Physical Sciences and Mathematics Commons^™

Photoacoustic Calorimetry Studies Of The Earliest Events In Horse Heart Cytochrome-C Folding, Tarah A. Word

USF Tampa Graduate Theses and Dissertations

The protein folding problem involves understanding how the tertiary structure of a protein is related to its primary structure. Hence, understanding the thermodynamics associated with the rate-limiting steps for the formation of the earliest events in folding is most crucial to understanding how proteins adopt native secondary and tertiary structures. In order to elucidate the mechanism and pattern of protein folding, an extensively studied protein, Cytochrome-c (Cc), was chosen as a folding system to obtain detailed time-resolved thermodynamic profiles for the earliest events in the protein folding process. Cytochrome-c is an ideal system for understanding the folding process for several …

Radial Versus Othogonal And Minimal Projections Onto Hyperplanes In L_4^3, Richard Alan Warner

USF Tampa Graduate Theses and Dissertations

In this thesis, we study the relationship between radial projections, and orthogonal and minimal projections in l_4^3. Specifically, we calculate the norm of the maximum radial projection and we prove that the hyperplane constant, with respect to the radial projection, is not achieved by a minimal projection in this space. We will also show our numerical results, obtained using computer software, and use them to approximate the norms of the radial, orthogonal, and minimal projections in l_4^3. Specifically, we show, numerically, that the maximum minimal projection is attained for ker{1,1,1} as well as compute the norms for the maximum radial …

Dual 7-Degree-Of-Freedom Robotic Arm Remote Teleoperation Using Haptic Devices, Yu-Cheng Wang

USF Tampa Graduate Theses and Dissertations

A teleoperated system of dual redundant manipulator will be controlled in this thesis. The robot used with the dual redundant manipulator in this thesis is Baxter. Baxter’s redundant robot arms are 7-degree-of-freedom arms. The problem that will be solved in this thesis is optimization of the 7-degree-of-freedom robot arms. The control algorithm of the 7-degree-of-freedom robot arms will be discussed and built. A simulation program will be built to test the control algorithm. Based on the control algorithm, a teleoperation system will be created for Baxter. The controller used is Omni, which is a six-joint haptic device. Omni will also …

Nanomechanical And Nanotribological Characterization Of Sub-Micron Polymeric Spheres, Himanshu Kumar Verma

USF Tampa Graduate Theses and Dissertations

Friction between nanoscale objects has been a subject of great interest and intense research effort for the last two decades. However, the vast majority of the work done in this area has focused upon the sliding friction between two rigid, atomically smooth surfaces. Thus the parameter most explored has been the corrugation in the atomic potentials and how this affects the force required to slide one object across another. In truth, many nanoscale objects whose translation force is of practical interest are more spherical in nature. We hypothesize that the factors that determine the translation force will be related, not …

Dead/Live Microbial Culture Technique, Michael Veri

USF Tampa Graduate Theses and Dissertations

New methodology has been utilized to provoke or increase targeted metabolic pathways in microbes. The low hanging fruit of natural products has been discovered over the last 50 years. To continue finding new metabolites to be used as possible drug candidates, methodology development such as those proposed herein are necessary. This methodology uses extracts from known pathogenic bacteria to elicit production of latent biosynthetic pathways from environmental bacterial isolates that may be active against the original pathogenic strains. A new compound, MAV-1 (1) of the diketopiperazine family (Figure 1) was isolated and identified utilizing these techniques. The structure of MAV-1 …

Insights Into The Challenges Of Modeling The Atmospheric Boundary Layer, Esa-Matti Tastula

USF Tampa Graduate Theses and Dissertations

This work approaches the topic of modeling the atmospheric boundary layer in four research projects, which are summarized below.

i) The diurnal cycles of near-surface meteorological parameters over Antarctic sea ice in six widely used atmospheric reanalyses were validated against observations from Ice Station Weddell. The station drifted from February through May 1992 and provided the most extensive set of meteorological observations ever collected in the Antarctic sea ice zone. For the radiative and turbulent surface fluxes, both the amplitude and shape of the diurnal cycles varied considerably among different reanalyses. Near-surface temperature, specific humidity, and wind speed in the …

Authentication Via Multiple Associated Devices, Jean-Baptiste Subils

USF Tampa Graduate Theses and Dissertations

This thesis presents a practical method of authentication utilizing multiple devices. The factors contributing to the practicality of the method are: the utilization of devices already commonly possessed by users and the amenability to being implemented on a wide variety of devices. The term “device” refers to anything able to perform cryptographic operations, store data, and communicate with another such device.

In the method presented herein, multiple devices need to be associated with a single user to provide this user an identity in the system. A public key infrastructure is used to provide this identity. Each of the devices associated …

Information Technology & Sustainability: An Empirical Study Of The Value Of The Building Automation System, Daphne Marie Simmonds

USF Tampa Graduate Theses and Dissertations

This study examines the environmental and economic effects of green information technology (IT). Green IT describes two sets of IT innovations: one set includes innovations that are implemented to reduce the environmental impact of IT services in organizations; and the other IT to reduce the environmental impact of other organizational processes. The two sets respond to the call for more environmentally friendly or “greener” organizational processes.

I developed and tested a preliminary model. The model applied the resource based view (RBV) of the firm (Wernerfelt 1984) the stakeholder theory (Freeman 1984) and included four constructs: (1) BAS implementation; environmental …

The Effect Of Urbanization On The Embodied Energy Of Drinking Water In Tampa, Florida, Mark Vincent Eli Santana

USF Tampa Graduate Theses and Dissertations

Increasing urbanization has serious implications for resource and energy use. One of these resources is drinking water. The increased amount of impervious surfaces associated with urban development is responsible for increased runoff during rain events, which may have a negative impact on the quality of nearby bodies of water, including drinking water sources. The growing populations associated with urbanization require a higher water demand. In addition, urban drinking water systems use energy to collect, treat, and distribute a safe reliable effluent to users. Therefore, this study focuses on the degree to which urbanization influences the embodied energy of drinking water …

Investigаtiоn Оf 3d Structures Оf Γ-Aaрeрtide Bаsed Peрtidоmimetics, Qiao Qiao

USF Tampa Graduate Theses and Dissertations

Oligomers which have a tendency to form well-defined secondary structures are called foldamers. They offer an attractive opportunity for the design of novel molecules that mimic the structures and functions of proteins and enzymes including biocatalysis and biomolecular recognition. Herein a new class of non-natural γ-AApeptides and their derivatives are synthesized and studied in our lab. Previous studies of γ-AApeptides have revealed that they are highly resistant to proteolysis, and have virtually limitless potential in functional group diversity. However, to improve the bio-activity and explore new bio-applications, the understanding of the folding conformation of γ-AApeptides are necessary. Thus, NMR spectroscopy …

Spatiotemporal Sensing And Informatics For Complex Systems Monitoring, Fault Identification And Root Cause Diagnostics, Gang Liu

USF Tampa Graduate Theses and Dissertations

In order to cope with system complexity and dynamic environments, modern industries are investing in a variety of sensor networks and data acquisition systems to increase information visibility. Multi-sensor systems bring the proliferation of high-dimensional functional Big Data that capture rich information on the evolving dynamics of natural and engineered processes. With spatially and temporally dense data readily available, there is an urgent need to develop advanced methodologies and associated tools that will enable and assist (i) the handling of the big data communicated by the contemporary complex systems, (ii) the extraction and identification of pertinent knowledge about the environmental …

Environmental Sustainability Of Wastewater Treatment Plants Integrated With Resource Recovery: The Impact Of Context And Scale, Pablo K. Cornejo

USF Tampa Graduate Theses and Dissertations

There is an urgent need for wastewater treatment plants (WWTPs) to adapt to a rise in water and energy demands, prolonged periods of drought, climate variability, and resource scarcity. As population increases, minimizing the carbon and energy footprints of wastewater treatment, while properly managing nutrients is crucial to improving the sustainability WWTPs. Integrated resource recovery can mitigate the environmental impact of wastewater treatment systems; however, the mitigation potential depends on various factors such as treatment technology, resource recovery strategy, and system size.

Amidst these challenges, this research seeks to investigate the environmental sustainability of wastewater treatment plants (WWTPs) integrating resource …

Effects Of Disorder And Low Dimensionality On Frozen Dynamics In Ca3co2-Xmnxo6, Brian Wesley Casas

USF Tampa Graduate Theses and Dissertations

Complex oxides represent an intersection of play grounds for the existence of exciting new fundamental physics and materials with potential technological implications. The realization of many exciting properties of these systems rely on the coupling of electronic, structural and magnetic degrees of freedom. Additionally, competing interactions within each type of coupling discussed previously lead to theoretically diverse ground states, which under the application of an external perturbation, can be tuned and probed.

Ca3Co¬2-xMnxO6 represent a quasi-one dimensional Ising spin chain system oriented in an antiferromagnetic triangular lattice. The exotic behavior of the undoped compound Ca3Co2O6 has inspired work on continuing …

Reconstructing Paleoenvironments Of The Plio-Pleistocene Tamiami Formation Of Florida With Benthic Foraminifera, Heather Bender

USF Tampa Graduate Theses and Dissertations

There is general agreement that a range of paleodepths and environments are represented in the individual shell units of the middle Pliocene to earliest Pleistocene Tamiami Formation of southwest Florida, but maximum depths remain poorly constrained. Here, benthic Foraminifera abundances are used as a paleoenvironmental proxy to compare the upper Tamiami from quarries in Sarasota, Florida to Recent modern coastal, bay, and reef habitats of Florida, the Grand Cayman Islands, and Puerto Rico, ranging in depth from 0 to 55 meters. I used: (1) ordination techniques, including detrended correspondence analysis (DCA) and cluster analysis, to compare upper Tamiami foraminiferal assemblages …

Development And Application Of Web-Based Open Source Drug Discovery Platforms, Yuri Pevzner

USF Tampa Graduate Theses and Dissertations

Computational modeling approaches have lately been earning their place as viable tools in drug discovery. Research efforts more often include computational component and the usage of the scientific software is commonplace at more stages of the drug discovery pipeline. However, as software takes on more responsibility and the computational methods grow more involved, the gap grows between research entities that have the means to maintain the necessary computational infrastructure and those that lack the technical expertise or financial means to obtain and include computational component in their scientific efforts. To fill this gap and to meet the need of many, …

Application And Development Of Computational Methods In Conformational Studies Of Bio-Molecules, Aleksandra Karolak

USF Tampa Graduate Theses and Dissertations

The work presented in my dissertation focuses on the conformational studies of bio-molecules including proteins and DNA using computational approaches. Conformational changes are important in numerous molecular bioprocesses such as recognition, transcription, replication and repair, etc. Proteins recognize specific DNA sequences and upon binding undergo partial or complete folding or partial unfolding in order to find the optimal conformational fit between molecules involved in the complex. In addition to sequence specific recognition, proteins are able to distinguish between subtle differences in local geometry and flexibility associated with DNA that may further affect their binding affinities. Experimental techniques provide high-resolution details …

Use Of Assessments In College Chemistry Courses: Examining Students' Prior Conceptual Knowledge, Chemistry Self-Efficacy, And Attitude, Sachel M. Villafañe-García

USF Tampa Graduate Theses and Dissertations

Students' retention in STEM-related careers is of great concern for educators and researchers, especially the retention of underrepresented groups such as females, Hispanics, and Blacks in these careers. Therefore it is important to study factors that could potentially influence students' decision to stay in STEM. The work described in this dissertation involved three research studies where assessments have been used in college chemistry courses to assess students' prior content knowledge, chemistry-self-efficacy, and attitude toward science. These three factors have been suggested to have an influence on students' performance in a course and could eventually be a retention factor.

The first …

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 …