The Adaptive Landscape Classification Procedure (ALCP), which links the advanced geospatial analysis capabilities of Geographic Information Systems (GISs) and Artificial Neural Networks (ANNs) and particularly Self-Organizing Maps (SOMs), is proposed as a method for establishing and reducing complex data relationships. Its adaptive and evolutionary capability is evaluated for situations where varying types of data can be combined to address different prediction and/or management needs such as hydrologic response, water quality, aquatic habitat, groundwater recharge, land use, instrumentation placement, and forecast scenarios. The research presented here documents and presents favorable results of a procedure that aims to be a powerful and flexible spatial data classifier that fuses the strengths of geoinformatics and the intelligence of SOMs to provide data patterns and spatial information for environmental managers and researchers. This research shows how evaluation and analysis of spatial and/or temporal patterns in the landscape can provide insight into complex ecological, hydrological, climatic, and other natural and anthropogenic-influenced processes. Certainly, environmental management and research within heterogeneous watersheds provide challenges for consistent evaluation and understanding of system functions. For instance, watersheds over a range of scales are likely to exhibit varying levels of diversity in their characteristics of climate, hydrology, physiography, ecology, and anthropogenic …

The search for the fundamental constituents of matter has been pursued and studied since the dawn of civilization. As early as the fourth century BCE, Democritus, expanding the teachings of Leucippus, proposed small, indivisible entities called atoms, interacting with each other to form the Universe. Democritus was convinced of this by observing the environment around him. He observed, for example, how a collection of tiny grains of sand can make out smooth beaches. Today, following the lead set by Democritus more than 2500 years ago, at the heart of particle physics is the hypothesis that everything we can observe in the Universe is made of a small number of fundamental particles interacting with each other. In contrast to Democritus, for the last hundred years we have been able to perform experiments that probe deeper and deeper into matter in the search for the fundamental particles of nature. Today's knowledge is encapsulated in the Standard Model of particle physics, a model describing the fundamental particles and their interactions. It is within this model that the work in this thesis is presented. This work attempts to add to the understanding of the Standard Model by measuring the relative branching fraction of the …

We measure the production cross section of t{bar t} events in p{bar p} collisions at {radical}s = 1.96 TeV. The data was collected by the CDF experiment in Run 2 of the Tevatron accelerator at the Fermi National Accelerator Laboratory between 2002 and 2007. 1.7 fb{sup -1} of data was recorded during this time period. We reconstruct t{bar t} events in the lepton+jets channel, whereby one W boson - resulting from the decay of the top quark pairs - decays leptonically and the other hadronically. The dominant background to this process is the production of W bosons in association with multiple jets. To distinguish t{bar t} from background, we identify soft electrons from the semileptonic decay of heavy flavor jets produced in t{bar t} events. We measure a cross section of {sigma}{sub p{bar p}} = 7.8 {+-} 2.4(stat) {+-} 1.6(syst) {+-} 0.5(lumi).

The Neutrino Factory has been proposed as a facility to provide an intense source of neutrinos suitable for the measurement of neutrino oscillation parameters and a possible CP violating phase to unprecedented precision. In the Neutrino Factory, neutrinos are produced by the decay of a muon beam with 20-50 GeV per muon. Initially, the muon beam occupies a large volume in phase space, which must be reduced before the beam can be accelerated. The proposed method to achieve this is to use a solenoidal ionisation colling channel.

GAMESS, a quantum chetnistry program for electronic structure calculations, has been freely shared by high-performance application scientists for over twenty years. It provides a rich set of functionalities and can be run on a variety of parallel platforms through a distributed data interface. While a chemistry computation is sophisticated and hard to develop, the resource sharing among different chemistry packages will accelerate the development of new computations and encourage the cooperation of scientists from universities and laboratories. Common Component Architecture (CCA) offers an enviromnent that allows scientific packages to dynamically interact with each other through components, which enable dynamic coupling of GAMESS with other chetnistry packages, such as MPQC and NWChem. Conceptually, a cotnputation can be constructed with "plug-and-play" components from scientific packages and require more than componentizing functions/subroutines of interest, especially for large-scale scientific packages with a long development history. In this research, we present our efforts to construct cotnponents for GAMESS that conform to the CCA specification. The goal is to enable the fine-grained interoperability between three quantum chemistry programs, GAMESS, MPQC and NWChem, via components. We focus on one of the three packages, GAMESS; delineate the structure of GAMESS computations, followed by our approaches to its component …

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The Main Injector Neutrino Oscillation Search (MINOS) is a long baseline neutrino oscillation experiment based at the Fermi National Accelerator Laboratory (FNAL) in Chicago, Illinois. MINOS measures neutrino interactions in two large iron-scintillator tracking/sampling calorimeters; the Near Detector on-site at FNAL and the Far Detector located in the Soudan mine in northern Minnesota. The Near Detector has recorded a large number of neutrino interactions and this high statistics dataset can be used to make precision measurements of neutrino interaction cross sections. The cross section for charged-current quasi-elastic scattering has been measured by a number of previous experiments and these measurements disagree by up to 30%. A method to select a quasi-elastic enriched sample of neutrino interactions in the MINOS Near Detector is presented and a procedure to fit the kinematic distributions of this sample and extract the quasi-elastic cross section is introduced. The accuracy and robustness of the fitting procedure is studied using mock data and finally results from fits to the MINOS Near Detector data are presented.

Three major high performance quantum chemistry computational packages, NWChem, GAMESS and MPQC have been developed by different research efforts following different design patterns. The goal is to achieve interoperability among these packages by overcoming the challenges caused by the different communication patterns and software design of each of these packages. A chemistry algorithm is hard to develop as well as being a time consuming process; integration of large quantum chemistry packages will allow resource sharing and thus avoid reinvention of the wheel. Creating connections between these incompatible packages is the major motivation of the proposed work. This interoperability is achieved by bringing the benefits of Component Based Software Engineering through a plug-and-play component framework called Common Component Architecture (CCA). In this thesis, I present a strategy and process used for interfacing two widely used and important computational chemistry methodologies: Quantum Mechanics and Molecular Mechanics. To show the feasibility of the proposed approach the Tuning and Analysis Utility (TAU) has been coupled with NWChem code and its CCA components. Results show that the overhead is negligible when compared to the ease and potential of organizing and coping with large-scale software applications.

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.

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.

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The work presented here is the first measurement of the fraction of top quark pair production through gluon-gluon fusion. We use an integrated luminosity of 0.96 {+-} 0.06 fb{sup -1} of p{bar p} collisions at {radical}s of 1.96 TeV collected by the CDF II detector. We select t{bar t} candidates by identifying a high-p{sub T} lepton candidate, a large missing E{sub T} as evidence for a neutrino candidate and at least four high E{sub T} jets, one of which has to be identified as originating from a b quark. The challenge is to discriminate between the two production processes with the identical final state, gg {yields} t{bar t} and q{bar q} {yields} t{bar t}. We take advantage of the fact that compared to a quark, a gluon is more likely to radiate a low momentum gluon and therefore, one expects a larger number of charged particles with low p{sub T} in a process involving more gluons. Given the large uncertainties associated with the modeling of the low p{sub T} charged particle multiplicity, a data-driven technique was employed. Using calibration data samples, we show there exists a clear correlation between the observed average number of low p{sub T} charged particles and …

Aptamers are short single-stranded nucleic acids that can bind to their targets with high specificity and high affinity. To study aptamer function and dynamics, the malachite green aptamer was chosen as a model. Malachite green (MG) bleaching, in which an OH- attacks the central carbon (C1) of MG, was inhibited in the presence of the malachite green aptamer (MGA). The inhibition of MG bleaching by MGA could be reversed by an antisense oligonucleotide (AS) complementary to the MGA binding pocket. Computational cavity analysis of the NMR structure of the MGA-MG complex predicted that the OH{sup -} is sterically excluded from the C1 of MG. The prediction was confirmed experimentally using variants of the MGA with changes in the MG binding pocket. This work shows that molecular reactivity can be reversibly regulated by an aptamer-AS pair based on steric hindrance. In addition to demonstrate that aptamers could control molecular reactivity, aptamer dynamics was studied with a strategy combining molecular dynamics (MD) simulation and experimental verification. MD simulation predicted that the MG binding pocket of the MGA is largely pre-organized and that binding of MG involves reorganization of the pocket and a simultaneous twisting of the MGA terminal stems around the pocket. …

The hadronic production cross section and the polarization of {psi}(2S) meson are measured by using the data from p{bar p} collisions at {radical}s = 1.96 TeV collected by the Collider Detector at Fermilab. The datasets used correspond to integrated luminosity of 1.1 fb{sup -1} and 800 pb{sup -1}, respectively. The decay {psi}(2S) {yields} {mu}{sup +}{mu}{sup -} is used to reconstruct {psi}(2S) mesons in the rapidity range |y({psi}(2S))| < 0.6. The coverage of the p{sub T} range is 2.0 GeV/c {le} p{sub T} ({psi}(2S)) < 30 GeV/c for the cross section analysis and pT {ge} 5 GeV/c for the polarization analysis. For events with p{sub T} ({psi}(2S)) > 2 GeV/c the integrated inclusive cross section multiplied by the branching ratio for dimuon decay is 3.17 {+-} 0.04 {+-} 0.28 nb . This result agrees with the CDF Run I measurement considering the increased center-of-mass energy from 1.8 TeV to 1.96 TeV. The polarization of the promptly produced {psi}(2S) mesons is found to be increasingly longitudinal as p{sub T} increases from 5 GeV/c to 30 GeV/c. The result is compared to contemporary theory models.

The WARP code is a robust electrostatic particle-in-cell simulation package used to model charged particle beams with strong space-charge forces. A fundamental operation associated with seeding detailed simulations of a beam transport channel is to generate initial conditions where the beam distribution is matched to the structure of a periodic focusing lattice. This is done by solving for periodic, matched solutions to a coupled set of ODEs called the Kapchinskij-Vladimirskij (KV) envelope equations, which describe the evolution of low-order beam moments subject to applied lattice focusing, space-charge defocusing, and thermal defocusing forces. Recently, an iterative numerical method was developed (Lund, Chilton, and Lee, Efficient computation of matched solutions to the KV envelope equations for periodic focusing lattices, Physical Review Special Topics-Accelerators and Beams 9, 064201 2006) to generate matching conditions in a highly flexible, convergent, and fail-safe manner. This method is extended and implemented in the WARP code as a Python package to vastly ease the setup of detailed simulations. In particular, the Python package accommodates any linear applied lattice focusing functions without skew coupling, and a more general set of beam parameter specifications than its predecessor. Lattice strength iteration tools were added to facilitate the implementation of problems with …

We calculate the exclusion region in the parameter space of {nu}{sub {mu}} {yields} {nu}{sub e} oscillations of the LSND type using a combined fit to the reconstructed energy distributions of neutrino candidate samples from the MiniBooNE data obtained with two different particle identification methods. The two {nu}{sub e} candidate samples are included together with a high statistics sample of {nu}{sub {mu}} events in the definition of a {chi}{sup 2} statistic which includes the correlations between the energy intervals of all three samples and handles the event overlap between the {nu}{sub e} samples. The {nu}{sub {mu}} sample is introduced to constrain the effect of systematic uncertainties. This analysis increases the exclusion limit in the region {Delta}m{sup 2} {approx}< 1eV{sup 2} when compared with the result previously published by the collaboration, which used a different technique.

Using approximately 1.3 fb{sup -1} of data collected by the D0 detector between 2002 and 2006, the lifetime of the B{sub c}{sup {+-}} meson is studied in the B{sub c}{sup {+-}} {yields} J/{psi}{mu}{sup {+-}} + X final state. Using an unbinned likelihood simultaneous fit to J/{psi} + {mu} invariant mass and lifetime distributions, a signal of 810 {+-} 80(stat.) candidates is estimated and a lifetime measurement made of: {tau}(B{sub c}{sup {+-}}) = 0.448{sub -0.036}{sup +0.038}(stat) {+-} 0.032(sys) ps.

A search for the muon neutrino magnetic moment was conducted using the Mini-BooNE low energy neutrino data. The analysis was performed by analyzing the elastic scattering interactions of muon neutrinos on electrons. The analysis looked for an excess of elastic scattering events above the Standard Model prediction from which a limit on the neutrino magnetic could be set. In this thesis, we report an excess of 15.3 {+-} 6.6(stat){+-}4.1(syst) {nu}{sub {mu}e} events above the expected background. At 90% C.L., we derived a limit on the muon neutrino magnetic moment of 12.7 x 10{sup -10} {micro}{sub B}. The other analysis reported in this thesis is a measurement of charged current single pion production (CC{pi}{sup +}) to charged current quasi elastic (CCQE) interactions cross sections ratio. This measurement was performed with two different fitting algorithms and the results from both fitters are consistent with each other.

We studied several {Xi}{sub c}{sup +} decay modes, most of them with a hyperon in the final state, and determined their branching ratios. The data used in this analysis come from the fixed target experiment SELEX, a multi-stage spectrometer with high acceptance for forward interactions, that took data during 1996 and 1997 at Fermilab with 600 GeV=c (mainly {Sigma}{sup -}, {pi}{sup -}) and 540 GeV/c (mainly p) beams incident on copper and carbon targets. The thesis mainly details the first observation of two Cabibbo-suppressed decay modes, {Xi}{sub c}{sup +} {yields} {Sigma}{sup +}{pi}{sup -}{pi}{sup +} and {Xi}{sub c}{sup +} {yields} {Sigma}{sup -}{pi}{sup +}{pi}{sup +}. The branching ratios of the decays relative to the Cabibbo-favored {Xi}{sub c}{sup +} {yields} {Xi}{sup -}{pi}{sup +}{pi}{sup +} are measured to be: {Lambda}({Xi}{sub c}{sup +} {yields} {Sigma}{sup -}{pi}{sup +}{pi}{sup +})/{Lambda}({Xi}{sub c}{sup +} {yields} {Xi}{sup -}{pi}{sup +}{pi}{sup +}) = 0.184 {+-} 0.086. Systematic studies have been performed in order to check the stability of the measurements varying all cuts used in the selection of events over a wide interval and we do not observe evidence of any trend, so the systematic error is negligible in the final results because the quadrature sum of the total error is not …

The Standard Model (SM) of particle physics successfully describes all of the observed interactions of the fundamental particles (with the exception of non-zero neutrino mass). Despite this enormous success, the SM is widely viewed as an incomplete theory. For example, the size of the asymmetry between matter and antimatter is not nearly large enough to account for the abundance of matter observed throughout the universe. It is thus believed that as-yet-unknown physical phenomena must exist that introduce new asymmetries between matter and antimatter. In this thesis, by studying decays that happen only rarely in the SM, we make measurements of asymmetries between matter and antimatter that are potentially sensitive to the existence of processes beyond the SM. At the PEP-II asymmetric-energy B Factory at SLAC, electrons and positrons are collided at the {Upsilon}(4S) resonance to create pairs of B mesons. The BABAR detector is used to measure the subsequent decay products. Using 383 million {Upsilon}(4S) {yields} B{bar B} decays, we study the decay B{sup 0} {yields} K{sup +}K{sup -}K{sup 0}. In the SM, this decay is dominated by loop amplitudes. Asymmetries between matter and antimatter (CP asymmetries) are extracted by measuring the time-dependence of the complex amplitudes describing the B{sup …

This thesis describes the measurement of the direct CP violation in the b {yields} sc{bar c} transition using the decay B{sup +} {yields} J/{psi}K{sup +}, and in the b {yields} dc{bar c} transition using the decay B{sup +} {yields} J/{psi}{pi}{sup +}. The decays of B{sup +} mesons are reconstructed in approximately 2.8 fb{sup -1} of data recorded by D0 detector in 2002-2007 during Run II of Fermilab Tevatron collider. Using the unbinned likelihood fit, a signal of 40,222 {+-} 242 of B{sup +} {yields} J/{psi}K{sup +} and 1,578 {+-} 119 of B{sup +} {yields} J/{psi}{pi}{sup +} events is obtained. The corresponding direct CP violation asymmetries are measured to be A{sub CP}(B{sup +} {yields} J/{psi}(1S)K{sup +}) = +0.0077 {+-} 0.0061(stat.) {+-} 0.0027(syst.), and A{sub CP}(B{sup +} {yields} J/{psi}(1S){pi}{sup +}) = - 0.089 {+-} 0.081(stat.) {+-} 0.028(syst.). The result on A{sub CP} (B{sup +} {yields} J/{psi}(1S)K{sup +}) is consistent with the 2007 world average and is the most precise measurement of this asymmetry, with uncertainty approaching the level of the Standard Model prediction. The result on A{sub CP} (B{sup +} {yields} J/{psi}(1S){pi}{sup +}) constitutes the first measurement of this asymmetry at the hadron collider, with uncertainty at the level of the 2007 …

The top quark is an extremely massive fundamental particle that is predominantly produced in pairs at particle collider experiments. The Standard Model of particle physics predicts that top quarks can also be produced singly by the electroweak force; however, this process is more difficult to detect because it occurs at a smaller rate and is more difficult to distinguish from background processes. The cross section of this process is related to the Cabbibo-Kobayashi-Maskawa matrix element |V{sub tb}|, and measurement of the single top quark production cross section is currently the only method to directly measure this quantity without assuming the number of generations of fermions. This thesis describes a measurement of the cross section of electroweak single top quark production in proton-antiproton collisions at a center-of-mass energy of 1.96 TeV. This analysis uses 2.2 fb{sup -1} of integrated luminosity recorded by the Collider Detector at Fermilab. The search is performed using a matrix element method which calculates the differential cross section for each event for several signal and background hypotheses. These numbers are combined into a single discriminant and used to construct templates from Monte Carlo simulation. A maximum likelihood fit to the data distribution gives a measurement of the …

A measurement of hadron production cross-sections for the simulation of accelerator neutrino beams and a search for muon neutrino to electron neutrino oscillations in the {Delta}m{sup 2} {approx} 1 eV{sup 2} region. This dissertation presents measurements from two different high energy physics experiments with a very strong connection: the Hadron Production (HARP) experiment located at CERN in Geneva, Switzerland, and the Mini Booster Neutrino Experiment (Mini-BooNE) located at Fermilab in Batavia, Illinois.