Physical Sciences and Mathematics Commons^™

Gene Regulatory Network Reconstruction Using Dynamic Bayesian Networks, Haoni Li

Dissertations

High-content technologies such as DNA microarrays can provide a system-scale overview of how genes interact with each other in a network context. Various mathematical methods and computational approaches have been proposed to reconstruct GRNs, including Boolean networks, information theory, differential equations and Bayesian networks. GRN reconstruction faces huge intrinsic challenges on both experimental and theoretical fronts, because the inputs and outputs of the molecular processes are unclear and the underlying principles are unknown or too complex.

In this work, we focused on improving the accuracy and speed of GRN reconstruction with Dynamic Bayesian based method. A commonly used structure-learning algorithm …

Dynamic Bioactive Stimuli-Responsive Polymeric Surfaces, Heather Marie Pearson

Dissertations

This dissertation focuses on the design, synthesis, and development of antimicrobial and anticoagulant surfaces of polyethylene (PE), polypropylene (PP), and poly(tetrafluoroethylene) (PTFE) polymers. Aliphatic polymeric surfaces of PE and PP polymers functionalized using click chemistry reactions by the attachment of –COOH groups via microwave plasma reactions followed by functionalization with alkyne moieties. Azide containing ampicillin (AMP) was synthesized and subsequently clicked into the alkyne prepared PE and PP surfaces. Compared to non-functionalized PP and PE surfaces, the AMP clicked surfaces exhibited substantially enhanced antimicrobial activity against Staphylococcus aureus bacteria. To expand the biocompatibility of polymeric surface …

Biological And Biologically Inspired Polymers For Interface Modification, Lea Clayton Paslay

Dissertations

Naturally occurring macromolecules are produced for a specific function and have the selectivity to accomplish objectives with little waste in energy. The scientific community strives to develop smart, efficient molecules on an economical scale, thus lessons can be learned from nature and applied to cost effective synthetic systems. First, the mimicry of naturally occurring antimicrobial peptides (AMPs) will be described. AMPs show great potential as alternatives to conventional antibiotics as they can selectively bind and eliminate pathogenic bacteria without harming eukaryotic tissues. Aqueous reversible addition–fragmentation chain transfer (RAFT) polymerization was utilized to prepare primary and tertiary amine containing AMP polymer …

Investigations Toward Tunability Of Mechanical, Thermal, And Impact Properties Of Thiol-Ene Networks For Novel High Energy Absorbing Materials, Olivia Devon Mcnair

Dissertations

The UV polymerization of thiols with electron rich alkenes is a highly resourceful reaction that has been utilized by scientists within various disciplines to produce an even more versatile display of applications. This dissertation focuses on a newer application, thiol-ene network (TEN) materials for energy absorption devices. TEN networks display a host of positive polymer properties such as low stress, high optical clarity and uniformity, but they also suffer from unfavorable mechanical properties such as low toughness and elongation at break. The poor mechanical properties demonstrated by TENs prohibit them as choice materials for applications requiring thicker material forms, including …

Synthesis Of Polyhedral Oligomeric Silsesquioxane (Poss) Functionalized Carbon Nanotubes For Improved Dispersion In Polyurethane Films, Xiaonan Kou

Dissertations

Carbon nanotube (CNT) polymer nanocomposites are promising advanced materials. These materials exhibit the advantages of traditional polymeric materials, such as being light weight and easy to process, combined with the potential to exhibit enhanced mechanical, thermal and electrical properties compared to pure polymers. To achieve substantial improvement of composite properties at low CNT loading, uniform dispersion of CNTs in the polymer matrix and strong CNT-polymer interfacial interaction are needed. However, it is difficult to achieve adequate dispersion and interfacial interactions due to the inert nature of CNTs. In this project, polyhedral oligomeric silsequioxane (POSS) will be used as a dispersing …

Nanoparticle Filled Polymeric Systems For Gas Barrier And Flame Retardant Properties, Yingji Wu

Dissertations

Polymer composite gas barrier and fire retardant properties were studied in this investigation. An increase in the gas barrier property was observed by adding silicate nanotubes or clay nanoparticles into polymeric systems. Oxygen permeability, diffusivity, solubility and water vapor permeability were determined for polyimide/silicate nanocomposites with 0 to 9.99% (vol/vol) filler loading. Both oxygen and water vapor permeability for the system gradually decreased when adding increasing amounts of nanofiller up to 4.50% (vol/vol) and increase again after that. The permeability decrease was caused by both the diffusivity and solubility coefficient changes, although diffusivity (the tortuous factor) is the main reason …

Utilizing Polymer Topology In Peptide-Based Block Copolymers: Unique Aqueous Assembly And Responsive Behavior, Jacob Griffin Ray

Dissertations

This document details work in the area of amphiphilic polypeptide-based block copolymers that are able to self-assemble into well-defined nanostructures in aqueous solution. The main focus of this work is to understand the impacts of polymer topology on self-assembly behavior and response to external stimulus, particularly pH. Poly(L-lysine) and poly(L-glutamic acid) are two pH-responsive, hydrophilic polypeptides that possess the unique property of undergoing α-helix to random coil secondary structure transitions with pH, and this responsiveness can lead to global morphology changes such as changes in aggregate size or even morphology transitions. These polypeptides are synthesized via ring opening polymerization of …

Photopolymerization And Characterization Of Modified Thiol-Ene Networks, Bradley James Sparks

Dissertations

Photopolymerization provides a unique ability to control variables typically uncontrollable using traditional thermally initiated polymerization, thus leading to its use in a broad range of commercial operations. Many of the traditional photopolymers suffer from several setbacks, including oxygen inhibition, unwanted stress buildup which leads to bulk shrinkage, etc., which ultimately lead to diminished polymer performance. The photopolymerization of multifunctional thiols and alkenes has been shown to provide a means to improve upon the weaknesses of traditional photoinitiated polymerizations. The free radical polymerization of thiol and –ene monomers occurs via a series of free radical chain transfer events, as a result, …

Relationships Between Cure Kinetics, Network Architecture, And Fluid Sensitivity In Glassy Epoxies, Katherine Lea Frank

Dissertations

Relationships between chemical structure, cure kinetics, network morphology and free volume have been correlated with fluid ingress for glassy epoxy network blends. Polymers synthesized from diglycidyl ether of bisphenol-A (DGEBA) and diglycidyl ether of bisphenol-F (DGEBF) were blended with varying amounts of triglycidyl-m-aminophenol (TGAP), tetraglycidyl-4,4-diaminodiphenylmethane (TGMP), napthylamine (NA), adamantylamine (AA), and aminopropylisobutyl polyhedral oliogmericsilsesquioxane (AI-POSS) and cured with 3,3’- and 4,4’- diaminodiphenylsulfone (DDS) to control fractional free volume, average hole size and morphology.

Varying curing profiles introduced morphological changes resulting in differences in network architectures. Epoxy with 10% NA had a smaller V_h (71 ų) …

Compositional And Structural Analysis Of Nitrogen Incorporated And Ion Implanted Diamond Thin Films, Elias James Garratt

Dissertations

Significant progress in area of nano-structured thin film systems has taken place in recent decades. In particular, diamond thin film systems are being widely studied for their wear resistant, optical and electronic properties. Of the various methods researchers use to modify the structure of such films, three techniques in particular are of interest due to their versatility: modification of the growth atmosphere, growth on metalized substrates, providing an interfacial layer, and modification through post-growth ion implantation. The aim of this study is to investigate the effects each has to the structure and composition of elements. Different techniques are applied in …

Engineered Interfaces And Nano-Scale Thin Films For Solid Oxide Fuel Cell Electrolytes, Manjula I. Nandasiri

Dissertations

Solid state electrolytes with high oxygen ionic conductivity at low temperatures are required to develop cost effective and efficient solid oxide fuel cells. This study investigates the influence of engineered interfaces on the oxygen ionic conductivity of nano-scale multilayer thin film electrolytes. The epitaxial Sm₂O₃ doped C_eO₂ (SDC) and Sc₂O₃ stabilized ZrO₂ (ScSZ) are selected as the alternative layers for the proposed multilayer thin film electrolyte based on the optimum structural, chemical, and electrical properties reported in the previous studies. The epitaxial SDC(111)/ScSZ(111) multilayer thin films are grown on high …

Metal-Organic And Supramolecular Architectures Based On Mechanically Interlocked Molecules, Isurika Rosini Fernando

Dissertations

The focus of this work is on mechanically interlocked molecules (MIMs), which have unusual physicochemical and mechanical properties with potential applications in nano-scale/molecular devices and high strength materials.

Rotaxanes, for example, consist of an axle-like molecule threaded through a wheel-like molecule, with bulky groups at the two ends of the axle preventing the wheel from dissociating. The position of the wheel along the axle can be switched in a controllable and reversible manner by applying external stimuli, a feature that might lead to the next generation of computers. Molecularly woven materials (MWMs), another example of molecules with mechanically interlocked features, …

A Computational Method For Estimating And Finding The Hconfidence Interval Of The Ratio Scale Parameters In The Two-Sample Problem, Mona Abdullah Alduailij

Dissertations

Testing equality of variances between two samples is applied in various fields. However, in the absence of non-normal assumptions, equality of variance tests would not yield robust results. In real life situation, the absence of such assumptions is even evident, which calls for more reliable tests to accommodate for the lack of these assumptions. There are abundant parametric and nonparametric methods for estimating the scale parameter; yet a distribution-free method for estimating and finding the confident interval ratio of scale parameters in the two-sample problem would be a reliable alternative. A comparison between existing parametric and non-parametric rank tests for …

Artificial Immune Systems And Particle Swarm Optimization For Solutions To The General Adversarial Agents Problem, Jeremy Mange

Dissertations

The general adversarial agents problem is an abstract problem description touching on the fields of Artificial Intelligence, machine learning, decision theory, and game theory. The goal of the problem is, given one or more mobile agents, each identified as either “friendly" or “enemy", along with a specified environment state, to choose an action or series of actions from all possible valid choices for the next “timestep" or series thereof, in order to lead toward a specified outcome or set of outcomes. This dissertation explores approaches to this problem utilizing Artificial Immune Systems, Particle Swarm Optimization, and hybrid approaches, along with …

Weighted Shifts Of Finite Multiplicity, Daniel S. Sievewright

Dissertations

We will discuss the structure of weighted shift operators on a separable, infinite dimensional, complex Hilbert space. A weighted shift is said to have multiplicity n when all the weights are n x n matrices. To study these weighted shifts, we will investigate which operators can belong to the Deddens algebras and spectral radius algebras, which can be quite large. This will lead to the necessary and sufficient conditions for these algebras to have a nontrivial invariant subspace.

A Comparative Study Of Exact Versus Propensity Matching Techniques Using Monte Carlo Simulation, Mukaria J. J. Itang'ata

Dissertations

Often researchers face situations where comparative studies between two or more programs are necessary to make causal inferences for informed policy decision-making. Experimental designs employing randomization provide the strongest evidence for causal inferences. However, many pragmatic and ethical challenges may preclude the use of randomized designs. In such situations, subject matching provides an alternative design approach for conducting causal inference studies. This study examined various design conditions hypothesized to affect matching procedures’ bias recovery ability.

See attachment for full abstract.

Localized Surface Plasmon Resonance Induced Structure-Property Relationships Of Metal Nanostructures, Subramanian Vilayurganapathy

Dissertations

The confluence of nanotechnology and plasmonics has led to new and interesting phenomena. The industrial need for fast, efficient and miniature devices which constantly push the boundaries on device performance tap into the happy marriage between these diverse fields. Designing devices for real life application that give superior performance when compared with existing ones are enabled by a better understanding of their structure-property relationships. Among all the design constraints, without doubt, the shape and size of the nanostructure along with the dielectric medium surrounding it has the maximum influence on the response and thereby the performance of the device. Hence …

Synthesis And Characterization Of New Light Emitting Probes For Sensitive Detection Of Bio-Molecules And Live Cells, Shyamala Pravin Pillai

Dissertations

A variety of contemporary analytical platforms in technical and biological applications take advantage of labeling the objects of interest with fluorescent or luminescent tracers. Luminescent tracers take advantage of the unique property of some lanthanide metals to absorb and emit light. Long lifetime of lanthanide emission allows temporal gating of the signal, which avoids the short-lived background of interfering sample components. This property in combination with large Stokes shift contributes to extreme sensitivity of detection (ca. 10^-13-10^-14 M), which makes lanthanide-based probes suitable for large variety of challenging tasks ( e.g., intracellular detection of single DNA/RNA, or …

Extension To Pv Optics To Include Front Electrode Design In Solar Cells, Debraj Guhabiswas

Dissertations

Proper optical designing of solar cells and modules is of paramount importance towards achieving high photovoltaic conversion efficiencies. Modeling softwares such as PV OPTICS, BIRANDY and SUNRAYS have been created to aid such optical designing of cells and modules; but none of these modeling packages take the front metal electrode architecture of a solar cell into account.

A new model, has been developed to include the front metal electrode architecture to finished solar cells for optical calculations. This has been implemented in C++ in order to add a new module to PV OPTICS (NREL’s photovoltaic modeling tool) to include …

Modeling Cell Proliferation In A Perfusion Tissue Engineering Bioreactor, Jeffrey Vincent Pohlmeyer

Dissertations

In this dissertation we develop a comprehensive model to simulate a tissue engineering experiment. The experiment takes place in a bioreactor in which a cell seeded porous scaffold is placed, and the scaffold experiences a perfused flow of a nutrient-rich culture medium. The goal of the model is to assist experimentalists in evaluation of different parameter scenarios as the time needed to simulate an experiment is significantly less than the time needed for the experiment itself. We provide the full two-dimensional model development, as well as investigation into possible variations of specific model choices, and we demonstrate the robustness and …

The Goodness-Of-Fit Tests For Geometric Models, Feiyan Chen

Dissertations

We propose two types of goodness-of-fit tests for geometric distribution and for a bivariate geometric distribution called BGD(B&D), based on their probability generating function (PGF). The first type is a special-case application of the general testing procedure for discrete distributions proposed by Kocherlakota and Kocherlakota (1986). The second type utilizes the supremum of the absolute value of the standardized difference between the PGF’s maximum likelihood estimator (MLE) and its empirical counterpart as the test statistic. We verify the asymptotic properties of the test statistics for the first type of test and explore the asymptotic behaviors of the test statistics for …

Development Of Luminescent Probes For Ultrasensitive Detection Of Biopolymers, Their Complexes, And Living Cells, Laura A. Wirpsza

Dissertations

New luminescent probes with enhanced brightness convenient for bioconjugation were synthesized and tested in major biological applications including the detection of nucleic acids and living cells. The first project used luminescent lanthanide ion probes that take advantage of hyper-sensitive acquisition of their long-lived emission signal in time- resolved mode, which avoids short-lived background fluorescence of the medium. Two model carbostyril fluorophores (cs 124-CH₃ and cs 124-CF₃) were modified by inclusion of two spacers (diamino and bi-phenyl) for the attachment of amine and thiol reactive cross-linking groups. In this project, time-resolved measurements are presented for spectroscopy and microscopy. …

Eye Detection Using Discriminatory Features And An Efficient Support Vector Machine, Shuo Chen

Dissertations

Accurate and efficient eye detection has broad applications in computer vision, machine learning, and pattern recognition. This dissertation presents a number of accurate and efficient eye detection methods using various discriminatory features and a new efficient Support Vector Machine (eSVM).

This dissertation first introduces five popular image representation methods - the gray-scale image representation, the color image representation, the 2D Haar wavelet image representation, the Histograms of Oriented Gradients (HOG) image representation, and the Local Binary Patterns (LBP) image representation - and then applies these methods to derive five types of discriminatory features. Comparative assessments are then presented to evaluate …

Theoretical Studies Of Structural And Electronic Properties In Transition Metal Oxides, Tsezar F. Seman

Dissertations

The following studies are presented: theory of K-edge resonant inelastic x-ray scattering and its application for La_0.5Sr_1.5MnO₄, effects of rare earth ion size on the stability of the coherent Jahn-Teller distortions in undoped perovskite manganites, and symmetry-mode-based classical and quantum mechanical formalism of lattice dynamics.

The formula based on tight-binding approach for the calculation of K-edge resonant inelastic x-ray scattering (RIXS) spectrum for transition metal oxides is presented first, by extending the previous existing result to include explicit momentum dependence and a basis with multiple core-hole sites. This formula is applied to layered charge, …

Handel's Maser-Soliton Theory Of Ball Lightning: The Creation Of Stable Three-Dimensional Cavitons By An Atmospheric Maser Within An Open Resonator, Glenn Andrew Carlson

Dissertations

This dissertation develops details of Handel’s Maser-Soliton Theory of ball lightning. The atmosphere between a thundercloud and the Earth’s surface is modeled as an idealized stable open resonator with water vapor as the active medium and the thundercloud and Earth’s surface as reflecting surfaces. The stable resonator generates a maser beam that narrows to the beam waist at the Earth’s surface, which is assumed to be planar. Two candidate rotational transitions are identified within the v1v2v3 = 010 vibrational band of water having wavelengths of 13.9 cm and 1.12 cm, and relevant spectroscopic parameters are retrieved from the HITRAN 2008 …

Use Of Sweet Potato To Develop A Medium For Cultivation Of Lactic Acid Bacteria, Saeed A. Hayek

Dissertations

This study investigated the use of sweet potatoes (Ipomoea batatas) as a basic component to develop a medium for cultivation of lactic acid bacteria (LAB). Extract from baked sweet potatoes was used to form a sweet potato medium (SPM). SPM was supplemented with 4 g/L of each nitrogen source (beef extract, yeast extract, and proteose peptone #3). Lactobacilli MRS was used as a control medium. Ten LAB strains were used to determine the suitability of SPM serving the growth of LAB. Our results showed no significant (p < 0.05) differences in the optical density, maximum specific growth rates, and bacterial populations between MRS and SPM. SPM also maintained higher pH values throughout the incubation period compared to that in MRS. The cost of SPM was 47% less than the cost of MRS. Further step was taken to determine the suitability of SPM serving LAB enzymatic activity. LAB strains growing in SPM showed relatively higher β-glucosidases, acid phosphatase, and phytase activities and lower a-glucosidase compared to that in MRS. Strains of L. reuteri showed the …

Tropical Cyclone Intensity Estimation Using Temporal And Spatial Features From Satellite Data, Gholamreza Fetanat Haghighi

Dissertations

Accurate intensity estimation of tropical cyclones (TC) is an important topic of research due to its economic impact and public safety concerns. An accurate measure of the current wind strength is necessary to accurately predict TC intensity. We have developed and tested automated method to estimate TC intensity based on the existing historical satellite images alone. The Hurricane Satellite data (HURSAT-B1) is used to develop the algorithm, which focuses on the North Atlantic from 1978-2009. The algorithm is trained and validated using aircraft reconnaissance-based data. Here, the data is restricted to include only fixes that are over water and are …

Adoption Of Green Building Practices And Rating System In Kenya: Potentials And Barriers, Peter Khaemba

Dissertations

This research study was undertaken to identify (a) green building rating attributes that could be adopted for Kenya, and (b) barriers to initial adoption of green building practices and a green building rating system in Kenya. The study was primarily built on the premise of select rating and adoption attributes in existing green building standards, especially Leadership in Energy and Environmental Design (LEED). A pilot phase of the study was conducted using a combination of focus groups and personal interviews. The pilot findings became the basis of a questionnaire that was utilized to survey a sample of 608 registered building …

The Rich Chemistry Of Cyclotriveratrylene (Ctv) And Ct-Inspired Reactions: Anthracenes With Organic Light-Emitting Diode (Oled) Applications And The Discovery Of Cascade Reactions, Samuel Sarsah

Dissertations

Cyclotriveratrylene (CTV) is a supramolecular scaffold with applications in host-guest chemistry, analytical detection, drug delivery and liquid crystals. We have discovered that CTV rearranges to a highly functionalized anthracene derivative that is ideal for the synthesis of 9,10-disubstituted anthracene derivatives that are useful for the construction of organic light-emitting diodes (OLEDs). Several diaryl anthracene derivatives have been synthesized and analyzed, and were found to have excellent electroluminescent properties, including one analog that exhibits an exceptionally high quantum yield. Red, green and blue are the primary colors needed for full color display, but blue fluorescence emitting organic compounds used in OLEDs …

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 …