The Main Injector Neutrino Oscillation Search (MINOS) is a two detector long-baseline neutrino experiment designed to study the disappearance of muon neutrinos. MINOS will test the {nu}{sub {mu}} {yields} {nu}{sub {tau}} oscillation hypothesis and measure precisely {Delta}m{sub 23}{sup 2} and sin{sup 2} 2{theta}{sub 23} oscillation parameters. The source of neutrinos for MINOS experiment is Fermilab's Neutrinos at the Main Injector (NuMI) beamline. The energy spectrum and the composition of the beam is measured at two locations, one close to the source and the other 735 km down-stream in the Soudan Mine Underground Laboratory in northern Minnesota. The precision measurement of the oscillation parameters requires an accurate prediction of the neutrino flux at the Far Detector. This thesis discusses the calculation of the neutrino flux at the Far Detector and its uncertainties. A technique that uses the Near Detector data to constrain the uncertainties in the calculation of the flux is described. The data corresponding to an exposure of 2.5 x 10{sup 20} protons on the NuMI target is presented and an energy dependent disappearance pattern predicted by neutrino oscillation hypotheses is observed in the Far Detector data. The fit to MINOS data, for given exposure, yields the best fit values …

Angle- and time-resolved two-photon photoemission (2PPE) was used to study systems of organic semiconductors on Ag(111). The 2PPE studies focused on electronic behavior specific to interfaces and ultrathin films. Electron time dynamics and band dispersions were characterized for ultrathin films of a prototypical n-type planar aromatic hydrocarbon, PTCDA, and representatives from a family of p-type oligothiophenes.In PTCDA, electronic behavior was correlated with film morphology and growth modes. Within a fewmonolayers of the interface, image potential states and a LUMO+1 state were detected. The degree to which the LUMO+1 state exhibited a band mass less than a free electron mass depended on the crystallinity of the layer. Similarly, image potential states were measured to have free electron-like effective masses on ordered surfaces, and the effective masses increased with disorder within the thin film. Electron lifetimes were correlated with film growth modes, such that the lifetimes of electrons excited into systems created by layer-by-layer, amorphous film growth increased by orders of magnitude by only a few monolayers from the surface. Conversely, the decay dynamics of electrons in Stranski-Krastanov systems were limited by interaction with the exposed wetting layer, which limited the barrier to decay back into the metal.Oligothiophenes including monothiophene, quaterthiophene, and …

This dissertation describes a search for the pair production of scalar top quarks, {tilde t}{sub 1}, using a luminosity of 995 pb{sup -1} of data collected in p{bar p} collisions with the D0 detector at the Fermilab Tevatron Collider at a center-of-mass energy {radical}s = 1.96 TeV. Both scalar top quarks are assumed to decay into a charm quark and a neutralino, {tilde {chi}}{sub 1}{sup 0}, where {tilde {chi}}{sub 1}{sup 0} is the lightest supersymmetric particle. This leads to a final state with two acoplanar charm jets and missing transverse energy. The yield of such events in data is found to be consistent with the expectations from known standard model processes. Sets of {tilde t}{sub 1} and {tilde {chi}}{sub 1}{sup 0} masses are excluded at the 95% confidence level that substantially extend the domain excluded by previous searches. With the theoretical uncertainty on the {tilde t}{sub 1} pair production cross section taken into account, the largest limit for m{sub {tilde t}{sub 1}} is m{sub {tilde t}{sub 1}} > 150 GeV, for m{sub {tilde {chi}}{sub 1}{sup 0}} = 65 GeV.

As predicted by numerous extensions of the Standard Model, leptoquarks (LQ) are hypothetical bosons allowing lepton-quark transitions. Under the assumption that they couple only to quarks and leptons of the same generation, three generations of leptoquarks can be distinguished. The search for the pair production of second generation scalar leptoquarks has been carried out in p{bar p} collisions at {radical}s = 1.96TeV, using an integrated luminosity of 1 fb{sup -1} collected by the D0 experiment at the Tevatron collider between August 2002 and February 2006. Topologies arising from the LQ{ovr LQ} {yields} {mu}q{nu}q and LQ{ovr LQ} {yields} {mu}q{mu}q decay modes have been investigated. In order to maximize the available statistics, a method for the combination of various prescaled triggers with an inclusive OR has been developed. Since no excess of data over the Standard Model prediction has been observed, upper limits on the leptoquark pair production cross section have been derived at 95% confidence level as function of the leptoquark mass and the branching fraction {beta} = Br(LQ {yields} {mu}q), and are interpreted as lower limits on the leptoquark mass as function of {beta}. For {beta} = 1, {beta} = 1/2 and {beta} = 0.1, the combination of the two …

Research at the interface between biomolecules and inorganic nanocrystals has resulted in a great number of new discoveries. In part this arises from the synergistic duality of the system: biomolecules may act as self-assembly agents for organizing inorganic nanocrystals into functional materials; alternatively, nanocrystals may act as microscopic or spectroscopic labels for elucidating the behavior of complex biomolecular systems. However, success in either of these functions relies heavily uponthe ability to control the conjugation and assembly processes.In the work presented here, we first design a branched DNA scaffold which allows hybridization of DNA-nanocrystal monoconjugates to form discrete assemblies. Importantly, the asymmetry of the branched scaffold allows the formation of asymmetric2assemblies of nanocrystals. In the context of a self-assembled device, this can be considered a step toward the ability to engineer functionally distinct inputs and outputs.Next we develop an anion-exchange high performance liquid chromatography purification method which allows large gold nanocrystals attached to single strands of very short DNA to be purified. When two such complementary conjugates are hybridized, the large nanocrystals are brought into close proximity, allowing their plasmon resonances to couple. Such plasmon-coupled constructs are of interest both as optical interconnects for nanoscale devices and as `plasmon ruler? biomolecular …

A measurement of the top quark mass in p{bar p} collisions at {radical}s = 1.96 TeV is presented. The analysis uses a template method, in which the overconstrained kinematics of the Lepton+Jets channel of the t{bar t} system are used to measure a single quantity, the reconstructed top quark mass, that is strongly correlated with the true top quark mass. in addition, the dijet mass of the hadronically decaying W boson is used to constrain in situ the uncertain jet energy scale in the CDF detector. Two-dimensional probability density functions are derived using a kernel density estimate-based machinery. Using 1.9 fb{sup -1} of data, the top quark mass is measured to be 171.8{sub -1.9}{sup +1.9}(stat.) {+-} 1.0(syst.)GeV/c{sup 2}.

Photosynthesis is the process by which light energy is used to drive reactions that generate sugars to supply energy for cellular processes. It is one of the most important fundamental biological reactions and occurs in both prokaryotic (e.g. bacteria) and eukaryotic (e.g. plants and algae) organisms. Photosynthesis is also remarkably intricate, requiring the coordination of many different steps and reactions in order to successfully transform absorbed solar energy into a biochemical usable form of energy. However, the net reaction for all photosynthetic organisms can be reduced to the following, deceptively general, equation developed by Van Niel[1] H{sub 2} - D + A {sub {implies}}{sup hv} A - H{sub 2} + D where H{sub 2}-D is the electron donor, e.g. H{sub 2}O, H{sub 2}S. A is the electron acceptor, e.g. CO{sub 2}, and A-H{sub 2} is the synthesized sugar. Amazingly, this simple net equation is responsible for creating the oxidizing atmosphere of Earth and the recycling of CO{sub 2}, both of which are necessary for the sustainment of the global ecosystem.

One of the biggest challenges in Chemical Dynamics is describing the behavior of complex systems accurately. Classical MD simulations have evolved to a point where calculations involving thousands of atoms are routinely carried out. Capturing coherence, tunneling and other such quantum effects for these systems, however, has proven considerably harder. Semiclassical methods such as the Initial Value Representation (SC-IVR) provide a practical way to include quantum effects while still utilizing only classical trajectory information. For smaller systems, this method has been proven to be most effective, encouraging the hope that it can be extended to deal with a large number of degrees of freedom. Several variations upon the original idea of the SCIVR have been developed to help make these larger calculations more tractable; these range from the simplest, classical limit form, the Linearized IVR (LSC-IVR) to the quantum limit form, the Exact Forward-Backward version (EFB-IVR). In this thesis a method to tune between these limits is described which allows us to choose exactly which degrees of freedom we wish to treat in a more quantum mechanical fashion and to what extent. This formulation is called the Tuning IVR (TIVR). We further describe methodology being developed to evaluate the prefactor …

We employ Runs 1-4 off-peak data sample (about 21.5 fb{sup -1}) to produce the current world-best spectra and production rates measurements for three strangely-flavored baryons: the {Lambda} hyperon, the cascade hyperon, and the {Omega} hyperon. These improved measurements shall enable theoretical and phenomelogical workers to generate more realistic models for the hadronization process, currently one of the unresolved problem areas in the standard model of particle physics. This analysis was conducted using codes from release 16 series. We report the production rate at 10.54 GeV for the {Lambda} as 0.0900 {+-} 0.0006(stat.) {+-} 0.0039(sys.) per hadronic event. Our measured production rate at the same energy for the cascade hyperon is 0.00562 {+-} 0.00013(stat.) {+-} 0.00045(sys.) per hadronic event, while that for the {Omega} hyperon is 0.00027 {+-} 0.00004(stat.) {+-} 0.0008(sys.) per hadronic event. The spectral measurements for the respective particles also constitute current world-best measurements.

This dissertation describes a measurement of the rate of associated production of the W boson with the charm jet in the proton and anti-proton collisions at the center-of-mass energy of 1.96 TeV at the Fermilab Tevatron Collider. The measurement has direct sensitivity to the strange quark content inside the proton. A direct measurement of the momentum distribution of the strange quark inside the proton is essential for a reliable calculation of new physics signal as well as the background processes at the collider experiments. The identification of events containing a W boson and a charm jet is based on the leptonic decays of the W boson together with a tagging technique for the charm jet identification based on the semileptonic decay of the charm quark into the muon. The charm jet recoiling against the W boson must have a minimum transverse momentum of 20 GeV and an absolute value of pseudorapidity less than 2.5. This measurement utilizes the data collected by the D0 detector at the Fermilab Collider. The measured rate of the charm jet production in association with the W boson in the inclusive jet production with the W boson is 0.074 {+-} 0.023, which is in agreement with …

A measurement of the top quark mass in proton-antiproton collisions at {radical}s = 1.96 TeV using 1040fb{sup -1} of data collected in D detector at Fermilab is presented. This analysis focuses on the all-hadronic decay mode of the top quark and therefore only events with six or more calorimeter jets in the final state are considered.

The Neutralized Drift Compression Experiment (NDCX) at Lawrence Berkeley National Laboratory is exploring the physical limits of compression and focusing of ion beams for heating material to warm dense matter (WDM) and fusion ignition conditions. The NDCX is a beam transport experiment with several components at a scale comparable to an inertial fusion energy driver. The NDCX is an accelerator which consists of a low-emittance ion source, high-current injector, solenoid matching section, induction bunching module, beam neutralization section, and final focusing system. The principal objectives of the experiment are to control the beam envelope, demonstrate effective neutralization of the beam space-charge, control the velocity tilt on the beam, and understand defocusing effects, field imperfections, and limitations on peak intensity such as emittance and aberrations. Target heating experiments with space-charge dominated ion beams require simultaneous longitudinal bunching and transverse focusing. A four-solenoid lattice is used to tune the beam envelope to the necessary focusing conditions before entering the induction bunching module. The induction bunching module provides a head-to-tail velocity ramp necessary to achieve peak axial compression at the desired focal plane. Downstream of the induction gap a plasma column neutralizes the beam space charge so only emittance limits the focused beam …

The Standard Model of elementary particles can not be the final theory. There are theoretical reasons to expect the appearance of new physics, possibly at the energy scale of few TeV. Several possible theories of new physics have been proposed, each with unknown probability to be confirmed. Instead of arbitrarily choosing to examine one of those theories, this thesis is about searching for any sign of new physics in a model-independent way. This search is performed at the Collider Detector at Fermilab (CDF). The Standard Model prediction is implemented in all final states simultaneously, and an array of statistical probes is employed to search for significant discrepancies between data and prediction. The probes are sensitive to overall population discrepancies, shape disagreements in distributions of kinematic quantities of final particles, excesses of events of large total transverse momentum, and local excesses of data expected from resonances due to new massive particles. The result of this search, first in 1 fb{sup -1} and then in 2 fb{sup -1}, is null, namely no considerable evidence of new physics was found.

Several reactions producing odd-Z transactinide compound nuclei were studiedwith the 88-Inch Cyclotron and the Berkeley Gas-Filled Separator at the LawrenceBerkeley National Laboratory. The goal was to produce the same compound nucleus ator near the same excitation energy with similar values of angular momentum via differentnuclear reactions. In doing so, it can be determined if there is a preference in entrancechannel, because under these experimental conditions the survival portion of Swiatecki, Siwek-Wilcznska, and Wilczynski's"Fusion By Diffusion" model is nearly identical forthe two reactions. Additionally, because the same compound nucleus is produced, theexit channel is the same. Four compound nuclei were examined in this study: 258Db, 262Bh, 266Mt, and 272Rg. These nuclei were produced by using very similar heavy-ion induced-fusion reactions which differ only by one proton in the projectile or target nucleus (e.g.: 50Ti + 209Bi vs. 51V + 208Pb). Peak 1n exit channel cross sections were determined for each reaction in each pair, and three of the four pairs' cross sections were identical within statistical uncertainties. This indicates there is not an obvious preference of entrancechannel in these paired reactions. Charge equilibration immediately prior to fusionleading to a decreased fusion barrier is the likely cause of this phenomenon. In addition …

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 …

We present a measurement of the W boson production charge asymmetry using the W {yields} e{nu} decay channel. We use data collected the Collider Detector at Fermilab (CDF) from p{bar p} collisions at {radical}s = 1.96 TeV. The data were collected up to February 2006 (Run II) and represent an integrated luminosity of 1 fb{sup -1}. The experimental measurement of W production charge asymmetry is compared to higher order QCD predictions generated using MRST2006 and CTEQ6 parton distribution functions (PDF). The asymmetry provides new input on the momentum fraction dependence of the u and d quark parton distribution functions (PDF) within the proton over the fraction of proton's momentum range from 0.002 < x < 0.8 corresponding to -3.0 < y{sub W} < 3.0 at Q{sup 2} {approx} M{sub W}{sup 2}.

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 …

During the directional solidification of peritectic alloys, a rich variety of two-phase microstructures develop, and the selection process of a specific microstructure is complicated due to the following two considerations. (1) In contrast to many single phase and eutectic microstructures that grow under steady state conditions, two-phase microstructures in a peritectic system often evolve under non-steady-state conditions that can lead to oscillatory microstructures, and (2) the microstructure is often governed by both the nucleation and the competitive growth of the two phases in which repeated nucleation can occur due to the change in the local conditions during growth. In this research, experimental studies in the Sn-Cd system were designed to isolate the effects of nucleation and competitive growth on the dynamics of complex microstructure formation. Experiments were carried out in capillary samples to obtain diffusive growth conditions so that the results can be analyzed quantitatively. At high thermal gradient and low velocity, oscillatory microstructures were observed in which repeated nucleation of the two phases was observed at the wall-solid-liquid junction. Quantitative measurements of nucleation undercooling were obtained for both the primary and the peritectic phase nucleation, and three different ampoule materials were used to examine the effect of different contact …

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 top quark pair production cross section measurement in the lepton+jets channel with b-tagging algorithm is described. About 900 pb{sup -1} data collected by the D0 detector at the Fermilab Tevatron are used for this analysis. In this thesis, event selection, background estimation, and cross section calculation are discussed in detail. In addition, calibration of the Luminosity Monitor readout electronics and a new b-tagging algorithm, the SLTNN tagger, are also discussed in this thesis.

I present a measurement of the t{bar t} production cross section at {radical}s = 1.96 TeV using 2034 pb{sup -1} of CDF Run II data using events with a high transverse momentum electron or muon, three or more jets, and missing transverse energy. The measurement assumes a t {yields} Wb branching fraction of 100 percent. Events consistent with t{bar t} decay are found by identifying jets containing heavy-flavor semileptonic decays to muons. The dominant backgrounds are evaluated directly from the data. Based on 248 candidate events and an expected background of 86.8 {+-} 5.6 events, I measure a production cross section of 8.7 {+-} 1.1{sub -0.8}{sup +0.9} {+-} 0.6 pb, in agreement with the Standard Model.

I present the results of a search for pair production of scalar top quarks ({tilde t}{sub 1}) in an R-parity violating supersymmetric scenario using 322 pb{sup -1} of p{bar p} collisions at {radical}s = 1.96 TeV collected by the upgraded Collider Detector at Fermilab. I assume each {tilde t}{sub 1} decays into a {tau} lepton and a b quark, with branching ratio {beta}, and search for final states containing either an electron or a muon from a leptonic {tau} decay, a hadronically decaying {tau} lepton, and two or more jets. Two candidate events pass my final selection criteria, consistent with the expectation from standard model processes. I present upper limits on the cross section times branching ratio squared {sigma}({tilde t}{sub 1}{bar {tilde t}}{sub 1}) x {beta}{sup 2} as a function of the stop mass m({tilde t}{sub 1}). Assuming {beta} = 1, I set a 95% confidence level limit m({tilde t}{sub 1}) > 153 GeV=c{sup 2}. These limits are also fully applicable to the case of a pair produced third generation scalar leptoquark that decays into a {tau} lepton and a b quark.

Matrix-assisted laser desorption/ionization(MALDI) mass spectrometry(MS) has been widely used for analysis of biological molecules, especially macromolecules such as proteins. However, MALDI MS has a problem in small molecule (less than 1 kDa) analysis because of the signal saturation by organic matrixes in the low mass region. In imaging MS (IMS), inhomogeneous surface formation due to the co-crystallization process by organic MALDI matrixes limits the spatial resolution of the mass spectral image. Therefore, to make laser desorption/ionization (LDI) MS more suitable for mass spectral profiling and imaging of small molecules directly from raw biological tissues, LDI MS protocols with various alternative assisting materials were developed and applied to many biological systems of interest. Colloidal graphite was used as a matrix for IMS of small molecules for the first time and methodologies for analyses of small metabolites in rat brain tissues, fruits, and plant tissues were developed. With rat brain tissues, the signal enhancement for cerebroside species by colloidal graphite was observed and images of cerebrosides were successfully generated by IMS. In addition, separation of isobaric lipid ions was performed by imaging tandem MS. Directly from Arabidopsis flowers, flavonoids were successfully profiled and heterogeneous distribution of flavonoids in petals was observed for …