Melanie Waltman's dissertation to be presented on March 24, 2010.

One of the central questions arising from human curiosity has always been what matter is ultimately made of, with the idea of some kind of elementary building-block dating back to the ancient greek philosophers. Scientific activities of multiple generations have contributed to the current best knowledge about this question, the Standard Model of particle physics. According to it, the world around us is composed of a small number of stable elementary particles: Electrons and two different kinds of quarks, called up and down quarks. Quarks are never observed as free particles, but only as bound states of a quark-antiquark pair (mesons) or of three quarks (baryons), summarized as hadrons. Protons and Neutrons, the constituents forming the nuclei of all chemical elements, are baryons made of up and down quarks. The electron and the electron neutrino - a nearly massless particle without electric charge - belong to a group called leptons. These two quarks and two leptons represent the first generation of elementary particles. There are two other generations of particles, which seem to have similar properties as the first generation except for higher masses, so there are six quarks and six leptons altogether. They were around in large amounts shortly …

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The COUPP collaboration has successfully used bubble chambers, a technology previously applied only to high-energy physics experiments, as direct dark matter detectors. It has produced the world's most stringent spin-dependent WIMP limits, and increasingly competitive spin-independent limits. These limits were achieved by capitalizing on an intrinsic rejection of the gamma background that all other direct detection experiments must address through high-density shielding and empirically-determined data cuts. The history of COUPP, including its earliest prototypes and latest results, is briefly discussed in this thesis. The feasibility of a new, windowless bubble chamber concept simpler and more inexpensive in design is discussed here as well. The dark matter limits achieved with a 15 kg windowless chamber, larger than any previous COUPP chamber (2 kg, 4 kg), are presented. Evidence of the greater radiopurity of synthetic quartz compared to natural is presented using the data from this 15 kg device, the first chamber to be made from synthetic quartz. The effective reconstruction of the three-dimensional positions of bubbles in a highly distorted optical field, with ninety-degree bottom lighting similar to cloud chamber lighting, is demonstrated. Another innovation described in this thesis is the use of the sound produced by bubbles recorded by an …

This dissertation focuses on the development of facile and rapid quantitative Raman spectroscopy measurements for the determination of conversion products in producing bioethanol from corn stover. Raman spectroscopy was chosen to determine glucose, xylose and ethanol in complex hydrolysis and fermentation matrices. Chapter 1 describes the motives and main goals of this work, and includes an introduction to biomass, commonly used pretreatment methods, hydrolysis and fermentation reactions. The principles of Raman spectroscopy, its advantages and applications related to biomass analysis are also illustrated. Chapter 2 and 3 comprise two published or submitted manuscripts, and the thesis concludes with an appendix. In Chapter 2, a Raman spectroscopic protocol is described to study the efficiency of enzymatic hydrolysis of cellulose by measuring the main product in hydrolysate, glucose. Two commonly utilized pretreatment methods were investigated in order to understand their effect on glucose measurements by Raman spectroscopy. Second, a similar method was set up to determine the concentration of ethanol in fermentation broth. Both of these measurements are challenged by the presence of complex matrices. In Chapter 3, a quantitative comparison of pretreatment protocols and the effect of enzyme composition are studied using systematic methods. A multipeak fitting algorithm was developed to …

Quantum mechanical (QM) calculations have the advantage of attaining high-level accuracy, however QM calculations become computationally inefficient as the size of the system grows. Solving complex molecular problems on large systems and ensembles by using quantum mechanics still poses a challenge in terms of the computational cost. Methods that are based on classical mechanics are an inexpensive alternative, but they lack accuracy. A good trade off between accuracy and efficiency is achieved by combining QM methods with molecular mechanics (MM) methods to use the robustness of the QM methods in terms of accuracy and the MM methods to minimize the computational cost. Two types of QM combined with MM (QM/MM) methods are the main focus of the present dissertation: the application and development of QM/MM methods for solvation studies and reactions on the Si(100) surface. The solvation studies were performed using a discreet solvation model that is largely based on first principles called the effective fragment potential method (EFP). The main idea of combining the EFP method with quantum mechanics is to accurately treat the solute-solvent and solvent-solvent interactions, such as electrostatic, polarization, dispersion and charge transfer, that are important in correctly calculating solvent effects on systems of interest. A …

Trust management techniques must be adapted to the unique needs of the application architectures and problem domains to which they are applied. For autonomic computing systems that utilize mobile agents and ant colony algorithms for their sensor layer, certain characteristics of the mobile agent ant swarm -- their lightweight, ephemeral nature and indirect communication -- make this adaptation especially challenging. This thesis looks at the trust issues and opportunities in swarm-based autonomic computing systems and finds that by monitoring the trustworthiness of the autonomic managers rather than the swarming sensors, the trust management problem becomes much more scalable and still serves to protect the swarm. After analyzing the applicability of trust management research as it has been applied to architectures with similar characteristics, this thesis specifies the required characteristics for trust management mechanisms used to monitor the trustworthiness of entities in a swarm-based autonomic computing system and describes a trust model that meets these requirements.

The MINOS experiment is a long-baseline neutrino oscillation experiment which sends a high intensity muon neutrino beam through two functionally identical detectors, a Near detector at the Fermi National Accelerator Laboratory in Illinois, 1km from the beam source, and a Far detector, 734km away, in the Soudan Mine in Minnesota. MINOS may be able to measure the neutrino mixing angle parameter sin{sup 2} 2{theta}{sub 13} for the first time. Detector granularity, however, makes it very hard to distinguish any {nu}{sub e} appearance signal events characteristic of a non-zero value of {theta}{sub 13} from background neutral current (NC) and short-track {nu}{sub {mu}} charged current (CC) events. Also, uncertainties in the hadronic shower modeling in the kinematic region characteristic of this analysis are relatively large. A new data-driven background decomposition method designed to address those issues is developed and its results presented. By removing the long muon tracks from {nu}{sub {mu}}-CC events, the Muon Removed Charge Current (MRCC) method creates independent pseudo-NC samples that can be used to correct the MINOS Monte Carlo to agree with the high-statistics Near detector data and to decompose the latter into components so as to predict the expected Far detector background. The MRCC method also provides …

The past decade has seen a strong evolution of the study of the hadron structure through exclusive processes, allowing to access to a more complete description of this structure. Exclusive processes include DVCS (Deeply Virtual Compton Scattering) as well as hard exclusive meson production. This document is particularly focussed on the latter, and more particularly on exclusive neutral pion production. In this thesis is described the analysis of triple coincidence events H(e, e'{gamma}{gamma})X, which were a consequent by-product of the DVCS experiment which occured during Fall 2004 at Jefferson Lab Hall A, to extract the ep {yields} ep{pi}{sup 0} cross section. This cross section has been measured at two values of four-momentum transfer Q{sup 2} = 1.9 GeV{sup 2} and Q{sup 2} = 2.3 GeV{sup 2}. The statistical precision for these measurements is achieved at better than 5 %. The kinematic range allows to study the evolution of the extracted cross section as a function of Q{sup 2} and W. Results are be confronted with Regge inspired calculations and Generalized (GPD) predictions. An intepretation of our data within the framework of semi-inclusive deep inelastic scattering is also discussed.

This dissertation presents the first search for the standard model Higgs boson (H) in decay topologies containing a muon, an imbalance in transverse momentum (E{sub T}) and jets, using p{bar p} collisions at {radical}s = 1.96 TeV with an integrated luminosity of 4.3 fb{sup -1} recorded with the D0 detector at the Fermilab Tevatron Collider. This analysis is sensitive primary to contributions from Higgs bosons produced through gluon fusion, with subsequent decay H {yields} WW {yields} {mu}{nu}jj where W represents a real or virtual W boson. In the absence of signal, limits are set at 95% confidence on the production and decay of the standard model Higgs boson for M{sub H} in the range of 115-200 GeV. For M{sub H} = 165 GeV, the observed and expected limits are factors of 11.2 larger than the standard model value. Combining this channel with e{nu}jj final states and including earlier data to increase the integrated luminosity to 5.4 fb{sup -1} produces observed(expected) limits of 5.5(3.8) times the standard model value.

The thesis is divided into two parts. In the first part a global optimization method is developed for the interface and surface structures optimization. Two prototype systems are chosen to be studied. One is Si[001] symmetric tilted grain boundaries and the other is Ag/Au induced Si(111) surface. It is found that Genetic Algorithm is very efficient in finding lowest energy structures in both cases. Not only existing structures in the experiments can be reproduced, but also many new structures can be predicted using Genetic Algorithm. Thus it is shown that Genetic Algorithm is a extremely powerful tool for the material structures predictions. The second part of the thesis is devoted to the explanation of an experimental observation of thermal radiation from three-dimensional tungsten photonic crystal structures. The experimental results seems astounding and confusing, yet the theoretical models in the paper revealed the physics insight behind the phenomena and can well reproduced the experimental results.

At a hadron collider, diphoton (γγ) production allows detailed studies of the Standard Model (SM), as well as as searches for new phenomena, such as new heavy resonances, extra spatial dimensions or cascade decays of heavy new particles. Within the SM, continuum γγ+X production is characterized by a steeply-falling γγ mass spectrum, on top of which a heavy resonance decaying into γγ can potentially be observed. In particular, this is considered one of the most promising discovery channels for a SM Higgs boson at the LHC, despite the small branching ratio of BR (H → γγ) {approx} 0.2% for 110 < M_Higgs < 140 GeV. At the Tevatron, the dominant SM Higgs boson production mechanism is gluon fusion, followed by associated production with a W or Z boson, and vector boson fusion. While the SM Higgs production rate at the Tevatron is not sufficient to observe it in the γγ mode, the Hgg and Hγγ couplings, being loop-mediated, are particularly sensitive to new physics effects. Furthermore, in some models beyond the SM, for instance, fermiophobic Higgs, with no couplings to fermions, the BR (H → γγ) can be enhanced significantly relative to the SM prediction, while has the SM-like production …

High Pressure Scanning Tunneling Microscopy (HP-STM) and Ambient Pressure X-ray Photoelectron Spectroscopy were used to study the structural properties and catalytic behavior of noble metal surfaces at high pressure. HP-STM was used to study the structural rearrangement of the top most atomic surface layer of the metal surfaces in response to changes in gas pressure and reactive conditions. AP-XPS was applied to single crystal and nanoparticle systems to monitor changes in the chemical composition of the surface layer in response to changing gas conditions. STM studies on the Pt(100) crystal face showed the lifting of the Pt(100)-hex surface reconstruction in the presence of CO, H₂, and Benzene. The gas adsorption and subsequent charge transfer relieves the surface strain caused by the low coordination number of the (100) surface atoms allowing the formation of a (1 x 1) surface structure commensurate with the bulk terminated crystal structure. The surface phase change causes a transformation of the surface layer from hexagonal packing geometry to a four-fold symmetric surface which is rich in atomic defects. Lifting the hex reconstruction at room temperature resulted in a surface structure decorated with 2-3 nm Pt adatom islands with a high density of step edge sites. Annealing …

An inductively coupled plasma-mass spectrometer (ICP-MS) is an elemental analytical instrument capable of determining nearly all elements in the periodic table at limits of detection in the parts per quadrillion and with a linear analytical range over 8-10 orders of magnitude. Three concentric quartz tubes make up the plasma torch. Argon gas is spiraled through the outer tube and generates the plasma powered by a looped load coil operating at 27.1 or 40.6 MHz. The argon flow of the middle channel is used to keep the plasma above the innermost tube through which solid or aqueous sample is carried in a third argon stream. A sample is progressively desolvated, atomized and ionized. The torch is operated at atmospheric pressure. To reach the reduced pressures of mass spectrometers, ions are extracted through a series of two, approximately one millimeter wide, circular apertures set in water cooled metal cones. The space between the cones is evacuated to approximately one torr. The space behind the second cone is pumped down to, or near to, the pressure needed for the mass spectrometer (MS). The first cone, called the sampler, is placed directly in the plasma plume and its position is adjusted to the point …

The Fermilab Booster is a nearly 40-year-old proton synchrotron, designed to accelerate injected protons from a kinetic energy of 400 MeV to 8 GeV for extraction into the Main Injector and ultimately the Tevatron. Currently the Booster is operated with a typical intensity of 4.5 x 10{sup 12} particles per beam, roughly twice the value of its design, because of the requirement for high particle flux in various experiments. Its relatively low injection energy provides certain challenges in maintaining beam quality and stability under these increasing intensity demands. An understanding of the effects limiting this intensity could provide enhanced beam stability and reduced downtime due to particle losses and subsequent damage to the accelerator elements. Design of future accelerators can also benefit from a better understanding of intensity effects limiting injection dynamics. Chapter 1 provides a summary of accelerator research during the 20th century leading to the development of the modern synchrotron. Chapter 2 puts forth a working knowledge of the terminology and basic theory used in accelerator physics, and provides a brief description of the Fermilab Booster synchrotron. Synergia, a 3d space-charge modeling framework, is presented, along with some simulation benchmarks relevant to topics herein. Emittance, a commonly used …

The top quark has been discovered by CDF and D0 experiments in 1995 at the proton-antiproton collider Tevatron. The amount of data recorded by both experiments makes it possible to accurately study the properties of this quark: its mass is now known to better than 1% accuracy. This thesis describes the measurement of the top pair cross section in the electron muon channel with 4, 3 fb^-1 recorded data between 2006 and 2009 by the D0 experiment. Since the final state included a muon, improvements of some aspects of its identification have been performed : a study of the contamination of the cosmic muons and a study of the quality of the muon tracks. The cross section measurement is in good agreement with the theoretical calculations and the other experimental measurements. This measurement has been used to extract a value for the top quark mass. This method allows for the extraction of a better defined top mass than direct measurements as it depends less on Monte Carlo simulations. The uncertainty on this extracted mass, dominated by the experimental one, is however larger than for direct measurements. In order to decrease this uncertainty, the ratio of the Z boson and …

Elucidating the nature of neutrino oscillation continues to be a goal in the vanguard of the efforts of physics experiment. As neutrino oscillation searches seek an increasingly elusive signal, a thorough understanding of the possible backgrounds becomes ever more important. Measurements of neutrino-nucleus interaction cross sections are key to this understanding. Searches for {nu}{sub {mu}} {yields} {nu}{sub e} oscillation - a channel that may yield insight into the vanishingly small mixing parameter {theta}{sub 13}, CP violation, and the neutrino mass hierarchy - are particularly susceptible to contamination from neutral current single {pi}{sup 0} (NC 1{pi}{sup 0}) production. Unfortunately, the available data concerning NC 1{pi}{sup 0} production are limited in scope and statistics. Without satisfactory constraints, theoretical models of NC 1{pi}{sup 0} production yield substantially differing predictions in the critical E{sub {nu}} {approx} 1 GeV regime. Additional investigation of this interaction can ameliorate the current deficiencies. The Mini Booster Neutrino Experiment (MiniBooNE) is a short-baseline neutrino oscillation search operating at the Fermi National Accelerator Laboratory (Fermilab). While the oscillation search is the principal charge of the MiniBooNE collaboration, the extensive data ({approx} 10{sup 6} neutrino events) offer a rich resource with which to conduct neutrino cross section measurements. This work concerns …

This work presents the first comprehensive measurement of neutrino-induced charged-current neutral pion production (CC{pi}{sup 0}) off a nuclear target. The Mini Booster Neutrino Experiment (MiniBooNE) and Booster Neutrino Beam (BNB) are discussed in detail. MiniBooNE is a high-statistics ({approx} 1,000,000 interactions) low-energy (E{sub {nu}} {element_of} 0.5-2.0 GeV) neutrino experiment located at Fermilab. The method for selecting and reconstructing CC{pi}{sup 0} events is presented. The {pi}{sup 0} and {mu}{sup -} are fully reconstructed in the final state allowing for the measurement of, among other things, the neutrino energy. The total observable CC{pi}{sup 0} cross-section is presented as a function of neutrino energy, along with five differential cross-sections in terms of the final state kinematics and Q{sup 2}. The results are combined to yield a flux-averaged total cross-section of <{sigma}>{sub {Phi}} = (9.2 {+-} 0.3{sub stat.} {+-} 1.5{sub syst}.) x 10{sup -39} cm{sup 2}/CH{sub 2} at energy 965 MeV. These measurements will aid future neutrino experiments with the prediction of their neutrino interaction rates.

What constitutes the spin of the nucleon? The answer to this question is still not completely understood. Although we know the longitudinal quark spin content very well, the data on the transverse quark spin content of the nucleon is still very sparse. Semi-inclusive Deep Inelastic Scattering (SIDIS) using transversely polarized targets provide crucial information on this aspect. The data that is currently available was taken with proton and deuteron targets. The E06-010 experiment was performed at Jefferson Lab in Hall-A to measure the single spin asymmetries in the SIDIS reaction n↑(e, e′π{sup ±}/K{sup ±})X using transversely polarized {sup 3}He target. The experiment used the continuous electron beam provided by the CEBAF accelerator with a beam energy of 5.9 GeV. Hadrons were detected in a high-resolution spectrometer in coincidence with the scattered electrons detected by the BigBite spectrometer. The kinematic coverage focuses on the valence quark region, x = 0.19 to 0.34, at Q{sup 2} = 1.77 to 2.73 (GeV/c){sup 2}. This is the first measurement on a neutron target. The data from this experiment, when combined with the world data on the proton and the deuteron, will provide constraints on the transversity and Sivers distribution functions on both the u …

The experiment E06010 measured the target single spin asymmetry (SSA) in the semiinclusive deep inelastic (SIDIS) n{up_arrow}(e, e'{pi}{sup -})X reaction with a transversely polarized {sup 3}He target as an e#11;ective neutron target. This is the very #12;rst independent measurement of the neutron SSA, following the measurements at HERMES and COMPASS on the proton and the deuteron. The experiment acquired data in Hall A at Je#11;erson Laboratory with a continuous electron beam of energy 5.9 GeV, probing the valence quark region, with x = 0.13 {rt_arrow} 0.41, at Q{sup 2} = 1.31 {rt_arrow} 3.1 GeV{sup 2}. The two contributing mechanisms to the measured asymmetry, viz, the Collins effect and the Sivers effect can be realized through the variation of the asymmetry as a function of the Collins and Sivers angles. The neutron Collins and Sivers moments, associated with the azimuthal angular modulations, are extracted from the measured asymmetry for the very #12;first time and are presented in this thesis. The kinematics of this experiment is comparable to the HERMES proton measurement. However, the COMPASS measurements on deuteron and proton are in the low-x region. The results of this experiment are crucial as the first step toward the extraction of quark transversity …

This thesis presents the measurement of the charged current quasi-elastic (CCQE) neutrino-nucleon cross section at neutrino energies around 1 GeV. This measurement has two main physical motivations. On one hand, the neutrino-nucleon interactions at few GeV is a region where existing old data are sparse and with low statistics. The current measurement populates low energy regions with higher statistics and precision than previous experiments. On the other hand, the CCQE interaction is the most useful interaction in neutrino oscillation experiments. The CCQE channel is used to measure the initial and final neutrino fluxes in order to determine the neutrino fraction that disappeared. The neutrino oscillation experiments work at low neutrino energies, so precise measurement of CCQE interactions are essential for flux measurements. The main goal of this thesis is to measure the CCQE absolute neutrino cross section from the SciBooNE data. The SciBar Booster Neutrino Experiment (SciBooNE) is a neutrino and anti-neutrino scattering off experiment. The neutrino energy spectrum works at energies around 1 GeV. SciBooNE was running from June 8th 2007 to August 18th 2008. In that period, the experiment collected a total of 2.65 x 10²⁰ protons on target (POT). This thesis has used full data collection in …

The CP violating phase {beta}{sub s}{sup J/{psi}{phi}} is measured in decays of B{sub s}{sup 0} {yields} J/{psi}{phi}. This measurement uses 5.2 fb{sup -1} of data collected in {radical}s = 1.96 TeV p{bar p} collisions at the Fermilab Tevatron with the CDF Run-II detector. CP violation in the B{sub s}{sup 0}-{bar B}{sub s}{sup 0} system is predicted to be very small in the Standard Model. However, several theories beyond the Standard Model allow enhancements to this quantity by heavier, New Physics particles entering second order weak mixing box diagrams. Previous measurements have hinted at a deviation from the Standard Model expectation value for {beta}{sub s}{sup J/{psi}{phi}} with a significance of approximately 2{sigma}. The measurement described in this thesis uses the highest statistics sample available to date in the B{sub s}{sup 0} {yields} J/{psi}{phi} decay channel, where J/{psi} {yields} {mu}{sup +}{mu}{sup -} and {phi} {yields} K{sup +}K{sup -}. Furthermore, it contains several improvements over previous analyses, such as enhanced signal selection, fully calibrated particle ID and flavour tagging, and the inclusion of an additional decay component in the likelihood function. The added decay component considers S-wave states of KK pairs in the B{sub s}{sup 0} {yields} J/{psi} K{sup +}K{sup -} channel. The …

This dissertation describes a measurement of the forward-backward asymmetry(A_FB) in p$\bar{p}$ → Z/γ* → ee events using 5.0 fb^-1 data collected by the D0 detector at the Fermilab Tevatron. The AFB is measured as a function of the invariant mass of the electron-positron pair. Along with obtaining normalized differential cross section 1/σ x dσ/dM and Z to light quark couplings, we measured the Standard Model(SM) fundamental parameter, the effective weak mixing angle sin² θ$lept\atop{eff}$, with an unprecedented precise in light quark sector, namely the single D0 measurement has surpassed the LEP combination of four experiment results of inclusive hadronic charge asymmetry.

Early measurements of a large forward-background asymmetry at the CDF and D0 experiments at Fermilab have generated much recent interest, but were hampered by large uncertainties. We present here a new measurement of the parton level forward-backward asymmetry of pair-produced top quarks, using a high-statistics sample with much improved precision. We study the rapidity, y_top, of the top quark production angle with respect to the incoming parton momentum in both the lab and t$\bar{t}$ rest frames. We find the parton-level forward-backward asymmetries to be A_fb^p$\bar{t}$ = 0.150 ± 0.050^stat ± 0.024^syst A_fb^t$\bar{t}$ = 0.158 ± 0.072{sup stat} ± 0.024^syst. These results should be compared with the small p$\bar{p}$ frame charge asymmetry expected in QCD at NLO, A_fb = 0.050 ± 0.015. Additionally, we introduce a measurement of the A_fb rapidity dependence dA_fb/d(Δy). We find this to be A_fb^p$\bar{t}$(|Δy| < 1.0) = 0.026 ± 0.104^stat ± 0.012 ^syst A_fb^p$\bar{t}$(|Δy| > 1.0) = 0.611 ± 0.210^stat ± 0.246^syst which we compare with model predictions 0.039 ± 0.006 and 0.123 ± 0.018 for the inner and outer rapidities, respectively.