Physical Sciences and Mathematics Commons^™

Development Of Interatomic Potentials For Large Scale Molecular Dynamics Simulations Of Carbon Materials Under Extreme Conditions, Romain Perriot

USF Tampa Graduate Theses and Dissertations

The goal of this PhD research project is to devise a robust interatomic potential for large scale molecular dynamics simulations of carbon materials under extreme conditions. This screened-environment dependent reactive empirical bond order potential (SED-REBO) is specifically designed to describe carbon materials under extreme compressive or tensile stresses. Based on the original REBO potential by Brenner and co workers, SED-REBO includes reparametrized pairwise interaction terms and a new screening term, which serves the role of a variable cutoff. The SED-REBO potential overcomes the deficiencies found with the most commonly used interatomic potentials for carbon: the appearance of artificial forces due …

Sustainable Livelihood Analysis Of An Irrigation Project In Ta Haen, Cambodia., Irene Rehberger Bescos

USF Tampa Graduate Theses and Dissertations

This study examines potential livelihood outcomes from a recently established irrigation project in Ta Haen, Cambodia, in a sustainable livelihoods framework. The aim of this SAUCE irrigation project is to provide water for drinking and irrigation purposes with the goal of enhancing food by producing an extra rice harvest, the staple, per year. Field research conducted in December 2011 provided qualitative data from questionnaires, key informant interviews, and participant and direct observation, in addition to quantitative data from water quality analysis focusing on arsenic (a potential risk), pH, EC and temperature. Most of the people in the village did not …

Responses To Chemical Exposure By Foraminifera: Distinguishing Dormancy From Mortality, Benjamin James Ross

USF Tampa Graduate Theses and Dissertations

The Deepwater Horizon blowout in 2010 released an estimated 4.9 million barrels of crude oil into the Gulf of Mexico in the 83 days between the initial explosion and the capping of the well. Response included extensive use of Corexit© oil dispersant. Although South Florida was spared exposure by currents, this event highlights the need for effective bioassay organisms for coral reefs. Amphistegina spp. are benthic foraminifers that host diatom symbionts in a relationship similar to that of coral and their zooxanthellae. Amphistegina spp. occur abundantly in reef communities nearly worldwide, are easily collected and maintained in culture, and are …

Stochastic Hybrid Dynamic Systems: Modeling, Estimation And Simulation, Daniel Siu

USF Tampa Graduate Theses and Dissertations

Stochastic hybrid dynamic systems that incorporate both continuous and discrete dynamics have been an area of great interest over the recent years. In view of applications, stochastic hybrid dynamic systems have been employed to diverse fields of studies, such as communication networks, air traffic management, and insurance risk models. The aim of the present study is to investigate properties of some classes of stochastic hybrid dynamic systems.

The class of stochastic hybrid dynamic systems investigated has random jumps driven by a non-homogeneous Poisson process and deterministic jumps triggered by hitting the boundary. Its real-valued continuous dynamic between jumps is described …

Use And Development Of Computational Tools In Drug Discovery: From Small Molecules To Cyclic Peptides, Daniel Navarrete Santiago

USF Tampa Graduate Theses and Dissertations

The scope of this work focuses on computationally modeling compounds with protein structures. While the impetus of drug discovery is the innovation of new therapeutic molecules, it also involves distinguishing molecules that would not be an effective drug. This can be achieved by inventing new tools or by refining old tools. Virtual screening (VS, also called docking), the computational modeling of a molecule in a receptor structure, is a staple in predicting a molecule's affinity for an intended target. In our Virtual Target Screening system (also called inverse-docking), VS is used to find high-affinity targets, which can potentially explain absorption, …

Properties Of Ferroelectric Perovskite Structures Under Non-Equilibrium Conditions, Qingteng Zhang

USF Tampa Graduate Theses and Dissertations

Ferroelectric materials have received lots of attention thanks to their intriguing properties such as the piezoelectric and pyroelectric effects, as well as the large dielectric constants and the spontaneous polarization which can potentially be used for information storage. In particular, perovskite crystal has a very simple unit cell structure yet a very rich phase transition diagram, which makes it one of the most intensively studied ferroelectric materials. In this dissertation, we use effective Hamiltonian, a first-principles-based computational technique to study the finite-temperature properties of ferroelectric perovskites. We studied temperature-graded

(BaxSr1-x )TiO3 (BST) bulk alloys as well as the dynamics of …

Methods And Algorithms For Scalable Verification Of Asynchronous Designs, Haiqiong Yao

USF Tampa Graduate Theses and Dissertations

Concurrent systems are getting more complex with the advent of multi-core processors and the support of concurrent programs. However, errors of concurrent systems are too subtle to detect with the traditional testing and simulation. Model checking is an effective method to verify concurrent systems by exhaustively searching the complete state space exhibited by a system. However, the main challenge for model checking is state explosion, that is the state space of a concurrent system grows exponentially in the number of components of the system. The state space explosion problem prevents model checking from being applied to systems in realistic size. …

Bayesian Inference On Mixed-Effects Models With Skewed Distributions For Hiv Longitudinal Data, Ren Chen

USF Tampa Graduate Theses and Dissertations

Statistical models have greatly improved our understanding of the pathogenesis of HIV-1 infection

and guided for the treatment of AIDS patients and evaluation of antiretroviral (ARV) therapies.

Although various statistical modeling and analysis methods have been applied for estimating the

parameters of HIV dynamics via mixed-effects models, a common assumption of distribution is

normal for random errors and random-effects. This assumption may lack the robustness against

departures from normality so may lead misleading or biased inference. Moreover, some covariates

such as CD4 cell count may be often measured with substantial errors. Bivariate clustered

(correlated) data are also commonly encountered in …

Crack Analysis In Silicon Solar Cells, Maria Ines Echeverria Molina

USF Tampa Graduate Theses and Dissertations

Solar cell business has been very critical and challenging since more efficient and low costs materials are required to decrease the costs and to increase the production yield for the amount of electrical energy converted from the Sun's energy. The silicon-based solar cell has proven to be the most efficient and cost-effective photovoltaic industrial device. However, the production cost of the solar cell increases due to the presence of cracks (internal as well as external) in the silicon wafer. The cracks of the wafer are monitored while fabricating the solar cell but the present monitoring techniques are not sufficient when …

Stable Isotope Analysis Of Busycon Sinistrum To Determine Fort Walton-Period Seasonality At St. Joseph Bay, Northwest Florida, Ryan Michael Harke

USF Tampa Graduate Theses and Dissertations

ABSTRACT

Recent archaeological investigations indicate that coastal Fort Walton cultures in the St. Joseph Bay region of northwest Florida emphasized marine and estuarine foraging. These late prehistoric (A.D. 1000-1500) peoples collected fish, shellfish, and other aquatic resources. At the Richardson's Hammock site (8Gu10), radiocarbon-dated to about A.D. 1300, as at dozens of other shell middens around this salty bay, large gastropods were a major subsistence component. This adaptation is in sharp contrast with that of contemporaneous inland Fort Walton societies, who relied on maize agriculture. It is unknown whether coastal groups represent separate hunter-gatherer-fisher populations or seasonal migrations by inland …

Linear Mixed-Effects Models: Applications To The Behavioral Sciences And Adolescent Community Health, Lizmarie Gabriela Maldonado

USF Tampa Graduate Theses and Dissertations

Linear mixed-effects (LME) modeling is a widely used statistical method for analyzing repeated measures or longitudinal data. Such longitudinal studies typically aim to investigate and describe the trajectory of a desired outcome. Longitudinal data have the advantage over cross-sectional data by providing more accuracy for the model. LME models allow researchers to account for random variation among individuals and between individuals.

In this project, adolescent health was chosen as a topic of research due to the many changes that occur during this crucial time period as a precursor to overall well-being in adult life. Understanding the factors that influence how …

Bi-Integrable And Tri-Integrable Couplings And Their Hamiltonian Structures, Jinghan Meng

USF Tampa Graduate Theses and Dissertations

An investigation into structures of bi-integrable and tri-integrable couplings is undertaken. Our study is based on semi-direct sums of matrix Lie algebras. By introducing new classes of matrix loop Lie algebras, we form new Lax pairs and generate several new bi-integrable and tri-integrable couplings of soliton hierarchies through zero curvature equations. Moreover, we discuss properties of the resulting bi-integrable couplings, including infinitely many commuting symmetries and conserved densities. Their Hamiltonian structures are furnished by applying the variational identities associated with the presented matrix loop Lie algebras.

The goal of this dissertation is to demonstrate the efficiency of our approach and …

Spatial And Temporal Variability Of Remotely Sensed Ocean Color Parameters In Coral Reef Regions, Daniel Brooks Otis

USF Tampa Graduate Theses and Dissertations

The variability of water-column absorption due to colored dissolved organic matter (CDOM) and phytoplankton in coral reef regions is the focus of this study. Hydrographic and CDOM absorption measurements made on the Bahamas Banks and in Exuma Sound during the spring of 1999 and 2000 showed that values of salinity and CDOM absorption at 440nm were higher on the banks (37.18 psu, 0.06 m^-1), compared to Exuma Sound (37.04 psu, 0.03 m^-1). Spatial patterns of CDOM absorption in Exuma Sound revealed that plumes of CDOM-rich water flow into Exuma Sound from the surrounding banks. To examine absorption variability in reef …

Remote Sensing Of Whitings In The Bahamas, Ryan Allen Lloyd

USF Tampa Graduate Theses and Dissertations

Whitings on both the Great Bahama Bank (GBB) and Little Bahama Bank (LBB) were evaluated using data collected from 2000-2010 by the Moderate Resolution Imaging Spectroradiometer (MODIS) instruments onboard the Terra and Aqua satellites. A semi-objective method was developed to classify whiting patches from other look-alike features using the recently developed Floating Algae Index (FAI) algorithm, an empirical cloud masking algorithm, and a gradient analysis from the 250-m resolution MODIS data. A total of 1,500 images with minimal cloud cover was used to calculate long-term and seasonal trends as well as an average daily coverage for both banks. Annual and …

Optical Detection And Classification Of Phytoplankton Taxa Through Spectral Analysis, Daniel Tyler Sensi

USF Tampa Graduate Theses and Dissertations

Phytoplankton serve as the bottom of the marine food web and therefore play an essential role in marine ecosystems. On the other hand, coastal phytoplankton communities can adversely affect the marine ecosystem and humans. A variety of techniques have been developed to measure and study phytoplankton, including in situ methods (e.g., flow cytometry) and laboratory methods (e.g., microscopic taxonomy). These provide accurate measurements of phytoplankton taxa and concentrations, yet they are limited in space and time, and synoptic information is difficult to obtain with these techniques.

Optical remote sensing may provide complementary information for its synoptic nature, as demonstrated by …

Design Of Novel Inhibitors For Infectious Diseases Using Structure-Based Drug Design: Virtual Screening, Homology Modeling And Molecular Dynamics, Divya Ramamoorthy

USF Tampa Graduate Theses and Dissertations

The main aim of the study in this thesis was to use structure-based protocols to design new drugs for enzymes, DXS and DXR in the non mevalonate pathway. Another aim of this study was to identify the dimer interface in E.coli FabH as an allosteric binding site for designing new class of anti-infective drugs. We have attempted to identify potential inhibitors for DXS by docking the NCI Diversity set compounds, compound libraries available from GSK-MMV and St. Jude's Children's research center. FabH dimer interface has been identified as a potential target using SiteMap, Alanine mutagenesis and docking studies.

The first …

Growth And Characterization Of Functional Nanoparticulate Films By A Microwave Plasma-Assisted Spray Deposition Process, Ted Wangensteen

USF Tampa Graduate Theses and Dissertations

Nanoparticle and nanoparticulate films have been grown by a unique approach combining a microwave and nebulized droplets where the concentration and thus the resulting particle size can be controlled. The goal of such a scalable approach was to achieve it with the least number of steps, and without using expensive high purity chemicals or the precautions necessary to work with such chemicals. This approach was developed as a result of first using a laser unsuccessfully to achieve the desired films and particles. Some problems with the laser approach for growing desired films were solved by substituting the higher energy microwave …

Assessment Of Methods To Manipulate Thermal Emission And Evaluate The Quality Of Thermal Radiation For Direct Energy Conversion, Samantha Wijewardane

USF Tampa Graduate Theses and Dissertations

ABSTRACT

Control of spectral thermal emission from surfaces may be desirable in some energy related applications, such as nano-scale antenna energy conversion and thermophotovoltaic conversion. There are a number of methods, from commercially available paints to advanced surface gratings that can be used to modify the thermal emission from a surface. To find out the proper emission controlling technique for a given energy conversion method all the surface emission controlling methods are comprehensively reviewed regarding the emission control capabilities and the range of possible applications. Radiation with high degree of coherence can be emitted using advanced surface emission controlling techniques. …

Chyd1 Solution Phase Synthesis Optimization And The Development Of A Novel Human Growth Hormone Antagonist And Agonist, Philip Murray

USF Tampa Graduate Theses and Dissertations

Inhibiting protein-protein interactions to achieve a therapeutically desired effect has been a goal in the field of drug discovery for decades. Recently, advances in peptidomimetics have led researches to the use of cyclized peptides to achieve this goal. Cyclization of linear peptides restricts the number of conformations of the peptide, increasing the peptide's affinity to binding to the desired target. Cyclization also stabilizes the peptide, allowing the peptide to be resistant to proteases. This study explores the optimization of solution phase synthesis of an important integrin-mediated cell adhesion cyclic peptide for the therapeutic inhibition of multiple myeloma, cHYD1. cHYD1 was …

Encapsulation Of High Temperature Phase Change Materials For Thermal Energy Storage, Rupa Nath

USF Tampa Graduate Theses and Dissertations

Thermal energy storage is a major contributor to bridge the gap between energy demand (consumption) and energy production (supply) by concentrating solar power. The utilization of high latent heat storage capability of phase change materials is one of the keys to an efficient way to store thermal energy. However, some of the limitations of the existing technology are the high volumetric expansion and low thermal conductivity of phase change materials (PCMs), low energy density, low operation temperatures and high cost. The present work deals with encapsulated PCM system, which operates at temperatures above 500°C and takes advantage of the heat …

Defining Earth Smarts: A Construct Analysis For Socioecological Literacy Based On Justly Maintaining Quality Of Life, Bryan H. Nichols

USF Tampa Graduate Theses and Dissertations

This paper describes the creation and validation of a new educational construct. Socioecological literacy, or earth smarts, describes the qualities we need to justly maintain or improve our quality of life in a changing world. It was created using construct analysis techniques and systems tools, drawing on an extensive, transdisciplinary body of literature. Concepts related to environmental, ecological and scientific literacy, sustainability and citizenship were combined with educational frameworks, new research in science education, and modern cognitive psychology. After the initial formulation, the results were considered by a variety of experts and professionals from the fields of ecology, environmental science …

Mangroves, Mudbanks And Seawalls: Political Ecology Of Adaptation To Sea Level Rise In Suriname, Ravic Nijbroek

USF Tampa Graduate Theses and Dissertations

This study seeks to understand how global discourses of sea level rise (SLR) and mangrove ecology influence national climate change adaptation policy to reduce coastal vulnerability in Suriname. A majority of the Surinamese population lives along the low elevation coastal zone and is highly exposed to projected SLR. Failure by the international community to reach agreement on climate change mitigation means that vulnerable coastal communities must adapt. The Suriname coast is predominantly shaped by mudbanks and mangroves which together provide protection against coastal erosion and trap sediments resulting in coastal accretion. Knowledge claims of mangrove ecology and utility in SLR …

Micronekton And Macrozooplankton Of The Western Antarctic Peninsula And The Eastern Ross Sea: Contrast Between Two Different Thermal Regimes, Melanie Leigh Parker

USF Tampa Graduate Theses and Dissertations

ABSTRACT

Micronekton and macrozooplankton were sampled from the Western Antarctic Peninsula (WAP) and eastern Ross Sea regions. Samples were collected over the course of six research cruises to the Southern Ocean. Four of those cruises were conducted in the Marguerite Bay region of the WAP during the austral fall and winter of 2001 and 2002. A fifth cruise sampled faunal assemblages at nine sites, ranging from Joinville Island at the northern tip of the WAP to Charcot Island near the southern extent of the WAP, during austral fall 2010. A sixth cruise was conducted in the pack ice within the …

Field And Laboratory Comparison Of The Hydraulic Performance Of Two Ceramic Pot Water Filters, Duncan Peabody

USF Tampa Graduate Theses and Dissertations

Currently 884 million people worldwide are living without access to an improved source of drinking water (WHO/UNICEF, 2011). Piped-water on premises is the ultimate goal of World Health Organization (WHO) due to the ability to treat all of the water and distribute it safely in pressurized pipes. However, Household Water Treatment and Safe Storage (HWTS) is an option for improving the quality of drinking water where that infrastructure is not yet developed, especially where there is a risk of recontamination between point of collection and point of use (Clasen, 2006).

This study analyzed one such HWTS, the ceramic pot water …

Shelf-Scale Mapping Of Fish Distribution Using Active And Passive Acoustics, Carrie Christy Wall

USF Tampa Graduate Theses and Dissertations

Fish sound production has been associated with courtship and spawning behavior. Acoustic recordings of fish sounds can be used to identify distribution and behavior. Passive acoustic monitoring (PAM) can record large amounts of acoustic data in a specific area for days to years. These data can be collected in remote locations under potentially unsafe seas throughout a 24-hour period providing datasets unattainable using observer-based methods. However, the instruments must withstand the caustic ocean environment and be retrieved to obtain the recorded data. This can prove difficult due to the risk of PAMs being lost, stolen or damaged, especially in highly …

Something Is Askew In Florida's Water: Arguing For A Better Descriptive Statistic For Positively Skewed Water-Quality Data, Amie October West

USF Tampa Graduate Theses and Dissertations

ABSTRACT

It may be of no surprise that water quality data is right-skewed, but what appears to be overlooked by some is that the arithmetic mean and standard deviation most often fail as measures of central tendency in skewed data. When using the arithmetic mean and arithmetic standard deviation with nutrient data, one standard deviation about the arithmetic mean can capture nearly all of the data and extend into negative values. Representing nutrient data this way can be misleading to viewers who are using the statistics, and making assumptions, to understand the characteristics of those waters. Through an in-depth statistical …

Asymmetric Intra- And Intermolecular Cyclopropanation By Co(Ii)- Based Metalloradical Catalysis, Xue Xu

USF Tampa Graduate Theses and Dissertations

Metal-catalyzed cyclopropanation of olefins with diazo reagents has attracted research interest because of its fundamental and practical importance. The resulting cyclopropyl units are recurrent motifs in biologically important molecules and can serve as versatile precursors in organic synthesis. Since they were first introduced in 2004, Co(II) complexes of D₂-symmetric chiral amidoporphyrins [Co(D₂-Por*)] have emerged as a new class of catalysts for asymmetric cyclopropanation. These metalloradical catalysts have been shown to be highly effective for asymmetric intermolecular cyclopropanation of a broad scope of substrates with different classes of carbene sources, particularly including electron-deficient olefins and acceptor/acceptor-substituted …

Spatial And Temporal Variations In The Air-Sea Carbon Dioxide Fluxes Of Florida Bay, Christopher Michael Dufore

USF Tampa Graduate Theses and Dissertations

The flux of CO2 between the ocean and the atmosphere is an important measure in determining local, global, and regional, as well as short term and long term carbon budgets. In this study, air-sea CO2 fluxes measured using a floating chamber were used to examine the spatial and temporal variability of CO2 fluxes in Florida Bay. Measurements of dissolved inorganic carbon and total alkalinity obtained concurrently with chamber measurements of CO2 flux allowed calculation of ΔpCO2 from flux measurements obtained at zero wind velocity. Floating chamber measurements of ΔpCO2 were subsequently coupled with wind speed data to provide a simple …

Investigating The Role Of The Internet In Women And Minority Stem Participation: A Case Study Of Two Florida Engineering Programs, Arland Nguema Ndong

USF Tampa Graduate Theses and Dissertations

Despite our awareness of the fascination modern humans have with the Internet, little is known about how and why colleges and universities create and maintain Websites. At the most general level, in this case study, I hypothesize that university Websites serve as communication and marketing tools in attracting students. At the most specific level, I postulate that civil engineering programs with Web pages depicting images of women and minorities would be more successful in recruiting and retaining women and students of color than civil engineering programs with Web pages displaying fewer or no images of women and minorities. The primary …

Quasi 3-Dimensional Electrical Resistivity Mapping Of Air-Filled Karst Conduits And Policy Implications, Charles W. Mccrackin

USF Tampa Graduate Theses and Dissertations

This study assesses the capability and practical applications of quasi 3-Dimensional (3D) electrical resistivity surveying (ER) for mapping air-filled karst conduits. Vadose zone caves within the Brooksville Ridge of West Central Florida are relatively similar in architecture, with N-S elongation, and do not consist of an interconnected network of conduits. A high resolution quasi-3D ER survey was performed over two mapped cave systems on the Brooksville Ridge. The resultant survey verified the general effectiveness of quasi-3D ER in locating the two known near-surface cave features. Several other locations in the survey show similar or stronger resistivity anomalies trending in a …