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 …

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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 …

The ratio of pion-kaon production by 120 GeV/c protons incident on carbon target is presented. The data was recorded with the Main Injector Particle Production experiment at Fermi National Accelerator Laboratory. Production ratios of K{sup +}/{pi}{sup +}, K{sup -}/{pi}{sup -}, K{sup -}/K{sup +}, and {pi}{sup -}/{pi}{sup +} are measured in 24 bins in longitudinal momentum from 20 to 90 GeV/c and transverse momentum up to 2 GeV/c. The measurement is compared to existing data sets, particle production Monte Carlo results from FLUKA-06, parametrization of proton-beryllium data at 400/450 GeV/c, and ratios measured by the MINOS experiment on the NuMI target.

Nuclear reaction study with radioactive ion beams is one of the most exciting research topics in modern nuclear physics. The development of radioactive ion beams has allowed nuclear scientists and engineers to explore many unknown exotic nuclei far from the valley of nuclear stability, and to further our understanding of the evolution of the universe. The recently developed radioactive ion beam facility at the Lawrence Berkeley National Laboratory's 88-inch cyclotron is denoted as BEARS and provides {sup 11}C, {sup 14}O and {sup 15}O radioactive ion beams of high quality. These moderate to high intensity, proton-rich radioactive ion beams have been used to explore the properties of unstable nuclei such as {sup 12}N and {sup 15}F. In this work, the proton capture reaction on {sup 11}C has been evaluated via the indirect d({sup 11}C, {sup 12}N)n transfer reaction using the inverse kinematics method coupled with the Asymptotic Normalization Coefficient (ANC) theoretical approach. The total effective {sup 12}N {yields} {sup 11}C+p ANC is found to be (C{sub eff}{sup 12{sub N}}){sup 2} = 1.83 {+-} 0.27 fm{sup -1}. With the high {sup 11}C beam intensity available, our experiment showed excellent agreement with theoretical predictions and previous experimental studies. This study also indirectly confirmed …

This dissertation describes a test of the Standard Model (SM) of particle physics by measuring the probability, or cross section, of simultaneously producing a W boson and a Z boson from proton-antiproton collisions. The SM predicts the cross section of WZ production to be 3.68 {+-} 0.25 pb. The SM and physics of WZ production are described in Chapter 2 of this dissertation. The 1.96 TeV center-of-mass energy proton-antiproton collisions are provided by the Fermi National Accelerator Laboratory (FNAL) Tevatron Collider. The W and Z particles are detected using the D0 detector, which is described in Chapter 3. The data were collected by the detector during 2002-2006 corresponding to 1 fb{sup -1} of p{bar p} collisions. This data set is described in Chapter 6. The measurement uses the trilepton (e{nu}ee, {mu}{nu}ee, e{nu}{mu}{mu}, and {mu}{nu}{mu}{mu}) decay channels, in which a W decays to a charged lepton plus a neutrino and a Z decays to a pair of charged leptons. The W and Z particle selection criteria, detection efficiency, and background determination are described in Chapter 7. We observe 13 candidate events in 1 fb{sup -1} of p{bar p} collisions. In this data set we expect to see 4.5 {+-} 0.6 background …

The work presented in this thesis is the search for Randall-Sundrum (RS) gravitons from an analysis of approximately 1 fb{sup -1} data collected with the D0 detector at Fermilab. The standard model has been a great success in explaining all experimental observations in particle physics. However, we also know that it has fundamental problems. One of these problems, called the hierarchy problem, is related to the large difference between the electroweak scale and the Planck scale. The model proposed by Randall and Sundrum presents a possible solution to the hierarchy problem by introducing physics beyond the standard model. Randall and Sundrum's theory postulates the existence of a 4th spatial dimension in addition to the conventional (3+1)-dimensional space. Gravity is localized on a 3+1 dimensional subspace, called a brane (Planck brane) that is separated in this new 4th spatial dimension from the standard model brane. As one moves away from this Planck brane, gravity is exponentially suppressed and this explains why gravity appears so weak at the standard model brane. In the simplest RS model, the only particles that propagate in the extra dimension are gravitons. The graviton manifests itself on the standard model brane as a series of excited states …

This thesis reports a time dependent measurement of the B{sup 0}{sub s}-{bar B}{sup 0}{sub s} oscillation frequency {Delta}m{sub s} using semileptonic decays B{sup 0}{sub s} {yields} D{sup -}{sub s}{ell}{sup +}X. We use a data sample of 1 fb{sup -1} of p{bar p} collisions at {radical}s = 1.96 TeV collected with the CDF II detector at the Fermilab Tevatron Collider to reconstruct {approx} 61, 500 semileptonic B{sup 0}{sub s} decays. This analysis of B{sup 0}{sub s}-{bar B}{sup 0}{sub s} mixing has a sensitivity of 19.4 ps{sup -1} and shows an evidence of B{sup 0}{sub s} oscillations at {Delta}m{sub s} {approx}17.75 ps{sup -1} with an amplitude significance of {approx}2. In combination with the analyses of {approx} 8,700 hadronic B{sup 0}{sub s} decays at CDF, we have made the first direct observation of time-dependent B{sup 0}{sub s}-{bar B}{sup 0}{sub s} flavor oscillations measuring {Delta}m{sub s} = 17.77 {sup +0.09}{sub -0.10} (stat) {+-} 0.07 (syst) ps{sup -1}. The obtained value of {Delta}m{sub s} agrees with the Standard Model expectation. When combined with the world average values for {Delta}m{sub d}, m{sub {bar B}0} and m{sub {bar B}0s}, along with other theoretical input, this result yields the ratio of CKM matrix elements |Vtd/Vts| = 0.2060 {+-} …

High-resolution NMR spectra of samples with anisotropicbroadening are simplified to their isotropic spectra by fast rotation ofthe sample at the magic angle 54.7 circ. This dissertation concerns thedevelopment of novel Nuclear Magnetic Resonance (NMR) methodologies basedwhich would rotate the magnetic field instead of the sample, rotatingfield NMR. It provides an over of the NMR concepts, procedures, andexperiments needed to understand the methodologies that will be used forrotating field NMR. A simple two-dimensional shimming method based onharmonic corrector rings which can provide arbitrary multiple ordershimming corrections were developed for rotating field systems, but couldbe used in shimming other systems as well. Those results demonstrate, forexample, that quadrupolar order shimming improves the linewidth by up toan order of magnitude. An additional order of magnitude reduction is inprinciple achievable by utilizing this shimming method for z-gradientcorrection and higher order xy gradients. A specialized pulse sequencefor the rotating field NMR experiment is under development. The pulsesequence allows for spinning away from the magic angle and spinningslower than the anisotropic broadening. This pulse sequence is acombination of the projected magic angle spinning (p-MAS) and magic angleturning (MAT) pulse sequences. This will be useful to rotating field NMRbecause there are limits on how fast a field …

High-resolution NMR spectra of samples with anisotropicbroadening are simplified to their isotropic spectra by fast rotation ofthe sample at the magic angle 54.7 circ. This dissertation concerns thedevelopment of novel Nuclear Magnetic Resonance (NMR) methodologies basedwhich would rotate the magnetic field instead of the sample, rotatingfield NMR. It provides an over of the NMR concepts, procedures, andexperiments needed to understand the methodologies that will be used forrotating field NMR. A simple two-dimensional shimming method based onharmonic corrector rings which can provide arbitrary multiple ordershimming corrections were developed for rotating field systems, but couldbe used in shimming other systems as well. Those results demonstrate, forexample, that quadrupolar order shimming improves the linewidth by up toan order of magnitude. An additional order of magnitude reduction is inprinciple achievable by utilizing this shimming method for z-gradientcorrection and higher order xy gradients. A specialized pulse sequencefor the rotating field NMR experiment is under development. The pulsesequence allows for spinning away from the magic angle and spinningslower than the anisotropic broadening. This pulse sequence is acombination of the projected magic angle spinning (p-MAS) and magic angleturning (MAT) pulse sequences. This will be useful to rotating field NMRbecause there are limits on how fast a field …

In the last two decades, the field of nanoscience andnanotechnology has witnessed tremendous advancement in the synthesis andapplication of group II-VI colloidal nanocrystals. The synthesis based onhigh temperature decomposition of organometallic precursors has becomeone of the most successful methods of making group II-VI colloidalnanocrystals. This method is first demonstrated by Bawendi and coworkersin 1993 to prepare cadmium chalcogenide colloidal quantum dots and laterextended by others to prepare other group II-VI quantum dots as well asanisotropic shaped colloidal nanocrystals, such as nanorod and tetrapod.This dissertation focuses on the chemistry of this type of nanocrystalsynthesis. The synthesis of group II-VI nanocrystals was studied bycharacterizing the molecular structures of the precursors and productsand following their time evolution in the synthesis. Based on theseresults, a mechanism was proposed to account for the 2 reaction betweenthe precursors that presumably produces monomer for the growth ofnanocrystals. Theoretical study based on density functional theorycalculations revealed the detailed free energy landscape of the precursordecomposition and monomerformation pathway. Based on the proposedreaction mechanism, a new synthetic method was designed that uses wateras a novel reagent to control the diameter and the aspect ratio of CdSeand CdS nanorods.

The family of R{sub 5}Si{sub x}Ge{sub 4-x} alloys demonstrates a variety of unique physical phenomena related to magneto-structural transitions associated with reversible breaking and reforming of specific bonds that can be controlled by numerous external parameters such as chemical composition, magnetic field, temperature, and pressure. Therefore, R{sub 5}Si{sub x}Ge{sub 4-x} systems have been extensively studied to uncover the mechanism of the extraordinary magneto-responsive properties including the giant magnetoresistance (GMR) and colossal magnetostriction, as well as giant magnetocaloric effect (GMCE). Until now, more than a half of possible R{sub 5}Si{sub x}Ge{sub 4-x} pseudobinary systems have been completely or partially investigated with respect to their crystallography and phase relationships (R = La, Pr, Nd, Gd, Tb, Dy, Er, Lu, Y). Still, there are other R{sub 5}Si{sub x}Ge{sub 4-x} systems (R = Ce, Sm, Ho, Tm, and Yb) that are not studied yet. Here, we report on phase relationships and structural, magnetic, and thermodynamic properties in the Yb{sub 5}Si{sub x}Ge{sub 4-x} and Sm{sub 5}Si{sub x}Ge{sub 4-x} pseudobinary systems, which may exhibit mixed valence states. The crystallography, phase relationships, and physical properties of Yb{sub 5}Si{sub x}Ge{sub 4-x} alloys with 0 {le} x {le} 4 have been examined by using single crystal and powder x-ray …

Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, …

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This report describes the development and application of a dispatch optimization algorithm for integrated energy systems (IES) comprised of on-site cogeneration of heat and electricity, energy storage devices, and demand response opportunities. This work is intended to aid commercial and industrial sites in making use of modern computing power and optimization algorithms to make informed, near-optimal decisions under significant uncertainty and complex objective functions. The optimization algorithm uses a finite set of randomly generated future scenarios to approximate the true, stochastic future; constraints are included that prevent solutions to this approximate problem from deviating from solutions to the actual problem. The algorithm is then expressed as a mixed integer linear program, to which a powerful commercial solver is applied. A case study of United States Postal Service Processing and Distribution Centers (P&DC) in four cities and under three different electricity tariff structures is conducted to (1) determine the added value of optimal control to a cogeneration system over current, heuristic control strategies; (2) determine the value of limited electric load curtailment opportunities, with and without cogeneration; and (3) determine the trade-off between least-cost and least-carbon operations of a cogeneration system. Key results for the P&DC sites studied include (1) in …

In the last two decades, the field of nanoscience andnanotechnology has witnessed tremendous advancement in the synthesis andapplication of group II-VI colloidal nanocrystals. The synthesis based onhigh temperature decomposition of organometallic precursors has becomeone of the most successful methods of making group II-VI colloidalnanocrystals. This methodis first demonstrated by Bawendi and coworkersin 1993 to prepare cadmium chalcogenide colloidal quantum dots and laterextended by others to prepare other group II-VI quantum dots as well asanisotropic shaped colloidal nanocrystals, such as nanorod and tetrapod.This dissertation focuses on the chemistry of this type of nanocrystalsynthesis. The synthesis of group II-VI nanocrystals was studied bycharacterizing the molecular structures of the precursors and productsand following their time evolution in the synthesis. Based on theseresults, a mechanism was proposed to account for the 2 reaction betweenthe precursors that presumably produces monomer for the growth ofnanocrystals. Theoretical study based on density functional theorycalculations revealed the detailed free energy landscape of the precursordecomposition and monomerformation pathway. Based on the proposedreaction mechanism, a new synthetic method was designed that uses wateras a novel reagent to control the diameter and the aspect ratio of CdSeand CdS nanorods.