Physical Sciences and Mathematics Commons^™

Investigation Of Bioactive Metabolites From The Antarctic Sponge Dendrilla Membranosa And Marine Microorganisms, Chris G. Witowski

USF Tampa Graduate Theses and Dissertations

Natural products continue to be a valuable source of compounds in research involving chemical ecology and drug discovery. Secondary metabolites are biosynthesized to benefit the host organism in its environment (feeding deterrence from predators, antibiotic properties to avoid infection, etc.) but these compounds also serve as useful scaffolds in drug discovery applications. The research herein describes both aspects of these two branches of natural products chemistry. The Antarctic sponge Dendrilla membranosa produces diterpenes, of which membranolide A, deters feeding of the predatory amphipod Gondogenia antarctica. A metabolomic study of several sponges was undertaken to determine environmental factors that govern …

Mid-Holocene Speleothem Climate Proxy Records From Florida And Belize, Anna L. Pollock

USF Tampa Graduate Theses and Dissertations

As global temperatures rise due to anthropogenic climate change, water resources, thus economies, are threatened. A geologically recent period of increased temperatures is the mid-Holocene and an investigation of its climate may allow for a better understanding of future precipitation and changes to regional water resources. The regions of interest are tropical Northern Central America and subtropical North America with Belize and Florida representing each climate zone. By reconstructing mid-Holocene climate in Florida and Belize, I hope to provide a better understanding of how increased temperatures and a reduced latitudinal temperature gradient impacts both precipitation patterns and variability. Today, drivers …

Quest Toward The Design And Synthesis Of Functional Metal-Organic Materials (Moms): A Supermolecular Building Layer Approach (Sbl), Hasnaa Mouttaki

USF Tampa Graduate Theses and Dissertations

Metal-Organic Materials (MOMs) represent an important division of coordination chemistry. They are self-assembled through the linking of metals with organic ligands. They gained their spotlight among scientists for their aptitude for design and facile synthesis via their multi-component coordination, and their readiness to functionalization. MOMs have been targeted for specific industrial and environmental applications such as gas storage, catalysis and CO₂ sequestration.

Throughout the past decade, studies have been conducted to develop systematic approaches toward the design and synthesis of functional MOMs. Their synthesis from targeted building units has facilitated their rational design and functionalization. The Molecular Building Block …

Active Tile Self-Assembly And Simulations Of Computational Systems, Daria Karpenko

USF Tampa Graduate Theses and Dissertations

Algorithmic self-assembly has been an active area of research at the intersection of computer science, chemistry, and mathematics for almost two decades now, motivated by the natural self-assembly mechanism found in DNA and driven by the desire for precise control of nanoscale material manufacture and for the development of nanocomputing and nanorobotics. At the theoretical core of this research is the Abstract Tile Assembly Model (aTAM), the original abstract model of DNA tile self-assembly. Recent advancements in DNA nanotechnology have been made in developing strand displacement mechanisms that could allow DNA tiles to modify themselves during the assembly process by …

The Evaluation And Study Of Modern Radiation Dosimetry Methods As Applied To Advanced Radiation Therapy Treatments Using Intensity Modulated Megavoltage Photon Beams, Cassandra Stambaugh

USF Tampa Graduate Theses and Dissertations

The purpose of this work is to evaluate quasi-3D arrays for use with intensity modulated radiation therapy (IMRT) and volumetric modulated arc therapy (VMAT) and to determine their clinical relevance. This is achieved using a Delta4 from Scandidos and ArcCheck from Sun Nuclear and the associated software. While certain aspects of these devices and software have been previously evaluated, the main goal of this work is to evaluate the new aspects, such as reconstructing dose on a patient CT set, and extending the capabilities. This includes the capability to reconstruct the dose based on a helical delivery as well as …

Aldehydic C-H Amination Reactions Via Co(Ii)-Based Metalloradical Catalysis And Construction Of Novel Chiral Meso-Amidoporphyrin Ligands, Christopher Lee Lizardi

USF Tampa Graduate Theses and Dissertations

Medium-sized organic ring synthesis poses a seemingly insurmountable challenge, and because of this it is a field under immense investigation. Heterocyclic containing medium-sized rings are common structural motifs in nature, which has caused researchers to investigate their potential biological activity and properties as materials. This research focused on the grand challenge of medium-sized heterocyclic ring synthesis, providing the synthesis community with new tools to generate these highly evasive products, while elucidating energetic and geometric properties of one of Nature's least understood organic ring systems.

Cobalt(II)-Amidoporphyrins, [Co(D₂-Por)], are an emerging class of metalloradical catalysts (MRC) which can facilitate …

Morphodynamics Of Mullet Key, West-Central Florida, Emeli Sandoval

USF Tampa Graduate Theses and Dissertations

Mullet Key is a right angle barrier island located at the mouth of Tampa Bay, west-central Florida. Based on historical shoreline data from 1873, the Gulf (west)-facing section of the beach has been dynamic illustrating large beach advances and retreats of up to 500 m on a decadal scale, while the south (channel)-facing section of the beach has shown to maintain a stable shoreline. This study focuses on the morphodynamics of the Gulf-facing beach. Since the 1920s, most of the Gulf-facing beach has been accreting except at the southern end near the Tampa Bay main channel. However, over the past …

The Speleogenesis Of Vallgornera Cave (Mallorca, Spain): A Mineralogical And Morphological Study, Jacqueline Amelia Diehl

USF Tampa Graduate Theses and Dissertations

Cova des Pas de Vallgornera (CPV) is morphologically and scientifically, the most prominent karst feature of Mallorca Island (Spain). It consists of over 74 km of passages developed within two carbonate lithologies (reef front and back reef facies) of Upper Miocene age. Two distinct cave patterns are recognized, both tightly controlled by the type of facies; spongework mazes and collapse chambers are characteristic for the reef front unit, whereas linear, fracture-guided galleries develop in the back reef carbonates. CPV is abundantly decorated with a variety of speleothems.

The overarching goal of this study is to provide evidence towards the cave's …

Dcms: A Data Analytics And Management System For Molecular Simulation, Meryem Berrada

USF Tampa Graduate Theses and Dissertations

Despite the fact that Molecular Simulation systems represent a major research tool in multiple scientific and engineering fields, there is still a lack of systems for effective data management and fast data retrieval and processing. This is mainly due to the nature of MS which generate a very large amount of data - a system usually encompass millions of data information, and one query usually runs for tens of thousands of time frames. For this purpose, we designed and developed a new application, DCMS (A data Analytics and Management System for molecular Simulation), that intends to speed up the process …

The Detection And Quantitative Analysis Of Endocannabinoids And Endogenous Fatty Acid Amides In Apis Mellifera And Tribolium Castaneum, Perry Robert Mitchell Jr.

USF Tampa Graduate Theses and Dissertations

Endocannabinoids, and the fatty acid amides from which they are a member, have garnered greater scientific interest in the last two decades due to the cannabimimetic properties of these endogenous molecules. The most well-known of these is Anandamide, which has thus far been discovered in several species of animal ranging from C. elegans, fruit flies, to bovine and humans. Because of the importance and increasing impact of these compounds a brief overview is first presented herein, with a major focus on the N-acyldopamines due to the direct impact they potentially pose to human physiology.

Secondly, the detection and …

Thermal Fluctuations Tunneling In Doped Conjugated Polymers, Troy C. Stedman

USF Tampa Graduate Theses and Dissertations

The possibility of using conducting polymers as organic alternatives to widely used inorganic materials for thermoelectric (TE) applications has received much attention in the past few decades. Since conducting polymers are generally inefficient compared to inorganic TE materials, research into their underlying transport mechanisms is required to improve their efficiency. We use a model based on the effects of local thermal fluctuations to characterize the transport in conducting polymer composites. With this model, full linear responses for the current and electronic heat current are obtained. From these responses, the local temperature dependent conductivity, electronic contribution to the thermal conductivity, and …

Design, Synthesis And Applications Of Polymer Biomaterials, Frankie Costanza

USF Tampa Graduate Theses and Dissertations

The emergence of antibiotic resistant bacteria has prompted the research into novel kinds of antibacterial small molecules and polymers. Nature has solved this issue with the use of cationic antimicrobial peptides, which act as nonspecific antibiotics against invading species. Herein, we have tried to mimic this general mechanism in a biocompatible and biodegradable polymer micelle based on the polymerization of naturally occurring amino acids lysine and phenylalanine linked to a PEG tether. This amphiphilic structure allows for the spontaneous collapse into stable nanoparticles in solution, which contains a hydrophilic outer layer and a hydrophobic core. Our polymers have shown activity …

Gamma-Aapeptides As A New Class Of Peptidomimetics: Synthesis, Structures, And Functions, Haifan Wu

USF Tampa Graduate Theses and Dissertations

Peptidomimetics are synthetic oligomers that resemble the activities of peptides. Their advantages over peptides include high stability towards proteolysis and enormous chemical diversity. Over the past two decades, there have been extensive efforts to develop peptide mimics, such as beta-peptides, peptoids, D-peptides, etc. The research on peptidomimetics have led to many important applications in both medicinal and material science. In order to explore new functions, the discovery of peptidomimetics with novel frameworks is essential. We reported the synthesis and evaluation of a new class of peptidomimetics, termed as gamma-AApeptides. Previous studies of gamma-AApeptides have revealed that gamma-AApeptides are highly resistant …

Design And Synthesis Of Bioactive Peptidomimetics, Yaogang Hu

USF Tampa Graduate Theses and Dissertations

Protein-Protein Interactions (PPIs) play a very important role in biological functions and therefore the inhibition of specific Protein-Protein Interactions has a huge therapeutic value. The most successful small molecular PPIs inhibitors do not fit with the prevalent `Rule of Five' drug profile. To overcome the disadvantages of small molecular PPIs inhibitors, peptide based PPIs inhibitors were developed. Herein we describe the development of a new class of peptidomimetics AA-peptides. The AApeptides were designed based on chiral PNA backbone. Substitution of nucleobases yields AApeptides that are resistant to proteolysis and capable of mimicking peptides. Two types of AApeptides were discussed in …

Optimization Of Aggregating Agents And Sers Substrates For Sers Detection Of Cotinine And Trans 3'-Hydroxycotinine, Sungyub Han

USF Tampa Graduate Theses and Dissertations

This dissertation mainly focuses on applications of Surface Enhance Raman Scattering (SERS) to detect tobacco-related biomarkers with optimized experimental conditions (pH and aggregating agents) and SERS substrates (silica core and silver shell nanoparticles). Cotinine (COT) and trans 3-hydroxycotinine (3HC), metabolized from nicotine as one of main chemicals of tobacco, have been used as tobacco biomarkers because their half-life are longer than that of nicotine, which enable to monitor the tobacco exposure. The effects of aggregating agents and pH on SERS detection of COT and 3HC were investigated. Aggregating agents play an important role in SERS detection of target molecules since …

Coherent Digital Holographic Adaptive Optics, Changgeng Liu

USF Tampa Graduate Theses and Dissertations

A new type of adaptive optics (AO) based on the principles of digital holography (DH) is proposed and developed for the use in wide-field and confocal retinal imaging. Digital holographic adaptive optics (DHAO) dispenses with the wavefront sensor and wavefront corrector of the conventional AO system. DH is an emergent imaging technology that gives direct numerical access to the phase of the optical field, thus allowing precise control and manipulation of the optical field. Incorporation of DH in an ophthalmic imaging system can lead to versatile imaging capabilities at substantially reduced complexity and cost of the instrument. A typical conventional …

Identification And Characterization Of N-Acyltransferase Enzymes That Are Involved In The Biosynthesis Of Fatty Acid Amides, Daniel Robert Dempsey

USF Tampa Graduate Theses and Dissertations

Fatty acid amides are an emerging family of bioactive lipids that consists of N-acylethanolamines, N-acylarylalkylamides, N-acylglycines, N-acyl amino acids, N-monoacylpolyamides, and primary fatty acid amides. Short chain fatty acid amides are products of inactivated biogenic amines such as dopamine, histamine, octopamine, and serotonin, whereas long chain fatty acid amides have been implicated in a number of physiological process such as the perception and inhibition of chronic pain through binding to their specific receptors. The most famous; therefore, the most studied long chain fatty acid amide is anandamide or also known as N-arachidonylethanolamine. The biosynthesis …

Design, Testing And Implementation Of A New Authentication Method Using Multiple Devices, Cagri Cetin

USF Tampa Graduate Theses and Dissertations

Authentication protocols are very common mechanisms to confirm the legitimacy of someone’s or something’s identity in digital and physical systems.

This thesis presents a new and robust authentication method based on users’ multiple devices. Due to the popularity of mobile devices, users are becoming more likely to have more than one device (e.g., smartwatch, smartphone, laptop, tablet, smart-car, smart-ring, etc.). The authentication system presented here takes advantage of these multiple devices to implement authentication mechanisms. In particular, the system requires the devices to collaborate with each other in order for the authentication to succeed. This new authentication protocol is robust …

Comparison Of Isotope-Based Biomass Pathways With Groundfish Community Structure In The Eastern Gulf Of Mexico, Sheri Ann Huelster

USF Tampa Graduate Theses and Dissertations

This study compared traditional community analysis with stable-isotope trophic analysis to define process-based trophic elements of community structure in the eastern Gulf of Mexico, and developed a predictive capability regarding changes to fish community structure that would be expected from increasing eutrophication. Specifically, it used an existing trawl survey program (SEAMAP) to compare invertebrate herbivore (sponge and sea urchin) isotopes with groundfish isotopes, and then compared the resulting spatial patterns with spatial variation in community structure, as identified by cluster analysis. The comparison was applied to seven NMFS survey zones that extended offshore from the Caloosahatchee River, FL northwest to …

Modeling Intrusive Geometries Of A Shallow Crustal Intrusion: New Evidence From Mount Ellsworth, Utah, Nathan Nushart

USF Tampa Graduate Theses and Dissertations

Surface displacements resulting from upper-crustal intrusion of melt are a paramount concern for communities and facilities located in or near active volcanic areas (e.g. Campi Flegrei, Yucca Mtn.). Study of active intrusions such as Campi Flegrei, Italy west of Mt. Vesuvius, is limited to remote observations through geophysical/geodetic procedures. While the surface displacement due to melt emplacement at depth can easily be determined, the geometries and depth of intrusions are often based on simplified assumptions (e.g. spheres and prolate or oblate ellipsoids). These models benefit from data constraining both the geometries of the individual intrusions, and the kinematics and mechanics …

Low Dimensionality Effects In Complex Magnetic Oxides, Paula J. Lampen Kelley

USF Tampa Graduate Theses and Dissertations

Complex magnetic oxides represent a unique intersection of immense technological importance and fascinating physical phenomena originating from interwoven structural, electronic and magnetic degrees of freedom. The resulting energetically close competing orders can be controllably selected through external fields. Competing interactions and disorder represent an additional opportunity to systematically manipulate the properties of pure magnetic systems, leading to frustration, glassiness, and other novel phenomena while finite sample dimension plays a similar role in systems with long-range cooperative effects or large correlation lengths. A rigorous understanding of these effects in strongly correlated oxides is key to manipulating their functionality and device performance, …

Relational Agency, Networked Technology, And The Social Media Aftermath Of The Boston Marathon Bombing, Megan M. Mcintyre

USF Tampa Graduate Theses and Dissertations

Agency is a foundational and ongoing concern for the field of Rhetoric and Composition. Long thought to be a product and possession of human action, rhetorical agency represents the most obvious connection between the educational and theoretical work of the field and the civic project of liberal arts and humanities education. Existing theories of anthropocentric rhetorical agency are insufficient, however, to account for the complex technological work of digitally enmeshed networks of humans and nonhumans. To better account for these complex networks, this project argues for the introduction of new materialist theories of distributed agency into conversations about agency within …

Organic-Inorganic Hybrid Materials Based On Oxyanion Linkers For Selective Adsorption Of Polarizable Gases, Mona Hanafy Mohamed

USF Tampa Graduate Theses and Dissertations

The separation of industrially important gases into pure supplies that can be used for many practical applications is based mainly on energy intensive methods such as the cryogenic distillation which is costly and energy intensive. Therefore other routes have been introduced to industrial separation of gases such as the selective adsorption using porous solid materials. Zeolites and activated carbon are the most widely used recyclable energy-efficient porous solid materials for industrial gas separations, however the low uptake and selectivity hurdles their commercialization in some separation applications. Metal organic frameworks (MOFs) have been extensively studied as solid porous materials in term …

Fabrication Of Tissue Precursors Induced By Shape-Changing Hydrogels, Olukemi O. Akintewe

USF Tampa Graduate Theses and Dissertations

Scaffold based tissue reconstruction inherently limits regenerative capacity due to inflammatory response and limited cell migration. In contrast, scaffold-free methods promise formation of functional tissues with both reduced adverse host reactions and enhanced integration. Cell-sheet engineering is a well-known bottom-up tissue engineering approach that allows the release of intact cell sheet from a temperature responsive polymer such as poly-N-isopropylacrylamide (pNIPAAm). pNIPAAm is an ideal template for culturing cell sheets because it undergoes a sharp volume-phase transition owing to the hydrophilic and hydrophobic interaction around its lower critical solution temperature (LCST) of 32°C, a temperature close to physiological temperature. Compared to …

Reducing The Control Burden Of Legged Robotic Locomotion Through Biomimetic Consonance In Mechanical Design And Control, Caitrin Elizabeth Eaton

USF Tampa Graduate Theses and Dissertations

Terrestrial robots must be capable of negotiating rough terrain if they are to become autonomous outside of the lab. Although the control mechanism offered by wheels is attractive in its simplicity, any wheeled system is confined to relatively flat terrain. Wheels will also only ever be useful for rolling, while limbs observed in nature are highly multimodal. The robust locomotive utility of legs is evidenced by the many animals that walk, run, jump, swim, and climb in a world full of challenging terrain.

On the other hand, legs with multiple degrees of freedom (DoF) require much more complex control and …

Ground-Coupled Air Waves: A Seismological Case Study Of The Explosion Quakes Of The 2007 Eruption Of Pavlof Volcano, Alaska, Cassandra Marie Smith

USF Tampa Graduate Theses and Dissertations

An abnormally high number of explosion quakes were noted during the monitoring effort for the 2007 eruption of Pavlof Volcano on the Alaskan Peninsula. In this study we manually counted the explosion quakes from their characteristic ground-coupled air waves. This study makes an effort at better quantifying the number of explosion quakes and how the characteristic ground-coupled air waves are affected by wind direction and wind speed. Additionally this study investigates how the ground coupled air waves might be used in a monitoring or analysis effort by calculating energy release and gas mass release. Over 3.2x10⁴ quakes were recorded. …

Population Dynamics Of The Little Gulper Shark (Centrophorus Uyato) And Community Analyses Of Elasmobranch Species In The Northern Gulf Of Mexico, Jacquelin Joye Hipes

USF Tampa Graduate Theses and Dissertations

In chapter 1 I describe the population dynamics of an understudied species of gulper shark, Centrophorus uyato (common name, the Little Gulper), found in the Northern Gulf of Mexico. Sharks in the family Centrophoridae are mid-sized, demersal fish, with seven species identified in North American waters. These deepwater species can be difficult to study due to the extreme depths at which they occur. During four longlining cruises from 2012-2014, 593 sharks were landed, predominantly in the Mississippi Canyon off the Louisiana coast. Mean depth of capture was 290 m. Supplementing these data are catch records for C. uyato from a …

Development Of Orally Bioavailable 4(1H)-Quinolones And 1,2,3,4-Tetrahydroacridin-9(10H)-Ones With Potent Anti-Malarial Activity, Jordany Richarlson Maignan

USF Tampa Graduate Theses and Dissertations

Although Malaria rates are on the decline due to the efforts of the World Health Organization and other organizations dedicated to the eradication of this disease, a relaxed attitude towards the development of new antimalarial entities would be flawed. Due to the emergence of resistance in the parasite, the almost 50% world-wide reduction in malarial death rates that have been produced over the past 15 years are threatening to be lost

New drugs are urgently needed and our approach focuses on the re-evaluation and optimization of the historic antimalarial ICI 56,780. Due to its causal prophylactic activity, along with its …

Computational Investigations Of Potential Energy Function Development For Metal-Organic Framework Simulations, Metal Carbenes, And Chemical Warfare Agents, Christian R. Cioce

USF Tampa Graduate Theses and Dissertations

Metal-Organic Frameworks (MOFs) are three-dimensional porous nanomaterials with a variety of applications, including catalysis, gas storage and separation, and sustainable energy. Their potential as air filtration systems is of interest for designer carbon capture materials. The chemical constituents (i.e. organic ligands) can be functionalized to create rationally designed CO2 sequestration platforms, for example. Hardware and software alike at the bleeding edge of supercomputing are utilized for designing first principles-based molecular models for the simulation of gas sorption in these frameworks. The classical potentials developed herein are named PHAST -- Potentials with High Accuracy, Speed, and Transferability, and thus are designed …

Nearest Neighbor Foreign Exchange Rate Forecasting With Mahalanobis Distance, Vindya Kumari Pathirana

USF Tampa Graduate Theses and Dissertations

Foreign exchange (FX) rate forecasting has been a challenging area of study in the past. Various linear and nonlinear methods have been used to forecast FX rates. As the currency data are nonlinear and highly correlated, forecasting through nonlinear dynamical systems is becoming more relevant. The nearest neighbor (NN) algorithm is one of the most commonly used nonlinear pattern recognition and forecasting methods that outperforms the available linear forecasting methods for the high frequency foreign exchange data. The basic idea behind the NN is to capture the local behavior of the data by selecting the instances having similar dynamic behavior. …