This dissertation contains five papers in the format required for journal publication which describe (in part) my research accomplishments as a graduate student at Iowa State University. This work can be broadly categorized as the binding of weakly-coordinating ligands to cationic organometallic ruthenium fragments, and consists of two main areas of study. Chapters 2-4 are investigations into factors that influence the binding of dibenzothiophenes to {l_brace}Cp'Ru(CO){sub 2}{r_brace}{sup +} fragments, where Cp' = {eta}{sup 5}-C{sub 5}H{sub 5} (Cp) and {eta}{sup 5}-C{sub 5}Me{sub 5} (Cp*). Chapters 5 and 6 present the synthesis and structural characterization of complexes containing corannulene buckybowls that are {eta}{sup 6}-coordinated to {l_brace}Cp*Ru{r_brace}{sup +} fragments. The first chapter contains a brief description of the difficulty in lowering sulfur levels in diesel fuel along with a review of corannulene derivatives and their metal complexes. After the final paper is a short summary of the work herein (Chapter 7). Each chapter is independent, and all equations, schemes, figures, tables, references, and appendices in this dissertation pertain only to the chapter in which they appear.

I present an analysis of b{bar b} pair production correlations, using dimuon-triggered data collected with the Collider Detector at Fermilab (CDF) in p{bar p} collisions at {radical}s = 1.96 TeV during Run II of the TeVatron. The leading order (LO) and next-to-leading order (NLO) b quark production processes are discriminated by the angular and momentum correlations between the b{bar b} pair. Track-level jets containing a muon are classified by b quark content and used to estimate the momentum vector of the progenitor b quark. The theoretical distributions given by the MC{at}NLO event generator are tested against the data.

The MINOS Far Detector is a 5.4 kiloton (5.2 kt steel plus 0.2 kt scintillator plus aluminum skin) magnetized tracking calorimeter located 710 meters underground in the Soudan mine in Northern Minnesota. MINOS is the first large, deep underground detector with a magnetic field and thus capable of making measurements of the momentum and charge of cosmic ray muons. Despite encountering unexpected anomalies in distributions of the charge ratio (N{sub {mu}{sup +}}/N{sub {mu}{sup -}}) of cosmic muons, a method of canceling systematic errors is proposed and demonstrated. The result is R{sub eff} = 1.346 {+-} 0.002 (stat) {+-} 0.016 (syst) for the averaged charge ratio, and a result for a rising fit to slant depth of R(X) = 1.300 {+-} 0.008 (stat) {+-} 0.016 (syst) + (1.8 {+-} 0.3) x 10{sup -5} x X, valid over the range of slant depths from 2000 < X < 6000 MWE. This slant depth range corresponds to minimum surface muon energies between 750 GeV and 5 TeV.

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The accurate and efficient simulation of coupled neutron-photon problems is necessary for several important radiation detection applications. Examples include the detection of nuclear threats concealed in cargo containers and prompt gamma neutron activation analysis for nondestructive determination of elemental composition of unknown samples.

In this dissertation, we present the results of a time-dependent angular analysis of B_s → J/ΨΦ decays performed with the use of initial-state flavor tagging. CP violation is observed in this mode through the interference of decay without net mixing and decay with net mixing, that is, B_s → J/ΨΦ and B_s → $\bar{B}$_s → J/ΨΦ . The time-dependent angular analysis is used to extract the decay widths of the heavy and light B_s eigenstates and the difference between these decay widths ΔΓ_s {triple_bond} Γ_s^L-Γ_s^H. Initial-state flavor tagging is used to determine the matter-antimatter content of the B_s mesons at production time. We combine flavor tagging with the angular analysis, which statistically determines the contributions of the CP-even and CP-odd components at decay time, to measure the CP-violating phase β_s. The phase β_s is expressed in terms of elements of the Cabibbo-Kobayashi-Maskawa matrix as β_s {triple_bond} arg (-V_tsV*_tb/V_csV*_cb), and is predicted by the Standard Model to be close to zero, β_s^SM = 0.02. In the measurement of ΔΓ_s, we use a dataset corresponding to 1.7 fb^-1 of luminosity, collected at the CDF experiment from proton-antiproton collisions at a center of mass energy √s = 1.96 TeV. In the measurement of …

The MINOS Far Detector is a 5400 ton iron calorimeter located at the Soudan state park in Soudan Minnesota. The MINOS far detector can observe atmospheric neutrinos and separate charge current {nu}{sub {mu}} and {bar {nu}}{sub {mu}} interactions by using a 1.4 T magnetic field to identify the charge of the produced muon. The CPT theorem requires that neutrinos and anti-neutrinos oscillate in the same way. In a fiducial exposure of 5.0 kilo-ton years a total of 41 candidate neutrino events are observed with an expectation of 53.1 {+-} 7.6(system.) {+-} 7.2(stat.) unoscillated events or 31.6 {+-} 4.7(system.) {+-} 5.6(stat.) events with {Delta}m{sup 2} = 2.4 x 10{sup -3} eV{sup 2}, sin{sup 2}(2{theta}) = 1.0 as oscillation parameters. These include 28 events which can have there charge identified with high confidence. These 28 events consist of 18 events consistent with being produced by {nu}{sub {mu}} and 10 events being consistent with being produced by {bar {nu}}{sub {mu}}. No evidence of CPT violation is observed.

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

Cross-sections are presented for 58 GeV {pi}, K, and p on a wide range of nuclear targets. These cross-sections are essential for determining the neutrino flux in measurements of neutrino cross-sections and oscillations. The E907 Main Injector Particle Production (MIPP) experiment at Fermilab is a fixed target experiment for measuring hadronic particle production using primary 120 GeV/c protons and secondary {pi}, K, and p beams. The particle identification is made by dE/dx in a time projection chamber, and by time-of-flight, differential Cherenkov and ring imaging Cherenkov detectors, which together cover a wide range of momentum from 0.1 GeV/c up to 120 GeV/c. MIPP targets span the periodic table, from hydrogen to uranium, including beryllium and carbon. The MIPP has collected {approx} 0.26 x 10{sup 6} events of 58 GeV/c secondary particles produced by protons from the main injector striking a carbon target.

Evidence from observational cosmology and astrophysics indicates that about one third of the universe is matter, but that the known baryonic matter only contributes to the universe at 4%. A large fraction of the universe is cold and non-baryonic matter, which has important role in the universe structure formation and its evolution. The leading candidate for the non-baryonic dark matter is Weakly Interacting Massive Particles (WIMPs), which naturally occurs in the supersymmetry theory in particle physics. The Cryogenic Dark Matter Search (CDMS) experiment is searching for evidence of a WIMP interaction off an atomic nucleus in crystals of Ge and Si by measuring simultaneously the phonon energy and ionization energy of the interaction in the CDMS detectors. The WIMP interaction energy is from a few keV to tens of keV with a rate less than 0.1 events/kg/day. To reach the goal of WIMP detection, the CDMS experiment has been conducted in the Soudan mine with an active muon veto and multistage passive background shields. The CDMS detectors have a low energy threshold and background rejection capabilities based on ionization yield. However, betas from contamination and other radioactive sources produce surface interactions, which have low ionization yield, comparable to that of …

There is an abundance of evidence that the majority of the mass of the universe is in the form of non-baryonic non-luminous matter that was non-relativistic at the time when matter began to dominate the energy density. Weakly Interacting Massive Particles, or WIMPs, are attractive cold dark matter candidates because they would have a relic abundance today of {approx}0.1 which is consistent with precision cosmological measurements. WIMPs are also well motivated theoretically. Many minimal supersymmetric extensions of the Standard Model have WIMPs in the form of the lightest supersymmetric partner, typically taken to be the neutralino. The CDMS II experiment searches for WIMPs via their elastic scattering off of nuclei. The experiment uses Ge and Si ZIP detectors, operated at <50 mK, which simultaneously measure the ionization and athermal phonons produced by the scattering of an external particle. The dominant background for the experiment comes from electromagnetic interactions taking place very close to the detector surface. Analysis of the phonon signal from these interactions makes it possible to discriminate them from interactions caused by WIMPs. This thesis presents the details of an important aspect of the phonon pulse shape analysis known as the ''Lookup Table Correction''. The Lookup Table Correction …

The use of boron neutron capture to boost tumor dose in fast neutron therapy has been investigated at several fast neutron therapy centers worldwide. This treatment is termed boron neutron capture enhanced fast neutron therapy (BNCEFNT). It is a combination of boron neutron capture therapy (BNCT) and fast neutron therapy (FNT). It is believed that BNCEFNT may be useful in the treatment of some radioresistant brain tumors, such as glioblastoma multiform (GBM). A boron neutron capture enhanced fast neutron therapy assembly has been designed for the Fermilab Neutron Therapy Facility (NTF). This assembly uses a tungsten filter and collimator near the patient's head, with a graphite reflector surrounding the head to significantly increase the dose due to boron neutron capture reactions. The assembly was designed using Monte Carlo radiation transport code MCNP version 5 for a standard 20x20 cm{sup 2} treatment beam. The calculated boron dose enhancement at 5.7-cm depth in a water-filled head phantom in the assembly with a 5x5 cm{sup 2} collimation was 21.9% per 100-ppm {sup 10}B for a 5.0-cm tungsten filter and 29.8% for a 8.5-cm tungsten filter. The corresponding dose rate for the 5.0-cm and 8.5-cm thick filters were 0.221 and 0.127 Gy/min, respectively; about …

The consideration of compliant mechanisms as Microelectromechanical Systems (MEMS) is the focus of this research endeavor. MEMS are micron to millimeter devices that combine electrical, mechanical, and information processing capabilities on the same device. These MEMS need some mechanical motion or parts that move relative to each other. This relative motion, using multiple parts, is not desired because of the assembly requirement and the friction introduced. Compliant devices limits or eliminates friction and the need for multi-component assembly. Compliant devices improve designs by creating single piece mechanisms. The purpose of this research is to validate surface micromachining as a viable fabrication process for compliant MEMS designs. Specifically, this research has sought to fabricate a micro-compliant gripper and a micro-compliant clamp to illustrate the process. While other researchers have created compliant MEMS, most have used comb-drive actuation methods and bulk micromachining processes. This research focuses on fully-compliant devices that use device flexibility for motion and actuation. Validation of these compliant MEMS is achieved by structural optimization of device design and functional performance testing. This research contributes to the ongoing research in MEMS by evaluating the potential of using surface micromachining as a process for fabricating compliant micro-mechanisms.

The new trigger processor, the Silicon Vertex Tracking (SVT), has dramatically improved the B physics capabilities of the upgraded CDF II Detector; for the first time in a hadron collider, the SVT has enabled the access to non-lepton-triggered B meson decays. Within the new available range of decay modes, the B{sub s}{sup 0} {yields} D{sub s}{sup -}{pi}{sup +} signature is of paramount importance in the measurement of the {Delta}m{sub s} mixing frequency. The analysis reported here is a step towards the measurement of this frequency; two where our goals: carrying out the absolute calibration of the opposite side flavor taggers, used in the {Delta}m{sub s} measurement; and measuring the B{sub d}{sup 0} mixing frequency in a B {yields} D{pi} sample, establishing the feasibility of the mixing measurement in this sample whose decay-length is strongly biased by the selective SVT trigger. We analyze a total integrated luminosity of 355 pb{sup -1} collected with the CDF II Detector. By triggering on muons, using the conventional di-muon trigger; or displaced tracks, using the SVT trigger, we gather a sample rich in bottom and charm mesons.

The thesis presented here includes two parts. The first part discusses the production of endcap modules for the ATLAS SemiConductor Tracker at the University of Geneva. The ATLAS experiment is one of the two multi-purpose experiments being built at the LHC at CERN. The University of Geneva invested extensive efforts to create an excellent and efficient module production site, in which 655 endcap outer modules were constructed. The complexity and extreme requirements for 10 years of LHC operation with a high resolution, high efficiency, low noise tracking system resulted in an extremely careful, time consuming production and quality assurance of every single module. At design luminosity about 1000 particles will pass through the tracking system each 25 ns. In addition to requiring fast tracking techniques, the high particle flux causes significant radiation damage. Therefore, modules have to be constructed within tight and accurate mechanical and electrical specification. A description of the ATLAS experiment and the ATLAS Semiconductor tracker is presented, followed by a detailed overview of the module production at the University of Geneva. My personal contribution to the endcap module production at the University of Geneva was taking part, together with other physicists, in selecting components to be assembled …

The fundamental motivation for the research presented in this dissertation was the need to development a more accurate prediction method for characterization of mixed radiation fields around medical electron accelerators (MEAs). Specifically, a model is developed for simulation of neutron and other particle production from photonuclear reactions and incorporated in the Monte Carlo N-Particle (MCNP) radiation transport code. This extension of the capability within the MCNP code provides for the more accurate assessment of the mixed radiation fields. The Nuclear Theory and Applications group of the Los Alamos National Laboratory has recently provided first-of-a-kind evaluated photonuclear data for a select group of isotopes. These data provide the reaction probabilities as functions of incident photon energy with angular and energy distribution information for all reaction products. The availability of these data is the cornerstone of the new methodology for state-of-the-art mutually coupled photon-neutron transport simulations. The dissertation includes details of the model development and implementation necessary to use the new photonuclear data within MCNP simulations. A new data format has been developed to include tabular photonuclear data. Data are processed from the Evaluated Nuclear Data Format (ENDF) to the new class ''u'' A Compact ENDF (ACE) format using a standalone processing …

The main focus of this dissertation is the design, development, and ground and microgravity validation of methods for monitoring drinking water quality on-board NASA spacecraft using clorimetric-solid phase extraction (C-SPE). The Introduction will overview the need for in-flight water quality analysis and will detail some of the challenges associated with operations in the absence of gravity. The ability of C-SPE methods to meet these challenges will then be discussed, followed by a literature review on existing applications of C-SPE and similar techniques. Finally, a brief discussion of diffuse reflectance spectroscopy theory, which provides a means for analyte identification and quantification in C-SPE analyses, is presented. Following the Introduction, four research chapters are presented as separate manuscripts. Chapter 1 reports the results from microgravity testing of existing C-SPE methods and procedures aboard NASA's C-9 microgravity simulator. Chapter 2 discusses the development of a C-SPE method for determining the total concentration of biocidal silver (i.e., in both dissolved and colloidal forms) in water samples. Chapter 3 presents the first application of the C-SPE technique to the determination of an organic analyte (i.e., formaldehyde). Chapter 4, which is a departure from the main focus of the thesis, details the results of an investigation …

The Cryogenic Dark Matter Search (CDMS) uses cryogenically-cooled detectors made of germanium and silicon in an attempt to detect dark matter in the form of Weakly-Interacting Massive Particles (WIMPs). The expected interaction rate of these particles is on the order of 1/kg/day, far below the 200/kg/day expected rate of background interactions after passive shielding and an active cosmic ray muon veto. Our detectors are instrumented to make a simultaneous measurement of both the ionization energy and thermal energy deposited by the interaction of a particle with the crystal substrate. A comparison of these two quantities allows for the rejection of a background of electromagnetically-interacting particles at a level of better than 99.9%. The dominant remaining background at a depth of {approx} 11 m below the surface comes from fast neutrons produced by cosmic ray muons interacting in the rock surrounding the experiment. Contamination of our detectors by a beta emitter can add an unknown source of unrejected background. In the energy range of interest for a WIMP study, electrons will have a short penetration depth and preferentially interact near the surface. Some of the ionization signal can be lost to the charge contacts there and a decreased ionization signal relative …

The work presented herein describes a fundamental investigations of carbon as electrode material by using the pyrolysis of photoresist to create an optically transparent material. The development of these carbon-based optically transparent electrodes (C-OTEs) enables investigations of molecular interactions within the electrical double layer, processes that are central to a wide range of important phenomena, including the impact of changes in the surface charge density on adsorption. The electrochemical importance of carbon cannot be understated, having relevance to separations and detection by providing a wide potential window and low background current in addition to being low cost and light weight. The interactions that govern the processes at the carbon electrode surface has been studied extensively. A variety of publications from the laboratories of McCreery and Kinoshita provide in depth summaries about carbon and its many applications in electrochemistry. These studies reveal that defects, impurities, oxidation, and a variety of functional groups create adsorption sites on carbon surfaces with different characteristics. The interest in C-OTEs was sparked by the desire to study and understand the behavior of individual molecules at electrified interfaces. It draws on the earlier development of Electrochemically Modulated Liquid Chromatography (EMLC), which uses carbon as the stationary phase. …

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.

Photonic band gap (PBG) crystals are periodic dielectric structures that manipulate electromagnetic radiation in a manner similar to semiconductor devices manipulating electrons. Whereas a semiconductor material exhibits an electronic band gap in which electrons cannot exist, similarly, a photonic crystal containing a photonic band gap does not allow the propagation of specific frequencies of electromagnetic radiation. This phenomenon results from the destructive Bragg diffraction interference that a wave propagating at a specific frequency will experience because of the periodic change in dielectric permitivity. This gives rise to a variety of optical applications for improving the efficiency and effectiveness of opto-electronic devices. These applications are reviewed later. Several methods are currently used to fabricate photonic crystals, which are also discussed in detail. This research involves a layer-by-layer micro-transfer molding ({mu}TM) and stacking method to create three-dimensional FCC structures of epoxy or titania. The structures, once reduced significantly in size can be infiltrated with an organic gain media and stacked on a semiconductor to improve the efficiency of an electronically pumped light-emitting diode. Photonic band gap structures have been proven to effectively create a band gap for certain frequencies of electro-magnetic radiation in the microwave and near-infrared ranges. The objective of this …

Magnetic resonance is the most powerful analytical tool used by chemists today. Its applications range from determining structures of large biomolecules to imaging of human brains. Nevertheless, magnetic resonance remains a relatively young field, in which many techniques are currently being developed that have broad applications. In this dissertation, two new techniques are presented, one that enables the determination of torsion angles in solid-state peptides and proteins, and another that involves imaging of heterogenous materials at ultra-low magnetic fields. In addition, structural studies of the prion protein via solid-state NMR are described. More specifically, work is presented in which the dependence of chemical shifts on local molecular structure is used to predict chemical shift tensors in solid-state peptides with theoretical ab initio surfaces. These predictions are then used to determine the backbone dihedral angles in peptides. This method utilizes the theoretical chemicalshift tensors and experimentally determined chemical-shift anisotropies (CSAs) to predict the backbone and side chain torsion angles in alanine, leucine, and valine residues. Additionally, structural studies of prion protein fragments are described in which conformationally-dependent chemical-shift measurements were made to gain insight into the structural differences between the various conformational states of the prion protein. These studies are of …

The D0 detector has recently undergone a major upgrade to maximize its potential to fully exploit Run II at the Tevatron 2 TeV proton-antiproton collider. The upgrade includes a completely new central tracking system with an outer scintillating fiber tracker and an inner silicon vertex detector. This thesis describes the development of the software to ''unpack'' the raw data from the central tracking detectors into a useful form, and the development of the Level 3 trigger algorithms to cluster the hit information from these detectors. One of the many areas of physics that is being studied by the D0 experiment is the physics of B mesons, particularly that involving CP violation. The second part of the thesis details a constrained mass fitting tool written to aid the reconstruction of B particles, and a Monte Carlo study into measuring the lifetime of B{sup +} and B{sup 0} mesons. This thesis lays the foundations for the means by which physics is extracted from the vast amount of Tevatron data--the trigger--and illustrates how analyses will proceed through the key reconstruction of heavy quarks.

The D0 detector underwent a major upgrade to maximize its ability to fully exploit Run II at the Fermilab Tevatron, the world's highest energy collider. The upgrade included a completely new central tracking system with an outer scintillating fiber tracker and an inner silicon vertex detector all within a 2T superconducting solenoid. This thesis describes the development of high level trigger algorithms including vertexing, impact parameter significance and invariant mass, that utilize tracks from these detectors. One of the main physics goals of Run II is the observation of B{sub s} oscillations. This measurement, which cannot be performed at the B factories, will significantly constrain the ''unitarity triangle'' associated with Cp violation and so probe the Standard Model of particle physics. Furthermore this is an interesting measurement as the study of mixing in meson systems has a long history for revealing new physics. The second part of this thesis presents a study of the hadronic decay B{sub s} {yields} D{sub s}{pi}. This important mode provides the best proper time resolution for B{sub s} mixing and is reconstructed for the first time at D0. Projections on the sensitivity to B{sub s} oscillations are then presented.