transformation kinetics. Factors that determine the extent of transformation, including diffusion, nucleation, and growth, are discussed.

Technicolor theory (TC) accomplishes the necessary electroweak symmetry breaking responsible for the mass of the elementary particles. TC postulates the existence of a new SU(N{sub TC}) gauge theory. Like QCD the exchange of gauge bosons causes the existence of a non-vanishing chiral condensate which dynamically breaks the SU(N{sub TC}){sub L} x SU(N{sub TC}){sub R} symmetry. This gives rise to N{sub TC}{sup 2}-1 Nambu-Goldstone Bosons. Three of these Goldstone Bosons become the longitudinal components of the W{sup {+-}} and Z which therefore acquire mass; the remaining ones are new particles (technihadrons) that can be produced at the high energy colliders and detected. The Technicolor Straw Man Model (TCSM) is a version of the dynamical symmetry breaking with a large number of technifermions and a relative low value of their masses. One of the processes predicted by the TCSM is q{bar q} {yields} V{sub T} {yields} W{pi}{sub T}, where V{sub T} is the Technicolor equivalent of the QCD vector meson and {pi}{sub T} is the equivalent of the pion. W is the electroweak gauge boson of the Standard Model. This dissertation describes the search for W{pi}{sub T} with the D0 detector, a multi-purpose particle detector located at one of the collision points …

This analysis describes a search for a standard model Higgs boson produced in association with a Z boson through the decay mode ZH {yields} e{sup +}e{sup -}b{bar b} in p{bar p} collisions at {radical}s = 1.96 TeV at the Fermilab Tevatron Collider. The data sample used in this analysis corresponds to 452 pb{sup -1} of integrated luminosity accumulated with the D{null} detector. Agreement between data and standard model predictions is observed. A 95% confidence level upper exclusion limit for the {sigma}(p{bar p} {yields} ZH) x BR(H {yields} b{bar b}) channel is set between 3.2-8.2 pb for Higgs masses of 105 to 145 GeV.

A search for neutral supersymmetric Higgs bosons and work relating to the improvement of the b-tagging and trigger capabilities at the D0 detector during Run II of the Fermilab Tevatron collider is presented. The search for evidence of the Higgs sector in the Standard Model (SM) and supersymmetric extensions of the SM are a high priority for the D0 collaboration, and b-tagging and good triggers are a vital component of these searches. The development and commissioning of the first triggers at D0 which use b-tagging is outlined, along with the development of a new secondary vertex b-tagging tool for use in the Level 3 trigger. Upgrades to the Level 3 trigger hit finding code, which have led to significant improvements in the quality and efficiency of the tracking code, and by extension the b-tagging tools, are also presented. An offline Neural Network (NN) b-tagging tool was developed, trained on Monte Carlo and extensively tested and measured on data. The new b-tagging tool significantly improves the b-tagging performance at D0, for a fixed fake rate relative improvements in signal efficiency range from {approx} 40% to {approx} 15%. Fake rates, for a fixed signal efficiency, are typically reduced to between a quarter …

The authors present a search for single top quarks produced in the s-channel electroweak production mode. The search is performed in the electron+jets decay channels, with one or more secondary-vertex tagged jets to indicate the presence of a b-jet and hence improving the signal:background ratio. Separation between signal and background is further enhanced by the use of Feed Forward Neural networks. 360 pb{sup -1} of Run II data used for this analysis was delivered by the Tevatron, and collected by D0 between August 2002 and August 2004. The resulting 95% confidence level upper limit is 4 pb.