Physical Sciences and Mathematics Commons^™

Mycobacteriosis-Associated Mortality In Wild Striped Bass (Morone Saxatilis) From Chesapeake Bay, Usa, D. T. Gauthier, R. J. Latour, D. M. Heisey, C. F. Bonzek, J. Gartland, E. J. Burge, W. K. Vogelbein

Biological Sciences Faculty Publications

The striped bass (Morone saxatilis) is an economically and ecologically important finfish species along the Atlantic seaboard of the United States. Recent stock assessments in Chesapeake Bay (USA) indicate that non-fishing mortality in striped bass has increased since 1999, concomitant with very high (>50%) prevalence of visceral and dermal disease caused by Mycobacterium spp. Current fishery assessment models do not differentiate between disease and other components of non-fishing mortality (e. g., senescence, predation); therefore, disease impact on the striped bass population has not been established. Specific measurement of mortality associated with mycobacteriosis in wild striped bass is …

Nutrient And Carbon Dynamics In The Chesapeake Bay Outflow Plume And Their Effect On The Coastal Ocean Environment, Katherine C. Filippino

OES Theses and Dissertations

Seasonally resolved nutrient and carbon fluxes from estuaries to the coastal ocean are poorly constrained. Nutrient and carbon cycling in highly productive regions like the Chesapeake Bay outflow plume and surrounding coastal environments greatly affect our global understanding of carbon cycling. The overall questions for the research described in this dissertation stem from the need to close global carbon budgets, and obtain a fundamental understanding of nutrient dynamics in a coastal region heavily influenced by seasonality and human impacts.

Within the framework of physical characteristics of the outflow plume and through the characterization of nutrient concentrations, primary productivity rates, and …

Biological Networks: Modeling And Structural Analysis, Emad Y. Ramadan

Computer Science Theses & Dissertations

Biological networks are receiving increased attention due to their importance in understanding life at the cellular level. There exist many different kinds of biological networks, and different models have been proposed for them. In this dissertation we focus on suitable network models for representing experimental data on protein interaction networks and protein complex networks (protein complexes are groups of proteins that associate to accomplish some function in the cell), and to design algorithms for exploring such networks. Our goal is to enable biologists to identify the general principles that govern the organization of protein-protein interaction networks and protein complex networks. …

Nonlinear Random Response Of Large-Scale Sparse Finite Element Plate Bending Problems, Swati Chokshi

Civil & Environmental Engineering Theses & Dissertations

Acoustic fatigue is one of the major design considerations for skin panels exposed to high levels of random pressure at subsonic/supersonic/hypersonic speeds. The nonlinear large deflection random response of the single-bay panels aerospace structures subjected to random excitations at various sound pressure levels (SPLs) is investigated. The nonlinear responses of plate analyses are limited to determine the root-mean-square displacement under uniformly distributed pressure random loads. Efficient computational technologies like sparse storage schemes and parallel computation are proposed and incorporated to solve large-scale, nonlinear large deflection random vibration problems for both types of loading cases: (1) synchronized in time and (2) …

Hypersonic Boundary Layer Receptivity To Acoustic Disturbances Over Cones, Kursat Kara

Mechanical & Aerospace Engineering Theses & Dissertations

The receptivity mechanisms of hypersonic boundary layers to free stream acoustic disturbances are studied using both linear stability theory (LST) and direct numerical simulations (DNS). A computational code is developed for numerical simulation of steady and unsteady hypersonic flow over cones by combining a fifth-order weighted essentially non-oscillatory (WENO) scheme with third-order total-variation-diminishing (TVD) Runge-Kutta method. Hypersonic boundary layer receptivity to free-stream acoustic disturbances in slow and fast modes over 5-degree, half-angle blunt cones and wedges are numerically investigated. The free-stream Mach number is 6.0, and the unit Reynolds number is 7.8×106/ft. Both the steady and unsteady solutions are obtained …

Catalytic Wet Air Oxidation Of Mono Azo Dye Orange Ii: Catalyst Selection, Reaction Kinetics, And Modeling, Pinar Ozdural

Civil & Environmental Engineering Theses & Dissertations

Wastewaters generated as byproducts of dyeing processes are not treatable with conventional methods. It has been estimated that among the 900,000 tons of different dyes produced annually in the world, approximately 10–15% are lost in wastewater streams during manufacturing and processing operations. Once in rivers and streams, dyes cause major problems, such as reducing light penetration, or displaying toxic effects on aquatic life. Therefore, it is essential that dyes are removed from wastewaters before being discharged into the environment.

This study focuses on the catalytic wet air oxidation (CWAO) of Orange II, a mono azo dye used in large amounts …

Massive Spatiotemporal Watershed Hydrological Storm Event Response Model (Mhserm) With Time-Lapsed Nexrad Radar Feed, Changqing Song

Civil & Environmental Engineering Theses & Dissertations

Correctly and efficiently estimating hydrological responses corresponding to a specific storm event at the streams in a watershed is the main goal of any sound water resource management strategy. Methods for calculating a stream flow hydrograph at the selected streams typically require a great deal of spatial and temporal watershed data such as geomorphological data, soil survey, landcover, precipitation data, and stream network information to name a few. However, extracting and preprocessing such data for estimation and analysis is a hugely time-consuming task, especially for a watershed with hundreds of streams and lakes and complicated landcover and soil characteristics. To …

Improved Constrained Global Optimization For Estimating Molecular Structure From Atomic Distances, Terri Marie Grant

Mathematics & Statistics Theses & Dissertations

Determination of molecular structure is commonly posed as a nonlinear optimization problem. The objective functions rely on a vast amount of structural data. As a result, the objective functions are most often nonconvex, nonsmooth, and possess many local minima. Furthermore, introduction of additional structural data into the objective function creates barriers in finding the global minimum, causes additional computational issues associated with evaluating the function, and makes physical constraint enforcement intractable. To combat the computational problems associated with standard nonlinear optimization formulations, Williams et al. (2001) proposed an atom-based optimization, referred to as GNOMAD, which complements a simple interatomic distance …

Dgm-Fd: A Finite Difference Scheme Based On The Discontinuous Galerkin Method, Anne Marguerite Fernando

Mathematics & Statistics Theses & Dissertations

Accurate and efficient numerical wave propagation is important in many areas of study such as computational aero-acoustics (CAA). While dissipation and dispersion errors influence the accuracy of a method, efficiency can be assessed by convergence rates and effective adaptability to different mesh structures. Finite difference and finite element methods are commonly used numerical schemes in CAA. Finite difference methods have the advantages of ease of use as well as high order convergence, but often require a uniform grid, and stable boundary closure can be non-trivial. Finite element methods adapt well to different mesh structures but can become difficult to implement …

Next-To-Leading Order Evolution Of Color Dipoles, Ian Balitsky, Giovanni A. Chirilli

Physics Faculty Publications

The small-x deep inelastic scattering in the saturation region is governed by the nonlinear evolution of Wilson-line operators. In the leading logarithmic approximation it is given by the Balitsky-Kovchegov equation for the evolution of color dipoles. In the next-to-leading order the Balitsky-Kovchegov equation gets contributions from quark and gluon loops as well as from the tree gluon diagrams with quadratic and cubic nonlinearities. We calculate the gluon contribution to the small-x evolution of Wilson lines (the quark part was obtained earlier).

Electroexcitation Of The Roper Resonance For 1.7 < Q² < 4.5gev² In Ep → Enπ+, Clas Collaboration, M. J. Amaryan, M. Bektasoglu, S. Bültmann, S. L. Careccia, K. V. Dharmawardane, G. E. Dodge, T. A. Forest, G. Gavalian, N. Guler, C. E. Hyde, A. Klein, S. E. Kuhn, L. M. Qin, L. B. Weinstein, J. Yun, J. Zhang

Physics Faculty Publications

The helicity amplitudes of the electroexcitation of the Roper resonance are extracted for 1.7 < Q² < 4.5 GeV² from recent high precision JLab-CLAS cross section and longitudinally polarized beam asymmetry data for π⁺ electroproduction on protons at W=1.15-1.69 GeV. The analysis is made using two approaches, dispersion relations and a unitary isobar model, which give consistent Q² behavior of the helicity amplitudes for the gamma*p -> N (1440)P₁₁ transition. It is found that the transverse helicity amplitude A _1/2, which is large and negative at Q²=0, becomes large and positive at Q² similar or equal …

First Measurement Of Target And Double Spin Asymmetries For Ep → Epπ° In The Nucleon Resonance Region Above The Δ (1232), Clas Collaborative, M. J. Amaryan, H. Bagdasaryan, S. Bültmann, G. E. Dodge, N. Guler, N. Kalantarians, A. Klein, S. E. Kuhn, S. Tkachenko, L. B. Weinstein, J. Zhang

Physics Faculty Publications

The exclusive channel polarized proton(polarized e,e' p)π⁰ was studied in the first and second nucleon resonance regions in the Q² range from 0.187 to 0.770 GeV² at Jefferson Lab using the CEBAF Large Acceptance Spectrometer (CLAS). Longitudinal target and beam-target asymmetries were extracted over a large range of center-of-mass angles of the π⁰ and compared to the unitary isobar model MAID, the dynamic model by Sato and Lee, and the dynamic model DMT. A strong sensitivity to individual models was observed, in particular for the target asymmetry and in the higher invariant mass region. This data …

Electroproduction Of ɸ(1020) Mesons At 1.4 ≤ Q² ≤ 3.8 Gev² Measured With The Clas Spectrometer, Clas Collaboration, M. J. Amaryan, H. Bagdasaryan, M. Bektasoglu, S. Bültmann, S. L. Careccia, K. V. Dharmawardane, G. E. Dodge, G. Gavalian, C. E. Hyde-Wright, H. G. Jungst, N. Kalantarians, A. Klien, A. V. Klimenko, S. E. Kuhn, R. A. Niyazov, T. Tkachenko, L. B. Weinstein, J. Zhang

Physics Faculty Publications

Electroproduction of exclusive ϕ vector mesons has been studied with the CLAS detector in the kinematic range 1.4 ⩽ Q² ⩽ 3.8 GeV² ,0.0 ⩽ t′ ⩽3.6 GeV² , and 2.0 ⩽ W ⩽ 3.0 GeV. The scaling exponent for the total cross section as 1/(Q² +M²_ϕ)ⁿ was determined to be n = 2.49 ± 0.33. The slope of the four-momentum transfer t′ distribution is b_ϕ = 0.98 ± 0.17 GeV^-2 . Under the assumption of s -channel helicity conservation, we determine the ratio of longitudinal to transverse cross sections …

Measurement Of Deeply Virtual Compton Scattering Beam-Spin Asymmetries, Clas Collaboration, H. Bagdasaryan, S. L. Careccia, K. V. Dharmawardane, G. E. Dodge, G. Gavalian, C. E. Hyde, H. G. Juengst, N. Kalantarians, A. Klein, A. V. Klimenko, S. E. Kuhn, J. Lachniet, S. Tkachenko, L. B. Weinstein, J. Zhang

Physics Faculty Publications

The beam-spin asymmetries in the hard exclusive electroproduction of photons on the proton (^→ep→epγ ) were measured over a wide kinematic range and with high statistical accuracy. These asymmetries result from the interference of the Bethe-Heitler process and of deeply virtual Compton scattering. Over the whole kinematic range (_xB from 0.11 to 0.58, Q² from 1 to 4.8  GeV², −t from 0.09 to 1.8  GeV²), the azimuthal dependence of the asymmetries is compatible with expectations from leading-twist dominance, A ≃ asinϕ/(1+ccosϕ). This extensive set of data can thus be used to …

Measurement Of Ep→Epπᵒ Beam Spin Asymmetries Above The Resonance Region, Clas Collaborative, M. J. Amaryan, H. Bagdasaryan, S. Bültmann, S. L. Careccia, K. V. Dharmawardane, G. E. Dodge, G. Gavalian, N. Guler, C. E. Hyde-Wright, N. Kalantarians, A. Klien, A. V. Klimenko, S. E. Kuhn, M. R. Niroula, S. Tkachenko, L. B. Weinstein, J. Zhang

Physics Faculty Publications

The beam spin asymmetry (BSA) in the exclusive reaction ^→ep→epπ0 was measured with the CEBAF 5.77 GeV polarized electron beam and Large Acceptance Spectrometer (CLAS). The x_B,Q²,t , and ϕ dependences of the π⁰ BSA are presented in the deep inelastic regime. The asymmetries are fitted with a sinϕ function and their amplitudes are extracted. Overall, they are of the order of 0.04–0.11 and roughly independent of t . This is the signature of a nonzero longitudinal-transverse interference. The implications concerning the applicability of a formalism based on generalized parton distributions, as well as …

Interactions Between Changing Pco2, N2 Fixation, And Fe Limitation In The Marine Unicellular Cyanobacterium Crocosphaera, Fei-Xue Fu, Margaret R. Mulholland, Nathan S. Garcia, Aaron Beck, Mark E. Warner, Sergio A. Sañudo, David A. Hutchins

OES Faculty Publications

We examined the physiological responses of steady-state iron (Fe)-replete and Fe-limited cultures of the biogeochemically critical marine unicellular diazotrophic cyanobacterium Crocosphaera at glacial (19 Pa; 190 ppm), current (39 Pa; 380 ppm), and projected year 2100 (76 Pa; 750 ppm) CO₂ levels. Rates of N₂ and CO₂ fixation and growth increased in step with increasing partial pressure of CO₂ (pCO₂), but only under Fe- replete conditions. N₂) and carbon fixation rates at 75 Pa CO₂ were 1.4-1.8-fold and 1.2-2.0-fold higher, respectively, relative to those at present day and glacial pCO_{2 …}

Creating Preservation-Ready Web Resources, Joan A. Smith, Michael L. Nelson

Computer Science Faculty Publications

There are innumerable departmental, community, and personal web sites worthy of long-term preservation but proportionally fewer archivists available to properly prepare and process such sites. We propose a simple model for such everyday web sites which takes advantage of the web server itself to help prepare the site's resources for preservation. This is accomplished by having metadata utilities analyze the resource at the time of dissemination. The web server responds to the archiving repository crawler by sending both the resource and the just-in-time generated metadata as a straight-forward XML-formatted response. We call this complex object (resource + metadata) a CRATE. …

Efficient Corona Training Protocols For Sensor Networks, Alan A. Bertossi, Stephan Olariu, Cristina M. Pinotti

Computer Science Faculty Publications

Phenomenal advances in nano-technology and packaging have made it possible to develop miniaturized low-power devices that integrate sensing, special-purpose computing, and wireless communications capabilities. It is expected that these small devices, referred to as sensors, will be mass-produced and deployed, making their production cost negligible. Due to their small form factor and modest non-renewable energy budget, individual sensors are not expected to be GPS-enabled. Moreover, in most applications, exact geographic location is not necessary, and all that the individual sensors need is a coarse-grain location awareness. The task of acquiring such a coarse-grain location awareness is referred to as training. …

Plasma Medicine, Mounir Laroussi, Alexander Fridman

Electrical & Computer Engineering Faculty Publications

Recent demonstrations of plasma technology in the treatment of living cells, tissues, and organs are creating a newfield at the intersection of plasma science and technology with biology and medicine - Plasma Medicine.

Vegetation Identification Based On Satellite Imagery, Vamsi K.R. Mantena, Ramu Pedada, Srinivas Jakkula, Yuzhong Shen, Jiang Li, Hamid R. Arabnia (Ed.)

Electrical & Computer Engineering Faculty Publications

Automatic vegetation identification plays an important role in many applications including remote sensing and high performance flight simulations. This paper presents a method to automatically identify vegetation based upon satellite imagery. First, we utilize the ISODATA algorithm to cluster pixels in the images where the number of clusters is determined by the algorithm. We then apply morphological operations to the clustered images to smooth the boundaries between clusters and to fill holes inside clusters. After that, we compute six features for each cluster. These six features then go through a feature selection algorithm and three of them are determined to …

Naturally Present Fatty Acids As Internal Calibrants For Fourier Transform Mass Spectra Of Dissolved Organic Matter, Rachel L. Sleighter, Georgina A. Mckee, Zhanfei Liu, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

The analysis of dissolved organic matter ( DOM) by Fourier transform ion cyclotron resonance mass spectrometry ( FTICR- MS) has gained wide interest recently, driven primarily by its ultrahigh resolving power and mass accuracy. Accurate calibration of mass spectra is a key step to successfully decipher the DOM components. We propose a simple and accurate method to internally calibrate the peaks in the complex spectra without the need to add a calibrant. Mass spectra of DOM samples from the Dismal Swamp, Virginia, and the lower Chesapeake Bay display the presence of naturally occurring fatty acids which can be readily recognized …

Absorption Spectral Slopes And Slope Ratios As Indicators Of Molecular Weight, Source, And Photobleaching Of Chromophoric Dissolved Organic Matter, John R. Helms, Aron Stubbins, Jason D. Ritchie, Elizabeth C. Minor, David J. Kieber, Kenneth Mopper

Chemistry & Biochemistry Faculty Publications

A new approach for parameterizing dissolved organic matter ( DOM) ultraviolet-visible absorption spectra is presented. Two distinct spectral slope regions ( 275-295 nm and 350-400 nm) within log-transformed absorption spectra were used to compare DOM from contrasting water types, ranging from wetlands (Great Dismal Swamp and Suwannee River) to photobleached oceanic water ( Atlantic Ocean). On the basis of DOM size-fractionation studies ( ultrafiltration and gel filtration chromatography), the slope of the 275-295- nm region and the ratio of these slopes (S_R; 275-295- nm slope : 350-400- nm slope) were related to DOM molecular weight ( MW) and …

Technical Note: Molecular Characterization Of Aerosol-Derived Water Soluble Organic Carbon Using Ultrahigh Resolution Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, A. S. Wozniak, J. E. Bauer, R. L. Sleighter, R. M. Dickhut, Patrick Hatcher

Chemistry & Biochemistry Faculty Publications

Despite the acknowledged relevance of aerosol-derived water-soluble organic carbon (WSOC) to climate and biogeochemical cycling, characterization of aerosol WSOC has been limited. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) was utilized in this study to provide detailed molecular level characterization of the hi(,h molecular weight (HMW; m/z>223) component of aerosol-derived WSOC collected from rural sites in Virginia and New York, USA. More than 3000 peaks were detected by ESI FT-ICR MS within a m/z range of 223-600 for each sample. Approximately 86% (Virginia) and 78% (New York) of these peaks were assigned molecular formulas …

Cold Atmospheric Pressure Air Plasma Jet For Medical Applications, Juergen Friedrich Kolb, A.-A H. Mohamed, R. O. Price, R. J. Swanson, A. Bowman, R. L. Chiavarini, Michael W. Stacey

Bioelectrics Publications

By flowing atmospheric pressure air through a direct current powered microhollow cathode discharge, we were able to generate a 2 cm long plasma jet. With increasing flow rate, the flow becomes turbulent and temperatures of the jet are reduced to values close to room temperature. Utilizing the jet, yeast grown on agar can be eradicated with a treatment of only a few seconds. Conversely, animal studies show no skin damage even with exposures ten times longer than needed for pathogen extermination. This cold plasma jet provides an effective mode of treatment for yeast infections of the skin.

Sublethal And Killing Effects Of Atmospheric-Pressure, Nonthermal Plasma On Eukaryotic Microalgae In Aqueous Media, Ying Zhong Tang, Xin Pei Lu, Mounir Laroussi, Fred C. Dobbs

OES Faculty Publications

In-depth studies on the interaction of nonthermal plasmas with microorganisms usually focus on bacteria; only little attention has been given to their effects on more complex eukaryotic cells. We report here nonthermal plasma's effects on cell motility, viability staining, and morphology of eukaryotic microalgae, with three marine dinoflagellates and a marine diatom as major targets. The effects on motility and viability staining depended on the time of exposure to plasma and the species of microalgae. We observed a strong pH decrease in aqueous samples (marine and freshwater algal cultures, their culture media, and deionized water) after exposure to plasma, and …

Lignin Degradation In Wood-Feeding Insects, Scott M. Geib, Timothy R. Filley, Patrick G. Hatcher, Kelli Hoover, John E. Carlson, Maria Del Mar Jimenez-Gasco, Akiko Nakagawa-Izumi, Rachel L. Sleighter, Ming Tien

Chemistry & Biochemistry Faculty Publications

The aromatic polymer lignin protects plants from most forms of microbial attack. Despite the fact that a significant fraction of all lignocellulose degraded passes through arthropod guts, the fate of lignin in these systems is not known. Using tetramethylammonium hydroxide thermochemolysis, we show lignin degradation by two insect species, the Asian longhorned beetle (Anoplophora glabripennis) and the Pacific dampwood termite (Zootermopsis angusticollis). In both the beetle and termite, significant levels of propyl side-chain oxidation (depolymerization) and demethylation of ring methoxyl groups is detected; for the termite, ring hydroxylation is also observed. In addition, culture-independent fungal gut …

Ratios Of 15N/12C And 4He/12C Inclusive Electroproduction Cross Sections In The Nucleon Resonance Region, P. E. Bosted, R. Fersch, G. Adams, M. Amaryan, S. Anefalos, M. Anghinolfi, G. Asryan, H. Avakian, H. Badasaryan, N. Baillie, M. Bektasoglu, S. Bültmann, S. L. Careccia, G. E. Dodge, K. V. Dharmawardane, T. A. Forest, G. Gavalian, N. Guler, C. E. Hyde-Wright, N. Kalantarians, A. Klein, S. E. Kuhn, J. Lachniet, R. A. Niyazov, L. M. Qin, F. Sabatié, S. Tkachenko, L. B. Weinstein, J. Zhang, Clas Collaboration

Physics Faculty Publications

The (W,Q²) dependence of the ratio of inclusive electron scattering cross sections for ¹⁵N/¹²C was determined in the kinematic ranges 0.8 < W < 2 GeV and 0.2 < Q² < 1 GeV² using 2.285 GeV electrons and the CLAS detector at Jefferson Lab. The ratios exhibit only slight resonance structure, in agreement with a simple phenomenological model and an extrapolation of deep-inelastic scattering ratios to low Q². Ratios of ⁴He/¹²C using 1.6 to 2.5 GeV electrons were measured with very high statistical precision and were used to correct for He in the N and C targets. …

Lipschitz Continuity Of The Best Approximation Operator In Vector-Valued Chebyshev Approximation, Martin Bartelt, John Swetits

Mathematics & Statistics Faculty Publications

When G is a finite dimensional Haar subspace of C(X, R^k), the vector-valued continuous functions (including complex-valued functions when k is 2) from a finite set X to Euclidean k-dimensional space, it is well-known that at any function f in C(X, R^k) the best approximation operator satisfies the strong unicity condition of order 2 and a Lipschitz (H˝older) condition of order 1/2. This note shows that in fact the best approximation operator satisfies the usual Lipschitz condition of order 1.

Studies Of Breakdown In A Pressurized Rf Cavity, M. Bastaninejad, A. A. Elmustafa, C. M. Ankenbrandt, A. Moretti, M. Popovic, K. Yonehara, D. M. Kaplan, M. Alsharo'a, P. M. Hanlet, R. P. Johnson, M. Kuchnir, D. Newsham, D. V. Rose, C. Thoma, D. R. Welch

Mechanical & Aerospace Engineering Faculty Publications

Microscopic images of the surfaces of metallic electrodes used in high-pressure gas-filled 805 MHz RF cavity experiments [1] have been used to investigate the mechanism of RF breakdown [2]. The images show evidence for melting and boiling in small regions of ∼10 micron diameter on tungsten, molybdenum, and beryllium electrode surfaces. In these experiments, the dense hydrogen gas in the cavity prevents electrons or ions from being accelerated to high enough energy to participate in the breakdown process so that the only important variables are the fields and the metallic surfaces. The distributions of breakdown remnants on the electrode surfaces …

Differences In The Performance Of Knowledge Transfer Across Projects: A Study Of Gender And Role Of Key Project Stakeholders, Rafael E. Landaeta, Catherine Vergopia, Rey N. Diaz

Engineering Management & Systems Engineering Faculty Publications

This investigation contributes empirical results of differences identified in key project stakeholders with respect to their use of knowledge transferred across projects. Gender and role were the two individual characteristics investigated. Project managers and members of project teams were the key stakeholders analyzed. Data was collected from 71 closed projects using a survey composed of closed-ended questions. The data collected was cross tabulated and statistically analyzed using Friedman's test and Spearman's correlation. The results provide evidence of the association of the performance of knowledge transfer across projects with (a) the individual factors of gender and role of key project stakeholders …