Physical Sciences and Mathematics Commons^™

An Insight Into The Biological Functions, The Molecular Mechanism And The Nature Of Interactions Of A Set Of Biologically Important Proteins., Adam A. Aboalroub

USF Tampa Graduate Theses and Dissertations

Characterization of protein structural properties is crucial to determine its role in normal and pathological conditions. In this dissertation, we have employed NMR spectroscopy in a combination of other biochemical and biophysical techniques to investigate the catalytic function, the molecular mechanism, and nature of the interactions of bmAANAT3, Cdc37, and TIMP2, respectively.

In the first project, we have employed an arylalkylamine N-acetyltransferases (AANATs) from Bombyx mori (bmAANAT3) to determine the role of the acetyl-group in coordinating the catalytic cycle in this family of enzymes. We have found that the occupancy of the acetyl-moiety in the catalytic funnel of these enzymes …

Phenomena Of Social Dynamics In Online Games, Essa Alhazmi

USF Tampa Graduate Theses and Dissertations

Online communities exhibit dynamic social phenomena that, if understood, can both influence the design of technical platforms and inform theories about general social dynamics. With increasing popularity, online games provide a rich recording of social dynamics that can contribute to understanding human behavior. This dissertation studies two phenomena of social dynamics at large scale using data traces from online games. The first phenomenon is team formation and the second is players mobility between gaming servers.

This dissertation first presents a framework for collecting data from online gaming through crawling. It includes the data sources and the tools used for data …

Design And Synthesis Of Novel Agents For The Treatment Of Tropical Diseases, Linda Corrinne Barbeto

USF Tampa Graduate Theses and Dissertations

Infectious diseases have had an impact on populations since the beginning of humanity. Despite huge advances in the fight against these conditions, they continue to be the leading cause of death and disability for a large portion of the world’s populace. Those most adversely affected predominately live in the more improvised areas of the developing world. Often treatments are made inaccessible to these areas due to cost, complicated administration requirements, severe side effects, and / or compound instability. Even when treatments are available the accelerated development of resistance has created an urgent need for the creation of new molecules with …

Simulation And Software Development To Understand Interactions Of Guest Molecules Inporous Materials, Douglas M. Franz

USF Tampa Graduate Theses and Dissertations

The effect of inclusion of explicit polarization is investigated through several theoret- ical studies of crystalline porous materials herein. In addition to the use of Monte Carlo simulation for such studies, a robust molecular dynamics software is presented which is suitable for analyzing time dependent properties of gases or other molecules in porous materials and other condensed phase systems. Metal-organic frameworks (MOFs) are the main focus of the work included here, a relatively young class of materials originally in- troduced in the early 1990s. These are usually three dimensional crystalline nanoporous materials that exhibit unique properties such as gas separation, …

Stable Isotope Geochemistry Of Shelled Marine Invertebrates: Wide-Ranging Applications, Nasser M. Al-Qattan

USF Tampa Graduate Theses and Dissertations

Mollusks grow by adding discrete growth layers throughout their lifetime (i.e., accretion). More specifically, most marine mollusks precipitate their shells in oxygen isotopic equilibrium with seawater or with a constant offset from equilibrium. The stable oxygen isotope values (δ¹⁸O) of their shells are determined by the temperature and δ¹⁸O values of the surrounding water during calcification without significant vital effects. In comparison, the stable carbon isotope values (δ¹³C) of their shells reflect those of the dissolved inorganic carbon (δ¹³C- DIC) and respired carbon dioxide. Therefore, variations in the oxygen and carbon isotope …

Statistical Learning Of Biomedical Non-Stationary Signals And Quality Of Life Modeling, Mahdi Goudarzi

USF Tampa Graduate Theses and Dissertations

Statistical learning is a set of tools for modeling and understanding complex datasets. It is a recently developed area in statistics and blends with parallel developments in computer science and, in particular, machine learning.

The classification of biomedical non-stationary signals such as Electroencephalogram (EEG) is always a challenging problem due to their complexity. The low spatial resolution on the scalp, curse of dimensionality, poor signal-to-noise ratio are disadvantages of working with biomedical signals. EEG signals are unstructured data which needs preprocessing steps to extract informative features which are measurable and predictive. In the first two chapters of this dissertation, EEG …

Solar Thermal Geothermal Hybrid System With A Bottoming Supercritical Organic Rankine Cycle, Francesca Moloney

USF Tampa Graduate Theses and Dissertations

Climate change has spurred an interest in renewable energy. Many renewable energy technologies are intermittent, such as solar energy, or are dependent on transient conditions such as the ambient temperature in the case of geothermal energy. While solar thermal energy is able to achieve high temperatures and efficiencies, geothermal energy is limited by its lower temperatures which results in low conversion efficiency. There is an opportunity to create a hybrid system using both solar thermal and geothermal energy to improve their stand-alone performance.

In the literature, solar-geothermal hybrid systems are limited by the temperature of the solar field and the …

Hierarchical Self-Assembly And Substitution Rules, Daniel Alejandro Cruz

USF Tampa Graduate Theses and Dissertations

A set of elementary building blocks undergoes self-assembly if local interactions govern how this set forms intricate structures. Self-assembly has been widely observed in nature, ranging from the field of crystallography to the study of viruses and multicellular organisms. A natural question is whether a model of self-assembly can capture the hierarchical growth seen in nature or in other fields of mathematics. In this work, we consider hierarchical growth in substitution rules; informally, a substitution rule describes the iterated process by which the polygons of a given set are individually enlarged and dissected. We develop the Polygonal Two-Handed Assembly Model …

Variations Of Global Ocean Salinity From Multiple Gridded Argo Products, Chao Liu

USF Tampa Graduate Theses and Dissertations

Salinity is one of the fundamental ocean state variables. Variations of ocean salinity can be used to infer changes in the global water cycle and air-sea freshwater exchange. Many institutions have developed gridded Argo products of global coverage. However, the existing gridded salinity products have not yet been dedicatedly intercompare and assessed. In this study, the mean state, annual and interannual variabilities, and decadal changes of ocean salinity from five Argo-based gridded salinity products, available from UK Met Office, JAMSTEC, Scripps Institution of Oceanography, China Second Institute of Oceanography, and International Pacific Research Center, are examined and compared for their …

Wireless Physical Layer Design For Confidentiality And Authentication, Tao Wang

USF Tampa Graduate Theses and Dissertations

As various of wireless techniques have been proposed to achieve fast and efficient data communication, it’s becoming increasingly important to protect wireless communications from being undermined by adversaries. A secure and reliable wireless physical layer design is essential and critical to build a solid foundation for upper layer applications. This dissertation present two works that explore the physical layer features to secure wireless communications towards the data confidentiality and user authentication.

The first work builds a reliable wireless communication system to enforce the location restricted service access control. In particular, the work proposes a novel technique named pinpoint waveforming to …

Design Of Variable Wall Thickness Geometry And Performance Mapping Of Scroll Expanders For Distributed Power Generation, Arun Kumar Narasimhan

USF Tampa Graduate Theses and Dissertations

Low-temperature heat sources such as industrial waste heat, solar, and geothermal are more suitable for small-scale power generation rather than utility scale. In order to maximize the electricity generated from low-temperature heat sources, an efficient expansion device for small-scale power output is necessary. This research work has focused on evaluating the use of a scroll expander and improving its geometrical design for the power output range of 1-25 kW_e.

The first part of the work focusses on modeling the performance of a scroll expander using two non-dimensionless parameters, namely, specific speed and specific diameter. Performance of a scroll …

Modeling And Assessing Lava Flow Hazards, Elisabeth Gallant

USF Tampa Graduate Theses and Dissertations

Lava flow hazards are one of the few constant themes across the wide spectrum of volcanic research in the solar system. These dynamic hazards are controlled by the location of the eruption, the topography and material properties of the land upon which the flow spreads, and the properties of the lava (e.g., volume, temperature, and rheology). Understanding the influences on eruption location and how lava flows modify the landscape are important steps to accurately forecast volcanic hazards. Three studies are presented in this dissertation that address di˙erent aspects of modeling and assessing vent opening and lava flow hazards.

The first …

Modulations Of Lipid Membranes Caused By Antimicrobial Agents And Helix 0 Of Endophilin, Nawal Kishore Khadka

USF Tampa Graduate Theses and Dissertations

Understanding the cellular membrane interaction with membrane active biomolecules and antimicrobial agents provides an insight in their working mechanism. Here, we studied the effect of antimicrobial agents; a recently developed peptidomimetics E107-3 and colistin as well as the N-terminal helix H0, of Endophilin A1 on the lipid bilayer.

It is important to discern the interaction mechanism of antimicrobial peptides with lipid membranes in battling multidrug resistant bacterial pathogens. We study the modification of structural and mechanical properties with a recently reported peptidomimetic on lipid bilayer. The compound referred to as E107-3 is synthesized based on the acylated reduced amide scaffold …

Framing Geologic Numeracy For The Purpose Of Geoscience Education: The Geoscience Quantitative Preparation Survey, Victor J. Ricchezza

USF Tampa Graduate Theses and Dissertations

The Geoscience Quantitative Preparation Survey (GQPS) was developed to address a deficiency in the available literature regarding the competency and preparation of early-career geologists in geoscience job-related quantitative skills – namely, geologic numeracy. The final version of the GQPS included self-confidence, usage, satisfaction, and demographic sections. The GQPS was expected to produce data that would allow for an evaluation of the geologic numeracy of early-career geologists and the success of approximately 20 years of increased focus on quantitatively literate geoscience graduates.

The self-confidence section of the GQPS included quantitative methods and quantitative skills. The usage section asked whether participants used …

Tracking Sediment Bypassing, Geomorphological Analysis, And Regional Sediment Management At Tidal Inlets, Tanya M. Beck

USF Tampa Graduate Theses and Dissertations

Tidal inlets on sandy shorelines separate barrier islands and serve as a conduit for transport of sand and water between embayments and oceans, seas, or other tidally influenced waterbodies. Tides and waves induce currents along the coastline that transport sediment across-shore and alongshore. Coastal managers must optimize barrier-inlet system stability while conserving limited sediment resources, and often base management decisions and engineering design upon geomorphic and numerical models that predict the morphological behavior of tidal inlets on short-to-medium timescales (years to decades). The overall goal of this study was threefold. First, to provide science-based practical guidance for regional sediment management …

A Machine Learning Approach To Predicting Community Engagement On Social Media During Disasters, Adel Alshehri

USF Tampa Graduate Theses and Dissertations

The use of social media is expanding significantly and can serve a variety of purposes. Over the last few years, users of social media have played an increasing role in the dissemination of emergency and disaster information. It is becoming more common for affected populations and other stakeholders to turn to Twitter to gather information about a crisis when decisions need to be made, and action is taken. However, social media platforms, especially on Twitter, presents some drawbacks when it comes to gathering information during disasters. These drawbacks include information overload, messages are written in an informal format, the presence …

Iron-Virus Interactions: Development And Testing Of The Ferrojan Horse Hypothesis, Chelsea Bonnain

USF Tampa Graduate Theses and Dissertations

Iron is an essential micronutrient for phytoplankton metabolism that limits growth in many regions of the surface ocean. More than 99.9% of oceanic dissolved iron is organically complexed to an iron-binding ligand, many of which have yet to be characterized. This thesis puts forth the Ferrojan Horse Hypothesis, which predicts a role for marine phages in oceanic iron cycling. Based on evidence from non-marine model systems, the Ferrojan Horse Hypothesis suggests that some marine phages (short for bacteriophages, or viruses that infect bacteria) can use iron as a “Trojan Horse” to gain access to host siderophore-bound iron receptors for infection. …

Reconstruction Of Radar Images By Using Spherical Mean And Regular Radon Transforms, Ozan Pirbudak

USF Tampa Graduate Theses and Dissertations

The goal of this study is the recovery of functions and finite parametric distributions from their spherical means over spheres and designing a general formula or algorithm for the reconstruction of a function f via its spherical mean transform. The theoretical study is and supported with a numerical implementation based on radar data. In this study, we approach the reconstruction problem in two different way. The first one is to show how the reconstruction problem could be converted to a Prony-type system of equations. After solving this Prony-type system of equations, one can extract the parameters that describe the corresponding …

Beyond Labels And Captions: Contextualizing Grounded Semantics For Explainable Visual Interpretation, Sathyanarayanan Narasimhan Aakur

USF Tampa Graduate Theses and Dissertations

One of the long-standing problems in artificial intelligence is the development of intelligent agents with complete visual understanding. Understanding entails recognition of scene attributes such as actors, objects and actions as well as reasoning about the common semantic structure that combines these attributes into a coherent description. While significant milestones have been achieved in the field of computer vision, majority of the work has been concentrated on supervised visual recognition where complex visual representations are learned and a few discrete categories or labels are assigned to these representations. This implies a closed world where the underlying assumption is that all …

A Decision-Making Framework For Hybrid Resource Recovery Oriented Wastewater Systems, Nader Rezaei

USF Tampa Graduate Theses and Dissertations

Water shortage, water contamination, and the emerging challenges in sustainable water resources management (e.g., the likely impacts of climate change and population growth) necessitate adopting a reverse logistics approach, which is the process of moving wastewater from its typical final destination back to the water supply chain for reuse purposes. This practice not only reduces the negative impacts of wastewater on the environment, but also provides an alternative to withdrawal from natural water resources, forming a closed-loop water supply chain. However, the design of such a supply chain requires an appropriate sustainability assessment, which simultaneously accounts for economic, environmental, and …

Sinkhole Lake Infiltration Of Contaminants Of Emerging Concern From Onsite Water Treatment Systems, Ethan A. Upton

USF Tampa Graduate Theses and Dissertations

The advancement in synthetic chemicals commonly referred to as contaminants of emerging concern (CECs) and their application has led to an increase in environmental pollution. The use of septic tanks otherwise referred to as onsite water treatment systems (OWTS), promotes the introduction of CECs into the environment while allowing little in the way of remediation. In order to study the impacts of CECs from OWTS as they infiltrate the environment and the aquifer system, water, sediment, and vegetation samples were collected around a sinkhole lake surrounded by residential housing using OWTSs. The main question of this research project is what …

The Distribution And Biogeochemistry Of Subtropical Intertidal Microbial Mats, Bert D. Anderson

USF Tampa Graduate Theses and Dissertations

Microbial mats have played an important role in the carbon (C) and nutrient cycles since the Archean Eon and modern mats are important contributors to the biogeochemistry of intertidal wetlands. Microbial mats are flat assemblages of microbes that are currently found in many unvegetated habitats globally. Intertidal salt pans are a common habitat for microbial mats, however little is known about the distribution of microbial mats within the intertidal landscape. Understanding the spatial distribution of microbial mats is critical to developing quantitative estimates of the impacts of microbial mats on their ecosystems. We photographically measured the presence and density of …

Habitat Suitability Index Model Of The Florida Sandhill Crane (Grus Canadensis Pratensis) In West-Central Florida, Courtney E. Buck

USF Tampa Graduate Theses and Dissertations

The Florida Sandhill Crane (Grus canadensis pratensis) is a state threatened endemic subspecies of the Sandhill Crane (Nesbitt & Tacha, 1997). With a population that was estimated at a maximum of 5,000 individuals in 2003 (Nesbitt & Hatchitt, 2008), it is imperative to identify potentially viable habitats, as Florida is rapidly developing. This research develops a Habitat Suitability Index model to determine unsuitable to optimally suitable habitat locations throughout west-central Florida. To do so, six suitability variables based on the crane’s life history were evaluated: Potential nesting area, immediate nesting area, wetland coverage, foraging area, brooding area, and road proximity. …

Synthesis, Discovery And Delivery Of Therapeutic Natural Products And Analogs, Zachary P. Shultz

USF Tampa Graduate Theses and Dissertations

Small molecule drug discovery relies heavily on synthetic organic chemistry to develop novel chemical entities that elicit desirable therapeutic effects. The development of targeted chemical syntheses is of paramount importance to access molecules for biological evaluation and is usually considered the bottleneck in most drug discovery campaigns. Targets for chemical syntheses commonly draw inspiration from molecules of natural origin. Nature harbors a wealth of chemical diversity that has established itself over millions of years through chemical and biological evolution. Organisms have an inherent ability to protect themselves from predators and harmful environments. In doing so, many of them evolve to …

Power Graphs Of Quasigroups, Dayvon L. Walker

USF Tampa Graduate Theses and Dissertations

We investigate power graphs of quasigroups. The power graph of a quasigroup takes the elements of the quasigroup as its vertices, and there is an edge from one element to a second distinct element when the second is a left power of the first. We first compute the power graphs of small quasigroups (up to four elements). Next we describe quasigroups whose power graphs are directed paths, directed cycles, in-stars, out-stars, and empty. We do so by specifying partial Cayley tables, which cannot always be completed in small examples. We then consider sinks in the power graph of a quasigroup, …

An Optimal Medium-Strength Regularity Algorithm For 3-Uniform Hypergraphs, John Theado

USF Tampa Graduate Theses and Dissertations

Szemere´di’s Regularity Lemma [32, 33] is an important tool in combinatorics, with numerous appli- cations in combinatorial number theory, discrete geometry, extremal graph theory, and theoretical computer science.

The Regularity Lemma hinges on the following concepts. Let G = (V, E) be a graph and let ∅ /= X, Y ⊂ V be a pair of disjoint vertex subsets. We define the density of the pair (X, Y ) by d_G(X, Y ) = |E[X, Y ]|/(|X||Y |) where E[X, Y ] denotes the …

Rethinking Map Literacy And An Analysis Of Quantitative Map Literacy, Ming Xie

USF Tampa Graduate Theses and Dissertations

Maps are increasingly being used in traditional and virtual media, and civic discourse on political, social, and environmental issues, among others, is more and more becoming influenced by them. The often-used expression of a “picture tells a 1000 words” has never been so apt in our progressively more visual world. Despite this increased role and importance of maps, map literacy, as a field of research, remains rather underdeveloped. This is especially so for thematic maps, the very type of map that is finding increasing currency in discourse. As part of this under-developed nature of map literacy, the quantitative skills used …

Design And Testing Of A Reciprocating Wind Harvester, Ahmet Topcuoglu

USF Tampa Graduate Theses and Dissertations

Renewable energy sources are vital to reduce dependence on fossil fuels that are harmful for the environment and release greenhouse gases causing global warming. Wind energy is a natural source of energy that is abundant in the environment. While wind turbines are most popular, convenient, and used to harvest energy at large scales, there have been recent studies focusing on harvesting energy from the wind for microdevices. Such micro wind energy harvesters can decrease dependence on batteries.

In this study, a novel, framed flag micro wind harvester was designed and tested, and its behavior at three different wind speeds was …

Measuring Influence Across Social Media Platforms: Empirical Analysis Using Symbolic Transfer Entropy, Abhishek Bhattacharjee

USF Tampa Graduate Theses and Dissertations

Social media platforms are interconnected environments that influence each other. Information from one social media platform spreads to another. This thesis proposes a platform-independent framework to analyze information transfer across social media platforms. This thesis uses Symbolic Transfer Entropy and Statistical Significance Test to measure influence and optimize the time window of influence between different platforms. To validate the framework, the thesis analyses the temporal activity dynamics and the information transfer across three different platforms, Reddit, Twitter and GitHub.

Two data driven studies are described in this thesis. The first study finds the optimum time windows of influence between the …

Prioritizing Rehabilitation Of Sanitary Sewers In Pinellas County, Fl, Jesse T. Hillman

USF Tampa Graduate Theses and Dissertations

Following large rain events, extraneous freshwater contributions known as inflow and infiltration (I/I) bypass the storm sewer and enter the sanitary sewer system. In areas with a high water table, like Pinellas County and the surrounding Tampa Bay area, a majority of the wastewater infrastructure is submerged year round exacerbating the rate of groundwater infiltration. This excess flow overloads the existing wastewater infrastructure leading to sanitary sewer overflows (SSOs). These SSOs result in serious problems for municipalities and utilities across the country.

This study was performed in order to assist Pinellas County Utilities in rehabilitating their southern sewer system. To …