Physical Sciences and Mathematics Commons^™

High Dimensional Non-Linear Optimization Of Molecular Models, Joseph C. Fogarty

USF Tampa Graduate Theses and Dissertations

Molecular models allow computer simulations to predict the microscopic properties of macroscopic systems. Molecular modeling can also provide a fully understood test system for the application of theoretical methods. The power of a model lies in the accuracy of the parameter values which govern its mathematical behavior. In this work, a new software, called ParOpt, for general high dimensional non-linear optimization will be presented. The software provides a very general framework for the optimization of a wide variety of parameter sets. The software is especially powerful when applied to the difficult task of molecular model parameter optimization. Three applications of …

Evaluation And Application Of Instruments Measuring Spatial Ability And Attitude For College Chemistry Students, Xiaoying Xu

USF Tampa Graduate Theses and Dissertations

Student performance in college chemistry courses remains a concern for educators seeking to help improve the future STEM workforce. Besides math ability and prior chemistry knowledge, spatial ability and attitude toward chemistry have been considered as important factors influencing college chemistry performance. This work includes five studies and uses data collected from instruments to examine the relationships of these two factors - spatial ability and attitude - with student chemistry performance, and provides psychometric evidence for using the Purdue Visualization of Rotations test (ROT) and Attitude toward the Subject of Chemistry Inventory (ASCIv2) to measure these two factors, respectively, in …

Co(Ii) Based Metalloradical Catalysis: Carbene And Nitrene Transfer Reactions, Joseph B. Gill

USF Tampa Graduate Theses and Dissertations

Radical chemistry has attracted a large amount of research interest over the last few decades and radical reactions have recently been recognized as powerful tools for organic synthesis. The synthetic applications of radicals have been demonstrated in many fields, including in the synthesis of complex natural products. Radical reactions have a number of inherent synthetic advantages over their ionic counterparts. For example, they typically proceed at fast reaction rates under mild and neutral conditions in a broad spectrum of solvents and show significantly greater functional group tolerance. Furthermore, radical processes have the capability of performing in a cascade fashion, allowing …

Mantle-Crust Interaction In Granite Petrogenesis In Post-Collisional Settings: Insights From The Danubian Variscan Plutons Of The Romanian Southern Carpathians, Ciprian Cosmin Stremtan

USF Tampa Graduate Theses and Dissertations

The issue of granite petrogenesis plays a key role in our overall understanding of the growth and differentiation of continents, as well as in our ability to unravel the tectonic histories of orogenic belts. Granites are ubiquitous magmatic products found in almost all tectonic settings: oceanic and continental rifts (i.e., plagiogranites - extreme basalt differentiates), active continental margins (e.g,. the granitic batholiths of central and southern Andes), continent-continent collision zones (e.g., the orogenic batholiths of the Himalayas, Western Anatolia), post-collisional settings (e.g., the Variscan provinces of Europe), complex within-plates settings (e.g., Limmo massif, Afar, Ethiopia). Furthermore, granitoids are characterized by …

Metallopeptides From Design To Catalysis: Structure, Oxidative Activities, And Inhibition Studies Of Designed And Naturally Occurring Metallopeptides, Alaa Hassan Hashim

USF Tampa Graduate Theses and Dissertations

Structural and mechanistic complexities of copper-dioxygen systems have attracted much attention in the field of bioinorganic chemistry, both in model systems and trapped protein intermediates. The research presented herein is focused on model and naturally occurring metallopeptide systems, from its design to catalysis. Copper is used as the coordinating metal ion, with cobalt and zinc as probes for metal binding. The bioinorganic chemistry of copper proteins and its coordination and spectroscopic properties are briefly discussed in chapter 1. The next two chapters are centered on the de novo design of a minimalistic metallopeptide system with an amino acid sequence of …

Magneto-Optical Kerr Eect Study Of Magnetic Anisotropy In Soft Ferromagnets, Tatiana Marie Eggers

USF Tampa Graduate Theses and Dissertations

The continued progress of modern information technology relies on understanding the influence of magnetic anisotropy on magnetic thin films. In this work, two sources of magnetic anisotropy are examined in two different soft ferromagnets: a uniaxial anisotropy induced during the fabrication of Ni₈₀Fe₂₀ and exchange anisotropy, or exchange bias, which occurs at the interface of Ni₇₇Fe₁₄Cu₅Mo₄/Fe₅₀Mn₅₀ bilayer. A home-built Magneto-optical Kerr effect magnetometer is used to measure the magnetic response of the soft ferromagnetic films and details of its construction are also discussed. A simple model …

Short- And Long-Term Trends In Ecological Interactions: From Predator-Prey Interactions To Phanerozoic Diversification, Subhronil Mondal

USF Tampa Graduate Theses and Dissertations

During the last two decades, a broad spectrum of short- and long-term studies on different taxonomic groups has enriched our understanding about how dynamics of taxonomic and ecological diversification have changed through geologic time. There are two major issues that have impacted these studies: the quality and quantity of data used are often insufficient in various ways and the methods used may produce results that are more equivocal than supposed. To investigate these issues more fully, this dissertation focuses on studies on two major aspects: 1) short-term studies examining the nature of successful and unsuccessful predatory attacks on Plio-Pleistocene bivalves; …

Growth Rates In Gulf Of Mexico Red Snapper, Lutjanus Campechanus, Before And After The Deepwater Horizon Blowout, Elizabeth Shea Herdter

USF Tampa Graduate Theses and Dissertations

The Deepwater Horizon blowout occurred on April 20^th, 2010 and released nearly 5 million barrels of crude oil into the northern Gulf of Mexico causing pollution of the water and sediment inhabited by many fishes for at least 87 days while the wellhead went uncapped. Populations of the Gulf of Mexico Red snapper, Lutjanus campechanus, an important fish to the ecology and economy in the region, exhibit affinity to shallow water oil infrastructure such as the Deepwater Horizon making them especially vulnerable to crude oil contamination. The objective of this study is to determine growth of Red …

Polycyclic Aromatic Hydrocarbon Metabolites As A Biomarker Of Exposure To Oil In Demersal Fishes Following The Deepwater Horizon Blowout, Susan Susan Snyder

USF Tampa Graduate Theses and Dissertations

The Deepwater Horizon blowout occurred on April 20th, 2010, releasing 4.9 million barrels of Louisiana crude oil into the Gulf of Mexico (GoM). Subsequent to the Deepwater Horizon blowout, sediment cores revealed oil on the northern GoM seafloor and abnormal skin lesions were seen in GoM fishes. Exposure to polycyclic aromatic hydrocarbons (PAHs), a component of crude oil, in fish has been associated with many sublethal effects, including cancer and population-level effects. Using a biomarker of exposure to PAHs, this thesis evaluates inter-species, temporal and spatial differences in exposure to hydrocarbon contamination between three species of fish with varying levels …

Verification And Comparison Of Two Commonly Used Numerical Modeling Systems In Hydrodynamic Simulation At A Dual-Inlet System, West-Central Florida, Ming Xie

USF Tampa Graduate Theses and Dissertations

Numerical modeling systems are very important tools to study tidal inlets. In order to test its capability and accuracy of solving multi-inlet system problems, this study selected two widely used numerical modeling systems: Coastal Modeling System (CMS) and Delft3D Modeling Package. The hydrodynamics modules of the two modeling systems were tested at John's Pass and Blind Pass, Florida, a dual-inlets system, based on a similar modeling scheme. Detailed bathymetric surveys and hydraulic measurements were conducted to collect water depths, tide conditions, wave and current velocities as the input data as well as verification data for the models.

A comparison study …

Use Of A Towed Camera System For Estimating Reef Fish Populations Densities On The West Florida Shelf, Sarah Elizabeth Grasty

USF Tampa Graduate Theses and Dissertations

Reef fish species tend to reside over high relief habitat which makes them difficult to sample with traditional gears such as nets and trawls. Therefore, implementing and understanding the strengths and weaknesses of new approaches which incorporate acoustic and optical methods has become a priority for reef fish stock assessment. Beginning in June of 2013, a towed camera system known as the Camera-Based Assessment Survey System (C-BASS) has been used to visualize over 500 kilometers of transect and record more than 80 hours of video over several habitats in the Gulf of Mexico. Surveys have been completed on the West …

Cloning And Characterization Of Il-1Β, Il-8, Il-10, And Tnfα From Golden Tilefish (Lopholatilus Chamaeleonticeps) And Red Snapper (Lutjanus Campechanus), Kristina L. Deak

USF Tampa Graduate Theses and Dissertations

Cytokines are pleiotropic and redundant signaling molecules that govern the inflammatory response and immunity, a critical ecological parameter for organism success and population growth. Produced at the site of injury or pathogen intrusion by a variety of cell types, cytokines mediate cell-signaling in either an autocrine or paracrine manner. The type and magnitude of the cytokine milieu produced subsequently dictates the strength and form of immune response. As the most diverse vertebrate group, with a high sensitivity to contaminants, fish represent an important foci for the evaluation of immune system evolution, function, and alteration upon toxicant exposure. While many cytokines …

Phenyl Functionalized Sol-Gel Silica Sorbent For Capillary Microextraction And Chromia-Based Sol-Gel Ucon Stationary Phase For Capillary Gas Chromatography, Michael M. Mclean

USF Tampa Graduate Theses and Dissertations

The first chapter of this thesis presents an introduction to sol-gel methodology whose usefulness as a synthetic route will be demonstrated with two applications in chromatography. The first application involves the fabrication of a capillary micro-extraction (CME) device by coating a phenyl functionalized extracting phase on the inner surface of a fused silica capillary for analyte pre-concentration. The device was coupled on-line to a RP-HPLC system and practicality was demonstrated using allergens as target analytes. The allergens chosen as model analytes are typically found in fragrance products and food. Most of the 26 fragrance allergens that are monitored by various …

Analysis Of Water Quality For Lake Tarpon, Pinellas County, Florida, Kristi Nichole Savio

USF Tampa Graduate Theses and Dissertations

Urbanization has taken a major toll on the water quality of Lake Tarpon. In response, there have been management strategies and legislation put in place to help improve water quality. Our objective was to identify what management strategies and other environmental factors were driving changes in Lake Tarpons water quality from 1970 - 2010. Trends in water quality were analyzed against precipitation, land use and water quality management strategies to achieve this. Results found that two water quality management strategies, the creation of the Lake Tarpon Outfall Canal and the closing of the Lake Tarpon Sink, improved water quality the …

Dynamics And Survival Of Coral And Octocoral Juveniles Following Disturbance On Patch Reefs Of The Florida Reef Tract, Lucy Bartlett

USF Tampa Graduate Theses and Dissertations

Over the past several decades, rapid decline in adult stony-coral (comprising the Orders Scleractinia and Anthomedusae, specifically Family Milleporidae) cover has occurred concurrent with an increase in adult octocoral (Octocorallia/gorgonian) cover along the Florida Reef Tract. In January 2010, the Florida Keys experienced extremely cold air and water temperatures, below the lethal threshold for many reef organisms including corals. Very high stony-coral mortality occurred on some patch reefs. The newly-available space created by this disturbance event provided the opportunity for recruitment and settlement of new coral larvae and other reef organisms.

The goal of this study was to examine post-disturbance …

Redox Chemistry In The Phosphorus Biogeochemical Cycle, Matthew A. Pasek, Jacqueline M. Sampson, Zachary Atlas

School of Geosciences Faculty and Staff Publications

The element phosphorus (P) controls growth in many ecosystems as the limiting nutrient, where it is broadly considered to reside as pentavalent P in phosphate minerals and organic esters. Exceptions to pentavalent P include phosphine—PH₃—a trace atmospheric gas, and phosphite and hypophosphite, P anions that have been detected recently in lightning strikes, eutrophic lakes, geothermal springs, and termite hindguts. Reduced oxidation state P compounds include the phosphonates, characterized by C−P bonds, which bear up to 25% of total organic dissolved phosphorus. Reduced P compounds have been considered to be rare; however, the microbial ability to use reduced P …

Groundwater Controls On Physical And Chemical Processes In Streamside Wetlands And Headwater Streams In The Kenai Peninsula, Alaska, Michael Kroh Callahan

USF Tampa Graduate Theses and Dissertations

For this dissertation I studied groundwater and surface water interactions in the Kenai Lowlands, Alaska. In particular, I examine two important aspects of groundwater and surface water interactions: 1) Groundwater's influence on surface-water temperature; and 2) Groundwater's role in forming hydrologic flow paths that can connect uplands to streamside wetlands and streams. Chapter 2 investigates the controls on stream temperature in salmon-bearing headwater streams in two common hydrogeologic settings: 1) drainage-ways, which are low-gradient streams that flow through broad valleys; and 2) discharge-slopes, which are high gradient streams that flow through narrow valleys. The results from chapter 2 showed significant …

Assessments Of Surface-Pelagic Drift Communities And Behavior Of Early Juvenile Sea Turtles In The Northern Gulf Of Mexico, Robert F. Hardy

USF Tampa Graduate Theses and Dissertations

Knowledge of species distribution and habitat associations are essential for conservation measures. Such information is lacking for many marine species due to their occupancy of broad and ephemeral habitats that are difficult to access for study. Sea turtles, specifically the surface-pelagic juvenile stage of some species, are a group for which significant knowledge gaps remain surrounding their distribution and habitat use. Recent research has confirmed the long-standing hypothesis that the surface-pelagic juvenile stage occurs within surface-pelagic drift communities (SPDC). Within the North Atlantic and surrounding basins, the holopelagic macroalgae Sargassum spp. dominates SPDC and serves as a remotely-detectable indicator of …

Distribution Of Dissolved Trace Metals And Carbon System Parameters In The Surface Waters Of The Hillsborough River And Tampa Bay, Matthew Matthias Elliott

USF Tampa Graduate Theses and Dissertations

This work represents a first look at the general spatial distribution of trace metals and the inorganic carbon system in the surface waters of Tampa Bay. Tampa Bay's chemical environment bears many influences ranging from hydrological and geological to anthropogenic and meteorological. A large y-shaped estuary on the west-central side of the Florida Peninsula, Tampa Bay extends over 400 square miles and has a 2200 square mile watershed that includes extensive swamps, scrub, agricultural lands and densely urbanized areas. Reaching 37 miles from the northernmost point of Old Tampa Bay to the mouth of the estuary near the Sunshine Skyway …

Photophysical And Electronic Properties Of Low-Bandgap Semiconducting Polymers, Evan Lafalce

USF Tampa Graduate Theses and Dissertations

In this Ph.D. work, we investigate the optoelectronic properties of low-bandgap semiconducting polymers and project the potential for employing these materials in electronic and photonics devices, with a particular emphasis on use in organic solar cells. The field of organic solar cells is well developed and many of the fundamental aspects of device operation and material requirements have been established. However, there is still more work to be done in order for these devices to ultimately reach their full potential and achieve commercialization. Of immediate concern is the low power conversion efficiency demonstrated in these devices so far. In order …

Sustainability Planning, Environmental Justice And Climate Change: Applications Of The Long Island Markal Model, David S. Friedman, Yehuda Klein, Jose Pillich, Michael T. Sullivan

Suburban Sustainability

As pointed out by many authors, sustainability is often vague and amorphous (See, for example, Dovers, 1989; Faber, et al, 2005; Glavič, et al. 2007). There is a clear need to make analytical and data-driven analyses of established and or proposed plans. MARKAL (MARKet ALlocation model) is an analytical tool that can be used characterize the impacts of sustainability plans at multiple spatial scales: global, national, regional, and local. In this study we apply the Long Island MARKAL model to answer three interrelated issues: 1, the development and incremental improvement of local and regional sustainability plans; 2, the impact of …

No More Hidden Secrets: Human Rights Violations And Remote Sensing, Tommy O'Connell, Stephen Young

Genocide Studies and Prevention: An International Journal

Aim: This study used both high resolution and medium resolution satellite imagery to test three semi-automated remote sensing methods, in an attempt to identify useful tools to support eye-witness testimony and reports on human rights violations. As huts are routinely burned down during attacks on a village, particularly in Sudan, the number of huts and villages burned can be used to corroborate on-the-ground reports.

Methods: Three remote sensing methods (Supervised Classification, Change Detection, and Feature Extraction) were performed on imagery from both before the attacks in February 2006 and after the attacks to examine any useful trends that could be …

The Biogeochemical Cycling Of Zinc And Zinc Isotopes In The North Atlantic Ocean, Tim M. Conway, Seth G. John

School of Geosciences Faculty and Staff Publications

Zinc (Zn) is a marine micronutrient, with an overall oceanic distribution mirroring the major macronutrients, especially silicate. Seawater Zn isotope ratios (δ⁶⁶Zn) are a relatively new oceanographic parameter which may offer insights into the biogeochemical cycling of Zn. To date, the handful of published studies of seawater δ⁶⁶Zn show the global deep ocean to be both remarkably homogeneous (approximately +0.5‰) and isotopically heavier than the marine sources of Zn (+0.1 to +0.3‰). Here we present the first high‐resolution oceanic section of δ⁶⁶Zn, from the U.S. GEOTRACES GA03 North Atlantic Transect, from Lisbon to …

Crystal Engineering Of Functional Metal-Organic Material Platforms For Gas Storage And Separation Applications, Sameh Khamis Elsaidi

USF Tampa Graduate Theses and Dissertations

Metal-organic materials (MOMs) represent a unique class of porous materials that captured a great scientific interest in various fields such as chemical engineering, physics and materials science. They are typically assembled from metal ions or metal clusters connected by multifunctional organic ligands. They represent a wide range of families of materials that varied from 0D to 3D networks: the discrete (0D) structures exemplified by metal-organic polyhedra (MOPs), cubes and nanoballs while the polymeric 1D, 2D and 3D structures exemplified by coordination polymers (CPs). Indeed, the porous 3D structures include metal-organic frameworks (MOFs), porous coordination polymers (PCPs) and porous coordination networks …

Caves In Caves: Evolution Of Post-Depositional Macroholes In Stalagmites, Nurit Shtober-Zisu, Henry P. Schwarcz, Tom Chow, Christopher R. Omelon, Gordon Southam

International Journal of Speleology

In a previous paper (Shtober-Zisu et al., 2012) we described millimeter to centime-sized fluid-free holes within the interiors of stalagmites of widely varying origin. We present here further observations of this phenomenon, using X-ray tomography, macroscopic and microscopic observation of sections of twenty-six stalagmites from various sites in North America and the Caribbean region. We can distinguish three types of cavities in speleothems: primary µm-sized fluid inclusions; mm to cm sized holes, aligned along the stalagmite growth axis which are clearly syngenetic; and µm to cm-sized holes away from the growth axis (“off-axis holes or OAHs”) deeply buried inside their …

Speleothem And Biofilm Formation In A Granite/Dolerite Cave, Northern Sweden, Therese Sallstedt, Magnus Ivarsson, Johannes Lundberg, Rabbe Sjöberg, Juan Ramón Vidal Romaní

International Journal of Speleology

Tjuv-Antes grotta (Tjuv-Ante's Cave) located in northern Sweden is a round-abraded sea cave ('tunnel cave'), about 30 m in length, formed by rock-water abrasion in a dolerite dyke in granite gneiss. Abundant speleothems are restricted to the inner, mafic parts of the cave and absent on granite parts. The speleothems are of two types: cylindrical (coralloid, popcorn-like), and flowstone (thin crusts). Coralloids correspond to terrestrial stromatolite speleothems in which layers of light calcite alternate with dark, silica-rich laminae. The dark laminae are also enriched in carbon and contain incorporated remains of microorganisms. Two types of microbial communities can be distinguished …

Book Review: Van Beynen, Karst Management, Arthur N. Palmer, Margaret V. Palmer

International Journal of Speleology

Not applicable

Analysis Of Selected Climatologically Observations Of Talus & Gorge Ice Caves In New England, David Holmgren, Andreas Pflitsch

The International Workshop on Ice Caves

Changing temperature regimes inside a field of debris with year-round ice blocks are the base of this study in northern New Hampshire, USA. This unique ecosystem shows strong temperature anomalies in comparison to the surrounding area and ice, especially year-round ice, is not common below 700 m a.s.l. Yearly mean air temperatures can be strongly connected to the yearly ice level variations. Besides the analysis of the complete dataset of five years and a comparison of the impact of different seasons onto the ice considering precipitation, air temperature and special weather phenomena, the question about the use of talus & …

Introduction For Proceedings Of The 6th International Workshop On Ice Caves, National Cave And Karst Research Institute

The International Workshop on Ice Caves

No abstract provided.

Full Proceedings Of The 6th International Workshop On Ice Caves, National Cave And Karst Research Institute

The International Workshop on Ice Caves

Welcome to the Sixth International Workshop on Ice Caves (IWIC VI) in Idaho Falls, Idaho, USA. The National Cave and Karst Research Institute is pleased to host the first IWIC to meet outside of Europe, which will include speakers from over half a dozen countries in Europe, Asia, and North America. The conference setting in this mountainous region of the northwestern United States will provide conference participants with multiple opportunities to visit ice caves, including two trips to Craters of the Moon National Monument. This is also the first IWIC to examine ice in lava tube caves.