Physical Sciences and Mathematics Commons^™

Exploring Computational Chemistry On Emerging Architectures, David Dewayne Jenkins

Doctoral Dissertations

Emerging architectures, such as next generation microprocessors, graphics processing units, and Intel MIC cards, are being used with increased popularity in high performance computing. Each of these architectures has advantages over previous generations of architectures including performance, programmability, and power efficiency. With the ever-increasing performance of these architectures, scientific computing applications are able to attack larger, more complicated problems. However, since applications perform differently on each of the architectures, it is difficult to determine the best tool for the job. This dissertation makes the following contributions to computer engineering and computational science. First, this work implements the computational chemistry variational …

Confinement Effects Of Solvation On A Molecule Physisorbed On A Metal Particle, Jacob Fosso Tande

Doctoral Dissertations

We describe and present results of the implementation of the surface and volume polarization for electrostatics~(SVPE) and the iso-density surface solvation models. Unlike most other implementation of the solvation models where the solute and the solvent are described with multiple numerical representation, our implementation uses a multiresolution, adaptive multiwavelet basis to describe both solute and the solvent. This requires reformulation to use integral equations throughout as well as a conscious management of numerical properties of the basis.

Likewise, we investigate the effects of solvation on the static properties of a molecule physisorbed on a spherical particle, modeled as a polarizable …

Parallel For Loops On Heterogeneous Resources, Frederick Edward Weber

Doctoral Dissertations

In recent years, Graphics Processing Units (GPUs) have piqued the interest of researchers in scientific computing. Their immense floating point throughput and massive parallelism make them ideal for not just graphical applications, but many general algorithms as well. Load balancing applications and taking advantage of all computational resources in a machine is a difficult challenge, especially when the resources are heterogeneous. This dissertation presents the clUtil library, which vastly simplifies developing OpenCL applications for heterogeneous systems. The core focus of this dissertation lies in clUtil's ParallelFor construct and our novel PINA scheduler which can efficiently load balance work onto multiple …

Growth And Characterization Of Hexagonal Lu-Fe-O Multiferroic Thin Films, Wenbin Wang

Doctoral Dissertations

In the quest for new types of information processing and storage, complex oxides stand out as one of the most promising material classes. The multiple functionalities of complex oxides naturally arise from the delicate energy balance between the various forms of order (structural, electronic, magnetic). In particular, multiferroic and magnetoelectric oxides which simultaneously exhibit more than one type of ferroic orders have many advantages over existing materials. Widespread practical applications will require a single-phase multiferroic material with a transition temperature that lies considerably above room temperature, large electric and magnetic polarizations, and strong coupling between ferroic orders.

Recently, multiferroic LuFe …

Dynamic Task Execution On Shared And Distributed Memory Architectures, Asim Yarkhan

Doctoral Dissertations

Multicore architectures with high core counts have come to dominate the world of high performance computing, from shared memory machines to the largest distributed memory clusters. The multicore route to increased performance has a simpler design and better power efficiency than the traditional approach of increasing processor frequencies. But, standard programming techniques are not well adapted to this change in computer architecture design.

In this work, we study the use of dynamic runtime environments executing data driven applications as a solution to programming multicore architectures. The goals of our runtime environments are productivity, scalability and performance. We demonstrate productivity by …

Towards A Unification Of Supercomputing, Molecular Dynamics Simulation And Experimental Neutron And X-Ray Scattering Techniques, Benjamin Lindner

Doctoral Dissertations

Molecular dynamics simulation has become an essential tool for scientific discovery and investigation. The ability to evaluate every atomic coordinate for each time instant sets it apart from other methodologies, which can only access experimental observables as an outcome of the atomic coordinates. Here, the utility of molecular dynamics is illustrated by investigating the structure and dynamics of fundamental models of cellulose fibers. For that, a highly parallel code has been developed to compute static and dynamical scattering functions efficiently on modern supercomputing architectures. Using state of the art supercomputing facilities, molecular dynamics code and parallelization strategies, this work also …

Boron And Metal Catalyzed C-C And C-H Bond Formation, Adam Barret Pippin

Doctoral Dissertations

Research efforts focused on the use of boron and metals to form new carbon-carbon and carbon-hydrogen bonds are summarized in this dissertation. Several novel reactions have been developed. These include: the deoxygenation of benzylic alcohols using chloroboranes; alkenylation of benzylic alcohols using boron trichloride; and dialkynlation of aryl aldehydes using dialkynylboron chloride. Numerous applications of these novel reactions have been developed. These include alternate routes to diphenylmethanes and 1,4-diynes from easily prepared dialkynylboron chlorides. In addition, E and Z alkenyl halides can now be prepared using boron trichloride without the use of butyllithium. The stereochemistry of the alkenyl halide can …

Synthesis, Evaluation And Applications Of Biologically Significant Molecules And Their Analogues, Sneha Ashesh Belapure

Doctoral Dissertations

Synthetic chemists are always looking for challenging problems to solve. Design and synthesis of novel molecules that can act as agents of chemical and biological modification are one of the foremost goals of a synthetic chemist. This dissertation describes advances and efforts made in this area.

Obesity is one of the critical problems of the modern age. Molecules that can remediate this condition are highly sought after. The first chapter of this dissertation describes synthetic strategies explored to prepare these valuable natural products along with their structural and stereochemical analogues to study structure and activity relationships (SAR). This method gives …

Structure And Dynamics Of High Temperature Superconductors, Jennifer Lynn Niedziela

Doctoral Dissertations

High temperature superconductivity in iron based compounds has presented a series of complex problems to condensed matter physics since being discovered in 2008. The stalwart basis of condensed matter physics is the “strength in numbers" aspect of crystalline periodicity. Perfect crystalline periodicity has made possible the reduction of the questions of structural and electronic properties to single dimensions, increasing the tractability of these problems. Nevertheless, modern complex materials stretch these assumptions to their limits, and it is at this point where our work starts. Using neutron and x-ray scattering, we have conducted a series of studies on the structural disorder …

Development Of A Novel Technique For Predicting Tumor Response In Adaptive Radiation Therapy, Rebecca Marie Seibert

Doctoral Dissertations

This dissertation concentrates on the introduction of Predictive Adaptive Radiation Therapy (PART) as a potential method to improve cancer treatment. PART is a novel technique that utilizes volumetric image-guided radiation therapy treatment (IGRT) data to actively predict the tumor response to therapy and estimate clinical outcomes during the course of treatment. To implement PART, a patient database containing IGRT image data for 40 lesions obtained from patients who were imaged and treated with helical tomotherapy was constructed. The data was then modeled using locally weighted regression. This model predicts future tumor volumes and masses and the associated confidence intervals based …

A Study Of Cellular Calcium Dynamics In Culture Using Fluorescence Microscopy – A Statistical And Mathematical Approach, Richard Adekola Idowu

Doctoral Dissertations

Calcium in its ionic form is very dynamic, especially in excitable cells such as muscle and brain cells, moving from the high concentration exterior of the cell to much lower concentrations inside the cell, where calcium is used as a second messenger. In brain cells, and neurons especially, calcium is a key signaling ion involved in memory and learning with excitatory neurotransmitters such as glutamate turning neurons "on." Glutamate excites the neurons in part by causing large and dynamic changes in the intracellular calcium concentration. While these dynamics are essential for normal signaling in the brain, excessive and sustained elevations …

Adaptive Grid Based Localized Learning For Multidimensional Data, Sheetal Saini

Doctoral Dissertations

Rapid advances in data-rich domains of science, technology, and business has amplified the computational challenges of "Big Data" synthesis necessary to slow the widening gap between the rate at which the data is being collected and analyzed for knowledge. This has led to the renewed need for efficient and accurate algorithms, framework, and algorithmic mechanisms essential for knowledge discovery, especially in the domains of clustering, classification, dimensionality reduction, feature ranking, and feature selection. However, data mining algorithms are frequently challenged by the sparseness due to the high dimensionality of the datasets in such domains which is particularly detrimental to the …

A Novel Microfluidic Enrichment Technique For Carbonylated Proteins, Bryant C. Hollins

Doctoral Dissertations

Proteins are the building blocks of cells in living organisms, and are composed of amino acids. The expression of proteins is regulated by the processes of transcription and translation. Proteins undergo post-translational modifications in order to dictate their role physiologically within a cell.

Not all post-translational modifications are beneficial for the protein or the cell. One type of post-translational modification, called carbonylation, irreversibly places a carbonyl group onto an amino acid residue, most commonly proline, lysine, arginine, and threonine. This modification can have severe consequences physiologically, including loss of solubility, loss of function, and protein aggregation.

Carbonylated proteins have commonly …

Ads/Cft In String Theory And M-Theory, Daniel R. Gulotta '03

Doctoral Dissertations

The AdS/CFT correspondence is a powerful tool that can help shed light on the relationship between geometry and field theory.

The first part of this thesis will focus on the construction of theories dual to Type IIB string theory on AdS₅ x Y⁵, where Y⁵ is a toric Sasaki-Einstein manifold. This thesis will introduce a consistency condition called "proper ordering" and demonstrate that it is equivalent to several other previously known consistency conditions. It will then give an efficient algorithm that produces a consistent field theory for any toric Sasaki-Einstein Y⁵.

The second part …

Understanding The Thermodynamic Behavior Of Nanoparticles To Tailor Polymer Nancomposite Structure, Mary Catherine Mutz

Doctoral Dissertations

The work presented in this dissertation is an attempt to understand the entropic and enthalpic forces that govern the dispersion and dissolution of nanoparticles in solutions and in thin polymer films with the end-goal of producing highly tailored products.

In the first part, neutron reflectivity was used to study the impact of nanoparticle presence on the surface segregation of deuterated polystyrene (dPS) in a polystyrene matrix. The impact of the presence of cylinders (carbon nanotubes), sheets (graphene), and spheres (polystyrene soft nanoparticles) on the surface segregation process and ultimate structure were examined. Experimental data indicate that the presence of the …

Formation And Alteration Of Basaltic Soils On Mars, Ian Oliver Mcglynn

Doctoral Dissertations

The current surface of Mars is an arid inhospitable environment, dominated by aeolian processes, composed of largely volcanic rocks that have little apparent indication of pervasive aqueous chemical weathering, and blanketed by dust. Rocks are composed of basalts and the “soil” sediments appear to be largely basaltic-derived, and are chemically similar on a global scale. If the climate was once warmer and wetter during the Noachian period, with environmental conditions favorable to the development of life, physically weathered remnants, such as large quantities of phyllosilicate minerals, should remain. Basaltic soils provide a crucial constraint on chemical and physical weathering processes, …

Development And Application Of Synthetic Lipid Probes To Study And Mimic Lipid Function, Heidi Elizabeth Bostic

Doctoral Dissertations

Lipids are biologically important molecules as they regulate a litany of key cellular processes that, when aberrant, result in disease. Since lipids control these regulation pathways, it is imperative to understand their properties and exploit them for use in advancing therapeutic strategies. The complex environments in which lipids exist have historically complicated their understanding, but recent advancements have facilitated this effort. In the chapters that follow, we have used synthetic lipid probes to investigate the role of signaling lipids as site-specific ligands in the binding of protein effectors and developed a high-throughput platform that can be used to rapidly classify …

Magnetic Excitations In The Iron Based Superconductors, Leland Weldon Harriger

Doctoral Dissertations

Presented within are neutron scattering studies detailing the spin dynamics of BaNi$_{x}$Fe$_{2-x}$As$_{2}$ for x = 0 (parent), 0.04 (underdoped), and 0.1 (optimal) dopings, and FeSe$_{x}$Te$_{1-x}$ for x = 0 (parent), 0.3 (underdoped), and 0.4 (optimal) dopings. These recently discovered Fe-based superconducting compounds are strikingly similar, in many respects, to the cuprate class of unconventional superconductors and share qualitatively similar phase diagrams consisting of a long range ordered magnetic ground state in the parents which, upon doping, is supplanted in favor of superconductivity. The dopings discussed herein allow us to tune through the phase diagram, beginning with long range ordered parents …

Select Reactions Of Organoboranes And Organostannanes, David W. Blevins

Doctoral Dissertations

Potassium aryl- and alkenyltrifluoroborates and tributyl(aryl)stannanes were found to undergo halodemetallation using trihalide salts. The hydrolysis of organotrifluoroborates was observed to be promoted by iron(III) chloride, zinc dust, and zinc oxide. A variety of potassium aryltrifluoroborates and an alkenyltrifluoroborate were found to undergo bromodeboronation at room temperature in a (1:1) THF/water solution in 30-40 minutes using pyridinium tribromide, providing good yields of aryl and vinyl bromides. Activated arenes underwent dibromination, but this was reduced by adding potassium bromide to the reaction. Potassium aryltrifluoroborates and an alkenyltrifluoroborate were observed to undergo iododeboronation in a (1:2) DMF/water solution at 80 degrees Celsius …

Sketchmate: A Computer-Aided Sketching And Simulation Tool For Teaching Graph Algorithms, Kristy Sue Van Hornweder

Doctoral Dissertations

In this dissertation, we developed and tested a sketching, visualization, and simulation tool called Sketchmate for demonstrating graph algorithms commonly taught in undergraduate computer science courses. For this research, we chose to focus on shortest path and network flow algorithms. Two versions of this tool have been implemented: 1) an instructor tool that supports computer-aided manual simulations of algorithms that augment traditional whiteboard presentations, allowing lectures to be more dynamic and interactive, and 2) a student tool that supports computer-aided manual practice of algorithms that enables students to work through homework problems more quickly while providing detailed incremental feedback about …

Study Of Local Structure, Stress And Dynamics In Disordered Materials Using Ab-Initio And Molecular Dynamics Simulation, Madhusudan Ojha

Doctoral Dissertations

Understanding the atomic structure and dynamics in structurally disordered systems has been a long-standing and most challenging problem in physics and material science. To begin with, it is difficult to describe disorder quantitatively and to differentiate the degree of disorder from one system to another. The majorities of experimental and theoretical approaches to the study of disordered systems are either transferred directly from the study of crystals or address the problem in the macroscopic scale where the atomic origin of behavior is obscured. First principle atomic level stresses and dynamic pair distribution functions described in this dissertation represent attempts to …

Novel Single-Site Titanosilicates With Targeted Connectivity And Nuclearity Of Titanium(Iv): Synthesis, Characterization And Catalytic Properties In Alkylphenol Oxidation, Nan Chen

Doctoral Dissertations

Titanosilicates are a family of porous materials that have shown excellent catalytic activity in olefin epoxidation and many other selective oxidation reactions. These materials have been extensively studied in the past few decades. One of the central questions in these investigations has been to define the catalytically active centers. The traditional synthesis of wet impregnation followed by calcination often produces more than one type of catalytic center within the same matrix, i.e. different coordination, connectivity and nuclearity. Each type potentially possesses unique catalytic activity. Co-existence of multiple catalytic centers makes it impossible to establish the relationship between the structure of …

Surface Structuring Strategies For Micro-Cantilever Sensing Platforms And Applications For Hydrogen Related Issues, James F. Patton

Doctoral Dissertations

Recent developments in microelectro-mechanical systems have enabled the exploration of transduction modes that involve mechanical energy and are based primarily on mechanical phenomena. As a result an innovative family of chemical and biological sensors has emerged which utilize a transducer in the form of microcantilevers (MCs). MCs offer greater sensitivity than comparable mass-responding sensors due in large part to their small dimension. These low cost devices can be deployed for remote testing, providing real-time information for the analyst. An additional advantage is the ability to employ MCs in an arrayed fashion adding a unique selectivity not available to many sensing …

New Approaches To Electroanalysis Of Metals And Pretreatment Of Biological And Environmental Samples, Stefanie Bragg

Doctoral Dissertations

Biological and environmental sample pretreatment followed by electrochemical sensing are the focus of this dissertation. The Advanced Oxidation Process (AOP) treatment using aqueous hydrogen peroxide and UV irradiation with acid deactivation of the enzyme catalase in blood has been developed and optimized. The kinetics of whole blood AOP in a single-cell reactor was studied, and the effect of pH on the AOP process has been investigated. A new method of dry ashing whole blood has been developed and optimized for trace metal analyses. The new method and subsequent metal analyses in the blood samples has been used to confirm results …

Secondary Light Particle Data Base Development Using A Thermodynamic Coalescence Model, Mahmoud Pourarsalan

Doctoral Dissertations

ABSTRACT

As heavy ions are transported through shielding and interact with shielding materials accurate values of total, elastic scattering, reactions cross sections and angular distributions of the emitted nucleons, light high energy particles such as deuteron, triton, helion, alpha particles and other heavy ions are required in order to design appropriate and adequate shielding to protect the human crews and instruments from ionizing radiations during long duration space missions. Double-differential (energy and angle) light energetic particle production cross sections must be known for ion energies from tens of MeV/nucleon to tens of GeV/nucleon for all emitted light energetic particles for …

Iron Pnictides: Superconductivity In Multi-Orbital Systems, Andrew David Nicholson

Doctoral Dissertations

This work focuses on the development and implementation of microscopic models as well as their numerical and analytical study to elucidate the properties of the iron pnictides. There are many first principle and phenomenological studies of these materials, but there is a need for unbiased numerical calculations following an approach similar to the one used in the study of the Hubbard and t-J models for the cuprates.

First a two orbital model for the pnictides, focusing on two hybridized Fe-d orbitals (dxz and dyz) is formulated, including hoppings between nearest and next nearest neighbors as well as on site Coulomb …

Microscopic Description Of Nuclear Fission At Finite Temperature, Jordan David Mcdonnell

Doctoral Dissertations

While a predictive, microscopic theory of nuclear fission has been elusive, advances in computational techniques and in our understanding of nuclear structure are allowing us to make significant progress. Through nuclear energy density functional theory, we study the fission of thorium and uranium isotopes in detail. These nuclides have been thought to possess hyperdeformed isomers in the third minima of their potential energy surfaces, but microscopic theories tend to estimate either shallow or non- existent third minima in these nuclei. We seek an explanation in terms of neutron shell effects. We study how the fission pathways, the symmetry, and the …

Synthesis And Temperature-Induced Phase Transfer Behavior Of Thermosensitive Hairy Particles Between Aqueous Solution And A Hydrophobic Ionic Liquid, Jonathan Michael Horton

Doctoral Dissertations

This dissertation presents the synthesis of a family of thermosensitive polymer brush-grafted silica particles and the study of their thermally induced phase transfer behavior between water and a hydrophobic ionic liquid, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide ([EMIM][TFSA]). The hairy particles were prepared by surface-initiated atom transfer radical polymerization.

Chapter 1 describes the synthesis and phase transfer behavior of a series of 205 nm silica particles grafted with thermosensitive polymers of methoxyoligo(ethylene glycol) methacrylates. The hairy particles with sufficiently high lower critical solution temperatures underwent reversible and quantitative transfer between water and [EMIM][TFSA] in response to temperature changes. The transfer temperature (T_{tr …}

Synthesis And Characterization Of Functionalized Nanomaterials: Heterogeneous Palladium Catalyst And Lithium-Doped Graphene Oxide, Benjamin E Estes

Doctoral Dissertations

As the Earth's population increases and natural resources decrease in supply, the development of new methods for energy storage and the efficient production of industrial chemicals becomes ever more important to humanity. The development of new nanomaterials may offer technological advances in the fields of sustainable energy production and storage, chemical production, medicine, and many others. The emerging field of nanoscience blends chemistry, physics, and engineering to create new materials that take advantage of properties found only on the nanoscale.

In this work, mesoporous silica spheres are used as a support for nanoparticles of palladium. This nanomaterial is shown to …

The Role Of Non-Bonding Interactions And Bonding Schemes In The Structure And Properties Of Multi-Component Polymer Systems, Caleb Will Dyer

Doctoral Dissertations

This dissertation addresses three aspects of multi-component polymer systems. Chapter 2 details work on understanding the effect of precise polymeric structure on the phase behavior of blends containing cellulose acetate chains with different levels of acetate substitution. The difference in degree substitution (Delta DS) between the two components in the blend is systematically changed from .06 to .63, where each blend is found to be partially miscible. The samples containing higher acetate content demonstrate decreased miscibility as Delta DS increases. The sample with the most hydroxyl groups, however, has greater miscibility than samples of similar Delta DS, but fewer hydroxyl …