Physical Sciences and Mathematics Commons^™

Zero-Inflated Models To Identify Transcription Factor Binding Sites In Chip-Seq Experiments, Sameera Dhananjaya Viswakula

Mathematics & Statistics Theses & Dissertations

It is essential to determine the protein-DNA binding sites to understand many biological processes. A transcription factor is a particular type of protein that binds to DNA and controls gene regulation in living organisms. Chromatin immunoprecipitation followed by highthroughput sequencing (ChIP-seq) is considered the gold standard in locating these binding sites and programs use to identify DNA-transcription factor binding sites are known as peak-callers. ChIP-seq data are known to exhibit considerable background noise and other biases. In this study, we propose a negative binomial model (NB), a zero-inflated Poisson model (ZIP) and a zero-inflated negative binomial model (ZINB) for peak-calling. …

Exploring The Effect Of Climate Change On Biological Systems, Nardos Sori

Chemistry & Biochemistry Theses & Dissertations

The present and potential future effect of global warming on the ecosystem has brought climate change to the forefront of scientific inquiry and discussion. For our investigation, we selected two organisms, one from cyanobacteria and one from a cereal plant to determine how climate change may impact these biological systems. The study involved understanding the physiological and adaptive responses at both the genetic and protein function levels to counteract environmental stresses. An increase in atmospheric carbon dioxide is a key factor in global climate change and can lead to alterations in ocean chemistry. Cyanobacteria are important, ancient and ubiquitous organisms …

Investigation Of The Potential For Algaenan To Produce Hydrocarbon Based Fuels From Algae By Hydrous Pyrolysis, Wassim Adel Obeid

Chemistry & Biochemistry Theses & Dissertations

The use of algae as a feedstock for hydrous pyrolysis has a high potential for producing biofuels. The non-food nature of algae in addition to the various advantages associated with the hydrous pyrolysis process makes this combination for the production of biofuels of high interest. However, current results from algae processing have alluded to some challenges: byproducts arising from the thermal transformation of carbohydrates and proteins, which become incorporated in the oil fraction, result in high oxygen and nitrogen contents of the oil. Accordingly, this produces an oil of low quality for refineries. This dissertation investigates use of a pretreatment …

Development Of Superconducting Spoke Cavities For High-Velocity Applications, Christopher Shawn Hopper

Physics Theses & Dissertations

To date, superconducting spoke cavities have been designed, developed, and tested for particle velocities up to β0 ~ 0.6, but there is a growing interest in possible applications of spoke cavities for high-velocity applications. The first task is to explore the design parameter space for low-frequency, high-velocity, single- and double-spoke superconducting cavities in order to determine how each design parameter affects the electromagnetic properties, in particular the surface electromagnetic fields and the shunt impedance. Once an electromagnetically optimized, high-velocity spoke cavity is designed, there are several other characteristics that need to be investigated. These include multipacting scenarios, higher-order mode excitation …

Catalysis Of Stark-Tuned Interactions Between Ultracold Rydberg Atoms, Aye Lu Win

Physics Theses & Dissertations

We present the study of the catalysis effect in the resonant energy transfer between ultracold ⁸⁵Rb Rydberg atoms. We have investigated the energy transfer process of 34p + 34p → 34s + 35s, and observed Stark-tuned Forster resonances. When additional Rydberg atoms of 34d state are included in the interaction, an increase in the population of 34s states atoms is observed. Although the 34d state atoms do not directly participate in the resonant energy transfer that produces 34s state atoms, they add an additional interaction channel 34p + 34 …

Meson Photo-Couplings From Lattice Quantum Chromodynamics, Christian J. P. Shultz

Physics Theses & Dissertations

We explore the calculation of three-point functions featuring a vector current insertion in lattice Quantum Chromodynamics. These three-point functions, in general, contain information about many radiative transition matrix elements simultaneously. We develop and implement the technology necessary to isolate a single matrix element via the use of optimized operators, operators designed to interpolate a single meson eigenstate, which are constructed as variationally optimized linear combination of meson interpolating fields within a large basis. In order to frame the results we also explore some well known phenomenology arising within the context of the constituent quark model before transitioning to a lattice …

Photoassociative Spectroscopy Of Ultracold Argon And Krypton Confined In A Magneto Optical Trap, Maha Khaled Omar

Physics Theses & Dissertations

Creating ultracold molecules has attracted considerable interest in the last decade. Once created, such molecules can be used for precision spectroscopy or to study chemical reactions at ultracold tem peratures. Several techniques have been developed to produce ultracold molecules; the most common is photoassociation where two ultracold atoms collide in the presence of light that induces a free-bound transition to an excited molecular state. Photoassociation can also be used to perform spectroscopy in order to map out the ro-vibrational levels of a molecular state. In this dissertaiotn, we report on our Photoasociative Spectroscopy (PAS) studies conducted separately in argon and …

Generation Of Multi-Charged Aluminum Ions From Femtosecond Laser Induced Plasma, Frederick Guy Wilson

Electrical & Computer Engineering Theses & Dissertations

Laser-induced plasma multi-charged ion (MCI) sources have gained in popularity over the last thirty years with the advent of reliable, high peak power, short temporal pulse laser systems. Utilization of laser-induced plasma MCI sources allows for production of a wide array of ion species from a variety of source target materials. In this thesis an investigation of the generation of MCis from an aluminum (Al) target source through laser-induced plasma from a femtosecond (fs) pulsed laser system is outlined and the results presented and analyzed. In order to characterize the production of the Al MCis resulting from the fs laser …

Toward A Theory Of Multi-Method Modeling And Simulation Approach, Mariusz A. Balaban

Computational Modeling & Simulation Engineering Theses & Dissertations

The representation via simulation models can easily lead to simulation models too simple for their intended purpose, or with too much detail, making them hard to understand. This problem is related to limitations of the modeling and simulation methods. A multi-method Modeling and Simulation (M&S) approach has the potential for improved representation by taking advantage of methods' strengths and mitigating their weaknesses. Despite a high appeal for using multiple M&S methods, several related problems should be addressed first. The current level of theoretical, methodological, and pragmatic knowledge related to a multi-method M&S approach is limited. It is problematic that there …

Java Animated Software For Teaching The Frank-Wolfe Algorithm For Static Traffic Network Equilibrium, Zhi Li

Computational Modeling & Simulation Engineering Theses & Dissertations

The popular Frank-Wolfe (FW) algorithm for solving the network equilibrium problems plays an important role in transportation simulation. Not only has the basic Frank Wolfe algorithm been studied, but also other variations of the FW algorithm (such as Conjugate Frank Wolfe and Bi-Conjugate Frank Wolfe algorithms) have been extensively studied by the research communities.

In this work, the basic Frank Wolfe algorithm is re-visited for the purpose of developing a useful, user-friendly, and appealing Java computer animation for enhancing the teaching effectiveness of this fundamental transportation static network equilibrium algorithm. Since the shortest path (SP) algorithms (such as the well-known …

Odu Hosts Fema Listening Session On New Flood Protection Standards, Public Affairs & News Bureau, Old Dominion University

News Items

No abstract provided.

What's Grad School All About?, Michele C. Weigle

Computer Science Presentations

PDF of a powerpoint presentation from the Capital region Celebration of Women in Computing (CAPWIC) Conference in Harrisonburg, Virginia, February 27, 2015. Also available on Slideshare.

New Coastal Resilience Director Brings Track Record, Expertise, Insideodu, Old Dominion University

News Items

No abstract provided.

Understanding Virginia’S Vulnerability To Climate Change, Tom Steinfeldt, Chris Coil, Hans-Peter Plag

MARI Documents

No abstract provided.

Simultaneous Analysis Of The Ballik-Ramsay And Phillips Systems Of C2 And Observation Of Forbidden Transitions Between Singlet And Triplet States, Wang Chen, Kentarou Kawaguchi, Peter F. Bernath, Jian Tang

Chemistry & Biochemistry Faculty Publications

6229 lines of the Ballik-Ramsay system (b₃Σ_g^--a₃Π_u) and the Phillips system (A¹Π_u-X¹Σ_g⁺) of C₂ up to v = 8 and J = 76, which were taken from the literature or assigned in the present work, were analyzed simultaneously by least-squares fitting with 82 Dunham-like molecular parameters and spin-orbit interaction constants between the b₃Σ_g^- and X¹Σ_g⁺ states with a standard deviation of 0.0037 cm^-1 for the whole data set. As a …

Storm Surge And Street-Level Inundation Modeling In New York City During Hurricane Sandy, Harry V. Wang, Derek Loftis, Zhou Liu, Jay Titlow, David Forrest, Joseph Zhang

January 23, 2015: Storm Surge Modeling Tools for Planning and Response

No abstract provided.

Introduction To Storm Surge Modeling, Rick Luettich

January 23, 2015: Storm Surge Modeling Tools for Planning and Response

No abstract provided.

Panel - Real World Applications: Overview Of Virginia Beach Center For Gis' Geoprocessing Of Storm Surge Models, Dave Arnold

January 23, 2015: Storm Surge Modeling Tools for Planning and Response

No abstract provided.

The Storm Surge Hazard, Jeff Orrock

January 23, 2015: Storm Surge Modeling Tools for Planning and Response

No abstract provided.

Applications Of The Adcirc Storm Surge, Tide, And Wind-Wave Model, Rick Luettich, Brian Blanton

January 23, 2015: Storm Surge Modeling Tools for Planning and Response

No abstract provided.

Agenda, Hr Adaptation Forum

January 23, 2015: Storm Surge Modeling Tools for Planning and Response

No abstract provided.

Imber- Research For Marine Sustainability: Synthesis And The Way Forward, Eileen Hofmann, Alida Bundy, Ken Drinkwater, Alberto R. Piola, Bernard Avril, Carol Robinson

CCPO Publications

The Integrated Marine Biogeochemistry and Ecosystem Research (IMBER) project aims at developing a comprehensive understanding of and accurate predictive capacity of ocean responses to accelerating global change and the consequent effects on the Earth system and human society. Understanding the changing ecology and biogeochemistry of marine ecosystems and their sensitivity and resilience to multiple drivers, pressures and stressors is critical to developing responses that will help reduce the vulnerability of marine-dependent human communities. This overview of the IMBER project provides a synthesis of project achievements and highlights the value of collaborative, interdisciplinary, integrated research approaches as developed and implemented through …

Dissolved Oxygen Dynamics During A Phytoplankton Bloom In The Ross Sea Polyna, Bastien Y. Queste, Karen J. Heywood, Walker O. Smith Jr., Daniel E. Kaufman, Timothy D. Jickells, Michael S. Dinniman

CCPO Publications

The Ross Sea polynya is one of the most productive regions in the Southern Ocean. However, limited access and high spatio-temporal variability of physical and biological processes limit the use of conventional oceanographic methods to measure early season primary productivity. High-resolution observations from two Seagliders provide insights into the timing of a bloom in the southern Ross Sea polynya in December 2010. Changes in chlorophyll and oxygen concentrations are used to assess bloom dynamics. Using a ratio of dissolved oxygen to carbon, net primary production is estimated over the duration of the bloom showing a sensitive balance between net autotrophy …

Acclimation, Adaptation, Traits And Trade-Offs In Plankton Functional Type Models: Reconciling Terminology For Biology And Modelling, Kevin J. Flynn, Michael St. John, John A. Raven, David O. F. Skibinski, J. Icarus Allen, Aditee Mitra, Eileen E. Hofmann

CCPO Publications

We propose definitions in terminology to enhance ongoing collaborations between biologists and modellers on plankton ecology. Organism "functional type" should refer to commonality in ecology not biogeochemistry; the latter is largely an emergent property of the former, while alignment with ecology is also consistent with usage in terrestrial science. Adaptation should be confined, as in genetics, to consideration of species inter-generational change; most so-called "adaptive" plankton models are thus acclimative, modifying vital rates in response to stimuli. Trait trade-off approaches should ideally only be considered for describing intra-generational interactions; in applications between generations, and certainly between unrelated species, such concepts …

Properties Of Cu(In,Ga,Al)Se² Thin Films Fabricated By Magnetron Sputtering, Talaat A. Hameed, Wei Cao, Bahiga A. Mansour, Inas K. Elzawaway, El-Metwally M. Abdelrazek, Hani E. Elsayed-Ali

Applied Research Center Publications

Cu (In,Ga,Al)Se₂ (CIGAS) thin films were studied as an alternative absorber layer material to Cu(In_xGa_1-x)Se₂. CIGAS thin films with varying Al content were prepared by magnetron sputtering on Si(100) and soda-lime glass substrates at 350 °C, followed by postdeposition annealing at 520 °C for 5 h in vacuum. The film composition was measured by an electron probe microanalyzer while the elemental depth profiles were determined by secondary ion mass spectrometry. X-ray diffraction studies indicated that CIGAS films are single phase with chalcopyrite structure and that the (112) peak clearly shifts to higher 2θ …

Changes To Climate Central’S Risk Finder Tool: A Usability Report, Justin Sikes

OUR Journal: ODU Undergraduate Research Journal

Students in the Fall English 231C Honors Climate Change and Crisis Communication course worked with instructor Megan McKittrick and Dr. Richards to conduct a usability test of Climate Central’s Risk Finder tool. Using the qualitative data, general trends that indicate potential areas of improvement for the website were identified. Students’ tasks were to find volunteers for the usability test through systematic sampling, conduct the test and analyze the audio recordings, and finally to code the data for themes to see if any trends became apparent. Several things became noticeable after looking at the responses of the four research participants, particularly …

Longitudinal Target-Spin Asymmetries For Deeply Virtual Compton Scattering, E. Seder, A. Biselli, S. Bültmann, A. Klein, S. E. Kuhn, Y. Prok, Clas Collaboration

Physics Faculty Publications

A measurement of the electroproduction of photons off protons in the deeply inelastic regime was performed at Jefferson Lab using a nearly 6 GeV electron beam, a longitudinally polarized proton target, and the CEBAF Large Acceptance Spectrometer. Target-spin asymmetries for e p → e'p'ɣ events, which arise from the interference of the deeply virtual Compton scattering and the Bethe-Heitler processes, were extracted over the widest kinematics in Q², x_B, t, and ɸ, for 166 four-dimensional bins. In the framework of generalized parton distributions, at leading twist the t dependence of these asymmetries provides insight into …

Measurements Of Ep → E'Π+N At 1.6 < W <2.0 Gev And Extraction Of Nucleon Resonance Electrocouplings At Clas, The Clas Collaboration, K. Park, K. P. Adhikari, M. J. Amaryan, L. El Fassi, Y. Prok, L. B. Weinstein

Physics Faculty Publications

Differential cross sections of the exclusive process ep -> e 'π⁺n were measured with good precision in the range of the photon virtuality Q² = 1.8-4.5 GeV² and the invariant mass range of the π⁺n final state W = 1.6-2.0 GeV using the Continuous Electron Beam Accelerator Facility Large Acceptance Spectrometer. Data were collected with nearly complete coverage in the azimuthal and polar angles of the n π⁺center-of-mass system. More than 37 000 cross-section points were measured. The contributions of the isospin I = ½ resonances N(1675) 5/2^-, N(1680) 5/2 …

Direct Observation Of Quark-Hadron Duality In The Free Neutron F2 Structure Function, I. Niculescu, G. Niculescu, W. Melnitchouk, J. Arrington, M. E. Christy, S. Kuhn

Physics Faculty Publications

Using the recently published data from the BONuS(Barely Off-shell Nucleon Structure) experiment at Jefferson Lab, which utilized a spectator tagging technique to extract the inclusive electron-free neutron scattering cross section, we obtain the first direct observation of quark-hadron duality in the neutron F₂ structure function. The data are used to reconstruct the lowest few (N = 2, 4, and 6) moments of F₂ in the three prominent nucleon resonance regions, as well as the moments integrated over the entire resonance region. Comparison with moments computed from global parametrizations of parton distribution functions suggest that quark-hadron duality holds locally …

Precise Determination Of The Deuteron Spin Structure At Low To Moderate Q² With Clas And Extraction Of The Neutron Contribution, The Clas Collaboration, N. Guler, S E. Kuhn, Y. Prok, K. P. Adhikari, D. Adikaram, M. J. Amaryan, L. El Fassi, C. E. Hyde, A. Klein, L. B. Weinstein, Z. W. Zhao

Physics Faculty Publications

We present the final results for the deuteron spin structure functions obtained from the full data set collected in 2000–2001 with Jefferson Lab's continuous electron beam accelerator facility (CEBAF) using the CEBAF large acceptance spectrometer (CLAS). Polarized electrons with energies of 1.6, 2.5, 4.2, and 5.8 GeV were scattered from deuteron (¹⁵ND₃ ) targets, dynamically polarized along the beam direction, and detected with CLAS. From the measured double-spin asymmetry, the virtual photon absorption asymmetry A^d₁ and the polarized structure function g^d₁ were extracted over a wide kinematic range (0.05GeV² < Q2 < 5GeV² and 0.9 …