Physical Sciences and Mathematics Commons^™

A Time Series Analysis Method Using Hidden Variables For Gene Network Reconstruction, Xi Wu

Dissertations

The DNA microarray technology can be applied to obtain time series data which contains thousands of genes and tens of time points. When confront the great amount of data points a fast and effective method must be constructed to extract useful information. The assumption that the interactions between genes are static in the time series data is made. After made the assumption how to reconstruct those interactions becomes a difficulty problem. Since the underlying interactions between genes are complicated, which involve transcription, translation and protein-protein interaction, to construct a model from physicochemistry is almost impossible/effortless. The popular methods constructed from …

Reification: A Process To Configure Java Realtime Processors, John Huddleston Heath

Dissertations

Real-time systems require stringent requirements both on the processor and the software application. The primary concern is speed and the predictability of execution times. In all real-time applications the developer must identify and calculate the worst case execution times (WCET) of their software. In almost all cases the processor design complexity impacts the analysis when calculating the WCET. Design features which impact this analysis include cache and instruction pipelining. With both cache and pipelining the time taken for a particular instruction can vary depending on cache and pipeline contents. When calculating the WCET the developer must ignore the speed advantages …

Understanding Corrosion Protection And Failure Through Model Polymers In Thin Films, Joshua Smith Hanna

Dissertations

When developing a model polymeric system to facilitate in the detection of molecular and microscopic events that preface macroscopic corrosive failure; a better understanding of how polymers can indicate corrosion was accomplished. Initially, the thought that molecular chain scission as a necessity for corrosion to occur had to be tested. Through the utilization of high molecular weight thermoplastic (HMWTP) model polymers, it was found that corrosion protection did not correlate to the quantity of weak bonds within an epoxy-amine polymer matrix. Therefore more sensitive methods of detecting corrosion had to be developed since changes within the polymer matrix did not …

Polymer Surface Engineering Via Thiol-Mediated Reactions, Ryan Matthew Hensarling

Dissertations

Synthesis of polymer brushes to decorate a surface with desired functionality typically involves surface-initiated polymerization (SIP) of functional, but non-reactive monomers. This approach suffers major drawbacks associated with synthesizing sufficiently thick polymer brushes containing surface-attached polymer chains of high molecular weight at high grafting density (i.e. cost, synthetic effort and functional group intolerance during polymerization). The research herein seeks to circumvent these limitations by the decoration of surfaces with polymer chains bearing specific pendent functional groups amenable to post-polymerization modification (PPM). In particular, this dissertation leverages PPM via a specific class of click reactions – thiol-click – that 1) enables …

Microstructure, Vacancies And Voids In Hydrogenated Amorphous Silicon, Rajendra Timilsina

Dissertations

This dissertation presents a theoretical and computational study of microstructure, vacancies and voids in hydrogenated amorphous silicon (a-Si:H). The microstructure consists of all possible silicon-hydrogen bonding configurations such as SiH, SiH₂, SiH₃ and SiH₄. However, it is highly dominated (approximately 75% or even more) by monohydride (SiH) configurations. Furthermore, the hydrogen atoms locate in both clustered and diluted phases; as a result, the distribution becomes highly inhomogeneous. Approximately 5% of hydrogen atoms reside in a form of isolated monohydrides at the lower (7 at.%) concentration whereas such configurations do not appear at the higher concentrations …

Radiative Double Electron Capture In Collisions Of Fully-Stripped Fluorine Ions With Thin Carbon Foils, Tamer Mohammad Samy Elkafrawy

Dissertations

Radiative double electron capture (RDEC) is a one-step process in ion-atom collisions occurring when two target electrons are captured to a bound state of the projectile simultaneously with the emission of a single photon. The emitted photon has approximately double the energy of the photon emitted due to radiative electron capture (REC), which occurs when a target electron is captured to a projectile bound state with simultaneous emission of a photon. REC and RDEC can be treated as timereversed photoionization (PI) and double photoionization (DPI), respectively, if loosely-bound target electrons are captured. This concept can be formulated with the principle …

Rule-Based Precise Localization Services In Mobile Environments, Mohammed Elbes

Dissertations

In recent years there has been great interest in the positioning of people and assets in indoor and outdoor environments. Many systems were constructed to accomplish this. The application of these systems depends on the environment and the precision required for localization. The Global Positioning System (GPS) cannot be used for a precise indoor localization due to the attenuation and scattering of the signals. For indoor environments, other technologies like Wireless LAN, laser, camera images and motion sensors are used in precise localization. GPS can be used in outdoor environments but if localization accuracy is a critical requirement, other technologies …

Integrated Approach For Hydrogeologic Investigations In Africa: Inferences From Space-Borne And Land-Based Gravity, Aeromagnetic, Gis, And Remote Sensing Data, Mohamed El Sayed Ahmed Ahmed

Dissertations

An integrated (space-borne and land-based gravity, aeromagnetic, GIS, and remote sensing) approach was developed, tested, and applied to investigate the following on regional scales (Africa) or local scales (El Qaa Plain, Sinai): (1) assess the capability of GRACE data (04/2002 to 08/2011) for monitoring elements of hydrologic systems on the sub-basin level (Task 1); (2) address the nature and the controlling factors (e.g., climatic and/or human pressure-related) affecting the inter-annual GRACE-derived Terrestrial Water Storage (TWS) trends over a large suite of hydrologic systems and domains in (Africa) (Task 2); and (3) identify the structural, geologic and hydrologic settings as well …

Boolean And Profinite Loops, Benjamin Andrew Phillips

Dissertations

A Quasigroup G consists of a set G together with a binary operation ∗ : G × G → G such that, for any elements a, b ∈ G there are unique solutions to the equations a ∗ x = b and y ∗ a = b within G. A loop is a quasigroup which also contains a 2-sided identity element. More heuristically, loops are essentially non-associative groups. However, without an associative binary operation, some of the familiar properties found in groups, such as 2-sided inverse, need not be present in loops.

The study of quasigroups and loops emerges …

The Characterization Of Volatiles Associated With Young Stellar Objects, Kari Anne Wojtkowski

Dissertations

In the first portion of this work, we searched for differences in volatiles within a single star forming region, Rho Ophiuchi. We determined the amount, temperature, and composition of two ice features, the bending modes of CO2 and H2O at 15 μm and 6 μm, respectively, toward 28 Young Stellar Objects (YSOs). We found that more than 50% of the YSOs studied contained a portion of crystalline CO2 ice. We also found that some sources with Flat or borderline Class II Spectral Energy Distributions (SEDs) have a larger abundance of CO2 ice with respect to H2O ice. In addition to …

Nanoporous Gold As A Solid Support For Protein Immobilization For The Development Of Immunoassays, And For Biomolecular Interaction Studies, Binod Prasad Pandey

Dissertations

Nanoporous gold (NPG) is a versatile material of high surface area to volume ratio that can be readily modified with self-assembled monolayers of alkanethiols to which biomolecules can be linked. NPG presents new opportunities for the development of immunoassays, and for the development of carbohydrate based assays. This thesis explores the use of NPG as a support for self-assembled monolayers, their linkage to antibody-enzyme conjugates for immunoassay development, and for the study and application of carbohydrate-protein interactions. Direct kinetic electrochemical immunoassays were developed on NPG for prostate specific antigen (PSA) and carcinoembryonic antigen (CEA). The decrease in enzymatic conversion of …

Fast Algorithms For Brownian Dynamics Simulation With Hydrodynamic Interactions, Zhi Liang

Dissertations

In the Brownian dynamics simulation with hydrodynamic interactions, one needs to generate the total displacement vectors of Brownian particles consisting of two parts: a deterministic part which is proportional to the product of the Rotne-Prager-Yamakawa (RPY) tensor D [1, 2] and the given external forces F; and a hydrodynamically correlated random part whose covariance is proportional to the RPY tensor. To be more precise, one needs to calculate Du for a given vector u and compute √Dv for a normally distributed random vector v. For an arbitrary N-particle configuration, D is a 3N x 3N matrix and u, v are …

Analytical And Computational Methods For The Study Of Rare Event Probabilities In Dispersive And Dissipative Waves, Daniel S. Cargill

Dissertations

The main focus of this dissertation is the application of importance sampling (IS) to calculate the probabilities associated with rare events in nonlinear, large-dimensional lightwave systems that are driven by noise, including models for fiber-based optical communication system and mode-locked lasers. Throughout the last decade, IS has emerged as a valuable tool for improving the efficiency of simulating rare events in such systems. In particular, it has shown great success in simulating various sources of transmission impairments found in optical communication systems, with examples ranging from large polarization fluctuations resulting from randomly varying fiber birefringence to large pulse-width fluctuations resulting …

Synthesis And Catalytic Applications Of Platinum(Ii) And Palladium(Ii)-Pta And Dapta Complexes, Sitaram Acharya

Dissertations

The cage-like tertiary phosphine, 1,3,5-triaza-7-phosphaadamantane (PTA) has recently received interest because of its water-solubility, air-stability, non-ionic, non-surfactant, and basic nature. These properties can solubilize transition metal complexes in the aqueous phase. A related air-stable derivative, N,N’-diacetyl-1-3-5-triaza-7-phosphaadamantane (DAPTA) has greater water-solubility than PTA, however, its coordination chemistry has not been significantly explored. This study involved the synthesis and characterization of a series of novel air-stable and water-soluble four-coordinated dialkyl, dialkynyl, dihalo, and halo(alkyl) complexes of platinum and palladium bearing PTA and DAPTA ligands. The alkyl complexes of the type MX(R)P2 (M = Pt, Pd; X = Cl, Br, I; R = …

Nickel Catalyzed Homoallylation Reactions And Synthesis Of Potent Inhibitors Of Yoph, Mahesh Prasad Paudyal

Dissertations

Amphidinolides are cytotoxic natural products isolated from marine dinoflagellate Amphidinium species. Amphidinolides C, C2 and F are active against cancer cell lines. Homoallylation of aldehydes with isoprene and triethylborane catalyzed by Ni(acac)2 gave hydroxyalkenes in good yield with excellent regio- and stereoselectivity. Cross metathesis of the hydroxyalkenes with methyl acrylate using second-generation Grubbs catalyst and copper(I) iodide afforded α,β-unsaturated esters, which underwent cyclization in the presence of DBU to produce tetrahydrofurans with the correct relative configuration for the C1-C9 fragment of amphidinolides C, C2, and F. Homoallylation of chiral and achiral diene carboxylate esters and dienecarboxamides with various aldehydes were …

Studies Toward Tetrahydrofuran-Containing Natural Products: Total Synthesis Of Amphidinolide C And Oxylipids, Sudeshna Roy

Dissertations

Tetrahydrofurans (thf) and tetrahydropyrans (thp) are important structural motifs found in a broad array of biologically relevant natural products such as polyether antibiotics and acetogenins. Classic methods used for thf- or thp-ring synthesis have their own advantages and disadvantages which tend to be substrate specific. Therefore, development of new and efficient methods is imperative especially to address the issue of diastereoselectivity when attainment of both cis- and trans-2,5-thf (or 2,6-thp) is highly desirable. Herein, a strategy of cross-metathesis and Pd(0)-catalyzed cyclization, useful for obtaining both cis- and trans-2,5-disubstituted thf (or 2,6-disubstituted thp), will be discussed along with its application in …

Coastal Hurricane Damage Assessment Via Wavelet Transform Of Remotely Sensed Imagery, Ricky Carl Crowsey

Dissertations

This dissertation uses post storm imagery processed using wavelet transforms to investigate the capability of wavelet transform-based methods to classify post storm damage of residential areas. Five level Haar, Meyer, Symlets, and Coiflets wavelet transform decompositions of the post storm imagery are inputs to damage classification models of post hurricane and tornado damage. Hurricanes Ike, Rita, Katrina, and Ivan are examined as are the 2011 Joplin and Tuscaloosa tornadoes.

Wavelet transform-based classification methods yielded varying classification accuracies for the four hurricanes examined, ranging from 67 percent to 89 percent classification accuracy for classification models informed by samples from the storms …

Characterizing And Supporting Change In Algebra Students' Representational Fluency In A Cas/Paper-And-Pencil Environment, Nicole L. Fonger

Dissertations

Representational fluency (RF) includes an ability to interpret, create, move within and among, and connect tool-based representations of mathematical objects. Taken as an indicator of conceptual understanding, there is a need to better support school algebra students’ RF in learning environments that utilize both computer algebra systems (CAS) and paper-and-pencil. The purpose of this research was to: (a) characterize change in ninth-grade algebra students’ RF in solving problems involving linear equations, and (b) determine conditions of a CAS and paper-and-pencil learning environment in which those students changed their RF.

Change in RF was measured by comparing results from initial to …

Modeling Transmission Of Photonic Crystal Waveguide Modes Enhanced By Kerr Nonlinearity, Buddhi M. Rai

Dissertations

Nonlinear modes of electromagnetic fields propagating in photonic crystal systems have been studied by implementing various computer simulation techniques using electromagnetic theory. The fundamentals of simulation of photonic crystals are analyzed using general purpose methodologies such as the FDTD or PWE methods. Information derived from the underlying physical insights into the systems could be utilized to describe the control mechanisms over the propagation of the modes around impurities in the photonic crystal lattice. The impurities trap the resonantly localized electromagnetic modes having a frequency in a stop band of the photonic crystal, suggesting novel optical controls in the photonic crystal …

Investigating The Biochemical Activity Of Some Flavonoids, Coumarins And Modified Gold-Nanoparticles As Anti-Breast-Cancer Agents, Amr Ezzat Mohamed Mahmoud

Dissertations

Polyphenols compounds are abundant natural products found in many plants as secondary metabolites. These compounds display many interesting pharmacological activities, which have motivated chemists over the years to explore them, and their synthetic derivatives, as potential drugs, especially anticancer drugs. Breast cancer is the most common cancer in women globally, and in the United States of America the estimated worldwide new breast cancer cases and the number of deaths are 1.38 million and 458 thousand, respectively. Currently in the USA there are 2.6 million women who have been treated for breast cancer, and the estimated number of deaths are 39,520 …

Adaptive Security-Aware Scheduling For Packet Switched Networks Using Real-Time Multi-Agent Systems, Ma'en Saleh Saleh

Dissertations

Conventional real-time scheduling algorithms are in care of timing constraints; they don’t pay any attention to enhance or optimize the real-time packet’s security performance. In this work, we propose an adaptive security-aware scheduling with congestion control mechanism for packet switching networks using real-time agentbased systems. The proposed system combines the functionality of real-time scheduling with the security service enhancement, where the real-time scheduling unit uses the differentiated-earliest-deadline-first (Diff-EDF) scheduler, while the security service enhancement scheme adopts a congestion control mechanism based on a resource estimation methodology.

The security service enhancement unit was designed based on two models: singlelayer and weighted …

Paleoclimatic Regimes Of The African Sahara Desert During Pleistocene And The Origin Of Groundwater In The Nubian Sandstone Aquifer System, Abdou A. Abouelmagd

Dissertations

This study involves an integrated three-fold approach to better understand the paleoclimatic regimes over the North African Sahara Desert with emphasis on the origin of groundwater in the Nubian Sandstone Aquifer System. Specifically, the nature and origin of the paleo-wind regimes that produced the precipitation that recharged the fossil aquifers in North Africa in the previous wet climatic periods are deciphered using inferences from stable isotope data, noble gases, remote sensing and GIS.

In the first phase, the progressive depletion trend of stable isotopic composition in the fossil groundwaters under influence of paleowesterlies across North African Sahara Desert is simulated …

Rank-Based Estimation And Prediction For Mixed Effects Models In Nested Designs, Yusuf K. Bilgic

Dissertations

Hierarchical designs frequently occur in many research areas. The experimental design of interest is expressed in terms of fixed effects but, for these designs, nested factors are a natural part of the experiment. These nested effects are generally considered random and must be taken into account in the statistical analysis. Traditional analyses are quite sensitive to outliers and lose considerable power to detect the fixed effects of interest.

This work proposes three rank-based fitting methods for handling random, fixed and scale effects in k-level nested designs for estimation and inference. An algorithm, which iteratively obtains robust prediction for both scale …

Study Of The Structure Of 9C Via Single Neutron Transfer, Scott T. Marley

Dissertations

This thesis describes a study of the nucleus ⁹C, produced in the single-neutron transfer reaction d(¹⁰C, t) ⁹C using a radioactive ¹⁰C beam. The structure of the neutron-deficient nucleus ⁹C is poorly known. Only a few excited states have been observed and no information exists of their single-particle characteristics. The measured ground-state magnetic dipole moment of ⁹C is anomalously small and could imply large contributions from sd-shell orbitals in the ground-state wave function. The positions of the ⁹C excited states and their single-particle properties are vital to furthering the …

Variations On A Graph Coloring Theme, Bryan Phinezy

Dissertations

Historically, the subject of graph colorings has been the most popular research area in graph theory. There are many problems in mathematics and in real life that can be represented by a graph and whose solution involves finding a specific coloring of this graph. Our research consists of two parts: (1) combinatorial problems and vertex colorings and (2) distance-defined colorings. In this research, we show that certain combinatorial puzzles and problems can be placed in a graph coloring setting and graph colorings can be defined in terms of distance in graphs that are useful in applications.

Two vertices u and …

Energy Methods For Reaction-Diffusion Problems, Xing Zhong

Dissertations

Nonlinear reaction-diffusion equations arise in many areas of applied sciences such as combustion modeling, population dynamics, chemical kinetics, etc. A fundamental problem in the studies of these equations is to understand the long time behavior of solutions of the associated Cauchy problem. These kinds of questions were originally studied in the context of combustion modeling.

For suitable nonlinearity and a monotone increasing one-parameter family of initial data starting with zero data, small values of the parameter lead to extinction, whereas large values of the parameter may lead to spreading, i.e., the solution converging locally uniformly to a positive spatially independent …

Structural Analysis And Auditing Of Snomed Hierarchies Using Abstraction Networks, Yue Wang

Dissertations

SNOMED is one of the leading healthcare terminologies being used worldwide. Due to its sheer volume and continuing expansion, it is inevitable that errors will make their way into SNOMED. Thus, quality assurance is an important part of its maintenance cycle.

A structural approach is presented in this dissertation, aiming at developing automated techniques that can aid auditors in the discovery of terminology errors more effectively and efficiently. Large SNOMED hierarchies are partitioned, based primarily on their relationships patterns, into concept groups of more manageable sizes. Three related abstraction networks with respect to a SNOMED hierarchy, namely the area taxonomy …

Instabilities In Newtonian Films And Nematic Liquid Crystal Droplets, Te-Sheng Lin

Dissertations

The instabilities of Newtonian films and nematic liquid crystal droplets within the framework of the long wave (lubrication) approximation are studied. For Newtonian films, it is found that, under destabilizing gravitational force, a contact line, modeled by a commonly used precursor film model, leads to free surface instabilities without any additional natural or imposed perturbations. In addition, there is a coupling between the surface instabilities and the transverse (fingering) instabilities which leads to complex behavior. All the observed phenomena are characterized by a single parameter D = (3Ca)^1/3 cot α where Ca is the capillary number and …

Effects Of Information Importance And Distribution On Information Exchange In Team Decision Making, Babajide James Osatuyi

Dissertations

Teams in organizations are strategically built with members from domains and experiences so that a wider range of information and options can be pooled. This strategic team structure is based on the assumption that when team members share the information they have, the team as a whole can access a larger pool of information than any one member acting alone, potentially enabling them to make better decisions. However, studies have shown that teams, unlike individuals, sometimes do not effectively share and use the unique information available to them, leading to poorer decisions. Research on information sharing in team decision making …

Evolution Of 3-D Magnetic Topology In Flare-Productive Active Regions, Yixuan Li

Dissertations

Solar eruptive phenomena, such as flares and coronal mass ejections (CMEs), derive their energy from complex magnetic fields and are the principal source of disturbances that affect space weather. Although physical mechanism and dynamic morphology of flares have been a subject of intense research, many aspects of the flaring process still remain unclear. The objective of this dissertation is to advance the understanding of the physics behind solar flares based on observations, simulations and nonlinear force-free (NLFF) field modeling of magnetic fields.

The data used in this study are obtained from several ground-based or space-borne instruments, including BBSO/DVMG, Hinode/SOT/SP, SDO/HMI …