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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.

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This is concerned with imaging and wave propagation in nonhomogeneous media, and includes a collection of computational techniques, such as level set methods with material transport, Dijkstra-like Hamilton-Jacobi solvers for first arrival Eikonal equations and techniques for data smoothing. The theoretical components include aspects of seismic ray theory, and the results rely on careful comparison with experiment and incorporation as input into large production-style geophysical processing codes. Producing an accurate image of the Earth's interior is a challenging aspect of oil recovery and earthquake analysis. The ultimate computational goal, which is to accurately produce a detailed interior map of the Earth's makeup on the basis of external soundings and measurements, is currently out of reach for several reasons. First, although vast amounts of data have been obtained in some regions, this has not been done uniformly, and the data contain noise and artifacts. Simply sifting through the data is a massive computational job. Second, the fundamental inverse problem, namely to deduce the local sound speeds of the earth that give rise to measured reacted signals, is exceedingly difficult: shadow zones and complex structures can make for ill-posed problems, and require vast computational resources. Nonetheless, seismic imaging is a crucial part …

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}.

Although the standard model of particle physics agrees perfectly with experimental data, it is unlikely the final theory describing particles and their interactions. New phenomena has been searched in the jets and missing transverse energy topology. Such phenomena may be due to the pair production of leptoquarks decaying into a quark and a neutrino or the pair production of stops decaying into a charm and a neutralino which is assumed to be the lightest supersymmetric particle. These searches have been performed with the D0 detector at hadronic collider TeVatron with a center of mass energy of 1.96 TeV. This kind of search needs a good understanding of the jet energy calibration. The determination of the relative jet energy scale has allowed them to reduce the systematic uncertainties on the jet energy measurement when comparing the data and the simulation. Moreover a new method has been developed in order to correct simulated jets for the differences observed in the jet energy scale, the jet energy resolution and the jet reconstruction efficiency between the data and the simulation. The data analysis, performed with an integrated luminosity of 310 pb{sup -1}, has not observed any excess. This result is interpreted in terms of …

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.

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Methods of analysis of the dynamics of ensembles of charged particles in collider rings are developed. The following problems are posed and solved using normal form transformations and other methods of perturbative nonlinear dynamics: (1) Optimization of the Tevatron dynamics: (a) Skew quadrupole correction of the dynamics of particles in the Tevatron in the presence of the systematic skew quadrupole errors in dipoles; (b) Calculation of the nonlinear tune shift with amplitude based on the results of measurements and the linear lattice information; (2) Optimization of the Muon Collider storage ring: (a) Computation and optimization of the dynamic aperture of the Muon Collider 50 x 50 GeV storage ring using higher order correctors; (b) 750 x 750 GeV Muon Collider storage ring lattice design matching the Tevatron footprint. The normal form coordinates have a very important advantage over the particle optical coordinates: if the transformation can be carried out successfully (general restrictions for that are not much stronger than the typical restrictions imposed on the behavior of the particles in the accelerator) then the motion in the new coordinates has a very clean representation allowing to extract more information about the dynamics of particles, and they are very convenient for …

In order to better understand the fundamental components that govern catalytic activity, two-dimensional model platinum nanocatalyst arrays have been designed and fabricated. These catalysts arrays are meant to model the interplay of the metal and support important to industrial heterogeneous catalytic reactions. Photolithography and sub-lithographic techniques such as electron beam lithography, size reduction lithography and nanoimprint lithography have been employed to create these platinum nanoarrays. Both in-situ and ex-situ surface science techniques and catalytic reaction measurements were used to correlate the structural parameters of the system to catalytic activity.

Many chemical reactions utilize organometallic complexes as catalysts. These complexes find use in reactions as varied as bond activation, polymerization, and isomerization. This thesis outlines the construction of a new ultrafast laser system with an emphasis on the generation of tunable mid-infrared pulses, data collection, and data analysis.

The shrinking of IC devices has followed the Moore's Law for over three decades, which states that the density of transistors on integrated circuits will double about every two years. This great achievement is obtained via continuous advance in lithography technology. With the adoption of complicated resolution enhancement technologies, such as the phase shifting mask (PSM), the optical proximity correction (OPC), optical lithography with wavelength of 193 nm has enabled 45 nm printing by immersion method. However, this achievement comes together with the skyrocketing cost of masks, which makes the production of low volume application-specific IC (ASIC) impractical. In order to provide an economical lithography approach for low to medium volume advanced IC fabrication, a maskless ion beam lithography method, called Maskless Micro-ion-beam Reduction Lithography (MMRL), has been developed in the Lawrence Berkeley National Laboratory. The development of the prototype MMRL system has been described by Dr. Vinh Van Ngo in his Ph.D. thesis. But the resolution realized on the prototype MMRL system was far from the design expectation. In order to improve the resolution of the MMRL system, the ion optical system has been investigated. By integrating a field-free limiting aperture into the optical column, reducing the electromagnetic interference …

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 …

Sum frequency generation (SFG) surface vibrational spectroscopy was used to characterize interfaces pertinent to current surface engineering applications, such as thin film polymers and novel catalysts. An array of advanced surface science techniques like scanning probe microscopy (SPM), x-ray photoelectron spectroscopy (XPS), gas chromatography (GC) and electron microscopy were used to obtain experimental measurements complementary to SFG data elucidating polymer and catalyst surface composition, surface structure, and surface mechanical behavior. Experiments reported in this dissertation concentrate on three fundamental questions: (1) How does the interfacial molecular structure differ from that of the bulk in real world applications? (2) How do differences in chemical environment affect interface composition or conformation? (3) How do these changes correlate to properties such as mechanical or catalytic performance? The density, surface energy and bonding at a solid interface dramatically alter the polymer configuration, physics and mechanical properties such as surface glass transition, adhesion and hardness. The enhanced sensitivity of SFG at the buried interface is applied to three systems: a series of acrylates under compression, the compositions and segregation behavior of binary polymer polyolefin blends, and the changes in surface structure of a hydrogel as a function of hydration. In addition, a catalytically active thin …