In the Tevatron accelerator at Fermilab protons and antiprotons are collided at a 1.96 TeV center of mass energy. CDF and D0 are the two experiments currently operating at the Tevatron. At these energies top quark is mostly produced via strong interactions as a top anti-top pair (t{bar t}). The top quark has an extremely short lifetime and according to the Standard Model it decays with {approx} 100% probability into a b quark and a W boson. In the ''lepton+jets'' channel, the signal from top pair production is detected for those events where one of the two W bosons decays hadronically in two quarks which we see as jets in the detector, and the other W decays into an electrically charged lepton and a neutrino. A relatively unambiguous identification in the detector is possible when we require that the charged lepton must be an electron or muon of either charge. The neutrino does not interact in the detector and its presence is inferred from an imbalance in the transverse energy of the event. They present a measurement of the top pair production cross section in p{bar p} collisions at 1.96 TeV, from a data sample collected at CDF between March …

The production of heavy quarkonium in hadronic collisions provides an ideal testing ground for our understanding of the production mechanisms for heavy quarks and the non-perturbative QCD effects that bind the quark pairs into quarkonium. In this analysis, the inclusive production cross section of the {Upsilon}(1S) bottomonium state is measured using the {Upsilon}(1S) {yields} {mu}{sup +}{mu}{sup -} decay mode. The data sample corresponds to an integrated luminosity of 159.1 {+-} 10.3 pb{sup -1}. We determine differential cross sections as functions of the {Upsilon}(1S) transverse momentum, p{sub T}{sup {Upsilon}}, for three ranges of the {Upsilon}(1S) rapidity: 0 < |y{sup {Upsilon}}| < 0.6,0.6 < |y{sup {Upsilon}}| < 1.2 and 1.2 < |y{sup {Upsilon}}| < 1.8. The shapes of d{sigma}/d{sub p{sub T}} cross sections show little variation with rapidity and are consistent with the published Run I CDF measurement over the rapidity range |y{sup {Upsilon}}| < 0.4.

Designing an adaptive optics (AO) system for extremely large telescopes (ELT's) will present new optical engineering challenges. Several of these challenges are addressed in this work, including first-order design of multi-conjugate adaptive optics (MCAO) systems, pyramid wavefront sensors (PWFS's), and laser guide star (LGS) spot elongation. MCAO systems need to be designed in consideration of various constraints, including deformable mirror size and correction height. The y,{bar y} method of first-order optical design is a graphical technique that uses a plot with marginal and chief ray heights as coordinates; the optical system is represented as a segmented line. This method is shown to be a powerful tool in designing MCAO systems. From these analyses, important conclusions about configurations are derived. PWFS's, which offer an alternative to Shack-Hartmann (SH) wavefront sensors (WFS's), are envisioned as the workhorse of layer-oriented adaptive optics. Current approaches use a 4-faceted glass pyramid to create a WFS analogous to a quad-cell SH WFS. PWFS's and SH WFS's are compared and some newly-considered similarities and PWFS advantages are presented. Techniques to extend PWFS's are offered: First, PWFS's can be extended to more pixels in the image by tiling pyramids contiguously. Second, pyramids, which are difficult to manufacture, can …

For this study, a high throughput method for identifying and testing regulatory elements was examined. In addition, the validity of promoters predicted by FirstEF was tested. It was found that by combining computer based promoter and first exon predictions from FirstEF (Davuluri et al., 2001) with PCR-based cloning to generate luciferase reporter constructs, and by testing reporter activity in cultured mammalian cells plated in a 96 well format one could identify promoter activity in a relatively high throughput manner. The data generated in this study suggest that FirstEF predictions are sometimes incorrect. Therefore, having a strategy for defining which FirstEF predicted promoters to test first may accelerate the process. Initially testing promoters that are at a confirmed transcription start site for a gene, at a possible alternate transcription start site or in a region of conserved sequence would be the best candidates, while promoters predicted in gene desert regions may not be as easy to confirm. The luciferase assay lent itself very well to the high throughput search, however the subcloning did not always go smoothly. The numerous steps that this traditional subcloning method requires were time consuming and increased the opportunities for errors. A faster method that skips many …

A measurement of the polarization of the W boson from top quark decay is an excellent test of the V-A form of the charged-current weak interaction in the standard model. Since the longitudinal W boson is intimately related to the electroweak symmetry breaking mechanism, and the standard model gives a specific prediction for the fraction of longitudinal W bosons from top decays, it is of particular interest for study. This thesis presents a measurement of W boson polarization in top quark decays through an analysis of the cos{theta}* distribution in the lepton-plus-jets channel of t{bar t} candidate events from p{bar p} collisions at {radical}s = 1.96 TeV. This measurement uses an integrated luminosity of {approx} 162 pb{sup -1} of data collected with the CDF Run II detector, resulting in 31 t{bar t} candidate events with at least one identified b jet. Using a binned likelihood fit to the cos{theta}* distribution from the t{bar t} candidate events found in this sample, the fraction of W bosons with longitudinal polarization is determined to be F{sub 0} = 0.99{sub -0.35}{sup +0.29}(stat.) {+-} 0.19(syst.), F{sub 0} > 0.33 {at} 95% CL. This result is consistent with the standard model prediction, given a top quark …

This thesis describes the analysis of the semileptonic decay D{sup 0} {yields} {bar K}{sup 0} {pi}{sup -} {mu}{sup +}{nu} using FOCUS data. FOCUS is a fixed target experiment at Fermilab that studies the physics of the charm quark. Particles containing charm are produced by photon-gluon fusion from the collision of a photon beam on a BeO target. The experiment is characterized by excellent vertex resolution and particle identification. The spectrometer consists of three systems for track reconstruction (two silicon systems and one multiwire proportional chamber system) and two magnets of opposite polarity. The polarity of the magnet is such that the events of e{sup +}e{sup -} pairs produced in the target (which constitutes the main background) travel through a central opening in the detectors without interactions. Particle momentum is measured from the deflection angle in the magnets. Three multicell Cerenkov counters are used for charged particle identification (for e, {pi}, K, and p). Two different tracking systems located after several interaction lengths of shielding material are used for muon identification. The energy of neutral pions and electrons is measured in two electromagnetic calorimeters, while an hadron calorimeter is used for measuring the neutron energy. During the last four years the …

The discovery that ultra-intense laser pulses (I > 10{sup 18} W/cm{sup 2}) can produce short pulse, high energy proton beams has renewed interest in the fundamental mechanisms that govern particle acceleration from laser-solid interactions. Experiments have shown that protons present as hydrocarbon contaminants on laser targets can be accelerated up to energies > 50 MeV. Different theoretical models that explain the observed results have been proposed. One model describes a front-surface acceleration mechanism based on the ponderomotive potential of the laser pulse. At high intensities (I > 10{sup 18} W/cm{sup 2}), the quiver energy of an electron oscillating in the electric field of the laser pulse exceeds the electron rest mass, requiring the consideration of relativistic effects. The relativistically correct ponderomotive potential is given by U{sub p} = ([1 + I{lambda}{sup 2}/1.3 x 10{sup 18}]{sup 1/2} - 1) m{sub o}c{sup 2}, where I{lambda}{sup 2} is the irradiance in W {micro}m{sup 2}/cm{sup 2} and m{sub o}c{sup 2} is the electron rest mass. At laser irradiance of I{lambda}{sup 2} {approx} 10{sup 20} W {micro}m{sup 2}/cm{sup 2}, the ponderomotive potential can be of order several MeV. A few recent experiments--discussed in Chapter 3 of this thesis--consider this ponderomotive potential sufficiently strong to accelerate …

When the field of modern publishing was on a collision course with telecommunications, publishing organizations had to come up to speed in fields that were, heretofore, completely foreign and technologically forbidding to them. For generations, the technology of publishing centered on offset lithography, typesetting, and photography--fields that saw evolutionary and incremental change from the time of Guttenberg. But publishing now includes making information available over the World Wide Web--Internet publishing--with its ever-accelerating rate of technological change and dependence on computers and networks. Clearly, we need a methodology to help anyone in the field of Internet publishing plan for the future, and there is a well-known, well-tested technique for just this purpose--Scenario Planning. Scenario Planning is an excellent tool to help organizations make better decisions in the present based on what they identify as possible and plausible scenarios of the future. Never was decision making more difficult or more crucial than during the years of this study, 1996-1999. This thesis takes the position that, by applying Scenario Planning, the Technical Information Department at LLNL, a large government laboratory (and organizations similar to it), could be confident that moving into the telecommunications business of Internet publishing stood a very good chance of …

The FOCUS experiment is designed to investigate charm particle decays. These charm particles are produced by the interaction of a photon beam with an average energy of 175 GeV on a BeO target and travel an average of few millimeters before decaying in the spectrometer. By reconstructing the daughters from the decay, we can infer properties of the charm particles. Semileptonic decays have been used to measure many CKM matrix elements. These decays are interesting due to the simplicity of their theoretical description but they are experimentally challenging due to the fact that a neutrino is not detected. Analysis of semileptonic decays in the charm sector are of great interest because they provide an excellent environment to test and to calibrate theoretical calculation that can be implemented in the determination of poorly known matrix elements such as V{sub ub}. In this thesis we report an analysis of the decays D{sup 0} {yields} {pi}{sup -}{mu}{sup +}{nu} and D{sup 0} {yields} K{sup -} {mu}{sup +}{nu}. We measure the relative branching ratio as well as the ratio of the form factors f{sub +}{sup {pi}}(0)/f{sub +}{sup K}(0). Using a weighting technique, we further report a parametric analysis of the q{sup 2} dependence for both …

This thesis presents the measurement of prompt diphoton production rate in proton-antiproton collisions at a center-of-mass energy of 1.96 TeV using the upgraded Collider Detector at Fermilab (CDF II). This process deserves some attention for the following reasons. The H {yields} {gamma}{gamma} decay mode is an important channel for the Standard Model (SM) Higgs boson searches in the low mass region (M{sub H} < 130 GeV) at the forth coming LHC. In many models involving physics beyond the SM, cascade decays of heavy new particles generate a {gamma}{gamma} signature. Some examples are supersymmetry with a light gravitino, radiative decays to a higgsino-LSP and models with large symmetry groups. The QCD production of prompt photon pairs with large invariant mass is the irreducible background to these searches. The rate is huge and requires to be quantitatively evaluated prior to any of the possible discoveries. In a hadronic collider environment such as LHC, prompt photon signals are contaminated by the production of neutral mesons which decay to multiple collinear photons. The experience of classifying background of neutral meson is very important. The process can be used to test the Next-to-Leading Order (NLO) calculation of Quantum Chromodynamics (QCD). The 4-momentum of particles in …

The author has measured the t{bar t} production cross section at {radical}s = 1.96 TeV using data collected by the D0 experiment at Fermilab. The integrated luminosity of the data set is 140 pb{sup -1} and a total of four candidate events are seen, with an expected background of 2.61 events. The measured cross section of {sigma}{sub t{bar t}} = 11.1{sub -9.3}{sup +22.1}(stat.){sub -4.5}{sup +4.3}(sys.) pb is in agreement with a NNLO calculation of 6.77 pb.

This thesis details the measurement of the p{bar p} {yields} W{gamma} + X {yields} {mu}{nu}{gamma} + X cross section at {radical}s = 1.96 TeV using the D0 detector at Fermilab, in 134.5 pb{sup -1} of integrated luminosity. From the photon E{sub T} spectrum limits on anomalous couplings of the photon to the W are obtained. At 95% confidence level, limits of -1.05 < {Delta}{kappa} < 1.04 for {lambda} = 0 and -0.28 < {lambda} < 0.27 for {Delta}{kappa} = 0 are obtained on the anomalous coupling parameters. The charge signed rapidity difference from the data is displayed, and its significance discussed.

This dissertation sets new limits on the mass of the scalar leptoquark from direct searches carried out at the Run II CDF detector using data from March 2001 to October 2003. The data analyzed has a total time-integrated measured luminosity of 198 pb{sup -1} of p{bar p} collisions with {radical}s = 1.96 TeV. Leptoquarks are assumed to be pair-produced and to decay into a lepton and a quark of the same generation. They consider two possible leptoquark decays: (1) {beta} = BR(LQ {yields} {mu}q) = 1.0, and (2) {beta} = BR(LQ {yields} {mu}q) = 0.5. For the {beta} = 1 channel, they focus on the signature represented by two isolated high-p{sub T} muons and two isolated high-p{sub T} jets. For the {beta} = 1/2 channel, they focus on the signature represented by one isolated high-p{sub T} muon, large missing transverse energy, and two isolated high-p{sub T} jets. No leptoquark signal is experimentally detected for either signature. Using the next to leading order theoretical cross section for scalar leptoquark production in p{bar p} collisions [1], they set new mass limits on second generation scalar leptoquarks. They exclude the existence of second generation scalar leptoquarks with masses below 221(175) GeV/c{sup 2} for …

Optical parametric amplification is an established broadband amplification technology based on a second-order nonlinear process of difference-frequency generation (DFG). When used in chirped pulse amplification (CPA), the technology has been termed optical parametric chirped pulse amplification (OPCPA). OPCPA holds a potential for producing unprecedented levels of peak and average power in optical pulses through its scalable ultrashort pulse amplification capability and the absence of quantum defect, respectively. The theory of three-wave parametric interactions is presented, followed by a description of the numerical model developed for nanosecond pulses. Spectral, temperature and angular characteristics of OPCPA are calculated, with an estimate of pulse contrast. An OPCPA system centered at 1054 nm, based on a commercial tabletop Q-switched pump laser, was developed as the front end for a large Nd-glass petawatt-class short-pulse laser. The system does not utilize electro-optic modulators or multi-pass amplification. The obtained overall 6% efficiency is the highest to date in OPCPA that uses a tabletop commercial pump laser. The first compression of pulses amplified in highly nondegenerate OPCPA is reported, with the obtained pulse width of 60 fs. This represents the shortest pulse to date produced in OPCPA. Optical parametric amplification in {beta}-barium borate was combined with laser amplification …

Knowledge discovery from large and complex collections of today's scientific datasets is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the increasing number of data dimensions and data objects is presenting tremendous challenges for data analysis and effective data exploration methods and tools. Researchers are overwhelmed with data and standard tools are often insufficient to enable effective data analysis and knowledge discovery. The main objective of this thesis is to provide important new capabilities to accelerate scientific knowledge discovery form large, complex, and multivariate scientific data. The research covered in this thesis addresses these scientific challenges using a combination of scientific visualization, information visualization, automated data analysis, and other enabling technologies, such as efficient data management. The effectiveness of the proposed analysis methods is demonstrated via applications in two distinct scientific research fields, namely developmental biology and high-energy physics.Advances in microscopy, image analysis, and embryo registration enable for the first time measurement of gene expression at cellular resolution for entire organisms. Analysis of high-dimensional spatial gene expression datasets is a challenging task. By integrating data clustering and visualization, analysis of complex, time-varying, spatial gene expression patterns and their formation …

A search for the Standard Model Higgs boson in proton-antiproton collisions with center-of-mass energy 1.96 TeV at the Tevatron is presented in this dissertation. The process of interest is the associated production of W boson and Higgs boson, with the W boson decaying leptonically and the Higgs boson decaying into a pair of bottom quarks. The dataset in the analysis is accumulated by the D0 detector from April 2002 to April 2008 and corresponding to an integrated luminosity of 2.7 fb{sup -1}. The events are reconstructed and selected following the criteria of an isolated lepton, missing transverse energy and two jets. The D0 Neural Network b-jet identification algorithm is further used to discriminate b jets from light jets. A multivariate analysis combining Matrix Element and Neural Network methods is explored to improve the Higgs boson signal significance. No evidence of the Higgs boson is observed in this analysis. In consequence, an observed (expected) limit on the ratio of {sigma} (p{bar p} {yields} WH) x Br (H {yields} b{bar b}) to the Standard Model prediction is set to be 6.7 (6.4) at 95% C.L. for the Higgs boson with a mass of 115 GeV.

Hard, wear-resistant coatings of thin film borides based on AlMgB{sub 14} have the potential to be applied industrially to improve the tool life of cutting tools and pump vanes and may account for several million dollars in savings as a result of reduced wear on these parts. Past work with this material has shown that it can have a hardness of up to 45GPa and be fabricated into thin films with a similar hardness using pulsed laser deposition. These films have already been shown to be promising for industrial applications. Cutting tools coated with AlMgB{sub 14} used to mill titanium alloys have been shown to substantially reduce the wear on the cutting tool and extend its cutting life. However, little research into the thin film fabrication process using pulsed laser deposition to make AlMgB{sub 14} has been conducted. In this work, research was conducted into methods to optimize the deposition parameters for the AlMgB{sub 14} films. Processing methods to eliminate large particles on the surface of the AlMgB{sub 14} films, produce films that were at least 1m thick, reduce the surface roughness of the films, and improve the adhesion of the thin films were investigated. Use of a femtosecond laser …

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The top quark was discovered in 1995 at the Fermilab National Accelerator Laboratory (Fermilab). One way to confirm if the observed top quark is really the top quark posited in the Standard Model (SM) is to measure its electric charge. In the Standard Model the top quark is the isospin partner of the bottom quark and is expected to have a charge of +2/3. However, an alternative 'exotic' model has been proposed with a fourth generation exotic quark that has the same characteristics, such as mass, as our observed top but with a charge of -4/3. This thesis presents the first CDF measurement of the top quark's charge via its decay products, a W boson and a bottom quark, using {approx} 1 fb{sup -1} of data. The data were collected by the CDF detector from proton anti-proton (p{bar p}) collisions at {radical}s = 1.96 TeV at Fermilab. We classify events depending on the charges of the bottom quark and associated W boson and count the number of events which appear 'SM-like' or 'exotic-like' with a SM-like event decaying as t {yields} W{sup +}b and an exotic event as t {yields} W{sup -}b. We find the p-value under the Standard Model …

In 2001, the D0 experiment entered a new era. Run II of the Tevatron at the Fermi National Accelerator Laboratory began, and the collider became the highest energy particle accelerator in the world. Accordingly, the D0 detector had already undergone a series of upgrades in order to fully exploit the physics now within reach. These included improvements to the tracking, calorimetry, muon detection and triggering capabilities. In the Standard Model, the Higgs boson is the last piece of the puzzle that remains to be discovered. The Higgs mechanism and consequently the Higgs boson is thought to be the fundamental ingredient by which particles acquire mass, and its existence (or lack of existence) is one of the most pressing issues in particle physics today. As such, one of the main goals of the Run II physics programme at D0 is to search for it. Armed with new accelerator capabilities, D0 will be able to impose tighter constraints on the mass of the Higgs, and perhaps even detect this elusive particle. If the Higgs does exist, it will be extremely difficult to find. One of the main challenges at a hadron-hadron collider is to reduce the large QCD background that masks the …

The D0 experiment is based at the Tevatron, which is currently the world's highest-energy accelerator. The detector comprises three major subsystems: the tracking system, the calorimeter and the muon detector. Jets, seen in the calorimeter, are the most common product of the proton-proton interactions at 2TeV. This thesis is divided into two parts. The first part focuses on jets and describes the derivation of a jet energy scale using p{bar p} {yields} (Z + jets) events as a cross-check of the official D0 jet energy scale (Versions 4.2 and 5.1) which is derived using p{bar p} {yields} {gamma} + jets events. Closure tests were also carried out on the jet energy calibration as a further verification. Jets from b-quarks are commonly produced at D0, readily identified and are a useful physics tool. These require a special correction in the case where the b-jet decays via a muon and a neutrino. Thus a semileptonic correction was also derived as an addition to the standard energy correction for jets. The search for the Higgs boson is one of the largest physics programs at D0. The second part of this thesis describes a search for the Standard Model Higgs boson in the ZH …

We report on a measurement of the rapidity distribution, d{sigma}/dy, for Z=Drell-Yan {yields} ee events produced in p{bar p} collisions at {radical}s = 1.96 TeV. The data sample consists of 2.13 fb{sup -1} corresponding to about 160,000 Z/Drell-Yan {yields} ee candidates in the Z boson mass region collected by the Collider Detector at Fermilab. The d{sigma}/dy distribution, which is measured over the full kinematic range for e{sup +}e{sup -} pairs in the invariant mass range 66 < M{sub ee} < 116 GeV/c{sup 2}, is compared with theory predictions. There is good agreement between the data and predictions of Quantum Chromodynamics in Next to Leading Order with the CTEQ6.1M Parton Distribution Functions.

Presented are the results of a search for direct CP violation in Cabibbo-suppressed decays of D{sup 0} to two charged daughters. The analysis described was performed on {approx}230 fb{sup -1} of the BABAR data sample, recorded at the Stanford Linear Accelerator Center and using the PEP-II electron storage rings. We measure CP asymmetries for decay to the KK and {pi}{pi} final states, as well as for the branching ratio, and develop a new technique for tagging-efficiency correction using the Cabibbo-favored K{pi} final state. We find some evidence for CP violation in decays to the KK final state and results that suggest CP violation in the {pi}{pi} final state as well.

This dissertation presents the first measurement of top quark pair production cross-section in events containing a muon and a tau lepton. The measurement was done with 1 fb{sup -1} of data collected during April 2002 through February 2006 using the D0 detector at the Tevatron proton-antiproton collider, located at Fermi National Accelerator Laboratory (Fermilab), Batavia, Illinois. Events containing one isolated muon, one tau which decays hadronically, missing transverse energy, and two or more jets (at least one of which must be tagged as a heavy flavor jet) were selected. Twenty-nine candidate events were observed with an expected background of 9.16 events. The top quark pair production cross-section is measured to be {sigma}(t{bar t}) = 8.0{sub -2.4}{sup +2.8}(stat){sub -1.7}{sup +1.8}(syst) {+-} 0.5(lumi) pb. Assuming a top quark pair production cross-section of 6.77 pb for Monte Carlo signal top events without a real tau, the measured {sigma} x BR is {sigma}(t{bar t}) x BR(t{bar t} {yields} {mu} + {tau} + 2{nu} + 2b) = 0.18{sub -0.11}{sup +0.13}(stat){sub -0.09}{sup +0.09}(syst) {+-} 0.01(lumi) pb.