A description of the development of the mc{_}runjob software package used to manage large scale computing tasks for the D0 Experiment at Fermilab is presented, along with a review of the Digital Front End Trigger electronics and the software used to control them. A tracking study is performed on detector data to determine that the D0 Experiment can detect charged B mesons, and that these results are in accordance with current results. B mesons are found by searching for the decay channel B{sup {+-}} {yields} J/{psi}K{sup {+-}}.

Ultra-sensitive native fluorescence detection of proteins with miniaturized one- and two-dimensional polyacrylamide gel electrophoresis was achieved with laser side-entry excitation, which provides both high excitation power and low background level. The detection limit for R-phycoerythrin protein spots in 1-D SDS-PAGE was as low as 15 fg, which corresponds to 40 thousand molecules only. The average detection limit of six standard native proteins was 5 pg per band and the dynamic range spanned more than 3 orders of magnitude. Approximately 150 protein spots from 30 ng of total Escherichia coli extraction were detected on a 0.8 cm x 1 cm gel in two-dimensional separation. Estrogen-DNA adducts as 4-OHE{sub 1}(E{sub 2})-1-N3Ade and 4-OHEI(E2)-2-NacCys were hypothesized as early risk assessment of prostate and breast cancers. Capillary electrophoresis, luminescence/absorption spectroscopy and LC-MS were used to characterize and detect these adducts. Monoclonal antibodies against each individual adduct were developed and used to enrich such compounds from urine samples of prostate and breast cancer patients as well as healthy people. Adduct 4-OHE{sub 1}-1-N3Ade was detected at much higher level in urine from subjects with prostate cancer patients compared to healthy males. The same adduct and 4-OHEI-2-NacCys were also detected at a much higher level in urine …

The D0 detector underwent an upgrade to its silicon vertex detector and triggering systems during the transition from Run IIa to Run IIb to maximize its ability to fully exploit Run II at the Fermilab Tevatron. This thesis describes improvements made to the tracking and vertexing algorithms used by the high level trigger in both Run IIa and Run IIb, as well as a search for resonant di-J/{psi} states using both Run IIa and Run IIb data. Improvements made to the tracking and vertexing algorithms during Run IIa included the optimization of the existing tracking software to reduce overall processing time and the certification and testing of a new software release. Upgrades made to the high level trigger for Run IIb included the development of a new tracking algorithm and the inclusion of the new Layer 0 silicon detector into the existing software. The integration of Layer 0 into the high level trigger has led to an improvement in the overall impact parameter resolution for tracks of {approx}50%. The development of a new parameterization method for finding the error associated to the impact parameter of tracks returned by the high level tracking algorithm, in association with the inclusion of Layer …

The first proposal for plasma based accelerators was suggested by 1979 by Tajima and Dawson. Since then there has been a tremendous progress both theoretically and experimentally. The theoretical progress is particularly due to the growing interest in the subject and to the development of more accurate numerical codes for the plasma simulations (especially particle-in-cell codes). The experimental progress follows from the development of multi-terawatt laser systems based on the chirped-pulse amplification technique. These efforts have produced results in several experiments world-wide, with the detection of accelerated electrons of tens of MeV. The peculiarity of these advanced accelerators is their ability to sustain extremely large acceleration gradients. In the conventional radio frequency linear accelerators (RF linacs) the acceleration gradients are limited roughly to 100 MV/m; this is partially due to breakdown which occurs on the walls of the structure. The electrical breakdown is originated by the emission of the electrons from the walls of the cavity. The electrons cause an avalanche breakdown when they reach other metal parts of the RF linacs structure.

The Fermilab Tevatron is currently the world's highest energy colliding beam facility. Its counter-rotating proton and antiproton beams collide at 2 TeV center-of-mass. Delivery of such intense beam fluxes to experiments has required improved knowledge of the Tevatron's beam optical lattice. An oscillating dipole magnet, referred to as an AC dipole, is one of such a tool to non-destructively assess the optical properties of the synchrotron. We discusses development of an AC dipole system for the Tevatron, a fast-oscillating (f {approx} 20 kHz) dipole magnet which can be adiabatically turned on and off to establish sustained coherent oscillations of the beam particles without affecting the transverse emittance. By utilizing an existing magnet and a higher power audio amplifier, the cost of the Tevatron AC dipole system became relatively inexpensive. We discuss corrections which must be applied to the driven oscillation measurements to obtain the proper interpretation of beam optical parameters from AC dipole studies. After successful operations of the Tevatron AC dipole system, AC dipole systems, similar to that in the Tevatron, will be build for the CERN LHC. We present several measurements of linear optical parameters (beta function and phase advance) for the Tevatron, as well as studies of …

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 work presents measurements of two diffractive production ratio for heavy flavour physics with the use of a reconstructed J/{psi} {yields} {mu}{sup +}{mu}{sup -} sample in p{bar p} collisions at {radical}s = 1.96 TeV using the D0 detector at Fermilab Tevatron. These events were selected using the Luminosity Monitor detectors, the calorimeter system and the muon system in a pseudo-rapidity region with range 2.7 {le} |{eta}| {le} 4.4. The measured ratio were estimated to be N{sub diff}{sup J/{psi}}/N{sub total}{sup J/{psi}} = (1.74 {+-} 0.16(stat) {+-} 0.13(syst))% e N{sub diff}{sup b}/N{sub total}{sup b} = (0.79 {+-} 0.11(stat) {+-} 0.23(syst))%.

A first study of single diffractive central high-p{sub T} dijet events in p{bar p} collisions at center-of-mass energy {radical}s = 1.96 TeV is presented, using data recorded by the D0 detector at the Tevatron during RunIIa in 2002-2004. The total integrated luminosity corresponding to the data sample is 398 pb{sup -1}. A diffractive sample is selected using a rapidity gap approach. A precise definition of the rapidity gap constitutes the first part of the thesis. The rapidity gap is defined by means of two parts of the D0 detector--luminosity detectors and calorimeter. Luminosity detectors serve as a basic indicators of diffractive candidates and the calorimeter is used to confirm the low energy activity in the forward region (a rapidity gap). Presented studies of energy deposited in forward part of calorimeter by various types of events yield two rapidity gap definitions. Both of them use a fixed rapidity interval in calorimeter |{eta}| {element_of} [2.6,5.2] and introduce an upper limit on the energy deposited in this region. First definition, which corresponds to the lowest systematical errors, uses a limit of 10 GeV, an energy limit in the second definition is set to 3 GeV. This alternative definition corresponds to the lowest contamination …

Measurements of the inclusive diffractive Z {yields} {mu}{sup +}{mu}{sup -} cross section with gap requirement for M{sub {mu}}{sub {mu}} > 40 GeV at {radical} s = 1.96 TeV and fraction of Z bosons produced diffractively with gap requirement from Z inclusive production are presented. The measurements are performed using a data sample corresponding to an integrated luminosity of 820 pb{sup -1}, collected with the D0 detector at the Tevatron, between 2002 to 2005. A total of 39945 di-muons events are selected and final results of: {sigma}{sub Diff}{sup gap} x Br(Z/{gamma}* {yields} {mu}{sup +}{mu}{sup -}) = 4.09 {+-} 0.64(stat.) {+-} 0.88(syst.) {+-} 0.27(lumi.) pb and, R{sub Diff}{sup gap} = 1.92 {+-} 0.30(stat.) {+-} 0.41(syst.) {+-} 0.12(lumi) % are obtained. In addition, d{sigma}/d{zeta} and d{sigma}/dy distributions are presented and they are compared with diffractive montecarlo (POMWIG). A reasonable agreement is obtained in this comparation. Finally, comparison of fraction of Z bosons produced diffractively with gap requirement (gap fraction) as measured with D0 during Run I of the Tevatron is compared. A good agreement is found for gap fraction results.

The first analysis of diffractively produced Z bosons in the muon decay channel is presented, using data taken by the D0 detector at the Tevatron at {radical}s = 1.96 TeV. The data sample corresponds to an integrated luminosity of 109 pb{sup -1}. The diffractive sample is defined using the fractional momentum loss {zeta} of the intact proton or antiproton measured using the calorimeter and muon detector systems. In a sample of 10791 (Z/{gamma})* {yields} {mu}{sup +}{mu}{sup -} events, 24 diffractive candidate events are found with {zeta} < 0.02. The first work towards measuring the cross section times branching ratio for diffractive production of (Z/{gamma})* {yields} {mu}{sup +}{mu}{sup -} is presented for the kinematic region {zeta} < 0.02. The first work towards measuring the cross section times branching ratio for diffractive production of (Z/{gamma})* {yields} {mu}{sup +}{mu}{sup -} is presented for the kinematic region {zeta} < 0.02. The systematic uncertainties are not yet sufficiently understood to present the cross section result. In addition, the first measurement of the efficiency of the Run II D0 Luminosity Monitor is presented, which is used in all cross section measurements. The efficiency is: {var_epsilon}{sub LM} = (90.9 {+-} 1.8)%.

Generalized Parton Distributions (GPDs), introduced in the late 90s, provide a universal description of hadrons in terms of the underlying degrees of freedom of Quantum Chromodynamics: quarks and gluons. GPDs appear in a wide variety of hard exclusive reactions and the advent of high luminosity accelerator facilities has made the study of GPDs accessible to experiment. Deeply Virtual Compton Scattering (DVCS) is the golden process involving GPDs. The first dedicated DVCS experiment ran in the Hall A of Jefferson Lab in Fall 2004. An electromagnetic calorimeter and a plastic scintillator detector were constructed for this experiment, together with specific electronics and acquisition system. The experiment preparation, data taking and analysis are described in this document. Results on the absolute cross section difference for opposite beam helicities provide the first measurement of a linear combination of GPDs as a function of the momentum transfer to the nucleon.

Both academia and industry alike have paid close attention to the mechanisms of microstructural selection during the solidification process. The forces that give rise to and the principles which rule the natural selection of particular morphologies are important to understanding and controlling new microstructures. Interfacial properties play a very crucial role to the selection of such microstructure formation. In the solidification of a metallic alloy, the solid-liquid interface is highly mobile and responds to very minute changes in the local conditions. At this interface, the driving force must be large enough to drive solute diffusion, maintain local curvature, and overcome the kinetic barrier to move the interface. Therefore, the anisotropy of interfacial free energy with respect to crystallographic orientation is has a significant influence on the solidification of metallic systems. Although it is generally accepted that the solid-liquid interfacial free energy and its associated anisotropy are highly important to the overall selection of morphology, the confident measurement of these particular quantities remains a challenge, and reported values are scarce. Methods for measurement of the interfacial free energy include nucleation experiments and grain boundary groove experiments. The predominant method used to determine anisotropy of interfacial energy has been equilibrium shape measurement. …

This dissertation describes a direct measurement of the W boson total decay width, {Lambda}{sub W}, using the D0 detector at the Fermilab Tevatron Collider. The measurement uses an integrated luminosity of 177.3 pb{sup -1} data, collected during the 2002-2003 run. The width is determined from the shape of the transverse mass distribution, M{sub T}, by fitting the data in the tail region 100 < M{sub T} < 200 GeV. The result if {Lambda}{sub W} = 2.011 {+-} 0.093(stat) {+-} 0.107(syst) GeV.

A direct measurement of the W boson total decay width is presented in proton-antiproton collisions at √s = 1.96 TeV using data collected by the CDF II detector. The measurement is made by fitting a simulated signal to the tail of the transverse mass distribution in the electron and muon decay channels. An integrated luminosity of 350 pb^-1 is used, collected between February 2002 and August 2004. Combining the results from the separate decay channels gives the decay width as 2.038 ± 0.072 GeV in agreement with the theoretical prediction of 2.093 ± 0.002 GeV. A system is presented for the management of detector calibrations using a relational database schema. A description of the implementation and monitoring of a procedure to provide general users with a simple interface to the complete set of calibrations is also given.

Magnetic monopoles are highly ionizing and curve in the direction of the magnetic field. A new dedicated magnetic monopole trigger at CDF, which requires large light pulses in the scintillators of the time-of-flight system, remains highly efficient to monopoles while consuming a tiny fraction of the available trigger bandwidth. A specialized offline reconstruction checks the central drift chamber for large dE/dx tracks which do not curve in the plane perpendicular to the magnetic field. We observed zero monopole candidate events in 35.7 pb{sup -1} of proton-antiproton collisions at {radical}s = 1.96 TeV. This implies a monopole production cross section limit {sigma} < 0.2 pb for monopoles with mass between 100 and 700 GeV, and, for a Drell-Yan like pair production mechanism, a mass limit m > 360 GeV.

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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 …

This thesis presents evidence for the B**{sup 0} and {Sigma}{sub b}{sup (*){+-}} hadrons in proton-antiproton collisions at a center of mass energy of 1.96 TeV, using data collected by the Collider Detector at Fermilab. In the search for B**{sup 0} {yields} B{sup {+-}} {pi}{sup {-+}}, two B{sup {+-}} decays modes are reconstructed: B{sup {+-}} {yields} J/{Upsilon}K{sup {+-}}, where J/{Upsilon} {yields} {mu}{sup +}{mu}{sup -}, and B{sup {+-}} {yields} {bar D}{sup 0}{pi}{sup {+-}}, where {bar D}{sup 0} {yields} K{sup {+-}} {pi}{sup {+-}}. Both modes are reconstructed using 370 {+-} 20 pb{sup -1} of data. Combining the B{sup {+-}} meson with a charged pion to reconstruct B**{sup 0} led to the observation and measurement of the masses of the two narrow B**{sup 0} states, B{sub 1}{sup 0} and B*{sub 2}{sup 0}, of m(B{sub 1}{sup 0}) = 5734 {+-} 3(stat.) {+-} 2(syst.) MeV/c{sup 2}; m(B*{sub 2}{sup 0}) = 5738 {+-} 5(stat.) {+-} 1(syst.) MeV/c{sup 2}. In the search for {Sigma}{sub b}{sup (*){+-}} {yields} {Lambda}{sub b}{sup 0}{pi}{sup {+-}}, the {Lambda}{sub b}{sup 0} is reconstructed in the decay mode {Lambda}{sub b}{sup 0} {yields} {Lambda}{sub c}{sup +}{pi}{sup -}, where {Lambda}{sub c}{sup +} {yields} pK{sup -} {pi}{sup +}, using 1070 {+-} 60 pb{sup -1} of data. Upon combining …

The top quark is by far the heaviest known fundamental particle with a mass nearing that of a gold atom. Because of this strikingly high mass, the top quark has several unique properties and might play an important role in electroweak symmetry breaking - the mechanism that gives all elementary particles mass. Creating top quarks requires access to very high energy collisions, and at present only the Tevatron collider at Fermilab is capable of reaching these energies. Until now, top quarks have only been observed produced in pairs via the strong interaction. At hadron colliders, it should also be possible to produce single top quarks via the electroweak interaction. Studies of single top quark production provide opportunities to measure the top quark spin, how top quarks mix with other quarks, and to look for new physics beyond the standard model. Because of these interesting properties, scientists have been looking for single top quarks for more than 15 years. This thesis presents the first discovery of single top quark production. An analysis is performed using 2.3 fb{sup -1} of data recorded by the D0 detector at the Fermilab Tevatron Collider at centre-of-mass energy {radical}s = 1.96 TeV. Boosted decision trees are …

Longitudinal compression of space-charge dominated beams can be achieved by imposing a head-to-tail velocity tilt on the beam. This tilt has to be carefully tailored, such that it is removed by the longitudinal space-charge repulsion by the time the beam reaches the end of the drift compression section. The transverse focusing lattice should be designed such that all parts of the beam stay approximately matched, while the beam smoothly expands transversely to the larger beam radius needed in the final focus system following drift compression. In this thesis, several drift compression systems were designed within these constraints, based on a given desired pulse shape at the end of drift compression systems were designed within these constraints, based on a given desired pulse shape at the end of drift compression. The occurrence of mismatches due to a rapidly increasing current was analyzed. In addition, the sensitivity of drift compression to errors in the initial velocity tilt and current profile was studied. These calculations were done using a new computer code that accurately calculates the longitudinal electric field in the space-charge dominated regime.

We discuss two examples of duality. The first arises in the context of toroidal compactification of the discrete light cone quantization of M-theory. In the presence of nontrivial moduli coming from the M-theory three form, it has been conjectured that the system is described by supersymmetric Yang-Mills gauge theory on a noncommutative torus. We are able to provide evidence for this conjecture, by showing that the dualities of this M-theory compactification, which correspond to T-duality in Type IIA string theory, are also dualities of the noncommutative supersymmetric Yang-Mills description. One can also consider this as evidence for the accuracy of the Matrix Theory description of M-theory in this background. The second type of duality is the self-duality of theories with U(1) gauge fields. After discussing the general theory of duality invariance for theories with complex gauge fields, we are able to find a generalization of the well known U(1) Born-Infeld theory that contains any number of gauge fields and which is invariant under the maximal duality group. We then find a supersymmetric extension of our results, and also show that our results can be extended to find Born-Infeld type actions in any even dimensional spacetime.

Current theories have been successful in explaining many nonlinear optical experiments in undoped semiconductors. However, these theories require a ground state which is assumed to be uncorrelated. Strongly correlated systems of current interest, such as a two dimensional electron gas in a high magnetic field, cannot be explained in this manner because the correlations in the ground state and the low energy collective excitations cause a breakdown of the conventional techniques. We perform ultrafast time-resolved four-wave mixing on $n$-modulation doped quantum wells, which contain a quasi-two dimensional electron gas, in a large magnetic field, when only a single Landau level is excited and also when two levels are excited together. We find evidence for memory effects and as strong coupling between the Landau levels induced by the electron gas. We compare our results with simulations based on a new microscopic approach capable of treating the collective effects and correlations of the doped electrons, and find a good qualitative agreement. By looking at the individual contributions to the model, we determine that the unusual correlation effects seen in the experiments are caused by the scattering of photo-excited electron-hole pairs with the electron gas, leading to new excited states which are not …

In May 2000, the Cerro Grande Fire burned approximately 17,200 ha in north-central New Mexico as the result of an escaped prescribed burn initiated by Bandelier National Monument. The interaction of large-scale fires, vegetation, and elk is an important management issue, but few studies have addressed the ecological implications of vegetative succession and landscape heterogeneity on ungulate populations following large-scale disturbance events. Primary objectives of this research were to identify elk movement pathways on local and landscape scales, to determine environmental factors that influence elk movement, and to evaluate movement and distribution patterns in relation to spatial and temporal aspects of the Cerro Grande Fire. Data collection and assimilation reflect the collaborative efforts of National Park Service, U.S. Forest Service, and Department of Energy (Los Alamos National Laboratory) personnel. Geographic positioning system (GPS) collars were used to track 54 elk over a period of 3+ years and locational data were incorporated into a multi-layered geographic information system (GIS) for analysis. Preliminary tests of GPS collar accuracy indicated a strong effect of 2D fixes on position acquisition rates (PARs) depending on time of day and season of year. Slope, aspect, elevation, and land cover type affected dilution of precision (DOP) values …

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