Current Search: reactions (x)
Pages
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Title
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THE GLYCINE AND PROLINE REDUCTASE SYSTEMS: AN EVOLUTIONARY PERSPECTIVE AND PRESCENCE IN ENTEROBACTERIACEAE.
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Creator
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Witt, Joshua, Self, William, University of Central Florida
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Abstract / Description
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The Glycine and Proline Reduction systems are two of the best characterized selenoenzymes in bacteria and have been found to occur in a wide variety of clostridia . These enzymes are utilized to reduce glycine or D-proline to obtain energy via substrate level phosporylation or membrane gradients, respectively [6, 7]. This includes the pathogens C. difficile and C. botulinum [5, 8]. Strains of C. difficile are activate toxigenic pathways whenever either of these pathways is active within the...
Show moreThe Glycine and Proline Reduction systems are two of the best characterized selenoenzymes in bacteria and have been found to occur in a wide variety of clostridia . These enzymes are utilized to reduce glycine or D-proline to obtain energy via substrate level phosporylation or membrane gradients, respectively [6, 7]. This includes the pathogens C. difficile and C. botulinum [5, 8]. Strains of C. difficile are activate toxigenic pathways whenever either of these pathways is active within the cell [5, 8]. Though evolutionary studies have been conducted on ammonia producing bacteria none has been done to directly characterize these two system by themselves. This includes an understanding of whether or not this system is transferred between organisms, as many of the clostridia that are to be studied are known to have an "open genome." [8, 10] With this information we were able to generate a phylogenic model of the proline and glycine reduction systems. Through this analysis, we were able to account for many clostridial organisms that contain the system, but also many other organisms as well. These included enterobacteriaceae including a strain of the model organism, Escherichia coli. It was further concluded that Glycine Reductase was a much less centralized system and included a wide range of taxa while Proline Reductase was much more centralized to being within the phyla of firmicutes. It was also concluded that the strain of E. coli has a fully functional operon for Glycine Reductase.
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Date Issued
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2013
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Identifier
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CFH0004506, ucf:45149
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFH0004506
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Title
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UNDERSTANDING THE ROLE OF A HEMERYTHRIN-LIKE PROTEIN IN MYCOBACTERIUM TUBERCULOSIS.
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Creator
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Herndon, Caitlyn, Rohde, Kyle, University of Central Florida
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Abstract / Description
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According to the Centers for Disease Control and Prevention (CDC), 8 million people each year are infected with Mycobacterium tuberculosis (Mtb) leading to 1.5 million deaths annually. This staggering number calls for advancements in understanding this bacterium so progress can be made in treating and preventing the disease. It is particularly important to understand mechanisms by which TB survives inside hostile host immune cells known as macrophages and within hypoxic granuloma lesions of...
Show moreAccording to the Centers for Disease Control and Prevention (CDC), 8 million people each year are infected with Mycobacterium tuberculosis (Mtb) leading to 1.5 million deaths annually. This staggering number calls for advancements in understanding this bacterium so progress can be made in treating and preventing the disease. It is particularly important to understand mechanisms by which TB survives inside hostile host immune cells known as macrophages and within hypoxic granuloma lesions of the lung. Preliminary microarray data has shown that a TB gene known as Rv2633c is induced upon macrophage invasion. Bioinformatic analysis of Rv2633c coding sequence shows the product of Rv2633c has homology with hemerythrin-like proteins. Hemerythrins are a class of proteins commonly used to bind oxygen and sense nitric oxide and iron, leading us to hypothesize a role for Rv2633c in surviving hypoxic or nitrosative stress encountered within macrophages and granulomas. My first aim will be to generate a reporter strain of Mycobacterium smegmatis (Msm) expressing the mCherry fluorescent protein driven by the Rv2633c promoter. This tool will allow us to determine the stress conditions (i.e. hypoxia, nitric oxide treatment, acid pH) that activate expression of this gene by measuring the change in fluorescence. Linking the regulation of Rv2633c to specific environmental cues relevant to infections in vivo will provide insight into the role of this unique protein. Secondly, a knockout mutant of Rv2633c in the attenuated M. bovis BCG will be constructed and characterized to determine the importance and function of this protein during TB infections.
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Date Issued
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2014
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Identifier
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CFH0004647, ucf:45291
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFH0004647
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Title
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From Excited Charge Dynamics to Cluster Diffusion: Development and Application of Techniques Beyond DFT and KMC.
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Creator
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Acharya, Shree Ram, Rahman, Talat, Chow, Lee, Stolbov, Sergey, Wu, Annie, University of Central Florida
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Abstract / Description
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This dissertation focuses on developing reliable and accurate computational techniques which enable the examination of static and dynamic properties of various activated phenomena using deterministic and stochastic approaches. To explore ultrafast electron dynamics in materials with strong electron-electron correlation, under the influence of a laser pulse, an ab initio electronic structure method based on time-dependent density functional theory (TDDFT) in combination with dynamical mean...
Show moreThis dissertation focuses on developing reliable and accurate computational techniques which enable the examination of static and dynamic properties of various activated phenomena using deterministic and stochastic approaches. To explore ultrafast electron dynamics in materials with strong electron-electron correlation, under the influence of a laser pulse, an ab initio electronic structure method based on time-dependent density functional theory (TDDFT) in combination with dynamical mean field theory (DMFT) is developed and applied to: 1) single-band Hubbard model; 2) multi-band metal Ni; and 3) multi-band insulator MnO. The ultrafast demagnetization in Ni reveal the importance of memory and correlation effects, leading to much better agreement with experimental data than previously obtained, while for MnO the main channels of charge response are identified. Furthermore, an analytical form of the exchange-correlation kernel is obtained for future applications, saving tremendous computational cost. In another project, size-dependent temporal and spatial evolution of homo- and hetero-epitaxial adatom islands on fcc(111) transition metals surfaces are investigated using the self-learning kinetic Monte Carlo (SLKMC) method that explores long-time dynamics unbiased by apriori selected diffusion processes. Novel multi-atom diffusion processes are revealed. Trends in the diffusion coefficients point to the relative role of adatom lateral interaction and island-substrate binding energy in determining island diffusivity. Moreover, analysis of the large data-base of the activation energy barriers generated for multitude of diffusion processes for variety of systems allows extraction of a set of descriptors that in turn generate predictive models for energy barrier evaluation. Finally, the kinetics of the industrially important methanol partial oxidation reaction on a model nanocatalyst is explored using KMC supplemented by DFT energetics. Calculated thermodynamics explores the active surface sites for reaction components including different intermediates and energetics of competing probable reaction pathways, while kinetic study attends to the selectivity of products and its variation with external factors.
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Date Issued
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2018
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Identifier
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CFE0006965, ucf:52910
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0006965
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Title
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Photochemistry and Applications of Diels-Alder Adducts and Photoacids in Materials Science.
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Creator
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Johns, Valentine, Liao, Yi, Miles, Delbert, Zou, Shengli, Gesquiere, Andre, Su, Ming, University of Central Florida
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Abstract / Description
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Utilizing light as an energy source for reactions has intrigued many chemists. This has led to the development of the principles of photochemistry. The Photo retro Diels Alder (PrDA) reaction is one such system that has potential for use in materials science as well as in the life sciences. However, there was no guide to predict whether a compound could undergo the PrDA reaction, which limits the widespread use of this reaction. Another system is that of photoacids (molecules that release...
Show moreUtilizing light as an energy source for reactions has intrigued many chemists. This has led to the development of the principles of photochemistry. The Photo retro Diels Alder (PrDA) reaction is one such system that has potential for use in materials science as well as in the life sciences. However, there was no guide to predict whether a compound could undergo the PrDA reaction, which limits the widespread use of this reaction. Another system is that of photoacids (molecules that release protons upon irradiation reversibly). Since most fundamental processes involve proton transfer, these types of photoacids have great potential which is yet to be explored. This thesis describes the design and synthesis of various aromatic DA adducts. These adducts were made to undergo the rDA reaction using UV (Ultra-Violet) light. Experimental results showed that the photoreactivity of these adducts depends on the electron-donating ability of the diene component and the electron-withdrawing ability of the dienophile component. In addition, mechanistic study of this reaction revealed the formation of a charge separated intermediate with a singlet excited state. The potential of the PrDA reaction was also explored in two ways. One was by designing isomeric DA adducts from pentacene and TCNE (tetracyanoethylene) which are capable of switching from one isomer to another via a PrDA process. The other way was the design and synthesis of a polymer with an anthracene diketone moeity which could undergo a PrDA reaction to change from an insulator to a semiconductor. Finally, the syntheses of a number of photoacids which not only become acidic upon irradiation but also respond to visible light reversibly have been explored. A rationale has been developed for the design of photoacids with desired photo-induced response. While electron donating and accepting groups in strategic positions help tune the pH; using different combinations of ethanol and water affect the rate of the forward and the backward processes. A photoacid monomer was also incorporated into three photoacid polymers which respond to visible light reversibly, hence promising widespread applications of these photoacids.
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Date Issued
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2012
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Identifier
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CFE0004556, ucf:49235
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0004556
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Title
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Diffusion and reaction in selected uranium alloy system.
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Creator
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Huang, Ke, Sohn, Yongho, An, Linan, Xu, Chengying, Coffey, Kevin, Heinrich, Helge, University of Central Florida
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Abstract / Description
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U-Mo metallic fuels with Al alloys as the matrix/cladding are being developed as low enriched uranium fuels under the Reduced Enrichment for Research and Test Reactor (RERTR) program. Significant interactions have been observed to occur between the U-Mo fuel and the Al alloy during fuel processing and irradiation. U-Zr metallic fuels with stainless steel claddings have been developed for the generation IV sodium fast reactor (SFR). The fuel cladding chemical interaction (FCCI) induced by the...
Show moreU-Mo metallic fuels with Al alloys as the matrix/cladding are being developed as low enriched uranium fuels under the Reduced Enrichment for Research and Test Reactor (RERTR) program. Significant interactions have been observed to occur between the U-Mo fuel and the Al alloy during fuel processing and irradiation. U-Zr metallic fuels with stainless steel claddings have been developed for the generation IV sodium fast reactor (SFR). The fuel cladding chemical interaction (FCCI) induced by the interdiffusion of components was also observed. These interactions induce deleterious effects on the fuel system, such as thinning of the cladding layer, formation of phases with undesirable properties, and thermal cracking due to thermal expansion mismatches and changes in molar volume. The interaction between the fuel and the cladding involves multi-component interdiffusion. To determine the ternary interdiffusion coefficients using a single diffusion couple, a new method based on regression via the matrix transformation approach is proposed in this study. This new method is clear in physical meaning and simple in mathematical calculation. The reliability and accuracy of this method have been evaluated through application to three case studies: a basic asymptotic concentration profile, a concentration profile with extrema and a smoothed concentration profile with noise. Generally, this new method works well in all three cases.In order to investigate the interdiffusion behavior in U-Mo alloys, U vs. Mo diffusion couples were assembled and annealed in the temperature range of 650 to 1000(&)deg;C. The interdiffusion microstructures and concentration profiles were examined via scanning electron microscopy (SEM) and electron probe microanalysis (EPMA), respectively. Interdiffusion coefficients and activation energies were calculated as functions of temperature and Mo composition. The intrinsic diffusion coefficients of U and Mo at the marker composition were also determined. The activity of U and the thermodynamic factor of the U-Mo alloy have been calculated using the ideal solution, the regular solution, and the subregular solution models based on the molar excess Gibbs free energy of the U-Mo alloy. The calculated intrinsic diffusivities of U and Mo along with the thermodynamic factor of the U-Mo alloy were employed to estimate the atomic mobilities and the vacancy wind effects of U and Mo according to Manning's description.To explore potential diffusion barrier materials for reducing the fuel cladding chemical interaction between the U-Mo fuel and the Al alloy matrix/cladding, the interdiffusion behavior between U-Mo alloys and Mo, Zr, Nb and Mg were systematically studied. U-10wt.%Mo vs. Mo, Zr and Nb diffusion couples were annealed in the temperature range from 600 to 1000(&)deg;C. A diffusion couple between U-7wt.%Mo and Mg was annealed at 550(&)deg;C for 96 hours. SEM and transmission electron microscopy (TEM) were applied to characterize the microstructure of the interdiffusion zone. X-ray energy dispersive spectroscopy (XEDS) and EPMA were utilized to examine the concentration redistribution and the phase constituents. For the U-Mo vs. Mo diffusion couples, the interdiffusion coefficients at high Mo concentrations ranging from 22 to 32 at.%Mo were determined for the first time. In the U-Mo vs. Zr diffusion couples, the Mo2Zr phase was found at the interface. The diffusion paths were estimated and investigated according to the Mo-U-Zr ternary phase diagram. Thermal cracks and pure U precipitates were found within the diffusion zone in the U-Mo vs. Nb system. The growth rate of the interdiffusion zone was found to be lower by about 103 times for Zr, 105 times for Mo and 106 times for Nb compared to those observed in the U-10wt.%Mo vs. Al or Al-Si systems. For the diffusion couple of U-Mo vs. Mg, the U-Mo was bonded very well to the Mg and there was negligible diffusion observed even after 96 hours annealing at 550(&)deg;C.For a more fundamental understanding of the complex diffusion behavior between U-Zr fuels and their stainless steel claddings, U vs. Fe, Fe-15wt.%Cr and Fe-15wt.%Cr-15wt.%Ni diffusion couples were examined to investigate the interdiffusion behaviors between U and Fe and the effects of the alloying elements Cr and Ni. The diffusion couples were annealed in the temperature range from 580 to 700(&)deg;C for various times. Two intermetallic phases, U6Fe and UFe2, developed in all of the diffusion couples with the U6Fe layer growing faster than the UFe2 layer. For the diffusion couples of U vs. Fe, extrinsic growth constants, intrinsic growth constants, integrated interdiffusion coefficients and activation energies in each phase were calculated. The results suggest that U6Fe impeded the growth of UFe2, and the boundary condition change caused by the allotropic transformation of U played a role in the growth of the U6Fe and UFe2 layers. The reasons why U6Fe grew much faster than UFe2 are also discussed. The additions of Cr and Ni into Fe affected the growth rates of U6Fe and UFe2. The solubility of Cr and Ni in U6Fe and UFe2 were determined, and it was found that Cr diffused into U more slowly than Fe or Ni.
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Date Issued
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2012
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Identifier
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CFE0004548, ucf:49238
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0004548
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Title
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First Principles Studies of Pattern Formations and Reactions on Catalyst Surfaces.
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Creator
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Le, Duy, Rahman, Talat, Roldan Cuenya, Beatriz, Schelling, Patrick, Sohn, Yongho, University of Central Florida
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Abstract / Description
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This dissertation undertakes theoretical research into the adsorption, pattern formation, and reactions of atoms, molecules, and layered materials on catalyst surfaces. These investigations are carried out from first-principles calculations of electronic and geometric structures using density functional theory (DFT) for predictions and simulations at the atomic scale. The results should be useful for further study of the catalytic activities of materials and for engineering functional...
Show moreThis dissertation undertakes theoretical research into the adsorption, pattern formation, and reactions of atoms, molecules, and layered materials on catalyst surfaces. These investigations are carried out from first-principles calculations of electronic and geometric structures using density functional theory (DFT) for predictions and simulations at the atomic scale. The results should be useful for further study of the catalytic activities of materials and for engineering functional nanostructures.The first part of the dissertation focuses on systematic first-principles simulations of the energetic pathways of CO oxidation on the Cu2O(100) surface. These simulations show CO to oxidize spontaneously on the O-terminated Cu2O(100) surface by consuming surface oxygen atoms. The O-vacancy on Cu2O(100) then is subsequently healed by dissociative adsorption of atmospheric O2 molecules.The second part discusses the pattern formation of hydrogen on two and three layers of Co film grown on the Cu(111) surface. It is found that increasing the pressure of H2 changes the hydrogen structure from 2H-(2 x 2) to H-p(1 x 1) through an intermediate structure of 6H-(3 x 3).The third part compares the results of different ways of introducing van der Waals (vdW) interactions into DFT simulations of the adsorption and pattern formation of various molecules on certain substrates. Examinations of the physisorption of five nucleobases on graphene and of n-alkane on Pt(111) demonstrate the importance of taking vdW interactions into account, and of doing so in a way that is best suited to the particular system in question. More importantly, as the adsorption of 1,4 diaminebenzene molecules on Au(111) shows inclusion of vdW interactions is crucial for accurate simulation of the pattern formation.The final part carries out first-principles calculations of the geometric and electronic structure of the Moire pattern of a single layer of Molybdenum disulfide (MoS2) on Cu(111). The results reveal three possible stacking types. They also demonstrate that the MoS2 layer to be chemisorbed, albeit weakly, and that, while Cu surface atoms are vertically disordered, the layer itself is not strongly buckled.
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Date Issued
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2012
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Identifier
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CFE0004224, ucf:48991
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0004224
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Title
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Analysis of Driver Behavior Modeling in Connected Vehicle Safety Systems Through High Fidelity Simulation.
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Creator
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Jamialahmadi, Ahmad, Pourmohammadi Fallah, Yaser, Rahnavard, Nazanin, Chatterjee, Mainak, University of Central Florida
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Abstract / Description
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A critical aspect of connected vehicle safety analysis is understanding the impact of human behavior on the overall performance of the safety system. Given the variation in human driving behavior and the expectancy for high levels of performance, it is crucial for these systems to be flexible to various driving characteristics. However, design, testing, and evaluation of these active safety systems remain a challenging task, exacerbated by the lack of behavioral data and practical test...
Show moreA critical aspect of connected vehicle safety analysis is understanding the impact of human behavior on the overall performance of the safety system. Given the variation in human driving behavior and the expectancy for high levels of performance, it is crucial for these systems to be flexible to various driving characteristics. However, design, testing, and evaluation of these active safety systems remain a challenging task, exacerbated by the lack of behavioral data and practical test platforms. Additionally, the need for the operation of these systems in critical and dangerous situations makes the burden of their evaluation very costly and time-consuming. As an alternative option, researchers attempt to use simulation platforms to study and evaluate their algorithms. In this work, we introduce a high fidelity simulation platform, designed for a hybrid transportation system involving both human-driven and automated vehicles. We decompose the human driving task and offer a modular approach in simulating a large-scale traffic scenario, making it feasible for extensive studying of automated and active safety systems. Furthermore, we propose a human-interpretable driver model represented as a closed-loop feedback controller. For this model, we analyze a large driving dataset to extract expressive parameters that would best describe different driving characteristics. Finally, we recreate a similarly dense traffic scenario within our simulator and conduct a thorough analysis of different human-specific and system-specific factors and study their effect on the performance and safety of the traffic network.
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Date Issued
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2018
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Identifier
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CFE0007573, ucf:52578
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0007573
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Title
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Invisible in Plain Sight: The Troubling Connections Between the National Hockey League and the Russian Mafia.
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Creator
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Ennion, Kayla, Crepeau, Richard, Gannon, Barbara, Walker, Ezekiel, University of Central Florida
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Abstract / Description
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Professional sports leagues in North America have seen scandals, controversies, and tragedies. There is, however, a forgotten scandal that happened in the 1990s: the Russian Mafia came dangerously close to the National Hockey League. This thesis explores the alleged Mafia connections by examining newspaper and magazine articles and documentaries focused on the issue. The limited public response to allegations of Russian Mafia involvement is contrasted with other professional sports...
Show moreProfessional sports leagues in North America have seen scandals, controversies, and tragedies. There is, however, a forgotten scandal that happened in the 1990s: the Russian Mafia came dangerously close to the National Hockey League. This thesis explores the alleged Mafia connections by examining newspaper and magazine articles and documentaries focused on the issue. The limited public response to allegations of Russian Mafia involvement is contrasted with other professional sports controversies that were met with an immediate response by the leagues and fans. How North Americans viewed Russians during the post-Soviet era is also explored in this paper. This thesis examines why evident Mafia involvement with National Hockey League players did not provoke attention and sanctions by the league nor an outcry from the fans. This study will conclude the League did not react to the allegations because it felt as if the games were not harmed directly. Also, hockey fans did not find the allegations surprising because of the media's constant reports of corruption within Russia's borders, especially involving organized crime. Perhaps the lack of reaction by the National Hockey League and its fans suggests why this particular scandal is forgotten a mere 20 years later.
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Date Issued
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2014
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Identifier
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CFE0005488, ucf:50363
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0005488
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Title
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Computational Approach to the Problems of Electro- and Photo-Catalysis.
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Creator
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Zuluaga, Sebastian, Stolbov, Sergey, Schelling, Patrick, Roldan Cuenya, Beatriz, Masunov, Artem, University of Central Florida
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Abstract / Description
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The main objective of this work is to gain basis for rational design of catalysts used in fuel cells for conversion of chemical energy stored in hydrogen molecules into electric energy, as well as photo-catalysts used for hydrogen production from water under solar irradiation. This objective is achieved by applying the first principles computational approach to reveal relationship among compositions of materials under consideration, their electronic structure and catalytic activity. A major...
Show moreThe main objective of this work is to gain basis for rational design of catalysts used in fuel cells for conversion of chemical energy stored in hydrogen molecules into electric energy, as well as photo-catalysts used for hydrogen production from water under solar irradiation. This objective is achieved by applying the first principles computational approach to reveal relationship among compositions of materials under consideration, their electronic structure and catalytic activity. A major part of the work is focused on electro-catalysts for hydrogen fuel cells. Platinum (Pt) is widely used in the electrodes of fuel cells due to its good catalytic properties. However, Pt is an expensive and scarce element, its catalytic activity is not optimal and also it suffers from CO poisoning at anode. Therefore the search for new catalytic materials is needed for large scale implementation of fuel cells. The main direction of search of more efficient electro-catalysts is based in the design in which an active element monoatomic layer (AE) is deposited on a metal substrate (MS) made of a cost-effective material. Two goals are achieved by doing this: on the one hand, the cost of the catalytic system is reduced by reducing the amount of the AE in the system and on the other hand the catalytic properties of the AE can be tuned through its interactions with the MS. In the first part of this work the Pd-based alloys and layered structures have been studied as promising electro-catalysts for the ORR on the fuel cell cathodes, more precisely Pd-Co alloys and Pd/M/Pd (M=Co,Fe). There exists a robust model linking the activity of a surface toward ORR to computable thermodynamic properties of the system and further to the binding energies of the ORR intermediates on the catalyst surface. A more challenging task is to find how to tune these binding energies through modification of the surface electronic structure that can be achieved by varying the surface composition and/or morphology. To resolve this challenge, the electronic structure, binding energies of intermediates and the ORR free energies have been calculated within the density functional theory (DFT) approximation. The results presented in this work show that in contrast to the widely accepted notion, the strain exerted by a substrate on AE hardly affects the surface activity toward ORR, while the hybridization of the electronic states of the AE-and MS-electronic states is the key factor controlling the catalytic properties of these systems. Next it is shown that the catalytic activity of the promising anode electrocatalysts, such as Pt/M, M=Au, Ru and Pd, is also determined by the AE-MS hybridization with a minor effect of the strain. Furthermore, we have shown that, if AE is weakly bound to the substrate (as it is for Pt/Au), surface reconstruction occurs. This leads to the breaking of the relation between the electronic structure of the clean surface and the reactivity of the sytem. Other kind of promising ORR catalysts is designed in the form of Ru nanoparticles modified by chalcogens. In this work, I present the results obtained for small Ru clusters and flat Ru facets modified with chalcogens (S, Se and Te). The O and OH binding energies are chosen as descriptors of the ORR. The results on the two systems are compared, concluding that large clusters with relative large flat facets have higher catalytic activity due to the absence of low coordinated and thus high reactive Ru atoms. Regarding the problem of the hydrogen production via photo-catalytic splitting of water, one of the challenges is tuning the band gap of the photo-anodes to optimal levels. Graphitic carbon nitride (g-C3N4) is a promising material to be used as a photo-anode, however, a reduction of the band gap width by rational doping of the material would improve the efficiency significantly. This issue is addressed in the last chapter of this work. Two problems are considered: a) the stability of the doped system and b) the band gap width. To address the first problem the ab-initio thermodynamics approach has been used, finding that the substitution of C and N with the doping agent (B, C, N, O, Si and P) is thermodynamically preferred over the interstitial addition of dopant to the g-C3N4 structure. However, due to high kinetic energy barriers for the detachment of C and N atoms, involved in the substitution doping, the interstitial addition found to be kinetically more favorable. Since the density functional theory fails to reproduce the band gap of semiconductors correctly, the GW approximation was used to study the band gap of the system. The results indicate that the g-C3N4 system maintain its semiconductor character if doped with B, O and P under certain conditions, while reducing the band gap.
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Date Issued
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2013
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Identifier
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CFE0005288, ucf:50546
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0005288
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Title
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A THREE-DIMENSIONAL BAY/ESTUARY MODEL TO SIMULATE WATER QUALITY TRANSPORT.
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Creator
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Yu, Jing, Yeh, Gour-Tsyh, University of Central Florida
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Abstract / Description
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This thesis presents the development of a numerical water quality model using a general paradigm of reaction-based approaches. In a reaction-based approach, all conceptualized biogeochemical processes are transformed into a reaction network. Through the decomposition of species governing equations via Gauss-Jordan column reduction of the reaction network, (1) redundant fast reactions and irrelevant kinetic reactions are removed from the system, which alleviates the problem of unnecessary and...
Show moreThis thesis presents the development of a numerical water quality model using a general paradigm of reaction-based approaches. In a reaction-based approach, all conceptualized biogeochemical processes are transformed into a reaction network. Through the decomposition of species governing equations via Gauss-Jordan column reduction of the reaction network, (1) redundant fast reactions and irrelevant kinetic reactions are removed from the system, which alleviates the problem of unnecessary and erroneous formulation and parameterization of these reactions, and (2) fast reactions and slow reactions are decoupled, which enables robust numerical integrations. The system of species transport equations is transformed to reaction-extent transport equations, which is then approximated with two subsets: algebraic equations and kinetic-variables transport equations. As a result, the model alleviates the needs of using simple partitions for fast reactions. With the diagonalization strategy, it makes the inclusion of arbitrary number of fast and kinetic reactions relatively easy, and, more importantly, it enables the formulation and parameterization of kinetic reactions one by one. To demonstrate the general paradigm, QAUL2E was recasted in the mode of a reaction network. The model then was applied to the Loxahatchee estuary to study its response to a hypothetical biogeochemical loading from its surrounding drainage. Preliminary results indicated that the model can simulate four interacting biogeochemical processes: algae kinetics, nitrogen cycle, phosphorus cycle, and dissolved oxygen balance.
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Date Issued
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2006
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Identifier
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CFE0001372, ucf:46991
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0001372
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Title
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INVESTIGATION OF NANOCERIA-MODIFIED PLATINUM-GOLD COMPOSITE ELECTRODES FOR THE ELECTROCHEMICAL REDUCTION OF OXYGEN IN ALKALINE MEDIA.
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Creator
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Hegishte, Rahul, Diaz, Diego, University of Central Florida
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Abstract / Description
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Platinum-gold and nanoceria-modified platinum-gold electrodes were prepared on a platinum surface via electrochemical reduction of solutions of platinum and gold salts in the dispersion of nanoceria. The molar ratios of Pt and Au were varied in both PtAu and PtAu/CeO2 electrodes while the total concentration of the metals was maintained at 2 x 10-3M and the concentration of nanoceria was maintained constant at 5 x 10-3M. The electrodes were characterized by their cyclic voltammetry curves in...
Show morePlatinum-gold and nanoceria-modified platinum-gold electrodes were prepared on a platinum surface via electrochemical reduction of solutions of platinum and gold salts in the dispersion of nanoceria. The molar ratios of Pt and Au were varied in both PtAu and PtAu/CeO2 electrodes while the total concentration of the metals was maintained at 2 x 10-3M and the concentration of nanoceria was maintained constant at 5 x 10-3M. The electrodes were characterized by their cyclic voltammetry curves in 0.5M sulfuric acid solution. The electrochemically active area of the electrodes was determined using the copper underpotential deposition method. The linear sweep voltammograms of the PtAu and PtAu/CeO2 electrodes were plotted from -1V to 0V vs. Ag/AgCl, 3M KCl reference electrode using the rotating disk electrodes for the rotation speeds from 200 to 3600rpm in an oxygen saturated 0.1M sodium hydroxide solution. The values of the kinetic controlled current density were determined from the rotating disk voltammetry. The values of the limiting current density for each rotation speed were used to plot the Koutecky-Levich plots for the electrodes. The rate constants were obtained from the Koutecky-Levich plots for each composition of the electrode. The values of kinetic current density and the rate constants indicated that the addition of Au enhances the ORR rates in both the PtAu and the PtAu/CeO2 electrodes. The values of the kinetic current densities of the PtAu/CeO2 were lower than that of the PtAu electrodes owing to the poor electrical conductivity of ceria. The Koutecky-Levich plots for the PtAu and the PtAu/CeO2 electrodes are linear for the four-electron reduction of oxygen in the alkaline media, which indicates that the overall reaction follows the first order kinetics. The electron transfer rate constants obtained from the Koutecky-Levich plots for the PtAu and the PtAu/CeO2 electrodes both were found to increase in values with the addition of Au. The Tafel plots were plotted for the PtAu and PtAu/CeO2 electrodes and the values of Tafel slopes were found to be in a small range for lower amounts of Au which indicated that the ORR rates were enhanced in lower amounts of Au. The values of Tafel slopes were found to be much higher for the ceria-modified PtAu electrodes as compared to the PtAu electrodes, which indicate the lower rates of ORR after the modification with ceria. Also, the ORR rates for the electrodes with smaller amounts of Au in PtAu/CeO2 were higher than those in the larger amounts of Au.
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Date Issued
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2011
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Identifier
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CFE0003639, ucf:48860
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0003639
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Title
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Tuning chemical and optical properties of nanomaterials: From extended surfaces to finite nanoclusters.
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Creator
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Hooshmand Gharehbagh, Zahra, Rahman, Talat, Kara, Abdelkader, Kaden, William, Uribe Romo, Fernando, University of Central Florida
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Abstract / Description
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Modifying the electronic and optical properties of surfaces and nanostructures are in the forefront of surface science. This dissertation's focus is on this problem. The first part is on the adsorption of functionalized naphthalene molecules on Cu(111) surface. The results show that changing the functional group results in modification of charge redistribution at the interface of molecule and surface and the electronic structure of Cu changes. The second part discusses the new Moir(&)#233;...
Show moreModifying the electronic and optical properties of surfaces and nanostructures are in the forefront of surface science. This dissertation's focus is on this problem. The first part is on the adsorption of functionalized naphthalene molecules on Cu(111) surface. The results show that changing the functional group results in modification of charge redistribution at the interface of molecule and surface and the electronic structure of Cu changes. The second part discusses the new Moir(&)#233; structure of h-BN on Rh(111) induced by intrinsic carbon impurities of Rh single crystals. We found that these impurities intercalate between h-BN and Rh(111) with new local properties such as charge transfer from Rh and C atoms to h-BN such as appearance of new states in the BN. The third part is about the study of CO super lattice structure at 1/2ML when adsorbed on Pd(111). By considering all the possible overlayer structures and using several different functionals, we found that two structures can be made by CO adsorbents and all the other structures convert to one of these two. The fourth part is on the electronic and optical properties of ligated Ag44 nanoclusters. Using DFT and TDDFT calculations we show that when the pH level of a solvent is changed, the protecting ligands deprotonate and their interaction with each other as well as the metal core varies and the new peaks in absorption spectrum arise from electron rich deprotonated ligands. The final part is on the adsorption of planar molecules on MoS2. We found that the isomers of di-iodobenzene adsorb with same strength on MoS2 and it is the symmetry of frontier orbitals that identifies their different behavior. Also the adsorption and dissociation of benzenethiol on MoS2 was studied and the results show that benzenethiol dissociates only in the presence of defects and heals the structure.
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Date Issued
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2018
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Identifier
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CFE0007337, ucf:52138
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0007337
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Title
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The Effects of Phosphatidylserine on Reaction Time and Cognitive Function Following an Exercise Stress.
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Creator
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Wells, Adam, Hoffman, Jay, Fragala, Maren, Stout, Jeffrey, University of Central Florida
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Abstract / Description
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Phosphatidylserine (PS) is an endogenously occurring phospholipid that has been shown to have cognition and mood enhancing properties in humans, possibly through its role as an enzyme co-factor in cellular signal transduction. Specifically, PS has been identified as activator of classical isoforms of protein kinase C, an enzyme known to be involved in the growth and differentiation of neural cells, and is therefore thought to play a role in the protection of neurons.The purpose of this study...
Show morePhosphatidylserine (PS) is an endogenously occurring phospholipid that has been shown to have cognition and mood enhancing properties in humans, possibly through its role as an enzyme co-factor in cellular signal transduction. Specifically, PS has been identified as activator of classical isoforms of protein kinase C, an enzyme known to be involved in the growth and differentiation of neural cells, and is therefore thought to play a role in the protection of neurons.The purpose of this study was to examine the effects of supplementation with PS and caffeine on measures of cognition, reaction time and mood prior to and following an exercise stress. Twenty, healthy, resistance trained males (17) and females (3) (mean (&)#177; SD; age: 22.75 (&)#177; 3.27 yrs; height: 177.03 (&)#177; 8.44cm; weight: 78.98 (&)#177; 11.24kg; body fat%: 14.28 (&)#177; 6.6), volunteered to participate in this randomized, double-blind, placebo-controlled study. Participants were assigned to a PS group (400mg/day PS; 100mg/day caffeine, N=9) or PL (16g/day Carbs, N=11) delivered in the form of 4 candy chews identical in size, shape and color. Subjects performed an acute bout of full body resistance exercise, prior to (T1) and following 14 days of supplementation (T2). Measures of reaction time (Dynavision(&)#174; D2 Visuomotor Training Device), cognition (Serial Subtraction Test, SST), and mood (Profile of Mood States, POMS) were assessed immediately before and following resistance exercise in both T1 and T2. Data was analyzed using two-way ANCOVA and repeated measures ANOVA.Supplementation with 400mg PS and 100mg caffeine did not have a significant impact upon measures of reaction time or cognition between groups at baseline or following acute resistance exercise. However, there was a non-significant trend to the attenuation of fatigue between groups, following acute resistance exercise (p = 0.071). Interestingly, our data suggests that acute resistance exercise alone may improve cognitive function.Although more research is necessary regarding optimal dosage and supplementation duration, the current findings suggest that supplementation 400mg/day PS with 100mg/day caffeine may attenuate fatigue following acute resistance exercise. It is possible that the lack of significance may be the result of both an inhibition of the PS activated pathway and a withdrawal effect from caffeine.
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Date Issued
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2012
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Identifier
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CFE0004457, ucf:49325
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0004457
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Title
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A NEW PARADIGM OF MODELING WATERSHED WATER QUALITY.
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Creator
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Zhang, Fan, Yeh, Gour-Tsyh, University of Central Florida
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Abstract / Description
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Accurate models to reliably predict sediment and chemical transport in watershed water systems enhance the ability of environmental scientists, engineers and decision makers to analyze the impact of contamination problems and to evaluate the efficacy of alternative remediation techniques and management strategies prior to incurring expense in the field. This dissertation presents the conceptual and mathematical development of a general numerical model simulating (1) sediment and reactive...
Show moreAccurate models to reliably predict sediment and chemical transport in watershed water systems enhance the ability of environmental scientists, engineers and decision makers to analyze the impact of contamination problems and to evaluate the efficacy of alternative remediation techniques and management strategies prior to incurring expense in the field. This dissertation presents the conceptual and mathematical development of a general numerical model simulating (1) sediment and reactive chemical transport in river/stream networks of watershed systems; (2) sediment and reactive chemical transport in overland shallow water of watershed systems; and (3) reactive chemical transport in three-dimensional subsurface systems. Through the decomposition of the system of species transport equations via Gauss-Jordan column reduction of the reaction network, fast reactions and slow reactions are decoupled, which enables robust numerical integrations. Species reactive transport equations are transformed into two sets: nonlinear algebraic equations representing equilibrium reactions and transport equations of kinetic-variables in terms of kinetically controlled reaction rates. As a result, the model uses kinetic-variables instead of biogeochemical species as primary dependent variables, which reduces the number of transport equations and simplifies reaction terms in these equations. For each time step, we first solve the advective-dispersive transport of kinetic-variables. We then solve the reactive chemical system node by node to yield concentrations of all species. In order to obtain accurate, efficient and robust computations, five numerical options are provided to solve the advective-dispersive transport equations; and three coupling strategies are given to deal with the reactive chemistry. Verification examples are compared with analytical solutions to demonstrate the numerical accuracy of the code and to emphasize the need of implementing various numerical options and coupling strategies to deal with different types of problems for different application circumstances. Validation examples are presented to evaluate the ability of the model to replicate behavior observed in real systems. Hypothetical examples with complex reaction networks are employed to demonstrate the design capability of the model to handle field-scale problems involving both kinetic and equilibrium reactions. The deficiency of current practices in the water quality modeling is discussed and potential improvements over current practices using this model are addressed.
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Date Issued
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2005
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Identifier
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CFE0000448, ucf:46405
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0000448
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Title
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INTERDIFFUSION BEHAVIOR OF U-MO ALLOYS IN CONTACT WITH AL AND AL-SI ALLOYS.
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Creator
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Perez, Emmanuel, Sohn, Yong-Ho, University of Central Florida
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Abstract / Description
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U-Mo dispersion and monolithic fuels embedded in Al-alloy matrix are under development to fulfill the requirements of research reactors to use low-enriched molybdenum stabilized uranium alloys as fuels. The system under consideration in this study consisted of body centered cubic (gamma) U-Mo alloys embedded in an Al structural matrix. Significant interaction has been observed to take place between the U-Mo fuel and the Al matrix during manufacturing of the fuel-plate system assembly and...
Show moreU-Mo dispersion and monolithic fuels embedded in Al-alloy matrix are under development to fulfill the requirements of research reactors to use low-enriched molybdenum stabilized uranium alloys as fuels. The system under consideration in this study consisted of body centered cubic (gamma) U-Mo alloys embedded in an Al structural matrix. Significant interaction has been observed to take place between the U-Mo fuel and the Al matrix during manufacturing of the fuel-plate system assembly and during irradiation in reactors. These interactions produce Al-rich phases with physical and thermal properties that adversely affect the performance of the fuel system and can lead to premature failure. In this study, interdiffusion and microstructural development in the U-Mo vs. Al system was examined using solid-to-solid diffusion couples consisting of U-7wt.%Mo, U-10wt.%Mo and U-12wt.%Mo vs. pure Al, annealed at 600°C for 24 hours. The influence of Si alloying addition (up to 5 wt.%) in Al on the interdiffusion microstructural development was also examined using solid-to-solid diffusion couples consisting of U-7wt.%Mo, U-10wt.%Mo and U-12wt.%Mo vs. pure Al, Al-2wt.%Si, and Al-5wt.%Si annealed at 550°C for 1, 5 and 20 hours. To further clarify the diffusional behavior in the U-Mo-Al and U-Mo-Al-Si systems, Al-rich 85.7Al-11.44U-2.86Mo, 87.5Al-10U-2.5Mo, 56.1Al-18.9Si-21.9U-3.1Mo and 69.3Al-11.9Si-18.8U (at.%) alloys were cast and homogenized at 500°C to determine the equilibrium phases of the system. Scanning electron microscopy (SEM), transmission electron microscopy (TEM) and electron probe microanalysis (EPMA) and X-ray diffraction (XRD) were employed to examine the phase development in the diffusion couples and the cast alloys. In ternary U-Mo-Al diffusion couples annealed at 600°C for 24 hours, the interdiffusion microstructure consisted of finely dispersed UAl3, UAl4, U6Mo4Al43, and UMo2Al20 phases while the average composition throughout the interdiffusion zone remained constant at approximately 80 at.% Al. The interdiffusion microstructures observed by EPMA, SEM and TEM analyses were correlated to explain the observed morphological development in the interdiffusion zones. The concept of thermodynamic degrees of freedom was used to justify that, although deviations are apparent, the interdiffusion zones did not significantly deviate from an equilibrium condition in order for the observed microstructures to develop. Selected diffusion couples developed periodic bands within the interdiffusion zone as sub-layers in the three-phase regions. Observation of periodic banding was utilized to augment the hypothesis that internal stresses play a significant role in the phase development and evolution of U-Mo vs. pure Al diffusion couples. The addition of Si (up to 5 wt.%) to the Al significantly reduced the growth rate of the interdiffusion zone. The constituent phases and composition within the interdiffusion zone were also modified. When Si was present in the Al terminal alloys, the interdiffusion zones developed layered morphologies with fine distributions of the (U,Mo)(Al,Si)3 and UMo2Al20 phases. The U6Mo4Al43 phase was observed scarcely in Si depleted regions within the interdiffusion zone. The phase development and evolution of the interdiffusion zone was described in terms of thermodynamic degrees of freedom with minimal deviations from equilibrium.
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Date Issued
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2011
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Identifier
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CFE0003747, ucf:48778
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0003747
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Title
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Physiological Reactions to Uncanny Stimuli: Substantiation of Self-Assessment and Individual Perception in User Enjoyment and Comfort.
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Creator
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Ballion, Tatiana, Sims, Valerie, Chin, Matthew, Jones, Donald, University of Central Florida
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Abstract / Description
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There is abundant anecdotal evidence substantiating Mori's initial observation of the "uncanny valley", a point at which human response to non-human entities drops sharply with respect to comfort (Mori, 1970), and the construct itself has a long-standing history in both Robotics and Psychology. Currently, many fields such as design, training, entertainment, and education make use of heuristic approaches to accommodate the anticipated needs of the user/consumer/audience in certain important...
Show moreThere is abundant anecdotal evidence substantiating Mori's initial observation of the "uncanny valley", a point at which human response to non-human entities drops sharply with respect to comfort (Mori, 1970), and the construct itself has a long-standing history in both Robotics and Psychology. Currently, many fields such as design, training, entertainment, and education make use of heuristic approaches to accommodate the anticipated needs of the user/consumer/audience in certain important aspects. This is due to the lack of empirical substantiation or, in some cases, the impossibility of rigorous quantification; one such area is with respect to the user's experience of uncanniness, a feeling of "eeriness" or "wrongness" when interacting with artefacts or environments. Uncanniness, however, continues to be defined and measured in a largely subjective way, and often after the fact; an experience or product's uncanny features are pointed out after the item has been markedly avoided or complained about by the general public. These studies are among the first seeking to determine a constellation of personality traits and physiological responses that incline the user to have a more frequent or profound (")uncanny" reaction when presented with stimuli meeting the criteria for a level of "eeriness". In study 1, 395 adults were asked to categorize 200 images as uncanny, neutral, pleasant, or other. In Study 2, physiological and eye-tracking data was collected from twenty two adults as they viewed uncanny, neutral and pleasant images culled from study 1. This research identifies components of the uncanny valley related to subjective assessment, personality factors (using the HEXACO and Anthropomorphic Tendencies Scale), and biophysical measures, and found that traits unique to Emotionality on the HEXACO inventory, compounded with a form of anthropomorphism demonstrates a level of relationship to the subjective experience of uncanny stimuli. There is evidence that HEXACO type and forms of anthropomorphic perception mediates the biophysical expression and the subjective perception of the stimuli. In keeping with psychological hypotheses, stimuli to which the participants had greatest response centered on death, the threat of death, or mismatched/absent facial features.
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Date Issued
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2012
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Identifier
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CFE0004354, ucf:49454
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0004354
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Title
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Nonlinear dynamic modeling, simulation and characterization of the mesoscale neuron-electrode interface.
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Creator
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Thakore, Vaibhav, Hickman, James, Mucciolo, Eduardo, Rahman, Talat, Johnson, Michael, Behal, Aman, Molnar, Peter, University of Central Florida
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Abstract / Description
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Extracellular neuroelectronic interfacing has important applications in the fields of neural prosthetics, biological computation and whole-cell biosensing for drug screening and toxin detection. While the field of neuroelectronic interfacing holds great promise, the recording of high-fidelity signals from extracellular devices has long suffered from the problem of low signal-to-noise ratios and changes in signal shapes due to the presence of highly dispersive dielectric medium in the neuron...
Show moreExtracellular neuroelectronic interfacing has important applications in the fields of neural prosthetics, biological computation and whole-cell biosensing for drug screening and toxin detection. While the field of neuroelectronic interfacing holds great promise, the recording of high-fidelity signals from extracellular devices has long suffered from the problem of low signal-to-noise ratios and changes in signal shapes due to the presence of highly dispersive dielectric medium in the neuron-microelectrode cleft. This has made it difficult to correlate the extracellularly recorded signals with the intracellular signals recorded using conventional patch-clamp electrophysiology. For bringing about an improvement in the signal-to-noise ratio of the signals recorded on the extracellular microelectrodes and to explore strategies for engineering the neuron-electrode interface there exists a need to model, simulate and characterize the cell-sensor interface to better understand the mechanism of signal transduction across the interface. Efforts to date for modeling the neuron-electrode interface have primarily focused on the use of point or area contact linear equivalent circuit models for a description of the interface with an assumption of passive linearity for the dynamics of the interfacial medium in the cell-electrode cleft. In this dissertation, results are presented from a nonlinear dynamic characterization of the neuroelectronic junction based on Volterra-Wiener modeling which showed that the process of signal transduction at the interface may have nonlinear contributions from the interfacial medium. An optimization based study of linear equivalent circuit models for representing signals recorded at the neuron-electrode interface subsequently proved conclusively that the process of signal transduction across the interface is indeed nonlinear. Following this a theoretical framework for the extraction of the complex nonlinear material parameters of the interfacial medium like the dielectric permittivity, conductivity and diffusivity tensors based on dynamic nonlinear Volterra-Wiener modeling was developed. Within this framework, the use of Gaussian bandlimited white noise for nonlinear impedance spectroscopy was shown to offer considerable advantages over the use of sinusoidal inputs for nonlinear harmonic analysis currently employed in impedance characterization of nonlinear electrochemical systems. Signal transduction at the neuron-microelectrode interface is mediated by the interfacial medium confined to a thin cleft with thickness on the scale of 20-110 nm giving rise to Knudsen numbers (ratio of mean free path to characteristic system length) in the range of 0.015 and 0.003 for ionic electrodiffusion. At these Knudsen numbers, the continuum assumptions made in the use of Poisson-Nernst-Planck system of equations for modeling ionic electrodiffusion are not valid. Therefore, a lattice Boltzmann method (LBM) based multiphysics solver suitable for modeling ionic electrodiffusion at the mesoscale neuron-microelectrode interface was developed. Additionally, a molecular speed dependent relaxation time was proposed for use in the lattice Boltzmann equation. Such a relaxation time holds promise for enhancing the numerical stability of lattice Boltzmann algorithms as it helped recover a physically correct description of microscopic phenomena related to particle collisions governed by their local density on the lattice. Next, using this multiphysics solver simulations were carried out for the charge relaxation dynamics of an electrolytic nanocapacitor with the intention of ultimately employing it for a simulation of the capacitive coupling between the neuron and the planar microelectrode on a microelectrode array (MEA). Simulations of the charge relaxation dynamics for a step potential applied at t = 0 to the capacitor electrodes were carried out for varying conditions of electric double layer (EDL) overlap, solvent viscosity, electrode spacing and ratio of cation to anion diffusivity. For a large EDL overlap, an anomalous plasma-like collective behavior of oscillating ions at a frequency much lower than the plasma frequency of the electrolyte was observed and as such it appears to be purely an effect of nanoscale confinement. Results from these simulations are then discussed in the context of the dynamics of the interfacial medium in the neuron-microelectrode cleft. In conclusion, a synergistic approach to engineering the neuron-microelectrode interface is outlined through a use of the nonlinear dynamic modeling, simulation and characterization tools developed as part of this dissertation research.
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Date Issued
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2012
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Identifier
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CFE0004797, ucf:49718
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Format
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Document (PDF)
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PURL
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http://purl.flvc.org/ucf/fd/CFE0004797
Pages