Physical Sciences and Mathematics Commons^™

Three-Body Dynamics In Single Ionization Of Atomic Hydrogen By 75 Kev Proton Impact, Aaron C. Laforge

Doctoral Dissertations

"Doubly differential cross sections (DDCS) for single ionization of atomic hydrogen by 75 keV proton impact have been measured as a function of the projectile scattering angle and energy loss. This pure three-body collision system represents a fundamental test case for the study of the reaction dynamics in few-body systems. A comparison between theory and experiment reveals that three-body dynamics is important at all scattering angles, and that an accurate description of the role of the projectile-target nucleus interaction as well as the second order projectile-electron interaction remains a major challenge to theory. However, progress is being made in understanding …

Nmr Investigations Of Biomass-To-Fuel Conversions By Hydrothermal Processes, Wenjia Zhang

Doctoral Dissertations

"Biofuels have gained significant attention as the most promising alternative energy and fuel supply for the near future because of two dominant reasons: first, biofuels are environmentally friendly; and second, they afford a sustainable technology. Biofuels can be synthesized from biomass by several different processes, among which, hydrothermal conversion is considered to be more energy efficient. However, scientific efforts to improve hydrothermal biomass-to-fuel (HT-BTF) conversion efficiencies are severely limited because little is known about the salient reaction mechanisms and intermediates. This study is aimed at a better understanding of the hydrothermal biomass degradation kinetics by advanced NMR spectroscopy and, accordingly, …

Effect Of Structure And Plasticizer On The Glass Transition Of Adsorbed Polymer, Boonta Hetayothin

Doctoral Dissertations

"The effect of molecular mass on adsorbed poly(methyl methacrylate) (PMMA) on silica was determined using temperature-modulated differential scanning calorimetry (TMDSC). A two-component model, based on loosely-bound polymer (glass transition temperature, T_g, similar to that of bulk) and tightly-bound polymer (T_g higher than that of bulk) was used to interpret the thermograms. Similar amounts of tightly-bound polymer were found for 450 and 85 kDa PMMA (0.78 mg/m²), while the 32 kDa sample had a smaller amount (0.48mg/m²). A comparison of adsorbed PMMA, poly(vinyl acetate) (PVAc), and poly(methyl acrylate) (PMA) on silica was made using the same technique. The …

Computational Methods For The Discovery And Analysis Of Genes And Other Functional Dna Sequences, Cyriac Kandoth

Doctoral Dissertations

"The need for automating genome analysis is a result of the tremendous amount of genomic data. As of today, a high-throughput DNA sequencing machine can run millions of sequencing reactions in parallel, and it is becoming faster and cheaper to sequence the entire genome of an organism. Public databases containing genomic data are growing exponentially, and hence the rise in demand for intuitive automated methods of DNA analysis and subsequent gene identification. However, the complexity of gene organization makes automation a challenging task, and smart algorithm design and parallelization are necessary to perform accurate analyses in reasonable amounts of time. …

Haart Drugs Induce Oxidative Stress And Mitochondrial Dysfunction In Blood-Brain Barrier, Kalyan Reddy Manda

Doctoral Dissertations

"The era of highly active antiretroviral therapy (HAART) has controlled AIDS and its related disorders considerably; however, the prevalence of HIV-1-associated neurocognitive disorders (HAND) has been on the rise in the post-HAART era. In view of these developments, we investigated whether a HAART drug combination of 3'-Azido-2', 3'-deoxythymidine (AZT) and Indinavir (IDV) can alter the functionality of the blood-brain barrier (BBB) endothelial cells, thereby exacerbating the condition. Viability of hCMEC/D3 cells (in vitro model of BBB) that were exposed to the drugs was significantly reduced after a 72 hr treatment, in a dose-dependent manner. Reactive oxygen species (ROS) were highly …

Structure And Content Semantic Similarity Detection Of Extensible Markup Language Documents Using Keys, Waraporn Viyanon

Doctoral Dissertations

"XML (eXtensible Mark-up Language) has become the fundamental standard for efficient data management and exchange. Due to the widespread use of XML for describing and exchanging data on the web, XML-based comparison is central issues in database management and information retrieval. In fact, although many heterogeneous XML sources have similar content, they may be described using different tag names and structures. This work proposes a series of algorithms for detection of structural and content changes among XML data. The first is an algorithm called XDoI (XML Data Integration Based on Content and Structure Similarity Using Keys) that clusters XML documents …

Analysis And Occurrence Of Disinfection By-Products In Fresh And Salt Water, Honglan Shi

Doctoral Dissertations

"Haloacetic acids, trihalomethanes, and bromate are important toxic water disinfection by-products (DBPs) that the US Environmental Protection Agency (USEPA) regulates in drinking water. Iodoacetic acids and halonitromethanes (HNMs) are the unregulated emerging DBPs that have been recently found in the disinfected drinking waters, and which have much higher toxicity than the regulated DBPs. The purpose of this study was to develop new analytical methods for analysis of these emerging DBPs, to study their occurrence in Missouri drinking water systems, and to investigate the occurrence and formation of these DBPs in saltwater and seawater based marine park aquaria. A new rapid …

Weak Shear Study Of Galaxy Clusters By Simulated Gravitational Lensing, David Coss

Doctoral Dissertations

"Gravitational lensing has been simulated for numerical galaxy clusters in order to characterize the effects of substructure and shape variations of dark matter halos on the weak lensing properties of clusters. In order to analyze realistic galaxy clusters, 6 high-resolution Adaptive Refinement Tree N-body simulations of clusters with hydrodynamics are used, in addition to a simulation of one group undergoing a merger. For each cluster, the three-dimensional particle distribution is projected perpendicular to three orthogonal lines of sight, providing 21 projected mass density maps. The clusters have representative concentration and mass values for clusters in the concordance cosmology. Two gravitational …

Quantum 1/F Noise In Infrared Detectors And Scanning Tunneling Microscopes, Amanda Marie Truong

Doctoral Dissertations

"Noise is, by definition, any random and persistent disturbance, which interferes with the clarity of a signal. Modern electronic devices are designed to limit noise, and in most cases the classical forms of noise have been eliminated or greatly reduced through careful design. However, there is a fundamental, quite unavoidable type of noise, called quantum 1/f noise, which occurs at low frequencies and is a fundamental consequence of the discrete nature of the charge carriers themselves. This quantum 1/f noise is present in any physical cross section or process rate, such as carrier mobility, diffusion rates and scattering processes. Although …

Investigating The Source Of Thermal Anomalies In The Northern United Arab Emirates (Uae) Desert Using Geophysical Methods, Khalid Ahmad

Doctoral Dissertations

"We conducted geophysical surveys to investigate the source of thermal anomalies and to delineate any potential water transport pathways from the recharge zones in the Oman Mountains to the location of the temporal thermal anomalies within the desert plain of the United Arab Emirates (UAE). In the visible region of the spectrum of both ASTER and MODIS satellite images, the desert plain of the UAE appears as a bare sandy surface. However, detailed examination of these images in the thermal bands reveal cooler thermal anomalies within the desert plain following major rainfall events. This anomaly has a cooler surface of …

Theoretical Study Of Electron Impact-Ionization Of Molecules, Ola Al-Hagan

Doctoral Dissertations

"There has been impressive progress in the area of theoretical treatments of electron impact ionization (e,2e) of atoms and molecules in the last decade. Most recently, low to intermediate incident electron energies have been reported for molecular systems. In this dissertation, different theoretical models will be used to calculate the fully differential cross section (FDCS) for (e,2e) processes for low to intermediate incident electron energies for a variety of final state electron angles and energies for the diatomic molecules H₂ and N₂, the triatomic molecule H₂O, and the biomolecule HCOOH.

In addition, there has been a large amount of interest …

Protein Secondary Structure Prediction Using Blast And Relaxed Threshold Rule Induction From Coverings, Leong Lee

Doctoral Dissertations

"Protein structure prediction has always been an important research area in bioinformatics and biochemistry. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q₃ accuracy of various computational prediction methods rarely has exceeded 75%; this status has changed little since 2003 when Rost stated that "the currently best methods reach a level around 77% three-state per-residue accuracy." The application of artificial neural network methods to this problem is revolutionary in the sense that those techniques employ the homologues of proteins for training and prediction. In this dissertation, a different …

Chemical Bath Deposition And Electrodeposition Of Epitaxial Semiconductor Materials For Application In Photovoltaic Devices, Guojun Mu

Doctoral Dissertations

"This dissertation investigates the chemical bath deposition of zinc oxide and electrodeposition of cuprous iodide on polycrystalline and single crystal substrates. Paper I describes the chemical bath deposition and characterization of titled epitaxial zinc oxide nanospears on Si(001) single crystal substrate. In Paper II, the chemical bath deposition of zinc oxide nanospears from highly alkaline solutions is discussed in detail, including a thermodynamic calculation of saturation and speciation of Zn(II) in aqueous solution, and a kinetic study of the deposition process. In this paper the epitaxial zinc oxide is reported grown on Au(100), (110), and (111) single crystals. Paper III …

The Stereochemistry Of Selected Supramolecular Complexes Of Cucurbiturils And The Effect Of Homogeneous Equilibria And Electron Transfer Of The Guest, Arumugam Thangavel

Doctoral Dissertations

"From a practical perspective, host-guest complexes are vehicles for understanding and using supramolecular interactions for purposeful function in sensors, molecular machines and switches, while from a fundamental perspective they may lead to novel supramolecular protection schemes in basic organic reactions. This dissertation examines the interactions of cucurbiturils as barrel-shaped hosts, exhibiting a hydrophobic cavity, with substituted benzoylpyrydinium, phenypyrylium, and diazaanthraquinonediium cations as guests. In water, N-methyl-4-(p-substituted benzoyl)pyridinium cations exist in equilibrium with their hydrated forms (gem-diols), whose concentrations depend on the para substituent. In the presence of cucurbit7uril (CB[7]), the benzoyl group shows a preference for the CB[7] cavity, and …

Adsorption And Segmental Dynamics Of Acrylate And Methacrylate Polymers Adsorbed On A Silica Surface, Piyawan Krisanangkura

Doctoral Dissertations

"Poly(isopropyl acrylate)-d₇ (PIPA- d₇) was studied using ²H solid-state NMR and modulated differential scanning calorimetry (MDSC). The polymer was deuterated on the methyl groups and side-chain methine. The PIPA- d₇ was adsorbed onto Cab-O-Sil silica. These two types of deuterons each showed their own characteristic deuterium nuclear magnetic resonance (NMR) spectra for bulk PIPA- d₇. The ²H NMR spectra of adsorbed PIPA- d₇ samples showed the presence of heterogeneity of the segmental dynamics. A residual powder pattern was found in the spectra of the surface samples at higher temperatures, indicating that the segments were tightly attached to the silica. The …

Open Heavy Flavor Measurement At Forward Angles For Cu+Cu Collisions At Center Of Mass Nn Collision Energy 200 Gev, Irakli Garishvili

Doctoral Dissertations

The main purpose of Relativistic Heavy Ion Collider (RHIC) program is to study the Quark-Gluon Plasma (QGP), a deconfined state of matter believed to be created in ultra-relativistic heavy ion collisions. Heavy quarks, expected to be produced during the earlier stages of heavy ion collisions, serve as an important probe of the QGP.‎

‎The following dissertation presents measurements of single muons resulting from the semileptonic decay of heavy flavor quarks in the rapidity range of $1.4 < \vert\eta\vert < 1.9$ for Cu+Cu nuclei collisions at $\sqrt{s_{NN}}=200$ GeV measured by the PHENIX experiment. Single muon spectra were measured for three different centrality classes (0 - 20 \% , 20 - 40 \%, 40 - 94 \%) within the $p_{T}$ range of 1.0 - 4.0 GeV/c.‎

‎To calculate single muon spectra, a full background estimate was statistically subtracted from inclusive spectra of muon candidate tracks reconstructed in the PHENIX muon …

Beta-Decay, Beta-Delayed Neutron Emission And Isomer Studies Around 78Ni, Mustafa Moiz Rajabali

Doctoral Dissertations

A study of nuclei with few nucleons outside the closed shell provides benchmarks for the nuclear shell model especially in this modern era of physics where exotic doubly magic nuclei can be tested. The subject of this thesis is to experimentally investigate the properties of nuclei near ⁷⁸Ni and to confront them with the predictions of modern large scale shell model calculations. In this regard, an experiment was performed at the National Superconducting Cyclotron Laboratory (NSCL) to measure excited states in ^71-73Ni populated via the beta-decay of ^71-73Co. Data collected from this experiment lead to partial level …

Controlled Self-Organization And Tunable Collective Phenomena In Surface-Based Nanostructures, Eun Ju Moon

Doctoral Dissertations

Nanostructure systems possessing certain desirable features can arise from the self-organization of fundamental building blocks. In this thesis we explore two types of controlled self-assembly mechanisms in hetero-epitaxy: (a) classical assembly of atom vacancies into quasi one-dimensional line structures and (b) quantum-driven assembly of atoms into atomically-smooth two-dimensional thin films. In the classical assembly phenomenon, adatom vacancies, created via elastic strain-relaxation in compressively strained atom chains on a silicon substrate, self-organize into meandering vacancy lines. The average spacing between these line defects can be varied by adjusting the chemical potential μ of the adsorbed atoms. We implemented a lattice model …

Biological Simulations And Biologically Inspired Adaptive Systems, Edgar Alfredo Duenez-Guzman

Doctoral Dissertations

Many of the most challenging problems in modern science lie at the interface of several fields. To study these problems, there is a pressing need for trans-disciplinary research incorporating computational and mathematical models. This dissertation presents a selection of new computational and mathematical techniques applied to biological simulations and problem solving: (i) The dynamics of alliance formation in primates are studied using a continuous time individual-based model. It is observed that increasing the cognitive abilities of individuals stabilizes alliances in a phase transition-like manner. Moreover, with strong cultural transmission an egalitarian regime is established in a few generations. (ii) A …

Physical Adsorption Of Ethylene On Mgo(100): Effects Of Substrate Ionicity And Symmetry On Wetting, Andi Barbour

Doctoral Dissertations

The wetting behavior of ethylene adsorbed on MgO(100) was investigated from 83{ 135 K using high resolution volumetric adsorption isotherms. Layering transitions for ethylene on MgO(100) are observed below the bulk triple point at 79.2 K and 98.4 K, respectively. From these isotherms, thermodynamic quantities associated with physical adsorption are determined. It was found that the average area occupied by ethylene on MgO(100) is around 22.6 squared angstroms per molecule. Using the two dimensional isothermal compressibility, the location of two potential phase transitions are identified at 108.6 K and 116.5 K for the first and second layer, respectively. The potential …

Sequence-Based Specification Of Embedded Systems, Jason Martin Carter

Doctoral Dissertations

Software has become integral to the control mechanism of modern devices. From transportation and medicine to entertainment and recreation, embedded systems integrate fundamentally with time and the physical world to impact our lives; therefore, product dependability and safety are of paramount importance.

Model-based design has evolved as an effective way to prototype systems and to analyze system function through simulation. This process mitigates the problems and risks associated with embedding software into consumer and industrial products. However, the most difficult tasks remain: Getting the requirements right and reducing them to precise specifications for development, and providing compelling evidence that the …

Studies Of Tungsten Alkyl Alkylidyne Compounds And Iron Porphyrin Derivatives, Brenda Ann Dougan

Doctoral Dissertations

This dissertation focuses on two research projects. The first project examines the reactions of tungsten(VI) alkyl alkylidyne and bis-alkylidene complexes with phosphines and water and the studies of thermodynamics and kinetics of the reactions. These studies have been conducted in part to determine the mechanistic pathway in the formation of novel tungsten(VI) species. The second portion of this dissertation focuses on the spin density and structures of biomimetic Fe(III) porphyrin derivatives using neutron and X-ray diffraction techniques. The spin density and magnetic properties of an Fe(III) porphyrin derivative has been determined by polarized neutron diffraction.

In the first portion of …

The Design And Synthesis Of Biotinylated Tylophorine Analogues For Use As Affinity Probes In The Elucidation Of The Cellular Targets Of Dcb-3503, Samson Francis

Doctoral Dissertations

The tylophorine analogue, DCB-3503 (1-62b, NSC-716802), has been found to exhibit broad spectrum activity in vitro in the National Cancer Institute’s (NCI) panel of 60 human-derived cell lines. Recent studies involving HepG2, a human hepatocellular carcinoma cell line, and two pancreatic ductal carcinoma cell lines (PANC-1 and HPAC), have suggested that DCB-3503 (1-62b) exerts its unique growth inhibition properties by modulating nuclear factor kappa B activity as well as through the inhibition of nuclear protein synthesis. However, the physiologically relevant protein binding partner(s) of DCB-3503 (1-62b) have not been identified. Herein, the design and …

Synthesis And Characterization Of Branched Polyelectrolytes: Star-Branched Napss, Daniel W. Holley

Doctoral Dissertations

In this thesis, we examined the effect of branching on the solution characteristics of polyelectrolytes using a set of star-branched NaPSS. The polystyrene precursors to these polyelectrolytes were synthesized using anionic polymerization allowing for the production of three distinct groups of star-branched polystyrenes with varying functionality and arm length.

Following sulfonation, several methods commonly employed in the literature for evaluation of sulfonation degree we established that sulfonation was quantitative. TGA was also demonstrated to reveal important characteristics of the sample.

We used aqueous SEC coupled with a multiple angle light scattering detector to determine several molecular characteristics of the star-branched …

Design And Synthesis Of Novel Tylophorine Analogs And Their Biological Activity, Julio Gutierrez

Doctoral Dissertations

Alkaloids containing the nitrogen atom in the bridgehead position of two rings, such as indolizidine, pyrrolizidine, and quinolizidine alkaloids, have a wide and varied distribution in nature. Some of these alkaloids demonstrate a broad range of pharmacological activities and have generated substantial synthetic interest. This thesis covers the total synthesis of novel tylophorine analogs called DCB 3503, DCB 3506, DCB 3507, DCB 3508, DCB 3509, and a derivative with a biotinylated chain attached to DCB 3506 for use as a biological probe. This thesis discusses the biological activity of these compounds as well.

Deciphering Climate From The Characterization Of Ring Width, Carbon, And Oxygen Isotopes In Latewood Tree-Ring Cellulose, Big Thicket National Preserve, Texas, Usa, Daniel Bruce Lewis

Doctoral Dissertations

Trees are excellent archives of paleoclimatic information. They can preserve records of past temperature, precipitation, drought, and extreme weather events. The focus of this dissertation is to use tree ring width, carbon isotopes, oxygen isotopes from multiple trees to characterize climate variability and the tree-ring tropical cyclone record. Living longleaf pine trees (Pinus palustris Mill.) were sampled from the Turkey Creek and Big Sandy Creek Units at Big Thicket National Preserve, Texas. Annual tree rings were measured and assigned yearly calendar dates. The latewood portion of each annual ring was shaved with a scalpel, and alpha-cellulose was extracted for …

Development And Implementation Of A New Technique To Study (P,Α) Reactions Relevant To Nucleosynthesis In Binary Systems, Brian Hossain Moazen

Doctoral Dissertations

The accurate determination of the strengths and energies of resonances in (p,alpha) reactions is important for understanding the influence of reaction cycles to element synthesis in many astrophysical environments. Thus far, (p,alpha) studies in inverse kinematics have employed solid polypropylene targets. These are not always advantageous, especially when the energy loss of the incoming beam in the solid target is significantly larger than the resonance width. At the Holifield Radioactive Ion Beam Facility, a new technique has been developed for measuring the strengths and energies of (p,alpha) reactions. In this technique, a large differentially-pumped scattering chamber is filled with hydrogen …

Static And Dynamic Scheduling For Effective Use Of Multicore Systems, Fengguang Song

Doctoral Dissertations

Multicore systems have increasingly gained importance in high performance computers. Compared to the traditional microarchitectures, multicore architectures have a simpler design, higher performance-to-area ratio, and improved power efficiency. Although the multicore architecture has various advantages, traditional parallel programming techniques do not apply to the new architecture efficiently. This dissertation addresses how to determine optimized thread schedules to improve data reuse on shared-memory multicore systems and how to seek a scalable solution to designing parallel software on both shared-memory and distributed-memory multicore systems.

We propose an analytical cache model to predict the number of cache misses on the time-sharing L2 cache …

Computational Exploration Of The Interaction Of Molecular Hydrogen With An Anionic Hydrogen Atom, Patrick Karl Moehlen

Doctoral Dissertations

The focus of this dissertation is to facilitate the computation of the infrared absorption line shape of solid para-hydrogen with an anionic hydrogen atom dopant. For this, we compute the complete potential energy surface for the interaction of H¯ with H². The coupled cluster with singles, doubles, and perturbative treatment of triple excitations method was used with augmented correlationconsistent polarized valence triple-zeta atom-centered basis sets and a set of bonding functions.

The focus then turns to describing the rovibrational Hamiltonian of the system with the coupledchannel method. We find bound and quasi-bound stationary states of the system for …

Wide-Range Characterization Of Current Conduction In Superconductors-Tuning Their Properties By Nanoscale Modification Of Materials, Özgür Polat

Doctoral Dissertations

Significant progress has been made in the development of YBa₂Cu₃O_7-x (YBCO)-based coated conductors (CCs) since the discovery of YBCO in 1987. Nowadays, high temperature superconductor (HTS) materials are advancing toward wide application areas in medical physics, industry, and science. The successful applications of these materials require clear understanding of the mechanisms controlling the current carrying capacity. It has been demonstrated the maximum current that a HTS can support is strongly affected by the vortex dynamics within the HTS materials. In this dissertation, we employed a combination of methods: conventional transport, magnetometry in a swept magnetic …