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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 …

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 …

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 …

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 main aim of physics research is to obtain a consistent description of nature leading to a detailed understanding of the phenomena observed in experiments. The field of particle physics focuses on the discovery and understanding of the fundamental particles and the forces by which they interact with each other. Using methods from group theory, the present knowledge can be mathematically described by the so-called ''Standard Model'', which interprets the fundamental particles (quarks and leptons) as quantum-mechanical fields interacting via the electromagnetic, weak and strong force. These interactions are mediated via gauge particles such as the photon (for the electromagnetic force), W{sup {+-}} and Z{sup 0} (for the weak force) and gluons (for the strong force). Gravitation is not yet included in this description as it presently cannot be formulated in a way to be incorporated in the Standard Model. However, the gravitational force is negligibly small on microscopic levels. The validity of this mathematical approach is tested experimentally by accelerating particles such as electrons and protons, as well as their antiparticles, to high energies and observing the reactions as these particles collide using sophisticated detectors. Due to the high energy of the particles involved, these detectors need to be …

The development of new odd-Z-projectile reactions leading to the production of transactinide elements is described. The cross section of the even-Z-projectile 208Pb(64Ni, n)271Ds reaction was measured at two new energies using the Berkeley Gas-filled Separator at the Lawrence Berkeley National Laboratory 88-Inch Cyclotron. In total, seven decay chains attributable to 271Ds were observed. These data, combined with previous results, establish an excitation function for the production of 271Ds. The maximum cross section was 20 +15 -11 pb at a center-of-target energy of 311.5 MeV in the laboratory frame.The data from the 271Ds experiments were used to estimate the optimum beam energy for the new odd-Z-projectile 208Pb(65Cu, n)272-111 reaction using the Fusion by Diffusion theory proposed by Swiatecki, Siwek-Wilczynska, and Wilczynski. A cross section for this reaction was measured for the first time, at a center-of-target energy of 321.1 MeV in the laboratory frame. The excitation energy f or compound nuclei formed at the target center was 13.2 MeV. One decay chain was observed, resulting in a measured cross section of 1.7 +3.9 -1.4 pb. This decay chain is in good agreement with previously published data on the decay of 272-111.The new odd-Z-projectile 208Pb(55Mn, n)262Bh reaction was studied at three different …

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 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 …

Thesis on the virtual compton scattering experiment in Hall A at Jefferson Lab.

In hadronic physics, the nucleon structure and the quarks confinement are still topical issues. The neutral pion electroproduction and virtual Compton scattering (VCS) reactions allow us to access new observables that describe this structure. This work is focused on the VCS experiment performed at Jefferson Lab in 1998.

The high temporal resolution and broad bandwidth of a femtosecond laser system are exploited in a pair of nonlinear optical studies of surfaces. The dephasing dynamics of resonances associated with the adatom dangling bonds of the Si(111)7 x 7 surface are explored by transient second-harmonic hole burning, a process that can be described as a fourth-order nonlinear optical process. Spectral holes produced by a 100 fs pump pulse at about 800 nm are probed by the second harmonic signal of a 100 fs pulse tunable around 800 nm. The measured spectral holes yield homogeneous dephasing times of a few tens of femtoseconds. Fits with a Lorentzian spectral hole centered at zero probe detuning show a linear dependence of the hole width on pump fluence, which suggests that charge carrier-carrier scattering dominates the dephasing dynamics at the measured excitation densities. Extrapolation of the deduced homogeneous dephasing times to zero excitation density yields an intrinsic dephasing time of {approx} 70 fs. The presence of a secondary spectral hole indicates that scattering of the surface electrons with surface optical phonons at 570 cm{sup -1} occurs within the first 200 fs after excitation. The broad bandwidth of femtosecond IR pulses is used to perform …

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.

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 …

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.

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The current practice of nondestructive assay (NDA) of fissile materials using neutrons is dominated by the {sup 3}He detector. This has been the case since the mid 1980s when Fission Multiplicity Detection (FMD) was replaced with thermal well counters and neutron multiplicity counting (NMC). The thermal well counters detect neutrons by neutron capture in the {sup 3}He detector subsequent to moderation. The process of detection requires from 30 to 60 {micro}s. As will be explained in Section 3.3 the rate of detecting correlated neutrons (signal) from the same fission are independent of this time but the rate of accidental correlations (noise) are proportional to this time. The well counters are at a distinct disadvantage when there is a large source of uncorrelated neutrons present from ({alpha}, n) reactions for example. Plastic scintillating detectors, as were used in FMD, require only about 20 ns to detect neutrons from fission. One thousandth as many accidental coincidences are therefore accumulated. The major problem with the use of fast-plastic scintillation detectors, however, is that both neutrons and gamma rays are detected. The pulses from the two are indistinguishable in these detectors. For this thesis, a new technique was developed to use higher-order time correlation …

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 …

Reliable group ordered delivery of multicast messages in a distributed system is a useful service that simplifies the programming of distributed applications. Such a service helps to maintain the consistency of replicated information and to coordinate the activities of the various processes. With the increasing popularity of the Internet, there is an increasing interest in scaling the protocols that provide this service to the environment of the Internet. The InterGroup protocol suite, described in this dissertation, provides such a service, and is intended for the environment of the Internet with scalability to large numbers of nodes and high latency links. The InterGroup protocols approach the scalability problem from various directions. They redefine the meaning of group membership, allow voluntary membership changes, add a receiver-oriented selection of delivery guarantees that permits heterogeneity of the receiver set, and provide a scalable reliability service. The InterGroup system comprises several components, executing at various sites within the system. Each component provides part of the services necessary to implement a group communication system for the wide-area. The components can be categorized as: (1) control hierarchy, (2) reliable multicast, (3) message distribution and delivery, and (4) process group membership. We have implemented a prototype of 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 …

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 …

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 …

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