Physical Sciences and Mathematics Commons^™

Reactive Molecular Dynamics Of Large Systems: Quantum Dynamics With Adaptable Gaussian Bases; Hydroxide Diffusion In A Polymeric Environment, Mohottige Sachith Prasanga Wickramasinghe

Theses and Dissertations

This dissertation describes our research in theory and applications of reactive molecular dynamics. Quantum dynamics provides the foundation for understanding chemical processes. However, the computational cost of describing a general quantum system scales exponentially with the system size. Thus, an efficient basis representation of wavefunctions is essential. Time-dependent Gaussian bases are often employed to describe the large-amplitude motion of high-dimensional systems. The time dependence of such bases is typically determined by (i) the variational principle or by (ii) classical dynamics. But those approaches have shortcomings due to intrinsic singularity of the variational equations in the full basis limit or due …

Phylogenetic Reconstruction Analysis On Gene Order And Copy Number Variation, Ruofan Xia

Theses and Dissertations

Genome rearrangement is known as one of the main evolutionary mechanisms on the genomic level. Phylogenetic analysis based on rearrangement played a crucial role in biological research in the past decades, especially with the increasing avail- ability of fully sequenced genomes. In general, phylogenetic analysis aims to solve two problems: Small Parsimony Problem (SPP) and Big Parsimony Problem (BPP). Maximum parsimony is a popular approach for SPP and BPP which relies on itera- tively solving a NP-hard problem, the median problem. As a result, current median solvers and phylogenetic inference methods based on the median problem all face se- rious …

Disinfection By-Products: Method Optimization For Quantification, Unknown Analysis, And Calculated Toxicity, Amy A. Cuthbertson

Theses and Dissertations

Disinfected drinking water contains hundreds of disinfection by-products (DBPs) that are formed by the reaction of disinfectants with natural and anthropogenic organic matter, bromide, and iodide. Understanding what these DBPs are is important because millions of people worldwide consume drinking water every day, and human epidemiologic studies have reported cancer, miscarriage, and birth defects from consuming such waters. While more than 700 DBPs are reported in the literature, very few studies quantify complete classes of chlorinated, brominated, and iodinated DBPs. The following document contains five chapters in the format designated for specific scientific journals on this subject. Chapter 1 describes …

Spatio-Temporal Analysis Of Precipitation And Flood Data From South Carolina, Haigang Liu

Theses and Dissertations

Spatio-temporal data are everywhere: we encounter them on TV, in newspapers, on computer screens, on tablets, and on plain paper maps. As a result, researchers in di- verse areas are increasingly faced with the task of modeling geographically-referenced and temporally-correlated data. In this dissertation, we propose two different spa- tiotemporal models to capture the behavior of rainfall and flood data in the state of South Carolina.

Both models are built using a Bayesian hierarchical framework, which involves specifying the true underlying process in the first level and the spatio-temporal ran- dom effect in the second level of the hierarchy. The …

An Instruction Embedding Model For Binary Code Analysis, Kimberly Michelle Redmond

Theses and Dissertations

Binary code analysis is important for understanding programs without access to the original source code, which is common with proprietary software. Analyzing binaries can be challenging given their high variability: due to growth in tech manufactur- ers, source code is now frequently compiled for multiple instruction set architectures (ISAs); however, there is no formal dictionary that translates between their assem- bly languages. The difficulty of analysis is further compounded by different compiler optimizations and obfuscated malware signatures. Such minutiae means that some vulnerabilities may only be detectable on a fine-grained level. Recent strides in ma- chine learning—particularly in Natural Language …

Instrumentation For, And Application Of, Novel Electrochemical Tools For In Vivo Analysis Of Neurotransmitters In The Context Of Psychiatric Disease, Rhiannon Robke

Theses and Dissertations

ABSTRACTSerotonin’s involvement in many physiological processes including anxiety, stress, compulsivity, and mood has been speculated for decades. Insufficient progress in our understanding of serotonin chemistry is due to the lack of effective tools to selectively measure this neurotransmitter on a neurotransmission-relevant time scale in vivo. An analytical technique for serotonin measurements, fast-scan cyclic voltammetry (FSCV), was pioneered in the last decade in anesthetized rodents and is beginning to shed light on the complexity of serotonergic activity on a sub-second timescale. Complementary, more recent technological innovations have enabled ambient neurotransmitter levels to be determined every few seconds using a method called …

Analysis Of Artificial Neural Networks In The Diagnosing Of Breast Cancer Using Fine Needle Aspirates, Janette Vazquez

Theses and Dissertations

This thesis examines how Artificial Neural Networks can be used to classify a set of samples from a fine needle aspirate dataset. The dataset is composed of various different attributes, each of which are used to come to the conclusion as to whether a sample is benign or malignant. To automate the process of analyzing the various attributes and coming to a correct prediction, a neural network was implemented. First, a Feedforward Neural Network was trained with the dataset using a Backpropagation training method and an activation sigmoid function with one hidden layer in the architecture of the network. After …

The Boundedness Of Hausdorff Operators On Function Spaces, Xiaoying Lin

Theses and Dissertations

For a fixed kernel function $\Phi$, the one dimensional Hausdorff operator is defined in the integral form by

\[

\hphi (f)(x)=\int_{0}^{\infty}\frac{\Phi(t)}{t}f(\frac{x}{t})\dt.

\]

By the Minkowski inequality, it is easy to check that the Hausdorff operator is bounded on the Lebesgue spaces $L^{p}$ when $p\geq 1$, with some size condition assumed on the kernel functions $\Phi$. However, people discovered that the above boundedness property is quite different on the Hardy space $H^{p}$ when $0

In this thesis, we first study the boundedness of $\hphi$ on the Hardy space $H^{1}$, and on the local Hardy space $h^{1}(\bbR)$. Our work shows that for …

A Weak Groethendieck Compactness Principle For Infinite Dimensional Banach Spaces, Kaitlin Bjorkman

Theses and Dissertations

The goal of this thesis is to give an exposition of the following recent result of Freeman, Lennard, Odell, Turett and Randrianantoanina. A Banach space has the Schur property if and only if every weakly compact set is contained in the closed convex hull of a weakly null sequence. This result complements an old result of Grothendieck (now called the Grothendieck Compactness Principle) stating that every norm compact subset of a Banach space is contained in the closed convex hull of a norm null sequence. We include many of the relevant definitions and preliminary results which are required in the …

Infinite Product Group, Keith G. Penrod

Theses and Dissertations

The theory of infinite multiplication has been studied in the case of the Hawaiian earring group, and has been seen to simplify the description of that group. In this paper we try to extend the theory of infinite multiplication to other groups and give a few examples of how this can be done. In particular, we discuss the theory as applied to symmetric groups and braid groups. We also give an equivalent definition to K. Eda's infinitary product as the fundamental group of a modified wedge product.

On-The-Fly Dynamic Dead Variable Analysis, Joel P. Self

Theses and Dissertations

State explosion in model checking continues to be the primary obstacle to widespread use of software model checking. The large input ranges of variables used in software is the main cause of state explosion. As software grows in size and complexity the problem only becomes worse. As such, model checking research into data abstraction as a way of mitigating state explosion has become more and more important. Data abstractions aim to reduce the effect of large input ranges. This work focuses on a static program analysis technique called dead variable analysis. The goal of dead variable analysis is to discover …

Real-Time Computer Optimized Scanning Potential Coulometry For Multi-Component Trace Analysis, Norman W. Petty

Theses and Dissertations

The instrumentation and methodology for real-time computer controlled scanning potential coulometry for multi-component trace analysis is described. The sensitivity limit was determined to be 10^-8 F for electrochemically reversible constituents. The sensitivity limit could be extended if measures were taken to compensate for the periodic signal found on the electrolysis current. Non-linear least squares curve fitting methods accurately resolved iron-platinum and silver-iron interferences to give accurate determinations for iron and silver. The resolving capability of this method was tested using theoretically generated scanning potential coulograms. The computer resolved sample constituents with a 1 to 100 concentration ratio and a formal …

The Chromatographic Purification Of Human Red Blood Cell Acetylcholinesterase, Richard P. Dunkley

Theses and Dissertations

A process of column chromatography of human erythrocyte acetylcholinesterase, using a cationic exchange resin, was investigated as a possible method for the primary partial purification of the enzyme on a large scale. The investigation was based, first; on a detailed study of the enzymatic stability to variation in hydrogen-ion and salt concentrations for periods of time extending to forty eight hours and, second; on an investigation of the degree of adsorption by the resin of the enzyme at various pH values within the pH range of enzyme stability. A method for the analysis of the enzyme activity of large numbers …

Biological Oxidation Of Copper Sulfide Minerals, Delmar Boyd Davis

Theses and Dissertations

This work represents a study of the biological oxidation of copper sulfide minerals. The principal objective of the study was to determine the extent of bacterial oxidation on copper containing sulfide minerals. It was also desired to determine if the bacteria could oxidize copper sulfides in the absence of iron. A better understanding of the nitrogen requirements of the organisms was desired. Minerals used in this study were Bingham Canyon Float Concentrate, chalcopyrite, covellite, calcocite, bornite, tetrahedrite, and reagent grade copper sulfide. The bacteria used were obtained from the mine waters of Bingham Canyon, Utah. To study the problem the …