Physical Sciences and Mathematics Commons^™

A Statistical Model To Determine Multiple Binding Sites Of A Transcription Factor On Dna Using Chip-Seq Data, Rasika Jayatillake

Mathematics & Statistics Theses & Dissertations

Protein-DNA interaction is vital to many biological processes in cells such as cell division, embryo development and regulating gene expression. Chromatin Immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a new technology that can reveal protein binding sites in genome with superior accuracy. Although many methods have been proposed to find binding sites for ChIP-seq data, they can find only one binding site within a short region of the genome. In this study we introduce a statistical model to identify multiple binding sites of a transcription factor within a short region of the genome using the ChIP-seq data. Mapped sequence …

Assessing Movement Of Fish Through Spectral Analysis Of Otolith Life History Scans, Renee Reilly Hoover

OES Theses and Dissertations

The ability to accurately measure movement timing across environmental gradients is fundamental for testing hypotheses in marine ecology that deal with ingress, egress, and migration of fish. Timing and patterns of movement have been estimated using life-history scans of the chemical signatures encoded in fish otoliths (ear stones). I provide a quantitative approach to examining life history scan data using spectral analysis, which retrospectively measures the movement timing for individual fish. Sagittal otoliths from juvenile Atlantic croaker (Micropogonias undulates) and adult black sea bass (Centropristis striata) were sampled using laser ablation inductively coupled plasma mass spectrometry …

Visualizing Digital Collections At Archive-It, Kalpesh Padia

Computer Science Theses & Dissertations

Archive-It, a subscription service from the Internet Archive, allows users to create,maintain, and view digital collections of web resources. The current interface of Archive-It is largely text-based, supporting drill-down navigation using lists of URIs.While this interface provides good searching capabilities, it is not efficient for browsing. In the absence of keywords, a user has to spend large amount of time trying to locate a web page of interest. In order to provide a better visual experience to the user, we have studied the underlying characteristics of Archive-It collections and implemented six different visualizations (treemap, time cloud, bubble chart, image plot, …

An Extensible Framework For Creating Personal Archives Of Web Resources Requiring Authentication, Matthew Ryan Kelly

Computer Science Theses & Dissertations

The key factors for the success of the World Wide Web are its large size and the lack of a centralized control over its contents. In recent years, many advances have been made in preserving web content but much of this content (namely, social media content) was not archived, or still to this day is not being archived,for various reasons. Tools built to accomplish this frequently break because of the dynamic structure of social media websites. Because many social media websites exhibit a commonality in hierarchy of the content, it would be worthwhile to setup a means to reference this …

Modeling, Visualizing, And Understanding Complex Tectonic Structures On The Surface And In The Sub-Surface, Steven Wild

Physics Theses & Dissertations

Plate tectonics is a relatively new theory with many details of plate dynamics which remain to be worked out. Moving plates can interact by divergence, lateral sliding, convergence, or collision. At a convergent plate boundary, a lithospheric slab of oceanic crust and upper mantle is subducted at a trench and dips down under a magmatic arc — either oceanic or continental. Textbooks show a static view of convergent boundaries but plate dynamics require that subduction zones and magmatic arcs must migrate with time. Therefore I develop animated models to help convey this motion. Also, convergent plate boundaries cannot continue along …

The Influence Of Non-Equilibrium Pressure On Rotating Flows, Irfan Rashid Zardadkhan

Mechanical & Aerospace Engineering Theses & Dissertations

This study was undertaken to investigate the influence of pressure relaxation on steady, incompressible flows with strong streamline curvature. In the early part of this dissertation research, the significance of non-equilibrium pressure forces in controlling the structure of a steady, two dimensional axial vortex was demonstrated. In order to extend the study of pressure relaxation influences on more complex rotating flows, this dissertation has examined other rotating flow features that can be associated with hurricanes, tornadoes and dust devils. To model these flows, modified boundary layer equations were developed for a fluid column rotating near a solid plane including the …

Incorporating Memory And Learning Mechanisms Into Meta-Raps, Arif Arin

Engineering Management & Systems Engineering Theses & Dissertations

Due to the rapid increase of dimensions and complexity of real life problems, it has become more difficult to find optimal solutions using only exact mathematical methods. The need to find near-optimal solutions in an acceptable amount of time is a challenge when developing more sophisticated approaches. A proper answer to this challenge can be through the implementation of metaheuristic approaches. However, a more powerful answer might be reached by incorporating intelligence into metaheuristics.

Meta-RaPS (Metaheuristic for Randomized Priority Search) is a metaheuristic that creates high quality solutions for discrete optimization problems. It is proposed that incorporating memory and learning …

Spectroscopic Characterization Of Dissolved Organic Matter: Insights Into Composition, Photochemical Transformation And Carbon Cycling, John Robert Helms

Chemistry & Biochemistry Theses & Dissertations

This dissertation explores processes affecting the composition of dissolved organic matter (DOM) and how DOM composition changes in sunlit surface waters and in the dark interior ocean. Simulated solar irradiations were used to investigate the impact of photochemistry on terrestrial waters and deep ocean DOM. The photochemically mediated processes observed in Dismal Swamp samples included (i) light induced flocculation of up to 12% of the organic matter and 84% of the dissolved iron originally present; (ii) 74-88% mineralization of dissolved organic carbon (DOC) and 95-99% bleaching of chromophoric DOM (CDOM) during 110 days of irradiation; and (iii) nearly complete loss …

De Novo Protein Structure Modeling From Cryoem Data Through A Dynamic Programming Algorithm In The Secondary Structure Topology Graph, Kamal H. Al Nasr

Computer Science Theses & Dissertations

Proteins are the molecules carry out the vital functions and make more than the half of dry weight in every cell. Protein in nature folds into a unique and energetically favorable 3-Dimensional (3-D) structure which is critical and unique to its biological function. In contrast to other methods for protein structure determination, Electron Cryorricroscopy (CryoEM) is able to produce volumetric maps of proteins that are poorly soluble, large and hard to crystallize. Furthermore, it studies the proteins in their native environment. Unfortunately, the volumetric maps generated by current advances in CryoEM technique produces protein maps at medium resolution about (~5 …

Application Of Chebyshev Formalism To Identify Nonlinear Magnetic Field Components In Beam Transport System, Michael Spata

Physics Theses & Dissertations

An experiment was conducted at Jefferson Lab's Continuous Electron Beam Accelerator Facility to develop a beam-based technique for characterizing the extent of the nonlinearity of the magnetic fields of a beam transport system. Horizontally and vertically oriented pairs of air-core kicker magnets were simultaneously driven at two different frequencies to provide a time-dependent transverse modulation of the beam orbit relative to the unperturbed reference orbit. Fourier decomposition of the position data at eight different points along the beamline was then used to measure the amplitude of these frequencies. For a purely linear transport system one expects to find solely the …

Multidentate Resorcinarene Surfactants For The Phase Transfer Of Metal Nanoparticles And Nanodiamonds: Applications In Catalysis And Diamond Film Growth, Vara Prasad Sheela

Chemistry & Biochemistry Theses & Dissertations

One main objective of the present work is to functionalize cuboctahedral platinum nanoparticles with various multidentate resorcinarene surfactants and study their influence in determining their catalytic activity. We hypothesized that catalytically active and recyclable catalysts can be achieved by incomplete yet strong passivation of the nanoparticle surfaces by using multidentate resorcinarene surfactants. We have developed phase transfer protocols for functionalizing cuboctahedral platinum nanoparticles with resorcinarene thiol or amine. Fluorescence assay confirmed that both these nanoparticles contained almost comparable unpassivated metal area. The activity of such phase transferred nanoparticles was tested in the catalytic hydrogenation of allyl alcohol. The conversion of …

Gravity Anomalies Along The East Scotia Ridge: Constraining The Relative Importance Of Magmatic And Tectonic Controls On Crustal Accretion, Briton Lee Nicholson

OES Theses and Dissertations

Similar to regions such as the Lau Basin and the Caribbean Sea, the eastern Scotia Sea is a geologically complex area that involves multiple plate boundary types. This study uses bathymetry and gravity data to infer upper mantle geodynamics in the eastern Scotia Sea region. Beneath this region is an intermediate-rate back-arc spreading center known as the East Scotia Ridge (ESR) that forms the boundary between the Scotia and Sandwich plates. To the east of the ESR are the South Sandwich island arc and the South Sandwich Trench. The ESR is a relatively young feature, with spreading estimated to have …

Friend: A Cyber-Physical System For Traffic Flow Related Information Aggregation And Dissemination, Samy S. El-Tawab

Computer Science Theses & Dissertations

The major contribution of this thesis is to lay the theoretical foundations of FRIEND — A cyber-physical system for traffic Flow-Related Information aggrEgatioN and Dissemination. By integrating resources and capabilities at the nexus between the cyber and physical worlds, FRIEND will contribute to aggregating traffic flow data collected by the huge fleet of vehicles on our roads into a comprehensive, near real-time synopsis of traffic flow conditions. We anticipate providing drivers with a meaningful, color-coded, at-a-glance view of flow conditions ahead, alerting them to congested traffic.

FRIEND can be used to provide accurate information about traffic flow and can be …

Response Surface Optimization Of Electron Beam Freeform Fabrication Depositions Using Design Of Experiments, Patricia A. Quigley

Engineering Management & Systems Engineering Theses & Dissertations

The Electron Beam Freeform Fabrication (EBF³ ) System is a material depositing, layer additive technique that produces three dimensional (3D) parts out of a wide range of metals in high vacuum, using an electron beam and wire feedstock. Screening deposition trials on a titanium alloy, Ti-6Al-4V, at the National Aeronautics Space Administration (NASA) revealed selective vaporization of the aluminum content of linear prototypes when subjected to chemical analysis. In this study, the aluminum content, bead height and bead width output responses were analyzed from a systematic study of the effects that the interactions of the EBF³ processing parameters …

Serious Game Design Principles: The Impact Of Game Design On Learning Outcomes, Michael W. Martin

Computational Modeling & Simulation Engineering Theses & Dissertations

This dissertation examines the research question "How do video game design principles affect learning outcomes in serious games?" This research first develops a theoretical foundation concerning the meaning of the terms "game" and "serious game". This conceptual clarification is broken down into analytic propositions, which state that games have participants, rules, goals and challenges, and synthetic propositions, which state that the games should be intrinsically compelling, provide meaningful choices, and be self encapsulated. Based on these synthetic propositions, three hypotheses were developed. The hypotheses are that games with an enhanced aesthetic presentation, more meaningful choices, or provide player competition will …

Population Structure And Connectivity Of An Important Pelagic Forage Fish In The Antarctic Ecosystem, Pleuragramma Antarcticum In Relation To Large Scale Circulation, Jason W. Ferguson

OES Theses and Dissertations

Ocean circulation has been identified as a major process controlling the distribution of biological material in marine systems. Large-scale transport by the Antarctic Circumpolar Current (ACC), the Ross and Weddell Gyres, and the Antarctic Coastal Current can promote spatially complex population structure in the Southern Ocean through advection. Antarctic silverfish (Pleuragramma antarcticum), a pelagic, neutrally buoyant notothenioid fish species, are distributed around the shelf systems of Antarctica and are considered an important species rivaling krill as prey for many birds, seals, whales, and other fish. We asked whether silverfish are distributed in independent, discrete populations along the shelf systems of …

Evaluation Of Electrophoretic Protein Extraction And Database-Driven Protein Identification From Marine Sediments, Eli K. Moore, Brook L. Nunn, Jessica F. Faux, David R. Goodlett, H. Rodger Harvey

OES Faculty Publications

Intact proteins comprise a major component of organic carbon and nitrogen produced globally and are likely an important fraction of organic matter in sediments and soils. Extracting the protein component from sediments and soils for mass spectral characterization and identification represents a substantial challenge given the range of products and functionalities present in the complex matrix. Multiple forms of gel electrophoresis were evaluated as a means of enhancing recovery of sedimentary protein before proteomic characterization and compared with a direct enzymatic digestion of proteins in sediments. Resulting tryptic peptides were analyzed using shotgun proteomics and tandem mass spectra were evaluated …

Coupled Physical And Biological Modeling Of Atlantic Surfclam Larval Transport And Sub-Population Connectivity In The Middle Atlantic Bight And Georges Bank, Xinzhong (Peter) Zhang, Dale B. Haidvogel, John M. Klinck, Roger Mann, Eric N. Powell

CCPO Publications

No abstract provided.

How Do Marine Protected Area Strategies Influence Metapopulation Genetic Connectivity? A Modeling Study With Oysters, Daphne Munroe, Eric N. Powell, John M. Klinck, Eileen E. Hofmann

CCPO Publications

No abstract provided.

Circulation, Vol. 17, No. 2, Center For Coastal Physical Oceanography, Old Dominion University, A. D. Kirwan Jr.

CCPO Circulation

Spring 2012 issue of CCPO Circulation featuring "CCPO Celebrates 20 Years: A retrospective" by A. D. Kirwan Jr., former CCPO faculty member

Section Abstracts: Environmental Science

Virginia Journal of Science

Abstracts of the Environmental Science Section for the 90th Annual Meeting of the Virginia Academy of Science, May 23-25, 2012, Norfolk State University, Norfolk, Virginia.

Section Abstracts: Computer Science

Virginia Journal of Science

Abstracts of the Computer Science Section for the 90th Annual Meeting of the Virginia Academy of Science, May 23-25, 2012, Norfolk State University, Norfolk, Virginia.

Section Abstracts: Astronomy, Mathematics And Physics With Materials Science

Virginia Journal of Science

Abstracts of the Astronomy, Mathematics, and Physics with Material Science Section for the 90th Annual Meeting of the Virginia Academy of Science, May 23-25, 2012, Norfolk State University, Norfolk, Virginia

Old Dominion University Climate Change And Sea Level Rise Initiative, Spring 2012, Larry P. Atkinson (Editor)

CCSLRI Newsletters

Summer 2012 Newsletter of the Old Dominion University Climate Change and Sea Level Rise Initiative

Section Abstracts: Chemistry

Virginia Journal of Science

Abstracts of the Chemistry Section for the 90th Annual Meeting of the Virginia Academy of Science, May 23-25, 2012, Norfolk State University, Norfolk, Virginia.

Measurement Of The Neutron F2 Structure Function Via Spectator Tagging With Clas, N. Baillie, S. Tkachenko, J. Zhang, P. Bosted, S. Bültmann, M. E. Christy, H. Fenker, K. A. Griffioen, C. E. Keppel, S. E. Kuhn, K. P. Adhikari, D. Adikaram, M. J. Amaryan, H. Baghdasaryan, G. Dodge, N. Guler, C. E. Hyde, A. Klein, A. Klimenko, L. B. Weinstein

Physics Faculty Publications

We report on the first measurement of the F₂ structure function of the neutron from the semi-inclusive scattering of electrons from deuterium, with low-momentum protons detected in the backward hemisphere. Restricting the momentum of the spectator protons to ≲ 100MeV/c and their angles to ≳ 100° relative to the momentum transfer allows an interpretation of the process in terms of scattering from nearly on-shell neutrons. The Fⁿ₂ data collected cover the nucleon-resonance and deep-inelastic regions over a wide range of Bjorken x for 0.65 < Q² < 4.52 GeV², with uncertainties from nuclear corrections estimated to be less …

Single And Double Spin Asymmetries For Pion Electro-Production From The Deuteron In The Resonance Region, Sharon L. Careccia

Physics Theses & Dissertations

The single and double spin asymmetries A_t and A_et have been measured in π^- electro-production off the deuteron using a longitudinally polarized electron beam and a polarized ND₃ target. The electron beam was polarized using a strained GaAs cathode and the target was polarized using Dynamic Nuclear Polarization. The data were collected at beam energies of 1.6, 1.7, 2.5 and 4.2 GeV in Hall B at Jefferson Lab in the spring of 2001. The final state particles were detected in the CEBAF Large Acceptance Spectrometer (CLAS). The d(e,e'π-p)p exclusive channel was identified using the missing mass …

Case Studies In Many-Body Physics, Ana Samolov

Physics Theses & Dissertations

The many-body problem refers to any physical problem made of more than two interacting particles. With increasing number of particles in a system, their coupling and entanglement becomes more complex, and there is no general analytic solution even for a three-body classical or quantum systems. However, some of the most fascinating phenomena in nature are products of collective effects. Therefore, significant efforts have been made in both experiment and theory to unravel some specific many-body problems. If we look at still unanswered physics questions we see that for most of these problems addressing the many-body interactions is a key issue. …

Image-Guided Robotic Dental Implantation With Natural-Root-Formed Implants, Xiaoyan Sun

Electrical & Computer Engineering Theses & Dissertations

Dental implantation is now recognized as the standard of the care for tooth replacement. Although many studies show high short term survival rates greater than 95%, long term studies (> 5 years) have shown success rates as low as 41.9%. Reasons affecting the long term success rates might include surgical factors such as limited accuracy of implant placement, lack of spacing controls, and overheating during the placement.

In this dissertation, a comprehensive solution for improving the outcome of current dental implantation is presented, which includes computer-aided preoperative planning for better visualization of patient-specific information and automated robotic site-preparation for superior …

Optimization Framework For A Radio Frequency Gun Based Injector, Alicia S. Hofler

Electrical & Computer Engineering Theses & Dissertations

Linear accelerator based light sources are used to produce coherent x-ray beams with unprecedented peak intensity. In these devices, the key parameters of the photon beam such as brilliance and coherence are directly dependent on the electron beam parameters. This leads to stringent beam quality requirements for the electron beam source. Radio frequency (RF) guns are used in such light sources since they accelerate electrons to relativistic energies over a very short distance, thus minimizing the beam quality degradation due to space charge effects within the particle bunch. Designing such sources including optimization of its beam parameters is a complex …