Physical Sciences and Mathematics Commons^™

Probing Reactivity And Substrate Specificity Of Both Subunits Of The Dimeric Mycobacterium Tuberculosis Fabh Using Alkyl-Coa Disulfide Inhibitors And Acyl-Coa Substrates, Sarbjot Sachdeva, Faik Musayev, Mamoun M. Alhamadsheh, J. Neel Scarsdale, H. Tonie Wright, Kevin A. Reynolds

Chemistry Faculty Publications and Presentations

The dimeric Mycobacterium tuberculosis FabH (mtFabH) catalyses a Claisen-type condensation between an acyl-CoA and malonyl-acyl carrier protein (ACP) to initiate the Type II fatty acid synthase cycle. To analyze the initial covalent acylation of mtFabH with acyl-CoA, we challenged it with mixture of C6-C20 acyl-CoAs and the ESI-MS analysis showed reaction at both subunits and a strict specificity for C12 acyl CoA. Crystallographic and ESI-MS studies of mtFabH with a decyl-CoA disulfide inhibitor revealed a decyl chain bound in acyl-binding channels of both subunits through disulfide linkage to the active site cysteine. These data provide the first unequivocal evidence that …

Trampling, Peeling And Nibbling Mussels: An Experimental Assessment Of Mechanical And Predatory Damage To Shells Of Mytilus Trossulus (Mollusca: Mytilidae), Carlos E. Cintra-Buenrostro

School of Earth, Environmental, & Marine Sciences Faculty Publications

Shell damage, if properly recognized, can provide information about biotic interactions between molluscs and their predators. However, it can be difficult to distinguish predatory damage from mechanical breakage, thus making interpretation of damaged modern and fossil shells problematic. To establish a clear-cut distinction between antemortem predatory crab damage and ante- and postmortem mechanical damage in Mytilus trossulus shells, a combined field and experimental approach was used. Mussels were exposed to predation by crabs, tumbled-live, tumbled-dead, and trampled. After 100 h of tumbling, live-collected mussel shells were abraded and disarticulated but not otherwise damaged. Eight percent of the dead-collected shells were …

Initial Studies On A Novel Target-Promoted Dna Alkylation System, Ting Xu

Theses and Dissertations

A novel target-promoted DNA alkylation system was designed, which consists of a DNA intercalating/alkylating quinone methide (QM) precursor, a removable amine linker, and a sequence-specific delivery. The QM in this system was regenerated by eliminating the amino linker promoted by the hydrophobic interaction between the target DNA and the intercalating QM precursor. Three alkylation model systems (methoxyl polycyclic system, intramolecular hydrogen bonding system and biaryl system) were proposed and synthesized. The potential DNA QM alkylation was investigated by deoxyadenosine (dA) and deoxyguanosine (dG) alkylation with the biaryl system. Only one deoxynucleoside adduct was observed when dA or dG reacted with …

An Evaluation Of Mold In Public Schools In The City Of Richmond, Va, Stephen Asante-Ansong

Theses and Dissertations

Forty-three (43) schools in the City of Richmond were used for this study. The rooms in these schools that were selected for testing were those rooms in which complaints about air quality were made by school staff. Tests were done to find out the counts of the different mold species present in these schools. Air-O-Cell (AOC) samples were taken in all schools, swab samples were taken in a few and in the rest biotapes were used. Samples that were taken were analyzed and interpreted at AmeriSci Laboratories, an accredited industrial hygiene laboratory. Documentation was done for the sampling methods. Statistical …

Integer Programming With Groebner Basis, Isabella Brooke Ginn

Theses and Dissertations

Integer Programming problems are difficult to solve. The goal is to find an optimal solution that minimizes cost. With the help of Groebner based algorithms the optimal solution can be found if it exists. The application of the Groebner based algorithm and how it works is the topic of research. The Algorithms are The Conti-Traverso Algorithm and the Original Conti-Traverso Algorithm. Examples are given as well as proofs that correspond to the algorithms. The latter algorithm is more efficient as well as user friendly. The algorithms are not necessarily the best way to solve and integer programming problem, but they …

Design Synthesis And Evaluation Of Diterpenones As Potent Chemopreventive Agents For Aflatoxin B1 Induced Carcinogenesis In Human Liver Cells, Miguel Angel Zuniga

Theses and Dissertations

DESIGN, SYNTHESIS, AND EVALUATION OF DITERPENONES AS POTENT CHEMOPREVENTIVE AGENTS FOR AFB1 INDUCED CARCINOGENISIS IN HUMAN LIVER CELLS By Miguel A. Zuniga, Ph.D. A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University. Major Director: Qibing Zhou, Ph.D Assistant Professor Department of Chemistry Terpene quinone methides (TPQMs) have been isolated from a variety of plants and show broad activities against bacteria, fungi, and cancerous cell lines. The biological activity has been attributed to the reactive electrophilic QM moiety, this structural feature has long been recognized as an intermediate in organic …

Supramolecular Usefulness Of Hexamethylenetetramine, Philias Daka

Masters Theses

Because non-covalent contacts are important to the design and construction of materials with functional applications, efforts that seek to uncover chemical features responsible for the assembly of multimolecular arrays hold current interest. The building-block approach is one strategy that has been successfully employed for the construction of molecular assemblies. By designing molecular components with complementary functional groups, the construction of predictable supramolecular motifs is possible. Although various modes of molecular alignment have been generated using this strategy, the extension of low dimensional motifs (discrete and 1-D patterns) to 2- and 3-D patterns remain a current challenge.

Studies Directed Toward The Diastereocontrolled Synthesis Of Heritol, Prashanth K. Padakanti

Masters Theses

3,3-Dichloro-4-indanyloxetan-2-one was synthesized and its double ring expansion in the presence of the Lewis acid magnesium bromide was investigated, which resulted only in a trans-fused butyrolactone in 25% yield. Of the natural products containing butyrolactones fused to 6-membered rings, trans is more common. This method of double ring expansion can be applied to the synthesis of the natural product heritol, whose core structure contains the butenolide moiety. A model study of the double ring expansion was performed with 3-chloro-4-indanyl-3-methyloxetane-2-one B6, but this study was not completed.

In order to apply the double ring expansion methodology to synthesize heritol, the preparation …

An Environmental Complexity Analysis For Robot-Environment System Design, Gang Yang

Theses and Dissertations

Recently, researchers have begun to investigate intelligent environments for robot applications. In this work, a robot and its work environment can be considered to be an integrated system. Currently, such robot-environment systems are designed on an ad-hoc basis, with the final performance of the system greatly dependent on the experience and preferences of the designer. This dissertation investigates a way to improve on this situation by looking at the complexity of an environment from the perspective of a robot. The objective of this research is to develop a method to evaluate environmental complexity and then use this information to help …

Computational Models To Predict The Inhibition Of Cytochrome P450 3a4 By Selected Natural Compounds, Sushma Thotakura

Theses and Dissertations

Cytochrome P450 3A4 (CYP3A4) plays a pivotal role in the metabolism of xenobiotics. Methylenedioxobenzene containing natural products have been shown to inhibit CYP3A4. Given that these compounds are widely distributed in nature there is a strong potential for drug interaction with many plants used for dietary or medicinal purposes. In this research we have developed two different computational models (Comparative Molecular Field Model and Artificial Neural Network Model) to assist in the identification of potentially strong inhibitors that could be further studied for potential inhibitory effects. These models were used to screen for the CYP3A4 inhibitory effects of 100 naturally …

Evaluation And Characterization Of Some Biologically Active Coumarin Derived Sulfonamides, Harish Gosike

Theses and Dissertations

Sulfonamide drugs discovered in the 1930's were the first effective chemotherapeutic agents to be employed for the prevention and cure of bacterial infections in humans. Bacterial resistance to these drugs over the years has led to the development of new variety of sulfonamide derivatives. Recently Chohan et al. synthesized a series of coumarin derived sulfonamides and their chemical structures have been established. In this report, we present some microbiological studies to establish the antibacterial characters of these compounds. In order to establish their chemical structure-biological activity relationship, electrochemical and spectroscopic studies have been conducted. Antibacterial studies conducted on these compounds …

Identification Of Potential Organic Contributors In Carbonaceous Aerosols: Enhanced Uv Absorption Spectra, Anand Mangu

Theses and Dissertations

Direct aerosol climate effects include light scattering and absorption that present the largest uncertainties in the assessment of radiative forcing. To estimate the overall effect of aerosols on climate the relative amounts of scattering and absorption must be known. Determination of aerosol UV-absorption spectra is the primary focus of this thesis research. Aerosol samples were collected in Mexico City in 2003 and 2006 as a part of Mexico City Metropolitan Area field study and also at Little Rock. UV-visible absorption spectra of these aerosol samples have been obtained by using an integrating sphere coupled to a UV-visible spectrometer and compared …

Mining Frequent Patterns From Sequences: Theory, Algorithm, Implementation, And Performance, Markus Petteri Turkia

Theses and Dissertations

Mining frequent patterns from sequences is an important data mining problem which has direct applications in many areas. In this thesis, we make three contributions to the state-of-the-art of the sequential frequent pattern mining. First of all, we propose a fast pattern-growth mining algorithm using a novel sequence database representation called First-Occurrence Linked WAP-tree (FLWAP-tree). The pattern-growth mining algorithm using the Pre-Order Linked WAP-tree (PLWAP-tree) was reported in the literature to be faster than other algorithms. We show that our pattern-growth using our FLWAP-tree outperforms the PLWAP-tree mining significantly and consistently. Secondly, we extend the pattern-growth algorithm with partial enumeration …

Synthesis And Characterization Of Highly Conductive Polypyrrole And Polypyrrole/Lignosulfonate/Graphite Composites, Aopeau Imvittaya

Theses and Dissertations

Polypyrrole (PPy) is one of the conductive polymers frequently used in commercial applications, mainly due to its long-term stability and the possibility of forming homopolymers or composites with optimal properties. Polypyrroles were prepared by the chemical polymerization of pyrrole using various methods. The effects of several parameters such as oxidant, dopant type, additives and reaction conditions on the properties of PPy were investigated. In addition, PPy/graphite composites were prepared because graphite is highly conductive and effectively incorporated into the polymer matrix during the polymerization. The amount of graphite in the composite was varied to determine the maximimum conductivity achievable in …

Singlet Oxygen Generation Using New Fluorene-Based Photosensitizers Under One- And Two-Photon Excitation, Stephen James Andrasik

Electronic Theses and Dissertations

Molecular oxygen in its lowest electronically excited state plays an important roll in the field of chemistry. This excited state is often referred to as singlet oxygen and can be generated in a photosensitized process under one- or two-photon excitation of a photosensitizer. It is particularly useful in the field of photodynamic cancer therapy (PDT) where singlet oxygen formation can be used to destroy cancerous tumors. The use of two-photon activated photosensitizers possesses great potential in the field of PDT since near-IR light is used to activate the sensitizer, resulting in deeper penetration of light into biological tissue, less photobleaching …

Two-Dimensional Guided Mode Resonant Structures For Spectral Filtering Applications, Sakoolkan Boonruang

Electronic Theses and Dissertations

Guided mode resonant (GMR) structures are optical devices that consist of a planar waveguide with a periodic structure either imbedded in or on the surface of the structure. The resonance anomaly in GMR structures has many applications as dielectric mirrors, tunable devices, sensors,and narrow spectral band reflection filters. A desirable response from a resonant grating filter normally includes a nearly 100% narrowband resonant spectral reflection (transmission), and a broad angular acceptance at either normal incidence or an oblique angle of incidence. This dissertation is a detailed study of the unique nature of the resonance anomaly in GMR structures with two-dimensional …

Discrimination Of Forensic Trace Evidence Using Laser Induced Breakdown Spectroscopy, Candice Bridge

Electronic Theses and Dissertations

Elemental analysis in forensic laboratories can be tedious and many trace evidence items are not analyzed to determine their elemental composition. Presently, scanning electron microscopy-energy dispersive x-ray spectroscopy (SEM-EDS) is the primary analytical tool for determining the elemental composition of trace evidence items. However, due to the time it takes to obtain the required vacuum and the limited number of samples that can be analyzed at any one time, SEM-EDS can be impractical for a high volume of evidence items. An alternative instrument that can be used for this type of analysis is laser ablation inductively coupled plasma mass spectrometry …

Raman Spectroscopic Study Of Single Red Blood Cells Infected By The Malaria Parasite Plasmodium Falciparum, William Carter

Electronic Theses and Dissertations

Raman micro-spectroscopy provides a non-destructive probe with potential applications as a diagnostic tool for cellular disorders. This study presents micro-Raman spectra of live erythrocytes infected with a malaria parasite and investigates the potential of this probe to monitor molecular changes which occur during differentiation of the parasite inside the cell. At an excitation wavelength of 633 nm the spectral bands are dominated by hemoglobin vibrations yielding information the on structure and spin state of the heme moiety. It also demonstrates the novel use of silica capillaries as a viable method for studying the erythrocytes in an environment that is much …

Scanning Fabry-Perot Spectrometer For Terahertz And Gigahertz Spectroscopy Using Dielectric Bragg Mirrors, Justin Cleary

Electronic Theses and Dissertations

A scanning Fabry-Perot transmission filter composed of a pair of dielectric mirrors has been demonstrated at millimeter and sub-millimeter wavelengths. The mirrors are formed by alternating quarter-wave optical thicknesses of silicon and air in the usual Bragg configuration. Detailed theoretical considerations are presented for determining the optimum design including factors that affect achievable finesse. Fundamental loss by lattice and free carrier absorption are considered. High resistivity in the silicon layers was found important for achieving high transmittance and finesse, especially at the longer wavelengths. Also considered are technological factors such as surface roughness, bowing, and misalignment for various proposed manufacturing …

Two-Photon 3d Optical Data Storage Via Fluorescence Modulation Of Fluorene Dyes By Photochromic Diarylethenes, Claudia Corredor

Electronic Theses and Dissertations

Three-dimensional (3D) optical data storage based on two-photon processes provides highly confined excitation in a recording medium and a mechanism for writing and reading data with less cross talk between multiple memory layers, due to the quadratic dependence of two photon absorption (2PA) on the incident light intensity. The capacity for highly confined excitation and intrinsic 3D resolution affords immense information storage capacity (up to 1012 bits/cm3). Recently, the use of photochromic materials for 3D memory has received intense interest because of several major advantages over current optical systems, including their erasable/rewritable capability, high resolution, and high sensitivity. This work …

Frequency Distribution Of Pyroxene Types And A Method To Separate The Composition Of Multiple Pyroxenes In A Sample, Jimmy Allen Davis

Electronic Theses and Dissertations

Determining mafic mineral composition of asteroid bodies is a topic reviewed by M.J. Gaffey et al. (2002). The iterative procedure discussed can be implemented as an algorithm, and such efforts revealed weaknesses that are examined in this work. We seek to illustrate the limits of this method and graphically determine its predictions. There are boundaries in the formulae given where the equations break down. In ranges where mafic mixtures are predicted, a method is illustrated that allows a decoupling of these mixtures into the constituents.

Spectroscopic Studies Of Laser Plasmas For Euv Sources, Simi A. George

Electronic Theses and Dissertations

With the availability of high reflectivity multilayer mirrors and zone plate lenses, the EUV region (5nm - 40nm) of the electromagnetic spectrum is currently being explored for applications of nanoscale printing and imaging. Advances made in this area have consequences for many areas of science. Research for producing a compact, bright EUV source for laboratory use has gained momentum in recent years. For this study, EUV radiation is produced by irradiating target materials using a focused laser beam. Focused laser beam ionizes the target to create a hot, dense, pulsed plasma source, where emission is a result of the relaxation …

Physically-Based Visualization Of Residential Building Damage Process In Hurricane, Dezhi Liao

Electronic Theses and Dissertations

This research provides realistic techniques to visualize the process of damage to residential building caused by hurricane force winds. Three methods are implemented to make the visualization useful for educating the public about mitigation measures for their homes. First, the underline physics uses Quick Collision Response Calculation. This is an iterative method, which can tune the accuracy and the performance to calculate collision response between building components. Secondly, the damage process is designed as a Time-scalable Process. By attaching a damage time tag for each building component, the visualization process is treated as a geometry animation allowing users to navigate …

Real-Time Tree Simulation Using Verlet Integration, Bobak Manavi

Electronic Theses and Dissertations

One of the most important challenges in real-time simulation of large trees and vegetation is the vast number of calculations required to simulate the interactions between all the branches in the tree when external forces are applied to it. This paper will propose the use of algorithms employed by applications like cloth and soft body simulations, where objects can be represented by a finite system of particles connected via spring-like constraints, for the structural representation and manipulation of trees in real-time. We will then derive and show the use of Verlet integration and the constraint configuration used for simulating trees …

Effect Of Inner Scale Atmospheric Spectrum Models On Scintillation In All Optical Turbulence Regimes, Kenneth Mayer

Electronic Theses and Dissertations

Experimental studies have shown that a "bump" occurs in the atmospheric spectrum just prior to turbulence cell dissipation.1,3,4 In weak optical turbulence, this bump affects calculated scintillation. The purpose of this thesis was to determine if a "non-bump" atmospheric power spectrum can be used to model scintillation for plane waves and spherical waves in moderate to strong optical turbulence regimes. Scintillation expressions were developed from an "effective" von Karman spectrum using an approach similar to that used by Andrews et al.8,14,15 in developing expressions from an "effective" modified (bump) spectrum. The effective spectrum extends the Rytov approximation into all optical …

Modeled And Observed N2 Lyman-Birge-Hopfield Band Emissions Earth's Dayglow: A Comparison, Donald Murray

Electronic Theses and Dissertations

Ultraviolet (UV) spectra obtained from Earth’s dayglow contain important information for understanding the thermosphere, and the N2 Lyman-Birge-Hopfield (LBH) bands are possibly the most useful emission. To be useful, a thorough understanding of how the LBH band emission varies with altitude and latitude is essential to present and future use of this emission by space-based remote sensors. Excited by photoelectron impact on N2 leading to transitions from the a 1Πg state to the ground state, the LBH emissions radiate between 1270 and 2400 Å. In addition to being populated by electron impact excitation, the a 1Πg state is populated by …

High Birefringence Liquid Crystals For Optical Communications, Amanda Jane Parish

Electronic Theses and Dissertations

High birefringence (Δn > 0.4) nematic liquid crystals are particularly attractive for infrared applications because they enable a thinner cell gap to be used for achieving fast response time and improved diffraction efficiency. In this thesis, the mesomorphic and electro‐optic properties of several new fluorinated isothiocyanate (NCS) terphenyl and phenyl tolane single compounds and mixtures are reported. The single compounds demonstrated Δn~0.35‐0.52 in the visible spectral region at room temperature and exhibit relatively low viscosity. It was found that lateral fluorine substitutions and short alkyl chains eliminate smectic phase and lower the melting temperature of the single compounds. However, the consequence …

Analytical Potential Of Polymerized Liposomes Bound To Lanthanide Ions For Qualitative And Quantitative Analysis Of Proteins, Marina Santos

Electronic Theses and Dissertations

One of the intriguing features of biological systems is the prevalence of highly selective and often very strong interactions among different cellular components. Such interactions play a variety of organizational, mechanical, and physiological roles at the cellular and organism levels. Antigen-antibody complexes are representative examples of highly selective and potent interactions involving proteins. The marked specificity of protein-antibody complexes have led to a wide range of applications in cellular and molecular biology related research. They have become an integral research tool in the present genomic and proteomic era. Unfortunately, the production of selective tools based on antigen-antibody interactions requires cumbersome …

Surface Characterization Of Thin Film Zno Capacitors By Capacitance-Voltage Measurements, Linda Smith

Electronic Theses and Dissertations

The main objective of the research was the fabrication and characterization of MOS/MIS capacitors with ZnO as the insulating layer. Comparison with the already well known behavior of MOS/MIS capacitors with SiO2 as insulator was used to facilitate determination of the ZnO characteristics. Moreover, thermal annealing of the samples led to increased understanding of the role of defects on the dielectric properties of the ZnO layers in the MOS/MIS devices. Hall-effect transport measurements and x-ray diffraction (XRD) spectroscopy are used to analyze the structure and electronic surface characteristics of the ZnO insulator. Capacitance-voltage (C-V) measurements are used to understand the …

Discrete Surface Solitons, Sergiy Suntsov

Electronic Theses and Dissertations

Surface waves exist along the interfaces between two different media and are known to display properties that have no analogue in continuous systems. In years past, they have been the subject of many studies in a diverse collection of scientific disciplines. In optics, one of the mechanisms through which optical surface waves can exist is material nonlinearity. Until recently, most of the activity in this area was focused on interfaces between continuous media but no successful experiments have been reported. However, the growing interest that nonlinear discrete optics has attracted in the last two decades has raised the question of …