The development of advanced lithium-ion batteries is key to the success of many technologies, and in particular, hybrid electric vehicles. In addition to finding materials with higher energy and power densities, improvements in other factors such as cost, toxicity, lifetime, and safety are also required. Lithium transition metal oxide and LiFePO₄/C composite materials offer several distinct advantages in achieving many of these goals and are the focus of this report. Two series of layered lithium transition metal oxides, namely LiNi_1/3Co_1/3-yM_yMn_1/3O₂ (M=Al, Co, Fe, Ti) and LiNi_0.4Co_0.2-yM_yMn_0.4O₂ (M = Al, Co, Fe), have been synthesized. The effect of substitution on the crystal structure is related to shifts in transport properties and ultimately to the electrochemical performance. Partial aluminum substitution creates a high-rate positive electrode material capable of delivering twice the discharge capacity of unsubstituted materials. Iron substituted materials suffer from limited electrochemical performance and poor cycling stability due to the degradation of the layered structure. Titanium substitution creates a very high rate positive electrode material due to a decrease in the anti-site defect concentration. LiFePO₄ is a very promising electrode material but suffers from poor electronic and ionic conductivity. To overcome this, two new techniques have been developed to synthesize high …

The electronic spin degree of freedom is of general fundamental importance to all matter. Understanding its complex roles and behavior in the solid state, particularly in highly correlated and magnetic materials, has grown increasingly desirable as technology demands advanced devices and materials based on ever stricter comprehension and control of the electron spin. However, direct and efficient spin dependent probes of electronic structure are currently lacking. Angle Resolved Photoemission Spectroscopy (ARPES) has become one of the most successful experimental tools for elucidating solid state electronic structures, bolstered by-continual breakthroughs in efficient instrumentation. In contrast, spin-resolved photoemission spectroscopy has lagged behind due to a lack of similar instrumental advances. The power of photoemission spectroscopy and the pertinence of electronic spin in the current research climate combine to make breakthroughs in Spin and Angle Resolved Photoemission Spectroscopy (SARPES) a high priority . This thesis details the development of a unique instrument for efficient SARPES and represents a radical departure from conventional methods. A custom designed spin polarimeter based on low energy exchange scattering is developed, with projected efficiency gains of two orders of magnitude over current state-of-the-art polarimeters. For energy analysis, the popular hemispherical analyzer is eschewed for a custom Time-of-Flight (TOF) …

The lifetime of the Λ⁰_b baryon (consisting of u, d and b quarks) is the theoretically most interesting of all b-hadron lifetimes. The lifetime of Λ⁰_b probes our understanding of how baryons with one heavy quark are put together and how they decay. Experimentally however, measurements of the Λ⁰_b lifetime have either lacked precision or have been inconsistent with one another. This thesis describes the measurement of Λ⁰_b lifetime in proton-antiproton collisions with center of mass energy of 1.96 TeV at Fermilab's Tevatron collider. Using 1070 ± 60pb^-1 of data collected by the Collider Detector at Fermilab (CDF), a clean sample of about 3,000 fully-reconstructed Λ⁰_b →Λ_c⁺π^- decays (with Λ⁺_c subsequently decaying via Λ⁺_c → p⁺ K^- π⁺) is used to extract the lifetime of the Λ⁰_b baryon, which is found to be cτ(Λ⁰_b) = 422.8 ± 13.8(stat) ± 8.8(syst)μm. This is the most precise measurement of its kind, and is even better than the current world average. It also settles the recent controversy regarding the apparent inconsistency between CDF's other measurement and the rest of the world.

Superconducting cavity resonators offer the advantage of high field intensity for a given input power, making them an attractive contender for particle accelerator applications. Power coupling into a superconducting cavity employed in a particle accelerator requires unique provisions to maintain high vacuum and cryogenic temperature on the cavity side, while operating with ambient conditions on the source side. Components introduced to fulfill mechanical requirements must show negligible obstruction of the propagation of the microwave with absence of critical locations that may give rise to electron multipaction, leading to a multiple section design, instead of an aperture, a probe, or a loop structure as found in conventional cavities. A coaxial power coupler for a superconducting multiple-cell cavity at 3.9 GHz has been developed. The cavity is intended to be employed as an accelerator to provide enhanced electron beam quality in a free-electron laser in Hamburg (FLASH) user facility. The design of the coupler called for two windows to sustain high vacuum in the cavity and two bellows to accommodate mechanical dimensional changes resulting from cryogenics. Suppression of multipacting was accomplished by the choice of conductor dimensions and materials with low second yield coefficients. Prior to integration with the cavity, the coupler …

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.

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.

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 magnetic flux structures in the intermediate state of bulk, pinning-free Type-I superconductors are studied using a high resolution magneto-optical imaging technique. Unlike most previous studies, this work focuses on the pattern formation of the coexisting normal and superconducting phases in the intermediate state. The influence of various parameters such as sample shape, structure defects (pinning) and applied current are discussed in relation to two distinct topologies: flux tubes (closed topology) and laminar (open topology). Imaging and magnetization measurements performed on samples of different shapes (cones, hemispheres and slabs), show that contrary to previous beliefs, the tubular structure is the equilibrium topology, but it is unstable toward defects and flux motion. Moreover, the application of current into a sample with the geometric barrier can replace an established laminar structure with flux tubes. At very high currents, however, there exists a laminar 'stripe pattern.' Quantitative analysis of the mean tube diameter is shown to be in good agreement with the prediction proposed by Goren and Tinkham. This is the first time that this model has been confirmed experimentally. Further research into the flux tube phase shows a direct correlation with the current loop model proposed in the 1990's by Goldstein, Jackson …

This thesis presents the results on a search for the neutral MSSM Higgs bosons decaying to tau pairs, with least one of these taus decays leptonically. The search was performed with a sample of 1.8 fb{sup -1} of proton-antiproton collisions at {radical}s = 1.96 TeV provided by the Tevatron and collected by CDF Run II. No significant excess over the Standard Model prediction was found and a 95% confidence level exclusion limit have been set on the cross section times branching ratio as a function of the Higgs boson mass. This limit has been translated into the MSSM Higgs sector parameter plane, tan{beta} vs. M{sub A}, for the four different benchmark scenarios.

Understanding chemical reactions requires the knowledge of the elementary steps of breaking and making bonds, and often a variety of experimental techniques are needed to achieve this goal. The initial steps occur on the femto- through picosecond time-scales, requiring the use of ultrafast spectroscopic methods, while the rate-limiting steps often occur more slowly, requiring alternative techniques. Ultrafast one and two-dimensional infrared and step-scan FTIR spectroscopies are used to investigate the photochemical reactions of four organometallic complexes. The analysis leads to a detailed understanding of mechanisms that are general in nature and may be applicable to a variety of reactions.

MINOS is a long baseline neutrino oscillation experiment. A manmade beam of predominantly muon neutrinos is detected both 1 km and 735 km from the production point by two functionally identical detectors. A comparison of the energy spectra measured by the two detectors shows the energy-dependent disappearance of muon neutrinos characteristic of oscillations and allows a measurement of the parameters governing the oscillations. This thesis presents work leading to measurements of disappearance in the 6% {bar {nu}}{sub {mu}} background in that beam. A calibration is developed to correct for time-dependent changes in the responses of both detectors, reducing the corresponding uncertainty on hadronic energy measurements from 1.8% to 0.4% in the near detector and from 0.8% to 0.4% in the far detector. A method of selecting charged current {bar {nu}}{sub {mu}} events is developed, with purities (efficiencies) of 96.5% (74.4%) at the near detector, and 98.8% (70.9%) at the far detector in the region below 10 GeV reconstructed antineutrino energy. A method of using the measured near detector neutrino energy spectrum to predict that expected at the far detector is discussed, and developed for use in the {bar {nu}}{sub {mu}} analysis. Sources of systematic uncertainty contributing to the oscillation measurements …

I describe a search for anomalous production of Z pairs through a new massive resonance X in 2.5-2.9 fb{sup -1} of p{bar p} collisions at {radical}s = 1.96 TeV using the CDFII Detector at the Fermilab Tevatron. I reconstruct Z pairs through their decays to electrons, muons, and quarks. To achieve perhaps the most efficient lepton reconstruction ever used at CDF, I apply a thorough understanding of the detector and new reconstruction software heavily revised for this purpose. In particular, I have designed and employ new general-purpose algorithms for tracking at large {eta} in order to increase muon acceptance. Upon analyzing the unblinded signal samples, I observe no X {yields} ZZ candidates and set upper limits on the production cross section using a Kaluza-Klein graviton-like acceptance.

The present work in this dissertation mainly focuses on the clean fivefold surfaces of i-Al-Pd-Mn quasicrystals as well as the nucleation and growth of Ag films on these surfaces. In addition, Ag film growth on NiAl(110) has been explored in the frame of this dissertation. First, we have investigated the equilibration of a fivefold surface of icosahedral Al-Pd-Mn quasicrystal at 900-915 K and 925-950 K, using Omicron variable temperature scanning tunneling microscope (STM). Annealing at low temperatures resulted in many voids on some terraces while the others were almost void-free. After annealing at 925-950K, void-rich terraces became much rarer. Our STM images suggest that through growth and coalescence of the voids, a different termination becomes exposed on host terraces. All of these observations in our study indicate that even after the quasicrystalline terrace-step structure appears, it evolves with time and temperature. More specifically, based on the STM observations, we conclude that during the annealing a wide range of energetically similar layers nucleate as surface terminations, however, with increasing temperature (and time) this distribution gets narrower via elimination of the metastable void-rich terraces. Next, we have examined the bulk structural models of icosahedral Al-Pd-Mn quasicrystal in terms of the densities, compositions …

The purpose of this research was to expand the chemiluminescence microscopy applications in live bacterial/mammalian cell imaging and to improve the detection sensitivity for ATP leaking or release events. We first demonstrated that chemiluminescence (CL) imaging can be used to interrogate single bacterial cells. While using a luminometer allows detecting ATP from cell lysate extracted from at least 10 bacterial cells, all previous cell CL detection never reached this sensitivity of single bacteria level. We approached this goal with a different strategy from before: instead of breaking bacterial cell membrane and trying to capture the transiently diluted ATP with the firefly luciferase CL assay, we introduced the firefly luciferase enzyme into bacteria using the modern genetic techniques and placed the CL reaction substrate D-luciferin outside the cells. By damaging the cell membrane with various antibacterial drugs including antibiotics such as Penicillins and bacteriophages, the D-luciferin molecules diffused inside the cell and initiated the reaction that produces CL light. As firefly luciferases are large protein molecules which are retained within the cells before the total rupture and intracellular ATP concentration is high at the millmolar level, the CL reaction of firefly luciferase, ATP and D-luciferin can be kept for a relatively …

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 …

Silver noble metal nanoparticles that are<10 nm often possess multiply twinned grains allowing them to adopt shapes and atomic structures not observed in bulk materials. The properties exhibited by particles with multiply twinned polycrystalline structures are often far different from those of single-crystalline particles and from the bulk. I will present experimental evidence that silver nanoparticles<10 nm undergo a reversible structural transformation under hydrostatic pressures up to 10 GPa. Results for nanoparticles in the intermediate size range of 5 to 10 nm suggest a reversible linear pressure-dependent rhombohedral distortion which has not been previously observed in bulk silver. I propose a mechanism for this transitiion that considers the bond-length distribution in idealized multiply twinned icosahedral particles. Results for nanoparticles of 3.9 nm suggest a reversible linear pressure-dependent orthorhombic distortion. This distortion is interpreted in the context of idealized decahedral particles. In addition, given these size-dependent measurements of silver nanoparticle compression with pressure, we have constructed a pressure calibration curve. Encapsulating these silver nanoparticles in hollow metal oxide nanospheres then allows us to measure the pressure inside a nanoshell using x-ray diffraction. We demonstrate the measurement of pressure gradients across nanoshells and show that these nanoshells have maximum resolved shear strengths …

This thesis describes a search for standard model Higgs bosons decaying to W boson pairs in proton-anti-proton collisions at a center of mass energy of 1.96 TeV using the CDF II detector. The decay to W bosons is dominant for Higgs masses greater than about 135 GeV. The final state examined consists of two leptons and missing transverse energy from the leptonic decay of one or more W bosons. The signal production mechanisms included are gluon fusion, associated production with a W or Z boson, and vector boson fusion. Matrix element calculations and artificial neural networks are used to discriminate signal from background for Higgs masses in the range 110 {le} M{sub H} {le} 200 GeV. No significant excess of events is observed at any of the Higgs masses investigated. Upper limits on the standard model Higgs cross section are set at 95% confidence for each Higgs mass investigated, the most stringent limit being 1.63 times the predicted standard model cross section for a Higgs mass of 160 GeV.

This thesis studies important dynamical observables of strong interactions such as form factors. It is known that Quantum Chromodynamics (QCD) is a theory which describes strong interactions. For large energies, one can apply perturbative techniques to solve some of the QCD problems. However, for low energies QCD enters into the nonperturbative regime, where different analytical or numerical tools have to be applied to solve problems of strong interactions. The holographic dual model of QCD is such an analytical tool that allows one to solve some nonperturbative QCD problems by translating them into a dual five-dimensional theory defined on some warped Anti de Sitter (AdS) background. Working within the framework of the holographic dual model of QCD, we develop a formalism to calculate form factors and wave functions of vector mesons and pions. As a result, we provide predictions of the electric radius, the magnetic and quadrupole moments which can be directly verified in lattice ca

This dissertation focused on new applications of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The diverse fields that were investigated show the versatility of the technique. In Chapter 2, LA-ICP-MS was used to investigate the rare earth element (REE) profiles of garnets from the Broken Hill Deposit in New South Wales, Australia. The normalized REE profiles helped to shed new light on the formation of deposits of sulfide ores. This information may be helpful in identifying the location of sulfide ore deposits in other locations. New sources of metals such as Pg, Zn, and Ag, produced from these ores, are needed to sustain our current technological society. The application of LA-ICP-MS presented in Chapter 3 is the forensics analysis of automotive putty and caulking. The elemental analysis of these materials was combined with the use of Principal Components Analysis (PCA). The PCA comparison was able to differentiate the automotive putty samples by manufacturer and lot number. The analysis of caulk was able to show a differentiation based on manufacturer, but no clear differentiation was shown by lot number. This differentiation may allow matching of evidence in the future. This will require many more analyses and the construction of a …

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).

Hard, wear-resistant coatings of thin film borides based on AlMgB{sub 14} have the potential to be applied industrially to improve the tool life of cutting tools and pump vanes and may account for several million dollars in savings as a result of reduced wear on these parts. Past work with this material has shown that it can have a hardness of up to 45GPa and be fabricated into thin films with a similar hardness using pulsed laser deposition. These films have already been shown to be promising for industrial applications. Cutting tools coated with AlMgB{sub 14} used to mill titanium alloys have been shown to substantially reduce the wear on the cutting tool and extend its cutting life. However, little research into the thin film fabrication process using pulsed laser deposition to make AlMgB{sub 14} has been conducted. In this work, research was conducted into methods to optimize the deposition parameters for the AlMgB{sub 14} films. Processing methods to eliminate large particles on the surface of the AlMgB{sub 14} films, produce films that were at least 1m thick, reduce the surface roughness of the films, and improve the adhesion of the thin films were investigated. Use of a femtosecond laser …

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.

Optimization techniques are finding their inroads into the field of nuclear physics calculations where the objective functions are very complex and computationally intensive. A vast space of parameters needs searching to obtain a good match between theoretical (computed) and experimental observables, such as energy levels and spectra. Manual calculation defies the scope of such complex calculation and are prone to error at the same time. This body of work attempts to formulate a design and implement it which would integrate the ab initio nuclear physics code MFDn and the VTDIRECT95 code. VTDIRECT95 is a Fortran95 suite of parallel code implementing the derivative-free optimization algorithm DIRECT. Proposed design is implemented for a serial and parallel version of the optimization technique. Experiment with the initial implementation of the design showing good matches for several single-nucleus cases are conducted. Determination and assignment of appropriate number of processors for parallel integration code is implemented to increase the efficiency and resource utilization in the case of multiple nuclei parameter search.

Various single-molecule techniques were utilized for ultra-sensitive early diagnosis of viral DNA and antigen and basic mechanism study of enzymatic reactions. DNA of human papilloma virus (HPV) served as the screening target in a flow system. Alexa Fluor 532 (AF532) labeled single-stranded DNA probes were hybridized to the target HPV-16 DNA in solution. The individual hybridized molecules were imaged with an intensified charge-coupled device (ICCD) in two ways. In the single-color mode, target molecules were detected via fluorescence from hybridized probes only. This system could detect HPV-16 DNA in the presence of human genomic DNA down to 0.7 copy/cell and had a linear dynamic range of over 6 orders of magnitude. In the dual-color mode, fluorescence resonance energy transfer (FRET) was employed to achieve zero false-positive count. We also showed that DNA extracts from Pap test specimens did not interfere with the system. A surface-based method was used to improve the throughput of the flow system. HPV-16 DNA was hybridized to probes on a glass surface and detected with a total internal reflection fluorescence (TIRF) microscope. In the single-probe mode, the whole genome and target DNA were fluorescently labeled before hybridization, and the detection limit is similar to the flow …