This work is the result of the researchers carried out during a three years Ph.D. period in the BABAR experiment. The first chapter consists in an introduction to the theoretical aspects of the D{sup 0} meson lifetime determination and CP violation parameters, as well as an overview of the CP violation in the B sector, which is the main topic of the experiment. The description of the experimental apparatus follows with particular attention to the Silicon Vertex Tracker detector, the most critical detector for the determination of decay vertices and thus of lifetimes and time dependent CP violation asymmetries. In the fourth chapter the operation and running of the vertex detector is described, as a result from the experience as Operation Manager of the SVT, with particular attention to the safety of the device and the data quality assurance. The last chapter is dedicated to the determination of the D{sup 0} meson lifetime with the BABAR detector, which is the main data analysis carried out by the candidate. The analysis is characterized by the selection of an extremely pure sample of D{sup 0} mesons for which the decay flight length and proper time is reconstructed. The description of the unbinned …

Presented is a precise measurement of the {bar B}{sup 0} {yields} D*{sup +}{ell}{sup -}{bar {nu}}{sub {ell}} branching fraction using 81.47 fb{sup -1} of data collected with the BABAR detector at the PEP-II e{sup +}e{sup -} storage ring at the Stanford Linear Accelerator Center. The measurement was performed by partially reconstructing the D*{sup +} meson from {bar B}{sup 0} {yields} D*{sup +}{ell}{sup -}{bar {nu}}{sub {ell}} decays using only the soft pion of the D*{sup +} {yields} D{sup 0}{pi}{sup +} decay to reconstruct its four vector. The branching fraction was measured to be {Beta}({bar B}{sup 0} {yields} D*{sup +}{ell}{sup -}{bar {nu}}{sub {ell}}) = (4.91 {+-} 0.01{sub stat} {+-} 0.15{sub syst})%.

SUBMITTED AS A DOCTORAL DISSERTATION IN COMPLETION OF REQUIREMENTS FOR THE DEGREE OF ED.D THROUGH WASHINGTON STATE UNIVERSITY. The overall purpose of this action research study was to explore the experiences of ten middle school science teachers involved in a three-year partnership program between scientists and teachers at a Department of Energy national laboratory, including the impact of the program on their professional development, and to improve the partnership program by developing a set of recommendations based on the study’s findings. This action research study relied on qualitative data including field notes recorded at the summer academies and data from two focus groups with teachers and scientists. Additionally, the participating teachers submitted written reflections in science notebooks, participated in open-ended telephone interviews that were transcribed verbatim, and wrote journal summaries to the Department of Energy at the end of the summer academy. The analysis of the data, collaboratively examined by the teachers, the scientists, and the science education specialist acting as co-researchers on the project, revealed five elements critical to the success of the professional development of science teachers. First, scientist-teacher partnerships are a unique contribution to the professional development of teachers of science that is not replicated in other …

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This thesis reports measurements of the time-dependent CP asymmetries in fully reconstructed B{sup 0} {yields} (D{sup (*){-+}} and B{sup 0} {yields} D{sup {-+}} {rho}{sup {+-}}) decays in approximately 232 million {Upsilon}(4S) {yields} B{bar B} events, collected with the BABAR detector at the PEP-II asymmetric-energy B factory at the Stanford Linear Accelerator Center in California, as published in Ref. [14]. The phenomenon of CP violation allows one to distinguish between matter and antimatter, and, as such, is one of the essential ingredients needed to explain the apparent abundance of matter over antimatter in the universe. The Standard Model describes the observed elementary particles in terms of three generations of quarks and leptons, as well as the weak, electromagnetic, and strong interactions between them. In the Standard Model, CP violation is incorporated in the Cabibbo-Kobayashi-Maskawa (CKM) matrix, which describes the weak interactions between the quarks. The weak interactions between quarks are described by coupling constants that are functions of three real parameters and one irreducible complex phase. The magnitude of all CP violating effects in the Standard Model is related to this complex phase. The measurement of the CP violating phase of the CKM matrix is an important part of the present …

The D{sub J}{sup 0} is a family of four orbitally excited mesons: D*{sub 2}(2460){sup 0}, D{sub 1}(2420){sup 0}, D{sub 1}(j = 1/2){sup -}, and D*{sub 0}(j = 1/2){sup 0}. This dissertation presents the measurements of the inclusive branching fractions, {Beta}(B{sup -} {yields} D*{sup +}{pi}{sup -}{pi}{sup -}) and {Beta}(B{sup -} {yields} D{sup +}{pi}{sup -}{pi}{sup -}). The D{sub J}{sup 0} provides an intermediate resonance for those two modes. The data used for this analysis consists of Runs 1-5 with total integrated luminosity of 343.38 fb{sup -1}, which is corresponding to 383.92 million B{bar B} pairs, provided by the BABAR detector at the PEP-II asymmetric B Factory. The values presented are: {Beta}(B{sup -} {yields} D{sup +}{pi}{sup -}{pi}{sup -}) = (1.12 {+-} 0.02 {+-} 0.08) x 10{sup -3}; {Beta}(B{sup -} {yields} D*{sup +}{pi}{sup -}{pi}{sup -}) = (1.67 {+-} 0.03 {+-} 0.13) x 10{sup -3}.

Note that the main goal of this thesis work is the measurement of the branching fractions, charge asymmetry, and Time-Dependent CP Violation in {eta}'K{sup 0} mode. All other measurements are reported here for completion because they are connected by similar physics arguments. They are part of the Milan analysis activity, done by undergraduate students. They should not be considered as done in this thesis work. The measurements of the two body-modes {eta}{eta}, {eta}{phi}, and {eta}'{phi} are used to determine a theoretical bound based on SU(3) flavor symmetry for the difference between SM prediction and the experimental measurements of CP violation parameters in b {yields} s loop-dominated modes. In general for this estimation we need to measure the branching fractions (or upper limits) of neutral B decays to two-body modes with {eta}', {eta}, {phi}, {omega}, {pi}{sup 0}, K{sup 0}, K*{sup 0} [13, 14, 15, 16]. There is an important issue related to the branching fractions of {eta}'K (charged and neutral) modes. Since the discover of B {yields} {eta}'K in 1997 [17] with high branching fraction (higher than expected), it was found that the corresponding mode with {eta} is suppressed. This fact was pointed out by Lipkin in 1991 [18]. In particular, …

The authors report the results of a study of the exclusive charmless semileptonic decay, B{sup 0} {yields} {pi}{sup -}{ell}{sup +}{nu}, undertaken with approximately 227 million B{bar B} pairs collected at the {Upsilon}(4S) resonance with the BABAR detector. The analysis uses events in which the signal B decays are reconstructed with an innovative loose neutrino reconstruction technique. They obtain partial branching fractions in 12 bins of q{sup 2}, the momentum transfer squared, from which they extract the f{sub +}(q{sup 2}) form-factor shape and the total branching fraction {Beta}(B{sup 0} {yields} {pi}{sup -}{ell}{sup +}{nu}) = (1.46 {+-} 0.07{sub stat} {+-} 0.08{sub syst}) x 10{sup -4}. Based on a recent unquenched lattice QCD calculation of the form factor in the range q{sup 2} > 16 GeV{sup 2}/c{sup 4}, they find the magnitude of the CKM matrix element |V{sub ub}| to be (4.1 {+-} 0.2{sub stat} {+-} 0.2{sub syst{sub -0.4}{sup +0.6}FF}) x 10{sup -3}, where the last uncertainty is due to the normalization of the form factor.

The rare decay B {yields} {pi}{ell}{sup +}{ell}{sup -} is the simplest manifestation of a b {yields} d{ell}{sup +}{ell}{sup -} flavor-changing neutral current (FCNC) process. This type of process only proceeds through penguin loop or box diagrams and is sensitive to physics at the electroweak scale. It can be used to constrain parameters of the Standard Model and its extensions. B {yields} {pi}{ell}{sup +}{ell}{sup -} events have not yet been observed; the branching fraction is expected to be an order of magnitude smaller than the measured branching fraction for the similar B {yields} K{ell}{sup +}{ell}{sup -} decay. Using 230 million B{bar B} meson pairs collected with the BABAR detector, we have done a search for the rare decay B {yields} {pi}{ell}{sup +}{ell}{sup -}. The data was produced in e+e? collision at the {Upsilon}(4S) resonance in the PEP-II collider between 1999 and 2004. Four exclusive B-meson decay modes have been reconstructed: B{sup +} {yields} {pi}{sup +}{ell}{sup +}{ell}{sup -} and B{sup 0} {yields} {pi}{sup 0}{ell}{sup +}{ell}{sup -}, where {ell}{sup +}{ell}{sup -} is either an electron pair (e{sup +}e{sup -}) or a muon pair ({mu}{sup +}{mu}{sup -}). We find no evidence for a signal, and we obtain upper limits on the branching fractions {Beta}. …

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In this work we presented measurements of CP violation and decay rates of B decays in final states not involving a charm quark in the final state. In particular, the time-dependent CP asymmetries of decays which proceed through b {yields} s elementary transition is a particularly sensitive probe of physics beyond the Standard Model. In fact, even if the precise measurements of CP conserving and CP violating processes show the success of the CKM picture of the flavour physics, the sector of b {yields} s transitions is still not strongly constrained and leaves room for new physics contributions. In particular, we considered the decays which have the cleanest theoretical prediction within the Standard Model: B{sup 0} {yields} {phi}K{sup 0} and B{sup 0} {yields} K{sub s}{sup 0}K{sub s}{sup 0}K{sub s}{sup 0} {beta}{sub eff}{sup SM} = 0.379. We examined the former with a completely new approach with respect to the past: the study of CP violation in the whole K{sup +}K{sup -}K{sup 0} phase space through a time-dependent Dalitz plot analysis. With this approach, we simultaneously measured the CP-violating asymmetries of the {phi}KJ{sup 0}, f{sub 0}(980)K{sup 0} resonant and K{sup +}K{sup -}K{sup 0} non-resonant contributions, avoiding one of the largest uncertainties which …

In the last two decades, the field of nanoscience andnanotechnology has witnessed tremendous advancement in the synthesis andapplication of group II-VI colloidal nanocrystals. The synthesis based onhigh temperature decomposition of organometallic precursors has becomeone of the most successful methods of making group II-VI colloidalnanocrystals. This method is first demonstrated by Bawendi and coworkersin 1993 to prepare cadmium chalcogenide colloidal quantum dots and laterextended by others to prepare other group II-VI quantum dots as well asanisotropic shaped colloidal nanocrystals, such as nanorod and tetrapod.This dissertation focuses on the chemistry of this type of nanocrystalsynthesis. The synthesis of group II-VI nanocrystals was studied bycharacterizing the molecular structures of the precursors and productsand following their time evolution in the synthesis. Based on theseresults, a mechanism was proposed to account for the 2 reaction betweenthe precursors that presumably produces monomer for the growth ofnanocrystals. Theoretical study based on density functional theorycalculations revealed the detailed free energy landscape of the precursordecomposition and monomerformation pathway. Based on the proposedreaction mechanism, a new synthetic method was designed that uses wateras a novel reagent to control the diameter and the aspect ratio of CdSeand CdS nanorods.

In the last two decades, the field of nanoscience andnanotechnology has witnessed tremendous advancement in the synthesis andapplication of group II-VI colloidal nanocrystals. The synthesis based onhigh temperature decomposition of organometallic precursors has becomeone of the most successful methods of making group II-VI colloidalnanocrystals. This methodis first demonstrated by Bawendi and coworkersin 1993 to prepare cadmium chalcogenide colloidal quantum dots and laterextended by others to prepare other group II-VI quantum dots as well asanisotropic shaped colloidal nanocrystals, such as nanorod and tetrapod.This dissertation focuses on the chemistry of this type of nanocrystalsynthesis. The synthesis of group II-VI nanocrystals was studied bycharacterizing the molecular structures of the precursors and productsand following their time evolution in the synthesis. Based on theseresults, a mechanism was proposed to account for the 2 reaction betweenthe precursors that presumably produces monomer for the growth ofnanocrystals. Theoretical study based on density functional theorycalculations revealed the detailed free energy landscape of the precursordecomposition and monomerformation pathway. Based on the proposedreaction mechanism, a new synthetic method was designed that uses wateras a novel reagent to control the diameter and the aspect ratio of CdSeand CdS nanorods.

The objective of this work is to investigate the thick diffusion limit of various spatial discretizations of the one-dimensional, steady-state, monoenergetic, discrete ordinates neutron transport equation. This work specifically addresses the two lowest order nodal methods, AHOT-N0 and AHOT-N1, as well as reconsiders the asymptotic limit of the Diamond Difference method. The asymptotic analyses of the AHOT-N0 and AHOT-N1 nodal methods show that AHOT-N0 does not possess the thick diffusion limit for cell edge or cell average fluxes except under very limiting conditions, which is to be expected considering the AHOT-N0 method limits to the Step method in the thick diffusion limit. The AHOT-N1 method, which uses a linear in-cell representation of the flux, was shown to possess the thick diffusion limit for both cell average and cell edge fluxes. The thick diffusion limit of the DD method, including the boundary conditions, was derived entirely in terms of cell average scalar fluxes. It was shown that, for vacuum boundaries, only when {sigma}{sub t}, h, and Q are constant and {sigma}{sub a} = 0 is the asymptotic limit of the DD method close to the finite-differenced diffusion equation in the system interior, and that the boundary conditions between the systems will …

Studies of colloidal nanocrystals and their assemblies are presented. Two of these studies concern the atomic-level structural characterization of the surfaces, interfaces, and interiors present in II-VI semiconductor nanorods. The third study investigates the crystallographic arrangement of cobalt nanocrystals in self-assembled aggregates. Crystallographically-aligned assemblies of colloidal CdSe nanorods are examined with linearly-polarized Se-EXAFS spectroscopy, which probes bonding along different directions in the nanorod. This orientation-specific probe is used, because it is expected that the presence of specific surfaces in a nanorod might cause bond relaxations specific to different crystallographic directions. Se-Se distances are found to be contracted along the long axis of the nanorod, while Cd-Se distances display no angular dependence, which is different from the bulk. Ab-initio density functional theory calculations upon CdSe nanowires indicate that relaxations on the rod surfaces cause these changes. ZnS/CdS-CdSe core-shell nanorods are studied with Se, Zn, Cd, and S X-ray absorption spectroscopy (XAS). It is hypothesized that there are two major factors influencing the core and shell structures of the nanorods: the large surface area-to-volume ratio, and epitaxial strain. The presence of the surface may induce bond rearrangements or relaxations to minimize surface energy; epitaxial strain might cause the core and shell lattices …

Conventional implementations of collective communications are based on point-to-point communications, and their optimizations have been focused on efficiency of those communication algorithms. However, point-to-point communications are not the optimal choice for modern computing clusters of SMPs due to their two-level communication structure. In recent years, a few research efforts have investigated efficient collective communications for SMP clusters. This dissertation is focused on platform-independent algorithms and implementations in this area. There are two main approaches to implementing efficient collective communications for clusters of SMPs: using shared memory operations for intra-node communications, and overlapping inter-node/intra-node communications. The former fully utilizes the hardware based shared memory of an SMP, and the latter takes advantage of the inherent hierarchy of the communications within a cluster of SMPs. Previous studies focused on clusters of SMP from certain vendors. However, the previously proposed methods are not portable to other systems. Because the performance optimization issue is very complicated and the developing process is very time consuming, it is highly desired to have self-tuning, platform-independent implementations. As proven in this dissertation, such an implementation can significantly out-perform the other point-to-point based portable implementations and some platform-specific implementations. The dissertation describes in detail the architecture of the platform-independent …

In this study, we applied the Nested Partitions method to a U-line balancing problem and conducted experiments to evaluate the application. From the results, it is quite evident that the Nested Partitions method provided near optimal solutions (optimal in some cases). Besides, the execution time is quite short as compared to the Branch and Bound algorithm. However, for larger data sets, the algorithm took significantly longer times for execution. One of the reasons could be the way in which the random samples are generated. In the present study, a random sample is a solution in itself which requires assignment of tasks to various stations. The time taken to assign tasks to stations is directly proportional to the number of tasks. Thus, if the number of tasks increases, the time taken to generate random samples for the different regions also increases. The performance index for the Nested Partitions method in the present study was the number of stations in the random solutions (samples) generated. The total idle time for the samples can be used as another performance index. ULINO method is known to have used a combination of bounds to come up with good solutions. This approach of combining different performance …

This work explores the development and application of chip-scale bioassays based on surface-enhanced Raman scattering (SERS) for high throughput and high sensitivity analysis of biomolecules. The size effect of gold nanoparticles on the intensity of SERS is first presented. A sandwich immunoassay was performed using Raman-labeled immunogold nanoparticles with various sizes. The SERS responses were correlated to particle densities, which were obtained by atomic force microscopy (AFM). The response of individual particles was also investigated using Raman-microscope and an array of gold islands on a silicon substrate. The location and the size of individual particles were mapped using AFM. The next study describes a low-level detection of Escherichia coli 0157:H7 and simulants of biological warfare agents in a sandwich immunoassay format using SERS labels, which have been termed Extrinsic Raman labels (ERLs). A new ERL scheme based on a mixed monolayer is also introduced. The mixed monolayer ERLs were created by covering the gold nanoparticles with a mixture of two thiolates, one thiolate for covalently binding antibody to the particle and the other thiolate for producing a strong Raman signal. An assay platform based on mixed self-assembled monolayers (SAMs) on gold is then presented. The mixed SAMs were prepared from …

Atomic clusters are unique objects, which occupy an intermediate position between atoms and condensed matter systems. For a long time it was thought that physical and chemical properties of atomic dusters monotonically change with increasing size of the cluster from a single atom to a condensed matter system. However, recently it has become clear that many properties of atomic clusters can change drastically with the size of the clusters. Because physical and chemical properties of clusters can be adjusted simply by changing the cluster's size, different applications of atomic clusters were proposed. One example is the catalytic activity of clusters of specific sizes in different chemical reactions. Another example is a potential application of atomic clusters in microelectronics, where their band gaps can be adjusted by simply changing cluster sizes. In recent years significant advances in experimental techniques allow one to synthesize and study atomic clusters of specified sizes. However, the interpretation of the results is often difficult. The theoretical methods are frequently used to help in interpretation of complex experimental data. Most of the theoretical approaches have been based on empirical or semiempirical methods. These methods allow one to study large and small dusters using the same approximations. However, …

Many of the current methods for pathogenic bacterial detection require long sample-preparation and analysis time, as well as complex instrumentation. This dissertation explores simple analytical approaches (e.g., flow cytometry and diffuse reflectance spectroscopy) that may be applied towards ideal requirements of a microbial detection system, through method and instrumentation development, and by the creation and characterization of immunosensing platforms. This dissertation is organized into six sections. In the general Introduction section a literature review on several of the key aspects of this work is presented. First, different approaches for detection of pathogenic bacteria will be reviewed, with a comparison of the relative strengths and weaknesses of each approach, A general overview regarding diffuse reflectance spectroscopy is then presented. Next, the structure and function of self-assembled monolayers (SAMs) formed from organosulfur molecules at gold and micrometer and sub-micrometer patterning of biomolecules using SAMs will be discussed. This section is followed by four research chapters, presented as separate manuscripts. Chapter 1 describes the efforts and challenges towards the creation of imunosensing platforms that exploit the flexibility and structural stability of SAMs of thiols at gold. 1H, 1H, 2H, 2H-perfluorodecyl-1-thiol SAM (PFDT) and dithio-bis(succinimidyl propionate)-(DSP)-derived SAMs were used to construct the platform. Chapter …

The combination of giant magnetoresistive sensors, magnetic labeling strategies, and biomolecule detection is just beginning to be explored. New readout methods and assay formats are necessary for biomolecules detection to flourish. The work presented in this dissertation describes steps toward the creation of a novel detection method for bioassays utilizing giant magnetoresistive sensors as the readout method. The introduction section contains a brief review of some of the current methods of bioassay readout. The theoretical underpinnings of the giant magnetoresistive effect are also discussed. Finally, the more prominent types of giant magnetoresistive sensors are described, as well as their complicated fabrication. Four data chapters follow the introduction; each chapter is presented as a separate manuscript, either already published or soon to be submitted. Chapter 1 presents research efforts toward the production of a bioassay on the surface of a gold-modified GMR sensor. The testing of this methodology involved the capture of goat a-mouse-coated magnetic nanoparticles on the mouse IgG-modified gold surface. The second, third and fourth chapters describe the utilization of a self-referenced sample stick for scanning across the GMR sensor. The sample stick consisted of alternating magnetic reference and bioactive gold addresses. Chapter 2 is concerned with the characterization …

Quantification in liquid chromatography (LC) is becoming very important as more researchers are using LC, not as an analytical tool itself, but as a sample introduction system for other analytical instruments. The ability of LC instrumentation to quickly separate a wide variety of compounds makes it ideal for analysis of complex mixtures. For elemental speciation, LC is joined with inductively coupled plasma mass spectrometry (ICP-MS) to separate and detect metal-containing, organic compounds in complex mixtures, such as biological samples. Often, the solvent gradients required to perform complex separations will cause matrix effects within the plasma. This limits the sensitivity of the ICP-MS and the quantification methods available for use in such analyses. Traditionally, isotope dilution has been the method of choice for LC-ICP-MS quantification. The use of naturally abundant isotopes of a single element in quantification corrects for most of the effects that LC solvent gradients produce within the plasma. However, not all elements of interest in speciation studies have multiple naturally occurring isotopes; and polyatomic interferences for a given isotope can develop within the plasma, depending on the solvent matrix. This is the case for reverse phase LC separations, where increasing amounts of organic solvent are required. For such …

Total internal reflection fluorescence microscopy (TIRFM) was used to study intermolecular interactions of DNAs with unpaired (sticky) ends of different lengths at water/fused silica interface at the single-molecule level. Evanescent field residence time, linear velocity and adsorption/desorption frequency were measured in a microchannel for individual DNA molecules from T7, Lambda, and PSP3 phages at various pH values. The longest residence times and the highest adsorption/desorption frequencies at the constant flow at pH 5.5 were found for PSP3 DNA, followed by lower values for Lambda DNA, and the lowest values for T7 DNA. Since T7, Lambda, and PSP3 DNA molecules contain none, twelve and nineteen unpaired bases, respectively, it was concluded that the affinity of DNAs for the surface increases with the length of the sticky ends. This confirms that hydrophobic and hydrogen-bonding interactions between sticky ends and fused-silica surface are driving forces for DNA adsorption at the fused-silica surface. Described single-molecule methodology and results therein can be valuable for investigation of interactions in liquid chromatography, as well as for design of DNA hybridization sensors and drug delivery systems.

The purposes of our research were: (1) To characterize subunits of highly fluorescent protein R-Phycoerythrin (R-PE) and check their suitability for single-molecule detection (SMD) and cell imaging, (2) To extend the use of R-PE subunits through design of similar proteins that will be used as probes for microscopy and spectral imaging in a single cell, and (3) To demonstrate a high-throughput spectral imaging method that will rival spectral flow cytometry in the analysis of individual cells. We first demonstrated that R-PE subunits have spectroscopic and structural characteristics that make them suitable for SMD. Subunits were isolated from R-PE by high-performance liquid chromatography (HPLC) and detected as single molecules by total internal reflection fluorescence microscopy (TIRFM). In addition, R-PE subunits and their enzymatic digests were characterized by several separation and detection methods including HPLC, capillary electrophoresis, sodium dodecyl sulfate-polyacrilamide gel electrophoresis (SDS-PAGE) and HPLC-electrospray ionization mass spectrometry (ESI-MS). Favorable absorption and fluorescence of the R-PE subunits and digest peptides originate from phycoerythrobilin (PEB) and phycourobilin (PUB) chromophores that are covalently attached to cysteine residues. High absorption coefficients and strong fluorescence (even under denaturing conditions), broad excitation and emission fluorescence spectra in the visible region of electromagnetic spectrum, and relatively low molecular …