Physical Sciences and Mathematics Commons^™

Predation Thresholds In Marine Microbial Communities Applied To Environments With Low Prey Abundances, Bonnie Bailey

OES Theses and Dissertations

Prokaryotes (Bacteria and Archaea) comprise the largest component of biomass in the world's oceans. Their abundances are controlled by resource availability, viral infections and protist grazing. Many pico- and nano-eukaryotic predators grow almost as quickly as their prey, and greatly increase in numbers as soon as their prey do, leading in tum to depletion in prokaryotes. It is still unclear however, as to what extent microbial predators are able to feed in low prey environments, most prominently in the largest biome on Earth, the deep sea (below l 000 m depth). It has been hypothesized that in low prey environments, …

Crustal Accretion And Mantle Geodynamics At Microplates: Constraints From Gravity Analysis And Numerical Modeling, Katherine Ames

OES Theses and Dissertations

This study investigates crustal accretion and mantle geodynamics at microplates using mantle Bouguer anomaly (MBA) gravity calculations and exploratory numerical models. The Easter and Juan Fernandez microplates are located in the eastern Pacific Ocean along the Pacific, Nazca, and Antarctic plate boundaries. Both microplates formed 3-5 Ma and they are currently rotating clockwise at 15° myr^-1 and 9° myr^-1,respectively [ e.g., Searle et al., 1993]. The study area also encompasses the Easter /Salas y Gomez mantle plume located near the Easter microplate. Both microplates show a difference in average MBA between their west and east ridges, with …

Discretized Agent-Based Model Of Infectious Disease Spread That Uses Contact Probability, Tyrell L. Gardner

Computational Modeling & Simulation Engineering Theses & Dissertations

This study uses contact probability in an agent-based model to simulate the spread of an infectious disease. In order to perform the study, the agent-based model must first be discretized into events. Each agent in the model is given its own infectious disease state machine taken from the Susceptible-Exposed-Infected-Recovered (SEIR) model. The agents move between squares in a grid environment where each square represents a group. Groups have a contact probability as an attribute that is used to predict whether an agent comes in close contact with another agent. The transitions between the states in the SEIR model are easily …

Organic Copper Binding Ligands And Thiol Compounds Produced By Bacteria And In The Elizabeth River, Virginia, Christina Louise Dryden

OES Theses and Dissertations

This dissertation presents work focusing on copper and organic copper binding ligands in laboratory cultures and the Elizabeth River, Virginia. Laboratory cultures of the marine bacterium Vibrio parahaemolyticus were used to demonstrate the influence of elevated copper concentrations on copper-complexing ligand and thiol production. Copper-complexing ligands similar in binding strength to the strongest natural ligands were detected in V. parahaemolyticus cultures (log K′_CuL = 11.8–13.2). A strong correlation (r² = 0.973) was found between total thiol and copper-complexing ligand concentrations at all copper concentrations examined.

A yearlong seasonal study was undertaken in a heavily polluted estuary to ascertain …

Meshless Mechanics And Point-Based Visualization Methods For Surgical Simulations, Rifat Aras

Computational Modeling & Simulation Engineering Theses & Dissertations

Computer-based modeling and simulation practices have become an integral part of the medical education field. For surgical simulation applications, realistic constitutive modeling of soft tissue is considered to be one of the most challenging aspects of the problem, because biomechanical soft-tissue models need to reflect the correct elastic response, have to be efficient in order to run at interactive simulation rates, and be able to support operations such as cuts and sutures.

Mesh-based solutions, where the connections between the individual degrees of freedom (DoF) are defined explicitly, have been the traditional choice to approach these problems. However, when the problem …

Bivariate Doubly Inflated Poisson And Related Regression Models, Pooja Sengupta

Mathematics & Statistics Theses & Dissertations

Count data are common in observational scientific investigations, and in many instances, such as twin or crossover studies, the data consists of dependent bivariate counts. An appropriate model for such data is the bivariate Poisson distribution given in Kocherlakota and Kocherlakota (2001). However, in situations where inflated count of (0, 0) occur, Lee et al. (2009) proposed the zero-inflated bivariate Poisson distribution which accounts for the inflated count. In this research, we introduce and study a bivariate distribution that accounts for an inflated count of the (k, k) cell for some k>0, in addition to the …

Analytic Evolution Of Singular Distribution Amplitudes In Qcd, Asli Tandogan

Physics Theses & Dissertations

Distribution amplitudes (DAs) are the basic functions that contain information about the quark momentum. DAs are necessary to describe hard exclusive processes in quantum chromodynamics. We describe a method of analytic evolution of DAs that have singularities such as nonzero values at the end points of the support region, jumps at some points inside the support region and cusps. We illustrate the method by applying it to the evolution of a flat (constant) DA, antisymmetric flat DA, and then use the method for evolution of the two-photon generalized distribution amplitude. Our approach to DA evolution has advantages over the standard …

Scalable Reasoning For Knowledge Bases Subject To Changes, Hui Shi

Computer Science Theses & Dissertations

ScienceWeb is a semantic web system that collects information about a research community and allows users to ask qualitative and quantitative questions related to that information using a reasoning engine. The more complete the knowledge base is, the more helpful answers the system will provide. As the size of knowledge base increases, scalability becomes a challenge for the reasoning system. As users make changes to the knowledge base and/or new information is collected, providing fast enough response time (ranging from seconds to a few minutes) is one of the core challenges for the reasoning system.

There are two basic inference …

Implications Of Climate Change For Cyanobacteria Over The Western Florida Shelf In The Gulf Of Mexico, Ivy Mara Osmon

OES Theses and Dissertations

Concentrations of atmospheric CO₂ are expected to double by year 2100 as a result of anthropogenic activities. Under elevated CO₂ conditions, cyanobacteria may reallocate energy from active accumulation and transport of dissolved inorganic carbon (C) required for photosynthesis to other growth processes. Stimulation of cyanobacterial production on the Western Florida Shelf in the Gulf of Mexico (GOM) could lead to improved nutritional status for the toxic, mixotrophic dinoflagellate Karenia brevis that utilizes newly fixed N₂ from co-occurring diazotrophic cyanobacteria and consumes unicellular cyanobacteria via grazing for growth. Culture studies performed by other researchers on the climate induced …

High Dimensional Data Set Analysis Using A Large-Scale Manifold Learning Approach, Loc Tran

Electrical & Computer Engineering Theses & Dissertations

Because of technological advances, a trend occurs for data sets increasing in size and dimensionality. Processing these large scale data sets is challenging for conventional computers due to computational limitations. A framework for nonlinear dimensionality reduction on large databases is presented that alleviates the issue of large data sets through sampling, graph construction, manifold learning, and embedding. Neighborhood selection is a key step in this framework and a potential area of improvement. The standard approach to neighborhood selection is setting a fixed neighborhood. This could be a fixed number of neighbors or a fixed neighborhood size. Each of these has …

Idpal – A Partially-Adiabatic Energy-Efficient Logic Family: Theory And Applications To Secure Computing, Mihail T. Cutitaru

Electrical & Computer Engineering Theses & Dissertations

Low-power circuits and issues associated with them have gained a significant amount of attention in recent years due to the boom in portable electronic devices. Historically, low-power operation relied heavily on technology scaling and reduced operating voltage, however this trend has been slowing down recently due to the increased power density on chips. This dissertation introduces a new very-low power partially-adiabatic logic family called Input-Decoupled Partially-Adiabatic Logic (IDPAL) with applications in low-power circuits. Experimental results show that IDPAL reduces energy usage by 79% compared to equivalent CMOS implementations and by 25% when compared to the best adiabatic implementation. Experiments ranging …

Investigation And Optimization Of A New Compact Superconducting Cavity For Deflecting And Crabbing Applications, Subashini Uddika De Silva

Physics Theses & Dissertations

Deflecting and crabbing structures have many applications in current accelerator systems. The primary use of a deflecting cavity is to separate a single beam into multiple beams. A crabbing cavity enables the head-on collision at the interaction point in particle colliders in order to increase the luminosity. The early uses of the deflecting structures have been in the early 1960s: these structures were disk loaded structures operating at room temperature. The crabbing structure which was installed at the NEK electron-positron collider was the first and only operational superconducting cavity of that kind. The most common design of superconducting deflecting and …

Improving Structural Features Prediction In Protein Structure Modeling, Ashraf Yaseen

Computer Science Theses & Dissertations

Proteins play a vital role in the biological activities of all living species. In nature, a protein folds into a specific and energetically favorable three-dimensional structure which is critical to its biological function. Hence, there has been a great effort by researchers in both experimentally determining and computationally predicting the structures of proteins.

The current experimental methods of protein structure determination are complicated, time-consuming, and expensive. On the other hand, the sequencing of proteins is fast, simple, and relatively less expensive. Thus, the gap between the number of known sequences and the determined structures is growing, and is expected to …

A Framework For Web Object Self-Preservation, Charles L. Cartledge

Computer Science Theses & Dissertations

We propose and develop a framework based on emergent behavior principles for the long-term preservation of digital data using the web infrastructure. We present the development of the framework called unsupervised small-world (USW) which is at the nexus of emergent behavior, graph theory, and digital preservation. The USW algorithm creates graph based structures on the Web used for preservation of web objects (WOs). Emergent behavior activities, based on Craig Reynolds’ “boids” concept, are used to preserve WOs without the need for a central archiving authority. Graph theory is extended by developing an algorithm that incrementally creates small-world graphs. Graph theory …

Feasibility Of Mainstream Nitrite Oxidizing Bacteria Out-Selection And Anammox Polishing For Enhanced Nitrogen Removal, Pusker Raj Regmi

Civil & Environmental Engineering Theses & Dissertations

Short-cut nitrogen removal avoids nitrite oxidation to nitrate by nitrite oxidizing bacteria (NOB) and allows a) reduction of formed nitrite to nitrogen gas via heterotrophic denitrification and/or b) oxidation of remaining ammonia with formed nitrite to nitrogen gas via anaerobic ammonia oxidation (anammox). The precondition for achieving shortcut nitrogen removal is suppression of NOB, which is favored by warm and high ammonia strength conditions found in internally generated ammonia-rich waste streams through anaerobic digestion of waste solids referred to as sidestreams or reject water. The discovery of anammox bacteria in the mid-1990s, which are capable of transforming NH₄+ …

Resource Allocation In Vehicular Cloud Computing, Puya Ghazizadeh

Computer Science Theses & Dissertations

Recently, we have witnessed the emergence of Cloud Computing, a paradigm shift adopted by information technology (IT) companies with a large installed infrastructure base that often goes under-utilized. The unmistakable appeal of cloud computing is that it provides scalable access to computing resources and to a multitude of IT services. Cloud computing and cloud IT services have seen and continue to see a phenomenal adoption rate around the world.

Recently, Professor Olariu and his coworkers through series of research introduced a new concept, Vehicular Cloud Computing. A Vehicular Cloud (VC) is a network of vehicles in a parking lot …

Measurement Of Single And Double Spin Asymmetries In Semi-Inclusive Deep-Inelastic Scattering On Proton And Deuteron, Suman Bandhu Koirala

Physics Theses & Dissertations

The EG1-DVCS experiment with CLAS at Jefferson Lab collected semi-inclusive pion electro-production data on longitudinally polarized solid state NH₃ and ND₃ targets with longitudinally polarized electrons of approximately 6 GeV energy. Data on all three pion channels, π +, π– and π⁰, were collected simultaneously. The charged pions were identified by their time-of-flight information whereas the neutral pions were reconstructed from the invariant mass of two photons. The experiment covered a wide kinematic range: 1 GeV ² ≤ Q² ≤ 3.2 GeV², 0.12 ≤ xB ≤ 0.48, 0.0 GeV ≤ P_{h⊥ …}

Assessing The Fit Between Child Welfare Information Systems And Frontline Workers: Development Of A Task-Technology Fit Instrument, Kurt William Heisler

Health Services Research Dissertations

States and the federal government continue to invest heavily in child welfare information systems (CWIS) to improve caseworkers' performance, but the extent to which these systems meet caseworkers' needs is unclear. In the field of child welfare there are no reliable user-evaluation measures states can use to assess the degree to which a CWIS meets caseworkers' needs, and identify which specific features of the CWIS most need improvement. The study developed such a measure based on the task-technology fit (TTF) framework, which posits that users will evaluate the usefulness of a technology based on how well it meets their tasks …

Density Functional Theory Modeling Of It-Stacking And Electrophilic Donor-Acceptor Interactions With Application To Therapeutic Targeting Of Zinc-Finger Proteins, Patricia Beall Lutz

Chemistry & Biochemistry Theses & Dissertations

Several viruses, including viruses that cause cancer, contain conserved zinc finger (ZF) proteins that are essential for viral reproduction, making them attractive drug targets for cancer and viral treatment. ZFs are small protein domains that have Zn²⁺ tetrahedrally coordinated to at least 2 Cys and His. They form three classes of ZFs depending on the amino acid ligands, CCHH, CCCH, and CCCC. Zn²⁺ is stable towards redox reactions; however, the Cys thiolates are redox active. Oxidation of the Cys thiolates release Zn²⁺, and the ZF loses its tertiary structure and can no longer bind DNA or …

A Comprehensive Evaluation Of C25 Highly Branched Isoprenoid Alkenes Of Marine Diatoms As Proxies For Sea Ice Extent In The Arctic Ocean, Tetiana Muniak

OES Theses and Dissertations

Sea Ice extent is one of the major factors regulating carbon cycling and ecosystem function in the modern Arctic Ocean. It is an essential component of climate models and is crucial for the evaluation of various oceanographic processes that influence a particular region. Yet it is also one of the most difficult attributes of the ocean with respect to our ability for its accurate reconstruction from paleo records. The lack of the detailed records prior to satellite information has encouraged the development of new proxy records for the reconstruction of past

sea ice conditions. In recent years, a new monounsaturated …

Spatial And Temporal Variability In Net Community Metabolism In The Middle Atlantic Bight, Georges Bank, And Gulf Of Maine: Observations Of Net Heterotrophic Phases In The Highly Productive Coastal Zone, Cory James Staryk

OES Theses and Dissertations

Net community metabolism (NCM), the balance between primary production and community respiration, was measured during two cruises, June 2011 and August 2012, in the Middle Atlantic Bight, Georges Bank and Gulf of Maine. Net heterotrophy was observed in Georges Bank and Gulf of Maine during the June 2011 cruise. During the August 2012 cruise, net heterotrophy was observed in the Middle Atlantic Bight and net autotrophy was observed in Georges Bank and the Gulf of Maine. Dark community respiration increased (DCR) with biomass and temperature. Gross community production (GCP) also increased with Chl a, bicarbonate uptake, and temperature. Net …

Computational Analysis Of Gene Expression And Connectivity Patterns In The Convoluted Structures Of Mouse Cerebellum, Tao Zeng

Computer Science Theses & Dissertations

One significant difference between evolved mammalian brains and other species is that mammalian brains exhibit increasingly convoluted structures in the cerebral cortex. Groove and ridge shaped structures named gyri and sulci expand surface area of cerebral cortex, making more functions possible. Prior studies using neuroimaging techniques such as dMRI and DTI have revealed that neural fibers are heavily connected to gyri comparing to those connected to sulci, such macro-scale experiments indicates that gyri are involved in large scale information processing while sulci process information locally. However, molecular and cellar level evidences, namely, gene expression pattern and its resulting neuronal connectivity …

Generating Combinatorial Objects- A New Perspective, Alexander Chizoma Nwala

Computer Science Theses & Dissertations

Combinatorics is the science of "possibilities." This definition, while not formal is a fair statement because all too often, in order to gain insight into the solution of many counting problems, we explore the possibilities. In some cases we seek to know how many options, while in other cases we seek to enumerate or list the options. Irrespective of the scenario, combinatorics plays a vital role today. In many instances such as exploring the options for choosing a new password for a combination lock, we employ combinatorics. In considering the possible license plate permutations for a state, or to see …

Document Classification In Support Of Automated Metadata Extraction Form Heterogeneous Collections, Paul K. Flynn

Computer Science Theses & Dissertations

A number of federal agencies, universities, laboratories, and companies are placing their documents online and making them searchable via metadata fields such as author, title, and publishing organization. To enable this, every document in the collection must be catalogued using the metadata fields. Though time consuming, the task of identifying metadata fields by inspecting the document is easy for a human. The visual cues in the formatting of the document along with accumulated knowledge and intelligence make it easy for a human to identify various metadata fields. Even with the best possible automated procedures, numerous sources of error exist, including …

Simulation Modeling And Analysis Of Customs-Regulated Container Terminal Operations With Multimodal Transportation, Mariam A. Kotachi

Engineering Management & Systems Engineering Theses & Dissertations

World trade has been increasing dramatically in the past two decades and, as a result, container exchange has grown significantly. Consequently and to meet this increase, several container terminals are expanding and many new ones are being established. A port with one or more container terminals is considered a complex system in which many entities interact to accomplish seamless handling of containers inbound and outbound. The level of complexity is drastically heightened for container terminals containing multimodal transportation systems as they typically involve ships, rail, and trucks arriving to one or more terminals delivering containers of different sizes to several …

Assessing Organizational Effectiveness Through The Competing Values Framework A Data Envelopment Approach, Raghavender Macherla

Engineering Management & Systems Engineering Theses & Dissertations

This study proposes a model to diagnose organizations using the mathematical principles of data envelopment analysis (DEA) to the variables generated using competing values framework (CVF) in order to evaluate overall organizational effectiveness. The notion of organizational effectiveness is abstract and difficult to measure due to its complexity and multi-functional nature. Over the years, measurement of organizational effectiveness has remained a challenge due to the lack of agreement on the factors that should be assessed to determine effectiveness. This research is aimed at shedding some light into this topic by using data envelopment analysis as a tool to measure relative …

Ray- And Wave-Theoretic Approach To Electromagnetic Scattering From Radially Inhomogeneous Spheres And Cylinders, Michael A. Pohrivchak

Mathematics & Statistics Theses & Dissertations

With applications in the areas of chemistry, physics, microbiology, meteorology, radar, astronomy, and many other fields, electromagnetic scattering is an important area of research. Many everyday phenomena that we experience are a result of the scattering of electromagnetic and acoustic waves. In this dissertation, the scattering of plane electromagnetic waves from radially inhomogeneous spheres and cylinders using both ray- and wave-theoretic principles is considered. Chapters 2 and 3 examine the use of the ray approach. The deviation undergone by an incident ray from its original direction is related to the angle through which the radius vector turns from the point …

Analyzing Cholera Dynamics In Homogeneous And Heterogeneous Environments, Drew Posny

Mathematics & Statistics Theses & Dissertations

Cholera continues to be a serious public health concern in developing countries and the global increase in the number of reported outbreaks suggests that activities to control the diseases and surveillance programs to identify or predict the occurrence of the next outbreaks are not adequate. Mathematical models play a critical role in predicting and understanding disease mechanisms, and have long provided basic insights in the possible ways to control infectious diseases. This dissertation is concerned with mathematical modeling and analysis of cholera dynamics. First, we study an autonomous model in a homogeneous environment with added controls that involves both direct …

Comparison Of Two Separation Methods For Biological Particles: Field-Flow Fractionation (Fff) And Sucrose Density Gradients, Cody E. Garrison

OES Theses and Dissertations

Sucrose gradient centrifugation and Field-flow fractionation (FFF) are two different particle separation methods that overcome the problems of similar size microorganisms clumping together during standard filtration methods. FFF separates particles based on size and density via the parabolic velocity profile of laminar flow in a ribbon-like channel. The sucrose method separates particles via centrifugation in a density gradient. Both techniques worked well in separating eukaryotic from prokaryotic microbes, with the preferred method depending on the type and relative abundance of organisms to be separated. Minicells were separated from mother cells in transformed Escherichia coli cultures, heterotrophic flagellates (e.g., Diplonema papillatum …

Markov Chain Monte Carlo Bayesian Predictive Framework For Artificial Neural Network Committee Modeling And Simulation, Michael S. Goodrich

Computational Modeling & Simulation Engineering Theses & Dissertations

A logical inference method of properly weighting the outputs of an Artificial Neural Network Committee for predictive purposes using Markov Chain Monte Carlo simulation and Bayesian probability is proposed and demonstrated on machine learning data for non-linear regression, binary classification, and 1-of-k classification. Both deterministic and stochastic models are constructed to model the properties of the data. Prediction strategies are compared based on formal Bayesian predictive distribution modeling of the network committee output data and a stochastic estimation method based on the subtraction of determinism from the given data to achieve a stochastic residual using cross validation. Performance for Bayesian …