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 …

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.

This thesis describes a measurement of the average proper decay time of the B{sub c}{sup {+-}} mesons, the ground state of bottom and charm quark bound states. The lifetime measurement is carried out in the decay modes B{sub c}{sup {+-}} {yields} J/{psi} + e{sup {+-}} + X and B{sub c}{sup {+-}} {yields} J/{psi} + {mu}{sup {+-}} + X, where the J/{psi} decays as J/{psi} {yields} {mu}{sup +}{mu}{sup -} and the X are unmeasured particles such as {nu}{sub e} or {nu}{sub {mu}}. The data are collect by the CDF II detector which measures the properties of particles created in {radical}s = 1.96 TeV p{bar p} collisions delivered by the Fermilab Tevatron. This measurement uses {approx} 1 fb{sup -1} of integrated luminosity. The measured average proper decay time of B{sub c}{sup {+-}} mesons, {tau} = 0.475{sub -0.049}{sup +0.053}(stat.) {+-} 0.018(syst.) ps, is competitive with the most precise measurements in the world and confirms previous measurements and theoretical predictions.

We have carried out a search for a charmed baryon {Omega}{sup *}{sub c} decaying to {Omega}{sup 0}{sub c} and a {gamma} where {Omega}{sub c} candidates are reconstructed using decay modes {Omega}{sup -}{pi}{sup +}(c1), {Omega}{sup -}{pi}{sup +}{pi}{sup 0}(c2), {Omega}{sup -}{pi}{sup +}{pi}{sup -}{pi}{sup +}(c3) and {Xi}{sup -}K{sup -}{pi}{sup +}{pi}{sup +}(c4). This search is performed by analyzing integrated luminosity of 230.7 fb{sup -1} data collected by the BABAR detector at the Stanford Linear Accelerator Center. In decay channel {Omega}{sup *}{sub c} {yields} {Omega}{sup 0}{sub c}({Omega}{sup -}{pi}{sup +}){gamma} (C1), we observe a signal yield of 39.2{sup +9.8}{sub -9.1}(stat){+-}6.0(syst) events with a significance of 4.2 standard deviations. In decay channels {Omega}{sup *}{sub c} {yields} {Omega}{sup 0}{sub c}({Omega}{sup -}{pi}{sup +}{pi}{sup 0}){gamma} (C2) and {Omega}{sup *}{sub c} {yields} {Omega}{sup 0}{sub c}({Xi}{sup -}K{sup -}{pi}{sup +}{pi}{sup +}){gamma} (C4), we observe signal yields of 55.2{sup 16.1}{sub -15.2} {+-} 5.6 and 20.2{sup +9.3}{sub -8.5} {+-} 3.1 with significances of 3.4 and 2.0 {sigma}, respectively. As for the {Omega}{sup *}{sub c} {yields} {Omega}{sup 0}{sub c}({Omega}{sup -}{pi}{sup +}{pi}{sup -}{pi}{sup +}){gamma} (C3) decay channel, we observe signal yields of -5.1{sup +5.3.8}{sub -4.7}{+-}1.0 without a positive significance. We assume the same production mechanism for the four decay channels of {Omega}{sup *}{sub c} studied. By combining …

High energy-density physics (HEDP) experiments examine the properties of materials under extreme conditions. These experiments rely on the measurement of one or two velocities. These velocities are used to obtain Hugoniot relationships and thermodynamic equations of state. This methodology is referred to as 'velocimetry' and an instrument used to measure the shock wave is called a 'velocimeter' or a '(velocity) diagnostic'. The two most-widely used existing velocity diagnostics are; photonic Doppler velocimetry (PDV) and velocity interferometer system for any reflector (VISAR). PDV's advantages are a fast rise-time and ease of implementation but PDV has an upper velocity limit. Traditional implementations of VISAR have a rise time 10 times slower than PDV and are not easily implemented but are capable of measuring any velocity produced during HEDP experiments. This thesis describes a novel method of combining the positive attributes of PDV and VISAR into a more cost effective diagnostic called a Single-Mode VISAR (SMV). The new diagnostic will consist of PDV parts in a VISAR configuration. This configuration will enable the measurement of any velocity produced during shock physics experiments while the components used to build the diagnostic will give the diagnostic a fast rise time and make it easy to …

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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.

Over the past decades the current theoretical description, the Standard Model of elementary particle physics, was solidified by many measurements as the basic theory describing fundamental particles and their interactions. It is extremely successful in explaining the high-precision data collected by experiments so far. The Standard Model includes several intrinsic parameters which have to be measured in experiments. Independent analyses of different physical processes can constrain those parameters. By combining those measurements physicists might be sensitive to physics beyond the Standard Model. If they are inconsistent it allows to get a hint on the theory that might supersede the Standard Model. The goal of the analysis presented in this thesis is to measure some of these parameters in the B{sub s} meson system. The B{sub s} meson, consisting of an anti-b and s quark, is not a pure mass eigenstate, thus allowing a B{sub s} meson to oscillate into its antiparticle via weak interacting processes. This is a general feature of any neutral meson. The history of meson mixing measurements is more then 50 years old. It was first observed in the kaon system. The oscillation in the B{sub d} system was measured very precisely by the B factories, whereas …

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 …

This dissertation describes a measurement of the shape of the boson transverse momentum distribution in p{bar p} {yields} Z/{gamma}* {yields} e{sup +}e{sup -} + X events at a center-of-mass energy of 1.96 TeV. The measurement is made for events with electron-positron mass between 70 < M{sub ee} < 110 GeV/c{sup 2} and uses 976 pb{sup -1} of data collected at the Fermilab Tevatron collider with the D0 detector. The shape is measured both for the inclusive sample and for the subset of events containing a boson with large rapidity. The large-rapidity distribution shows better agreement with theory when the calculation is done using traditional Collins-Soper-Sterman resummation than when using a recent resummed form factor with modifications in the small-x region.

Understanding the world -- This aim drives humankind since the beginning of conscious thinking. Especially the nature of matter has been of major interest. Nowadays, we have a complex image of the constitution of matter. Atoms consist of electrons and nucleons. But even nucleons are not elementary. Their basic constituents are called quarks. Physicists developed a model describing the elementary components of matter as well as the forces between them: the standard model of elementary particle physics. The substructure of matter is only visible in scattering experiments. In high energy physics, these experiments are done at particle accelerators. The world's highest energetic collider, the Tevatron, is hosted by the Fermi National Accelerator Laboratory (FNAL), also called Fermilab, in the vicinity of Chicago. The proton-antiproton collisions with a center-of-mass energy of {radical}s = 1.96 TeV are recorded by two multipurpose detectors, namely D0 and CDF II.

The evidence is compelling that neutrinos undergo flavor change as they propagate. In recent years, experiments have observed this phenomenon of neutrino oscillations using disparate neutrino sources: the sun, fission reactors, accelerators, and secondary cosmic rays. The standard model of particle physics needs only simple extensions - neutrino masses and mixing - to accommodate all neutrino oscillation results to date, save one. The 3.8{sigma}-significant {bar {nu}}{sub e} excess reported by the LSND collaboration is consistent with {bar {nu}}{sub {mu}} {yields}{bar {nu}}{sub e} oscillations with a mass-squared splitting of {Delta}m{sup 2} {approx} 1 eV{sup 2}. This signal, which has not been independently verified, is inconsistent with other oscillation evidence unless more daring standard model extensions (e.g. sterile neutrinos) are considered.

Additional gauge bosons are introduced in many theoretical extensions to the Standard Model. A search for a new heavy charged gauge boson W{prime} decaying into an electron and a neutrino is presented. The data used in this analysis was taken with the D0 detector at the Fermilab proton-antiproton collider at a center-of-mass energy of 1.96 TeV and corresponds to an integrated luminosity of about 1 fb{sup -1}. Since no significant excess is observed in the data, an upper limit is set on the production cross section times branching fraction {sigma}{sub W{prime}}xBr (W{prime} {yields} e{nu}). Using this limit, a W{prime} boson with mass below {approx}1 TeV can be excluded at the 95% confidence level assuming that the new boson has the same couplings to fermions as the Standard Model W boson.

I present time-varying Reeb graphs as a topological framework to support the analysis of continuous time-varying data. Such data is captured in many studies, including computational fluid dynamics, oceanography, medical imaging, and climate modeling, by measuring physical processes over time, or by modeling and simulating them on a computer. Analysis tools are applied to these data sets by scientists and engineers who seek to understand the underlying physical processes. A popular tool for analyzing scientific datasets is level sets, which are the points in space with a fixed data value s. Displaying level sets allows the user to study their geometry, their topological features such as connected components, handles, and voids, and to study the evolution of these features for varying s. For static data, the Reeb graph encodes the evolution of topological features and compactly represents topological information of all level sets. The Reeb graph essentially contracts each level set component to a point. It can be computed efficiently, and it has several uses: as a succinct summary of the data, as an interface to select meaningful level sets, as a data structure to accelerate level set extraction, and as a guide to remove noise. I extend these uses …

Much of the previous work in the large data visualization area has solely focused on handling the scale of the data. This task is clearly a great challenge and necessary, but it is not sufficient. Applying standard visualization techniques to large scale data sets often creates complicated pictures where meaningful trends are lost. A second challenge, then, is to also provide algorithms that simplify what an analyst must understand, using either visual or quantitative means. This challenge can be summarized as improving the legibility or reducing the complexity of massive data sets. Fully meeting both of these challenges is the work of many, many PhD dissertations. In this dissertation, we describe some new techniques to address both the scale and legibility challenges, in hope of contributing to the larger solution. In addition to our assumption of simultaneously addressing both scale and legibility, we add an additional requirement that the solutions considered fit well within an interoperable framework for diverse algorithms, because a large suite of algorithms is often necessary to fully understand complex data sets. For scale, we present a general architecture for handling large data, as well as details of a contract-based system for integrating advanced optimizations into a …

The castor bean plant (Ricinus communis) is a member of the family Euphorbiaceae. In spite of its common name, the castor plant is not a true bean (i.e., leguminous plants belonging to the family, Fabaceae). Ricinus communis is native to tropical Africa, but because the plant was recognized for its production of oil with many desirable properties, it has been introduced and cultivated in warm temperate regions throughout the world (Armstrong 1999 and Brown 2005). Castor bean plants have also been valued by gardeners as an ornamental plant and, historically, as a natural rodenticide. Today, escaped plants grow like weeds throughout much of the southwestern United States, and castor seeds are even widely available to the public for order through the Internet. In this study, multiple loci of chloroplast noncoding sequence data and a few nuclear noncoding regions were examined to identify DNA polymorphisms present among representatives from a geographically diverse panel of Ricinus communis cultivated varieties. The primary objectives for this research were (1) to successfully cultivate castor plants and extract sufficient yields of high quality DNA from an assortment of castor cultivated varieties, (2) to use PCR and sequencing to screen available universal oligos against a small panel …

The authors searched for decays of the type B{sub (s)}{sup 0} {yields} h{sup +}h{prime}{sup -} (where h, h{prime} = K or {pi}) in a sample corresponding to 180 pb{sup -1} of p{bar p} collisions at {radical}s = 1.96 TeV, collected by the upgraded Collider Detector at the Fermilab Tevatron. A total signal of approximately 900 events was reconstructed, and the relative branching fractions ({Beta}) of each decay mode were determined with a likelihood fit.

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 …

In this dissertation, they present a study of the untagged decay of B{sub s}{sup 0} {yields} J/{psi}{phi}, the final state of which is a superposition of the CP-even and CP-odd states. Within the framework of the standard model (SM), to a good approximation, the two CP eigenstates of the (B{sub s}{sup 0}, {bar B}{sub s}{sup 0}) system are equivalent to mass eigenstates. The data collected by the D0 detector between June 2002 to August 2004 (an integrated luminosity of approximately 450 pb{sup -1}) has been used for the analysis presented in this thesis. From a simultaneous fit to the B{sub s}{sup 0} candidate mass, lifetime, and the angular distribution of the decay products, they obtain the CP-odd fraction in the final state at production time to be 0.16 {+-} 0.10(stat) {+-} 0.02(syst). The average lifetime of the (B{sub s}{sup 0}, {bar B}{sub s}{sup 0}) system is measured to be 1.39{sub -0.16}{sup +0.13}(stat){sub -0.02}{sup +0.01}(syst) ps, with the relative width difference between the heavy and light mass eigenstates, {Delta}{Gamma}/{bar {Gamma}} = ({Gamma}{sup L}/{Gamma}{sup H})/{bar {Gamma}} = 0.24{sub -0.38}{sup +0.28}(stat){sub -0.04}{sup +0.03}(syst). With the additional constraint from the world average of the B{sub s}{sup 0} lifetime measurements using semileptonic decays, they find …

In this thesis the author has described the first measurement performed at a hadron collider of the branching fraction of the Cabibbo-suppressed mode B{sup +} {yields} {bar D}{sup 0} K{sup +}. The analysis has been performed with 360 pb{sup -1} of data collected by the CDF II detector.

In this thesis we present a new technique to analyze events containing two highly energetic leptons, as a probe of the Standard Model. The philosophy is to consider the data in a more global way, as opposed to the more traditional process dependent approach of extracting a given signal over the expected backgrounds by using various kinematical requirements. We use our global technique to simultaneously measure the cross sections of the main Standard Model processes; the t{bar t}, WW and Z {yields} {tau}{tau} production from p{bar p} collisions at {radical}s = 1.96 TeV in the CDF detector at Fermilab. We select events by requiring they contain two highly energetic leptons (e{mu}, ee, or {mu}{mu}), and make no other kinematic requirements, except for the ee and {mu}{mu} channels. We then use a likelihood fit of the data in the two-dimensional phase space defined by the missing transverse energy (E{sub T}) and the number of jets in the event (N{sub jet}), to the expected Standard Model distributions, to simultaneously extract the production cross-sections of the main process contributing to our dilepton sample.