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Title: Spatio-Temporal Evolutions of Non-Orthogonal Equatorial Wave Modes Derived from Observations.
Creator: Barton, Cory, Cai, Ming, Niu, Xufeng, Clarke, Allan J., Speer, Kevin G. (Kevin George), Sura, Philip, Florida State University, College of Arts and Sciences, Program in...
Show moreBarton, Cory, Cai, Ming, Niu, Xufeng, Clarke, Allan J., Speer, Kevin G. (Kevin George), Sura, Philip, Florida State University, College of Arts and Sciences, Program in Geophysical Fluid Dynamics
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Abstract/Description: Equatorial waves have been studied extensively due to their importance to the tropical climate and weather systems. Historically, their activity is diagnosed mainly in the wavenumber-frequency domain. Recently, many studies have projected observational data onto parabolic cylinder functions (PCFs), which represent the meridional structure of individual wave modes, to attain time-dependent spatial wave structures. The non-orthogonality of wave modes has yet posed a problem when attempting to...
Show moreEquatorial waves have been studied extensively due to their importance to the tropical climate and weather systems. Historically, their activity is diagnosed mainly in the wavenumber-frequency domain. Recently, many studies have projected observational data onto parabolic cylinder functions (PCFs), which represent the meridional structure of individual wave modes, to attain time-dependent spatial wave structures. The non-orthogonality of wave modes has yet posed a problem when attempting to separate data into wave fields where the waves project onto the same structure functions. We propose the development and application of a new methodology for equatorial wave expansion of instantaneous flows using the full equatorial wave spectrum. By creating a mapping from the meridional structure function amplitudes to the equatorial wave class amplitudes, we are able to diagnose instantaneous wave fields and determine their evolution. Because all meridional modes are shared by some subset of the wave classes, we require constraints on the wave class amplitudes to yield a closed system with a unique solution for all waves' spatial structures, including IG waves. A synthetic field is analyzed using this method to determine its accuracy for data of a single vertical mode. The wave class spectra diagnosed using this method successfully match the correct dispersion curves even if the incorrect depth is chosen for the spatial decomposition. In the case of more than one depth scale, waves with varying equivalent depth may be similarly identified using the dispersion curves. The primary vertical mode is the 200 m equivalent depth mode, which is that of the peak projection response. A distinct spectral power peak along the Kelvin wave dispersion curve for this value validates our choice of equivalent depth, although the possibility of depth varying with time and height is explored. The wave class spectra diagnosed assuming this depth scale mostly match their expected dispersion curves, showing that this method successfully partitions the wave spectra by calculating wave amplitudes in physical space. This is particularly striking because the time evolution, and therefore the frequency characteristics, is determined simply by a timeseries of independently-diagnosed instantaneous horizontal fields. We use the wave fields diagnosed by this method to study wave evolution in the context of the stratospheric QBO of zonal wind, confirming the continuous evolution of the selection mechanism for equatorial waves in the middle atmosphere. The amplitude cycle synchronized with the background zonal wind as predicted by QBO theory is present in the wave class fields even though the dynamics are not forced by the method itself. We have additionally identified a time-evolution of the zonal wavenumber spectrum responsible for the amplitude variability in physical space. Similar to the temporal characteristics, the vertical structures are also the result of a simple height cross-section through multiple independently-diagnosed levels.
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Date Issued: 2016
Identifier: FSU_2016SP_Barton_fsu_0071E_13099
Format: Thesis

Title: An Analysis of Conjugate Harmonic Components of Monogenic Functions and Lambda Harmonic Functions.
Creator: Ballenger-Fazzone, Brendon Kerr, Nolder, Craig, Harper, Kristine, Aldrovandi, Ettore, Case, Bettye Anne, Quine, J. R. (John R.), Ryan, John Barry, Florida State University,...
Show moreBallenger-Fazzone, Brendon Kerr, Nolder, Craig, Harper, Kristine, Aldrovandi, Ettore, Case, Bettye Anne, Quine, J. R. (John R.), Ryan, John Barry, Florida State University, College of Arts and Sciences, Department of Mathematics
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Abstract/Description: Clifford analysis is seen as the higher dimensional analogue of complex analysis. This includes a rich study of Clifford algebras and, in particular, monogenic functions, or Clifford-valued functions that lie in the kernel of the Cauchy-Riemann operator. In this dissertation, we explore the relationships between the harmonic components of monogenic functions and expand upon the notion of conjugate harmonic functions. We show that properties of the even part of a Clifford-valued function...
Show moreClifford analysis is seen as the higher dimensional analogue of complex analysis. This includes a rich study of Clifford algebras and, in particular, monogenic functions, or Clifford-valued functions that lie in the kernel of the Cauchy-Riemann operator. In this dissertation, we explore the relationships between the harmonic components of monogenic functions and expand upon the notion of conjugate harmonic functions. We show that properties of the even part of a Clifford-valued function determine properties of the odd part and vice versa. We also explore the theory of functions lying in the kernel of a generalized Laplace operator, the λ-Laplacian. We explore the properties of these so-called λ-harmonic functions and give the solution to the Dirichlet problem for the λ-harmonic functions on annular domains in Rⁿ.
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Date Issued: 2016
Identifier: FSU_2016SP_BallengerFazzone_fsu_0071E_13136
Format: Thesis

Title: The Role of Evolution in Maintaining Coexistence of Competitors.
Creator: Pastore, Abigail I. (Abigail Ilona), Miller, Thomas E., Bertram, R. (Richard), Inouye, Brian D., Steppan, Scott J., Winn, Alice A., Florida State University, College of Arts and...
Show morePastore, Abigail I. (Abigail Ilona), Miller, Thomas E., Bertram, R. (Richard), Inouye, Brian D., Steppan, Scott J., Winn, Alice A., Florida State University, College of Arts and Sciences, Department of Biological Science
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Abstract/Description: Species interactions can regulate a population’s density and therefore can act as a selective force on that population. Such evolutionary responses have the potential to feedback and change ecological interactions between species. For species that compete for resources, the interaction between ecological and evolutionary dynamics will regulate the stability of the species interactions, determining whether competing species can coexist. The outcome of competition between species is determined...
Show moreSpecies interactions can regulate a population’s density and therefore can act as a selective force on that population. Such evolutionary responses have the potential to feedback and change ecological interactions between species. For species that compete for resources, the interaction between ecological and evolutionary dynamics will regulate the stability of the species interactions, determining whether competing species can coexist. The outcome of competition between species is determined by two factors: (1) niche overlap, or the similarity in how species use resources and are affected by their environment, and (2) fitness differences, or differences in how efficiently each species uses resources in their environment. Decreasing niche overlap will decrease competitive interactions, thereby stabilizing coexistence. Decreasing fitness differences makes species more equal in their competitive abilities, facilitating coexistence. In the absence of evolutionary constraints, both niche overlap and fitness differences among species are subject to change as a consequence of evolution among competitors, and thus ecological dynamics between two species will also change. In this dissertation, I develop a broader understanding of (1) how niche overlap and fitness differences between species change after evolution in response to competition, (2) how changes in niche overlap and fitness differences are mediated through changes in resource use of protists, and (3) what role evolutionary history plays in shaping ecological and evolutionary dynamics. I address these goals with a suite of approaches including theoretical models, an experimental lab system, and comparative methods. I constructed a quantitative genetic model of trait evolution, where the trait of a species determined its resource use, and found that species are prone to change in their niche overlap as well as their fitness differences as a result of trait evolution. However, the magnitude of changes in niche overlap and fitness differences were determined by the resource availability within the environments. When resources were broadly available, species changed more in their niche overlap, whereas when resources were narrowly available, species changed more in their fitness difference. To test these predictions, I developed a system in the laboratory where protists competed for a bacterial resource. Species were allowed to evolve in either monoculture or a two-species mixture; the effects of evolution on competition, niche overlap and fitness differences were quantified using parameterized models. In general I found that species tended to converge in their niche as a result of evolution, however, changes in fitness differences between species were larger and more influential on coexistence than changes in niche differences. Both increases in niche overlap, and increases in fitness differences decreased coexistence among species pairs. By describing the bacterial communities associated with these protists before and after selection I determined that protists tended to converge or not change in which bacteria they were consuming as a result of selection. Additionally, for eleven protist species, I determined whether traits or relatedness predicted competitive ability by placing species on a molecular phylogeny and conducting pairwise competition experiments for all pairs. I found no correlations, suggesting neither traits, nor evolutionary history was informative for explaining current ecological and evolutionary interactions in this deeply divergent clade. There are two major conclusions from this dissertation: (1) when species evolve in response to competition, changes in fitness differences may often be more important than changes in niche overlap, (2) evolution can, and may be likely to, decrease the ability of species to coexist through increases in niche overlap and increases in fitness differences. This work suggests that one must simultaneously consider the role of evolutionary and ecological processes to understand community processes. Specifically, when researchers are attempting to explain mechanisms of coexistence between species, they must consider how evolutionary dynamics may change the ecological interactions within communities of competitors.
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Date Issued: 2017
Identifier: FSU_FALL2017_Pastore_fsu_0071E_14135
Format: Thesis

Title: Composition and Stability of Single-Stranded DNA Viral Populations in Wastewater Treatment Plants.
Creator: Pearson, Victoria M., Rokyta, Darin, Beerli, Peter, Dennis, Jonathan Hancock, Hughes, Kimberly A., Tang, Hengli, Florida State University, College of Arts and Sciences,...
Show morePearson, Victoria M., Rokyta, Darin, Beerli, Peter, Dennis, Jonathan Hancock, Hughes, Kimberly A., Tang, Hengli, Florida State University, College of Arts and Sciences, Department of Biological Science
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Abstract/Description: Regular emergence and re-emergence of viral pathogens emphasizes the importance of understanding viral biogeography and migration. Single-stranded DNA (ssDNA) viruses are among the least understood groups of microbial pathogens, yet the group contains known agricultural pathogens, which infect both livestock and crops (Circoviridae and Geminiviridae), and model organisms (Microviridae). Wastewater treatment plants (WWTPs) receive water from multiple sources, becoming reservoirs for the...
Show moreRegular emergence and re-emergence of viral pathogens emphasizes the importance of understanding viral biogeography and migration. Single-stranded DNA (ssDNA) viruses are among the least understood groups of microbial pathogens, yet the group contains known agricultural pathogens, which infect both livestock and crops (Circoviridae and Geminiviridae), and model organisms (Microviridae). Wastewater treatment plants (WWTPs) receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a large range of hosts. Investigations utilizing high-throughput sequencing have determined that local viral diversity is extremely high but does not scale to produce an exponentially higher global diversity. It follows that similar genotypes can be found great distances apart, although they may not be permanent constituents of any single population. Transient genotypes have been observed in temporal surveys of closed systems, where genotypes migrate between individual populations. This study focused on the geographic and temporal population stability of single-stranded DNA (ssDNA) viruses in open systems. Sampling from WWTPs in three neighboring cities in Northwest Florida, which receive constant inflow and potentially receive the same viruses from the local environment, was conducted across a nine-month time span. A combination of polyethylene glycol (PEG) precipitation and filter concentration was used to isolate whole viral particles from the complex wastewater samples. The ssDNA viruses were isolated from larger viruses using a sucrose gradient for size selection and rolling circle amplification was performed to both bias the sample towards ssDNA and prepare the samples for high-throughput sequencing. Amplified genomes were sequenced using Illumina platforms and de novo assembled. Given the increased potential for migration, we expected the populations would be mostly homogenous with relatively few viruses that are unique to individual WWTPs. Viral genotypes with genetic similarity to Circoviridae, Geminiviridae, and Microviridae were recovered from all three WWTPs, however <25% of recovered genes match genotypes (>80% amino acid identity) recovered from neighboring sample sites. We determined that <10% of the genotypes were present in all three plants and the majority of genotypes were specific to one WWTP. Unexpectedly, the WWTPs that were closest to each other geographically were the least similar, and the plants geographically distant from each other had the most observed genetic overlap. These results highlight the high level of diversity within each population, while the high observed heterogeneity indicates localized genetic success and limited migration opportunities between the WWTPs. Throughout time the communities experienced a large degree of genetic turnover. Only 30% of the genotypes were present in more than one time point, 5% were recovered in three of more samplings and <1% were present in all five time points. This thesis concludes that viral genomes are continually moving through the environment and their presence in any given area may be temporary. Therefore, viruses are a continual selective force on their host species through the sheer volume of genetic potential in an area at any given time.
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Date Issued: 2017
Identifier: FSU_FALL2017_Pearson_fsu_0071E_14170
Format: Thesis

Title: Threat Processing in the Human Sensory Cortex.
Creator: You, Yuqi, Li, Wen, Kabbaj, Mohamed, Kelley, Colleen M., Wang, Zhi, Wang, Zuoxin, Feng, Jian, Florida State University, College of Arts and Sciences, Department of Psychology
Abstract/Description: The need for expedient detection of and response to signals of danger compels the development of sophisticated neural circuits for threat processing. This threat neural circuitry should support not only identification of and response to innately threatening stimuli, but also learning and memory of sensory cues predictive of such threats. While extensive rodent and human research has established an essential role of the amygdala in processing innate and learned threats, increasing evidence...
Show moreThe need for expedient detection of and response to signals of danger compels the development of sophisticated neural circuits for threat processing. This threat neural circuitry should support not only identification of and response to innately threatening stimuli, but also learning and memory of sensory cues predictive of such threats. While extensive rodent and human research has established an essential role of the amygdala in processing innate and learned threats, increasing evidence suggests the existence of extra-amygdala neural circuits that are capable of independent threat processing. The sensory cortex emerges as an important part of the threat circuitry, demonstrating heightened neural response to innately threatening stimuli and persistent neural plasticity as a result of threat learning. In three separate yet conceptually-integrated experiments, employing a combination of electrophysiological and functional magnetic resonance imaging (fMRI) methods, this dissertation examines threat processing in the human sensory cortex, and importantly, disentangles its unique contribution from that of the amygdala. Study 1 (Chapter 2) indicated that the ventral visual cortex was capable of fast, refined processing of threat scenes, relatively independent of the amygdala. Studies 2 and 3 (Chapters 3 and 4) further applied threat conditioning to examine possible learning and memory mechanisms by which the sensory cortex contributes to the processing of threat. Study 2 demonstrated immediate and long-term plastic changes in the olfactory cortex to learned threat odors, combining fMRI, olfactory aversive conditioning, and a long-term memory retention test (on Day 9). Lastly, Study 3 revealed visual cortical and amygdala contributions to immediate and lasting plastic changes to learned visual threats, respectively, combining brain electrophysiology, visual aversive conditioning, and a long-term memory retention test (on Day 16). Together, these three experiments demonstrate the critical role the sensory cortex plays in threat encoding and the origin of such sensory cortical threat codes via associative learning.
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Date Issued: 2017
Identifier: FSU_FALL2017_You_fsu_0071E_14136
Format: Thesis

Title: Against Reason a Defense of Moderate Normative Skepticism.
Creator: Vadakin, Aron, Mele, Alfred R., Kavka, Martin, Rawling, Piers, Clarke, Randolph K., Florida State University, College of Arts and Sciences, Department of Philosophy
Abstract/Description: This dissertation both surveys contemporary work in metanormativity and argues for a position that I call moderate normative skepticism. I begin by evaluating efforts to characterize the normative domain and conclude that while some normative concepts and properties are amenable to naturalistic programs of reduction and analysis, other normative concepts and properties are not. I proceed to clarify accounts of reasons, reasoning, and rationality; this establishes argumentative room to...
Show moreThis dissertation both surveys contemporary work in metanormativity and argues for a position that I call moderate normative skepticism. I begin by evaluating efforts to characterize the normative domain and conclude that while some normative concepts and properties are amenable to naturalistic programs of reduction and analysis, other normative concepts and properties are not. I proceed to clarify accounts of reasons, reasoning, and rationality; this establishes argumentative room to maneuver for my moderate normative skepticism. Next, I evaluate moral error theories, which I count as close cousins of my own thesis, and I note how these error theories have more profound implications than their authors realize. I claim that, understood properly, these error theories extend to the domain of normative reasons in general. I accept and defend the extension of error theory as a viable position. In the final chapter of my dissertation, I defend my position against charges of self-defeat and attempt to anticipate and defuse potential criticisms.
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Date Issued: 2017
Identifier: FSU_FALL2017_Vadakin_fsu_0071E_14258
Format: Thesis

Title: Monte Carlo Scheme for a Singular Control Problem: Investment-Consumption under Proportional Transaction Costs.
Creator: Tsai, Wan-Yu, Fahim, Arash, Atkins, Jennifer, Zhu, Lingjiong, Florida State University, College of Arts and Sciences, Department of Mathematics
Abstract/Description: Nowadays free boundary problems are considered as one of the most important directions in the mainstream of partial differential equations (PDEs) analysis, with an abundance of applications in various sciences and real world problems. Free boundary problems on finance have been extended in many areas, such as optimal portfolio selection, control credit risks, and different American style products etc. To modelling these financial problems in the real world, the qualitative and quantitative...
Show moreNowadays free boundary problems are considered as one of the most important directions in the mainstream of partial differential equations (PDEs) analysis, with an abundance of applications in various sciences and real world problems. Free boundary problems on finance have been extended in many areas, such as optimal portfolio selection, control credit risks, and different American style products etc. To modelling these financial problems in the real world, the qualitative and quantitative behaviors of the solution to a free boundary problem are still not well understood and also numerical solutions to free boundary problems remain a challenge. Stochastic control problems reduce to free-boundary problems in partial differential equations while there are no bounds on the rate of control. In a free boundary problem, the solution as well as the domain to the PDE need to be determined simultaneously. In this dissertation, we concern the numerical solution of a fully nonlinear parabolic double obstacle problem arising from a finite time portfolio selection problem with proportional transaction costs. We consider optimal allocation of wealth among multiple stocks and a bank account in order to maximize the finite horizon discounted utility of consumption. The problem is mainly governed by a time-dependent Hamilton-Jacobi-Bellman equation with gradient constraints. We propose a numerical method which is composed of Monte Carlo simulation to take advantage of the high-dimensional properties and finite difference method to approximate the gradients of the value function. Numerical results illustrate behaviors of the optimal trading strategies and also satisfy all qualitative properties proved in Dai et al. (2009) and Chen and Dai (2013).
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Date Issued: 2017
Identifier: FSU_FALL2017_Tsai_fsu_0071E_14174
Format: Thesis

Title: Reaction Discovery Using Neopentylene-Tethered Coupling Partners: Methodology and Applications of Dienyne Cycloisomerizations.
Creator: Kramer, Nicholas J. James, Dudley, Gregory B., Frederich, James H., Fadool, James M., Alabugin, Igor V., Shatruk, Mykhailo, Florida State University, College of Arts and...
Show moreKramer, Nicholas J. James, Dudley, Gregory B., Frederich, James H., Fadool, James M., Alabugin, Igor V., Shatruk, Mykhailo, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
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Abstract/Description: Within the past few decades, metal-catalysis has emerged as a key facet in synthetic organic chemistry, perpetuating a continuous need for the development of methods within this sect of chemistry. In tandem, cycloisomerization reactions of tethered enynes have garnered considerable interest as emphasis on annulation strategies to access polycyclic systems becomes necessary for the generation of important bioactive structures. Driven by both methodological and total synthesis applications,...
Show moreWithin the past few decades, metal-catalysis has emerged as a key facet in synthetic organic chemistry, perpetuating a continuous need for the development of methods within this sect of chemistry. In tandem, cycloisomerization reactions of tethered enynes have garnered considerable interest as emphasis on annulation strategies to access polycyclic systems becomes necessary for the generation of important bioactive structures. Driven by both methodological and total synthesis applications, metal-catalyzed cycloisomerizations remain at the forefront of interest for effective atom-economic reactions. We have identified a strategic gap in the methodology of 1,6-enyne cycloisomerizations bearing heteroatom, methylene, and malonate tethers. Herein will be described a method for the [4 + 2] formal Diels-Alder cycloisomerization of neopentylene-tethered dienynes, closing the gap previously mentioned and highlighting a valuable reactivity profile of this new tether. Also demonstrated is significant progress in the Diels-Alder cyclization of electron-deficient dienynes, for which the literature has shown to be relatively unexplored, presumably due to the apparent poor reactivity of these substrates. Further investigation into isolation of the [4 + 2] Diels-Alder products as well as elaboration on the previously published fragmentation/olefination methodology is included in this manuscript. Using these effective annulation strategies developed in our lab, we have sought to gain access to sesquiterpene natural products of particular interest bearing the gem-dimethylcyclopentane, an extension of the indane core. These methods have been employed in a six-step total synthesis of Alcyopterosin A and in the efforts toward the synthesis of Fomajorin D.
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Date Issued: 2017
Identifier: FSU_FALL2017_Kramer_fsu_0071E_14204
Format: Thesis

Title: Estimation of Nitrogen Load from Septic Systems to Surface Waterbodies in Indian River County, FL.
Creator: Lei, Hongzhuan, Ye, Ming, Wang, Xiaoqiang, Shanbhag, Sachin, Florida State University, College of Arts and Sciences, Department of Scientific Computing
Abstract/Description: Excessive nitrogen loading to surface water bodies has resulted in serious environmental, economical, ecological, and human health problems, such as groundwater contamination and eutrophication in surface water. One important source of nitrogen in the environment, especially in densely populated coastal areas in Florida, is due to wastewater treatment using onsite sewage treatment and disposal systems (OSTDS) (a.k.a., septic systems). Moreover, due to the population expansion, nitrogen loads...
Show moreExcessive nitrogen loading to surface water bodies has resulted in serious environmental, economical, ecological, and human health problems, such as groundwater contamination and eutrophication in surface water. One important source of nitrogen in the environment, especially in densely populated coastal areas in Florida, is due to wastewater treatment using onsite sewage treatment and disposal systems (OSTDS) (a.k.a., septic systems). Moreover, due to the population expansion, nitrogen loads from septic systems are expected to increase. Therefore, sustainable decision-making and management of nitrogen pollution due to septic systems are urgently needed. In this thesis, two software are used to simulate the whole process of nitrogen (ammonium and nitrate) transport starting from septic systems to finally reach the surface waterbodies. One software is VZMOD, and the other one is the ArcGIS-based Nitrogen Load Estimation Toolkit (ArcNLET). VZMOD is seamlessly integrated with ArcNLET in the way as follows. VZMOD is firstly used to simulate the flow and nitrogen transport in the vadose zone, which is between drain field infiltrative surface and water table, based on the assumption of steady-state, one-dimensional vertical reactive transport with constant incoming fluxes of water, ammonium, and nitrate. The ammonium and nitrate concentrations, given by VZMOD at the water table, are then used as the inputs to the modeling of ammonium and nitrate fate and transport in groundwater in ArcNLET, considering heterogeneous hydraulic conductivity and porosity as well as spatial variability of septic system locations, surface water bodies, and distances between septic systems and surface water bodies. In addition, the key mechanisms controlling nitrogen transport, including advection, dispersion, and denitrification, are also considered in ArcNLET. The study sites of this thesis research are the Main-South Canal (MSC) drainage basin and the City of Sebastian located in Indian River County in southeast Florida. Surface water bodies (e.g., rivers and streams) and groundwater at the two site discharge to the Southern Indian River Lagoon, where the ecological and biological integrity has deteriorated in the last several decades due to the decline in water quality caused in part by nitrogen pollution. There are in total 12,741 septic systems in the MSC area, while in the City of Sebastian, the number of septic systems is 4,883. The process of simulating nitrogen reactive transport from septic tanks to surface water bodies consists of the following three steps: (1) based on the site-specific data, such as DEM, waterbodies, septic locations, hydraulic conductivity and porosity, forward models of VZMOD and ArcNLET is developed, (2) based on the measured data of system state variables, such as water level and nitrogen concentration, the forward models are calibrated, and (3) the calibrated models are used to simulate nitrogen plumes and to estimate nitrogen load from the septic systems to surface water bodies. Considering the modeling ability and the site complexity, two questions, (1) what are the nitrogen characteristics of these two sites, (2) can my model be able to capture these nitrogen characteristics, have been investigated in this study, and the major findings are as follows: (1) The simulated nitrogen plumes and load estimates exhibit substantial spatial variability in the both sites, and the depth from drainfields to water table is important to nitrogen reactive transport, especially the ammonium nitrification to nitrate. (2) Ammonium and nitrate loads for the Main-South Canal drainage basin are largely located in the south to the South Canal drainage basin. Along the ditches and canals, the ammonium concentration is lower due to the small distance between water table and drainfields. There exists a region located in the southeast drainage basin where ammonium loading is high. (3) Incomplete nitrification process is exposed under the vadose zone while the denitrification process is mostly complete in the saturated zone in the Main-South Canal area. (4) The nitrification process is largely complete under the unsaturated zone while the denitrification process is incomplete in the saturated zone in the City of Sebastian area. (5) Reduction ratio is lower while nitrogen loading to surface waterbodies per septic system is larger in the City of Sebastian area than in the Main-South Canal area. (6) The flow model calibration in the City of Sebastian area is not as satisfactory as in the Main-South Canal area, because of the simplified assumption that water table is a subdued replica of topography used in ArcNLET is not satisfied at the study site. These results can be used to support the on-going Basin Management Action Plan. More efforts, such as investigating the soil condition (e.g. micro-bacteria content, dissolved oxygen or dissolved organic carbon and pH) and specific septic system environment, are also needed to verify these results and to develop more insights about the nitrogen processes in the study areas.
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Date Issued: 2017
Identifier: FSU_FALL2017_Lei_fsu_0071N_14260
Format: Thesis

Title: Evolution of the Material Properties of Mineralized Dental Tissues.
Creator: Kay, David Ian, Erickson, Gregory M., Lenhert, Steven John, Oates, William, Steppan, Scott J., Florida State University, College of Arts and Sciences, Department of Biological...
Show moreKay, David Ian, Erickson, Gregory M., Lenhert, Steven John, Oates, William, Steppan, Scott J., Florida State University, College of Arts and Sciences, Department of Biological Science
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Abstract/Description: During their 473 million-year diversification, gnathostomes came to exploit an unprecedented variety of trophic niches. Modifications to dental form and mineralized tissue constituents (i.e. enamel, dentines and in a few taxa, cementum) facilitated their exploitation of novel prey and/or plant matter. In general, it has been assumed that the intra-tissue level biomechanics of these constituents had little bearing on whole-tooth functionality, aside from enamel in mammals showing dental...
Show moreDuring their 473 million-year diversification, gnathostomes came to exploit an unprecedented variety of trophic niches. Modifications to dental form and mineralized tissue constituents (i.e. enamel, dentines and in a few taxa, cementum) facilitated their exploitation of novel prey and/or plant matter. In general, it has been assumed that the intra-tissue level biomechanics of these constituents had little bearing on whole-tooth functionality, aside from enamel in mammals showing dental occlusion. Specifically, many mammals possess teeth that self-wear to functionality and show a diversity of derived dental tissues (e.g. prismatic enamel fabrics, coronal cementum) – some which have been shown to possess unique biomechanical attributes to resist wear and fracture. Here I formally test the hypothesis that the primitive gnathostome hard tissue material properties remained static prior to the cladogenesis of Mammalia. An ancillary goal is to glean initial insights on how the material properties of these dental tissues in non-mammalian and mammalian taxa may contribute to whole-tooth form, function, performance and diets. Properties were tested and examined using two standardized material science techniques, microindentation and nanoindentation, as well as a novel technique for quantifying fracture propagation from cracks formed during microindentation. The results from this investigation suggest these material properties are highly variable among gnathostome dentitions. Aside from hardness, there is not a significant relationship between most material properties and diet aside from enamel hardness. There are also complex fracture patterns seen in the enamels of mammals and chondrichthyans, showing that gnathostome lineages independently evolved properties to control fracture and damage done to tooth enamel. Overall, this study suggests that in the case of enamel hardness, natural selection operated at the tissue level to bring about shifts in tooth functionality throughout the gnathostome radiation. More material properties (i.e. fracture toughness) need to be investigated to uncover the true functional import of material properties in dental tissues and establish how the tissue complexes contributed to whole tooth function.
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Date Issued: 2017
Identifier: FSU_FALL2017_Kay_fsu_0071N_14152
Format: Thesis

Title: Examining the Effect of Treatment on the Distribution of Blood Pressure in the Population Using Observational Data.
Creator: Kucukemiroglu, Saryet Alexa, McGee, Daniel, Slate, Elizabeth H., Hurt, Myra M., Huffer, Fred W. (Fred William), Florida State University, College of Arts and Sciences,...
Show moreKucukemiroglu, Saryet Alexa, McGee, Daniel, Slate, Elizabeth H., Hurt, Myra M., Huffer, Fred W. (Fred William), Florida State University, College of Arts and Sciences, Department of Statistics
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Abstract/Description: Since the introduction of anti-hypertensive medications in the mid-1950s, there has been an increased use of blood pressure medications in the US. The growing use of anti-hypertensive treatment has affected the distribution of blood pressure in the population over time. Now observational data no longer reflect natural blood pressure levels. Our goal is to examine the effect of anti-hypertensive drugs on distributions of blood pressure using several well-known observational studies. The...
Show moreSince the introduction of anti-hypertensive medications in the mid-1950s, there has been an increased use of blood pressure medications in the US. The growing use of anti-hypertensive treatment has affected the distribution of blood pressure in the population over time. Now observational data no longer reflect natural blood pressure levels. Our goal is to examine the effect of anti-hypertensive drugs on distributions of blood pressure using several well-known observational studies. The statistical concept of censoring is used to estimate the distribution of blood pressure in populations if no treatment were available. The treated and estimated untreated distributions are then compared to determine the general effect of these medications in the population. Our analyses show that these drugs have an increasing impact on controlling blood pressure distributions in populations that are heavily treated.
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Date Issued: 2017
Identifier: FSU_FALL2017_Kucukemiroglu_fsu_0071E_14275
Format: Thesis

Title: Memory Consolidation during Post-encoding Wakeful Rest.
Creator: Komsky, Jane C. (Jane Claire), Bishop, Michael A., Johnson, Frank, Boot, Walter Richard, Nee, Derek Evan, Florida State University, College of Arts and Sciences, Department of...
Show moreKomsky, Jane C. (Jane Claire), Bishop, Michael A., Johnson, Frank, Boot, Walter Richard, Nee, Derek Evan, Florida State University, College of Arts and Sciences, Department of Psychology
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Abstract/Description: Engaging in post-encoding wakeful rest has been shown to lead to better retention of encoded information versus engaging in a post-encoding task. Brain imaging studies have shown that there is reactivation during post-encoding rest of brain areas that were active during initial encoding, and this process has been attributed to memory consolidation, leading to the improvements in recall. The present set of experiments investigated the impact of conscious thoughts occurring during post-encoding...
Show moreEngaging in post-encoding wakeful rest has been shown to lead to better retention of encoded information versus engaging in a post-encoding task. Brain imaging studies have shown that there is reactivation during post-encoding rest of brain areas that were active during initial encoding, and this process has been attributed to memory consolidation, leading to the improvements in recall. The present set of experiments investigated the impact of conscious thoughts occurring during post-encoding wakeful rest on delayed recall performance for both younger and older adults. Recall was tested across two tests separated by a rest period while verbalizing conscious thoughts or engaging in a visuo-spatial task while verbalizing thoughts. The present set of experiments demonstrated that both younger and older adults engage in post-encoding conscious reply that relates to delayed recall organization. The role of conscious replay in post-encoding processing is discussed.
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Date Issued: 2017
Identifier: FSU_FALL2017_Komsky_fsu_0071E_14232
Format: Thesis

Title: Like a Rolling Stone: Moving Toward Methodologies for Analysis of Multimodal Musical Performance.
Creator: Burgess, Andrew D. (Andrew David), Fleckenstein, Kristie S., Houck, Davis W., Yancey, Kathleen Blake, Neal, Michael R., Florida State University, College of Arts and Sciences,...
Show moreBurgess, Andrew D. (Andrew David), Fleckenstein, Kristie S., Houck, Davis W., Yancey, Kathleen Blake, Neal, Michael R., Florida State University, College of Arts and Sciences, Department of English
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Abstract/Description: As a means for understanding a wide range of multimodal phenomena, multimodal analysis poses methodological challenges for the novice researcher intent on investigating multimodal communication, especially communication that involves multimodal musical performance (MMP), an understudied communicative act. As a response to these challenges, this project examines three approaches to multimodal analysis identified by Carey Jewitt in The Routledge Handbook of Multimodal Analysis as central to...
Show moreAs a means for understanding a wide range of multimodal phenomena, multimodal analysis poses methodological challenges for the novice researcher intent on investigating multimodal communication, especially communication that involves multimodal musical performance (MMP), an understudied communicative act. As a response to these challenges, this project examines three approaches to multimodal analysis identified by Carey Jewitt in The Routledge Handbook of Multimodal Analysis as central to studying multimodality writ large: social-semiotic multimodal analysis (SSMA), multimodal discourse analysis (MDA), and multimodal interactional analysis (MIA). However, while these approaches each provide a theory and key concepts for analysis, they lack a practicable methodology—necessary for the novice research—and, thus, provide no concrete way to pursue multimodal analysis or to assess the strengths and deficits of a particular approach when applied to the analysis of MMPs. In this project, I conduct a critical analysis that includes a theoretical and pragmatic examination of these approaches to multimodal analysis and assess them for strengths and deficits in terms of a particular MMP because such a performance is an important and under-explored variety of multimodal text. Thus, this project asks three questions of each approach and its methods: 1) What are the strengths of each approach to multimodal analysis of musical performance as multimodal communication? 2) What are the deficits of each approach to multimodal analysis of musical performance as multimodal communication? 3) And, finally, given the strengths and deficits of competing approaches to multimodal analysis of musical performance as multimodal communication, what do we need moving forward in order to fully, robustly, and capaciously analyze and understand musical performance as multimodal communication? I respond to these questions by devising a synthesized, practicable methodology for each approach, one derived from the work in key chapters in The Routledge Handbook identified by Jewitt as employing a specific approach. I apply each of these methodologies to a single musical performance: video footage from Bob Dylan’s July 25, 1965 performance at the Newport Folk Festival—which is often seen as a pivotal moment in popular music history—collected on the 2011 blu-ray release of Murray Lerner’s concert film The Other Side of the Mirror: Bob Dylan Live At Newport Folk Festival 1963-1965. I assess the results of my application of each methodology and its methods to determine the strengths and deficits of each approach for analyzing MMPs. Finally, I offer two options to bolster strengths and address deficits of these three approaches to the multimodal analysis of MMPs, one crafted from combining approaches, and one crafted from a new perspective—that of sonic imaginations (Sterne)—thus informing methodology with attention to the sonic aspects of MMPs. This dissertation offers three key results important for the novice researcher. First, it provides a practicable methodology for each approach, a necessary step in the process of assessing an approach's strengths and deficits. Second, it offers the novice researcher insight into each methodology’s potential. For instance, analyses indicated that SSMA possesses, among its five strengths, a focus on the sign-maker, while at the same time, it possesses, among its three deficits, no mechanism through which to consider the multiple sign-makers involved in an MMP. Similarly, MDA possesses, among its six strengths, a focus on the multimodal phenomenon, while at the same time, it possesses, among its four deficits, a lack of a systematic means for delineating levels of discourse. And, MDA possesses, among its five strengths, a focus on interaction between social actors involved in an MMP, while at the same time, it possesses, among its five deficits, a requirement for a considerable amount of guesswork on the part of the researcher. Third, while demonstrating that no approach to multimodal analysis offers a “best” methodology for the analysis of MMPs, this dissertation offers two directions for methodological inspiration. It concludes that, through a deliberate courting of emotion by tapping into elements of music criticism and through a deliberate courting of messiness by embracing the union of emotion and analysis, methodologies for analysis can be crafted that align with the demands of MMPs.
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Date Issued: 2017
Identifier: FSU_FALL2017_Burgess_fsu_0071E_14194
Format: Thesis

Title: Semi-Parametric Generalized Estimating Equations with Kernel Smoother: A Longitudinal Study in Financial Data Analysis.
Creator: Yang, Liu, Niu, Xufeng, Cheng, Yingmei, Huffer, Fred W. (Fred William), Tao, Minjing, Florida State University, College of Arts and Sciences, Department of Statistics
Abstract/Description: Longitudinal studies are widely used in various fields, such as public health, clinic trials and financial data analysis. A major challenge for longitudinal studies is repeated measurements from each subject, which cause time dependent correlation within subjects. Generalized Estimating Equations can deal with correlated outcomes for longitudinal data through marginal effect. My model will base on Generalized Estimating Equations with semi-parametric approach, providing a flexible structure...
Show moreLongitudinal studies are widely used in various fields, such as public health, clinic trials and financial data analysis. A major challenge for longitudinal studies is repeated measurements from each subject, which cause time dependent correlation within subjects. Generalized Estimating Equations can deal with correlated outcomes for longitudinal data through marginal effect. My model will base on Generalized Estimating Equations with semi-parametric approach, providing a flexible structure for regression models: coefficients for parametric covariates will be estimated and nuisance covariates will be fitted in kernel smoothers for non-parametric part. Profile kernel estimator and the seemingly unrelated kernel estimator (SUR) will be used to deliver consistent and efficient semi-parametric estimators comparing to parametric models. We provide simulation results for estimating semi-parametric models with one or multiple non-parametric terms. In application part, we would like to focus on financial market: a credit card loan data will be used with the payment information for each customer across 6 months, investigating whether gender, income, age or other factors will influence payment status significantly. Furthermore, we propose model comparisons to evaluate whether our model should be fitted based on different levels of factors, such as male and female or based on different types of estimating methods, such as parametric estimation or semi-parametric estimation.
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Date Issued: 2017
Identifier: FSU_FALL2017_YANG_fsu_0071E_14219
Format: Thesis

Title: Transport Properties of Semimetallic Transition Metal Dichalcogenides.
Creator: Zhou, Qiong, Balicas, Luis, Bonesteel, N. E., Andrei, Petru, Xiong, Peng, Wahl, Horst, Florida State University, College of Arts and Sciences, Department of Physics
Abstract/Description: The Weyl semimetal requires the breaking of either the time-reversal symmetry (TRS) or the lattice inversion symmetry. When the TRS and inversion symmetry coexist, a pair of degenerate Weyl points may exist, leading to the related Dirac semimetal phase. In other words, a Dirac semimetallic state can be regarded as two copies of Weyl semimetal states. In this dissertation, we study tellurium based compounds like the Weyl semimetal candidate MoTe2 and the Dirac semimetal candidate PtTe2 within...
Show moreThe Weyl semimetal requires the breaking of either the time-reversal symmetry (TRS) or the lattice inversion symmetry. When the TRS and inversion symmetry coexist, a pair of degenerate Weyl points may exist, leading to the related Dirac semimetal phase. In other words, a Dirac semimetallic state can be regarded as two copies of Weyl semimetal states. In this dissertation, we study tellurium based compounds like the Weyl semimetal candidate MoTe2 and the Dirac semimetal candidate PtTe2 within the transition metal dichalcogenides family. Firstly, we report a systematic study on the Hall-effect of the semi-metallic state of bulk MoTe2, which was recently claimed to be a candidate for a novel type of Weyl semi-metallic state. The temperature (T) dependence of the carrier densities and of their mobilities, as estimated from a numerical analysis based on the isotropic two-carrier model, indicates that its exceedingly large and non-saturating magnetoresistance may be attributed to a near perfect compensation between the densities of electrons and holes at low temperatures. A sudden increase in hole density, with a concomitant rapid increase in the electron mobility below T ∼ 40 K, leads to comparable densities of electrons and holes at low temperatures suggesting a possible electronic phase-transition around this temperature. Secondly, the electronic structure of semi-metallic transition-metal dichalcogenides, such as WTe2 and orthorhombic γ−MoTe2, are claimed to contain pairs of Weyl points or linearly touching electron and hole pockets associated with a non-trivial Chern number. For this reason, these compounds were recently claimed to conform to a new class, deemed type-II, of Weyl semi-metallic systems. A series of angle resolved photoemission experiments (ARPES) claim a broad agreement with these predictions detecting, for example, topological Fermi arcs at the surface of these crystals. We synthesized single-crystals of semi-metallic MoTe2 through a Te flux method to validate these predictions through measurements of its bulk Fermi surface (FS) via quantum oscillatory phenomena. We find that the superconducting transition temperature of γ−MoTe2 depends on disorder as quantified by the ratio between the room- and low-temperature resistivities, suggesting the possibility of an unconventional superconducting pairing symmetry. Similarly to WTe2, the magnetoresistivity of γ−MoTe2 does not saturate at high magnetic fields and can easily surpass 106 %. Remarkably, the analysis of the de Haas-van Alphen (dHvA) signal superimposed onto the magnetic torque, indicates that the geometry of its FS is markedly distinct from the calculated one. The dHvA signal also reveals that the FS is affected by the Zeeman-effect precluding the extraction of the Berry-phase. A direct comparison between the previous ARPES studies and density-functional-theory (DFT) calculations reveals a disagreement in the position of the valence bands relative to the Fermi level εF . Here, we show that a shift of the DFT valence bands relative to εF , in order to match the ARPES observations, and of the DFT electron bands to explain some of the observed dHvA frequencies, leads to a good agreement between the calculations and the angular dependence of the FS cross-sectional areas observed experimentally. However, this relative displacement between electron- and hole-bands eliminates their crossings and, therefore, the Weyl type-II points predicted for γ−MoTe2. Finally, we investigate the electronic structure and transport properties in single crystals of the semi-metallic platinum ditelluride (PtTe2), recently claimed to be a novel type-II Dirac semimetal, via a methodology similar to that applied to γ−MoTe2, i.e. the temperature and angular dependence of the SdH and dHvA effects. Our high-quality PtTe2 crystal displays a large non-saturating magnetoresistance under magnetic field up to 61 T. The dHvA oscillation and SdH effect reveal several high and low frequencies suggesting a rather complex Fermi surface. We also find evidence for a non-trivial Berry phase. The crystal quality improved considerably under subsequent annealing at high-temperatures leading to the observation of linear in field magnetoresistivity. Combined with effective masses in the order of ∼ 0.1 free electron mass, these results further suggest that PtTe2 displays bulk Dirac-like bands.
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Date Issued: 2017
Identifier: FSU_FALL2017_Zhou_fsu_0071E_14145
Format: Thesis

Title: Developing SRSF Shape Analysis Techniques for Applications in Neuroscience and Genomics.
Creator: Wesolowski, Sergiusz, Wu, Wei, Bertram, R. (Richard), Srivastava, Anuj, Beerli, Peter, Mio, Washington, Florida State University, College of Arts and Sciences, Department of...
Show moreWesolowski, Sergiusz, Wu, Wei, Bertram, R. (Richard), Srivastava, Anuj, Beerli, Peter, Mio, Washington, Florida State University, College of Arts and Sciences, Department of Mathematics
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Abstract/Description: Dissertation focuses on exploring the capabilities of the SRSF statistical shape analysis framework through various applications. Each application gives rise to a specific mathematical shape analysis model. The theoretical investigation of the models, driven by real data problems, give rise to new tools and theorems necessary to conduct a sound inference in the space of shapes. From theoretical standpoint the robustness results are provided for the model parameters estimation and an ANOVA...
Show moreDissertation focuses on exploring the capabilities of the SRSF statistical shape analysis framework through various applications. Each application gives rise to a specific mathematical shape analysis model. The theoretical investigation of the models, driven by real data problems, give rise to new tools and theorems necessary to conduct a sound inference in the space of shapes. From theoretical standpoint the robustness results are provided for the model parameters estimation and an ANOVA-like statistical testing procedure is discussed. The projects were a result of the collaboration between theoretical and application-focused research groups: the Shape Analysis Group at the Department of Statistics at Florida State University, the Center of Genomics and Personalized Medicine at FSU and the FSU's Department of Neuroscience. As a consequence each of the projects consists of two aspects—the theoretical investigation of the mathematical model and the application driven by a real life problem. The applications components, are similar from the data modeling standpoint. In each case the problem is set in an infinite dimensional space, elements of which are experimental data points that can be viewed as shapes. The three projects are: ``A new framework for Euclidean summary statistics in the neural spike train space''. The project provides a statistical framework for analyzing the spike train data and a new noise removal procedure for neural spike trains. The framework adapts the SRSF elastic metric in the space of point patterns to provides a new notion of the distance. ``SRSF shape analysis for sequencing data reveal new differentiating patterns''. This project uses the shape interpretation of the Next Generation Sequencing data to provide a new point of view of the exon level gene activity. The novel approach reveals a new differential gene behavior, that can't be captured by the state-of-the art techniques. Code is available online on github repository. ``How changes in shape of nucleosomal DNA near TSS influence changes of gene expression''. The result of this work is the novel shape analysis model explaining the relation between the change of the DNA arrangement on nucleosomes and the change in the differential gene expression.
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Date Issued: 2017
Identifier: FSU_FALL2017_Wesolowski_fsu_0071E_14177
Format: Thesis

Title: Dissipation of Mesoscale Energy by Vortex-Topography Interaction.
Creator: Bishnu, Siddhartha, Dewar, William K., Chassignet, Eric P., Clarke, Allan J., Kopriva, David A., Florida State University, College of Arts and Sciences, Department of Earth,...
Show moreBishnu, Siddhartha, Dewar, William K., Chassignet, Eric P., Clarke, Allan J., Kopriva, David A., Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
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Abstract/Description: Energy is introduced into the oceans primarily at large scales by means of wind, tides and surface buoyancy forcing. This energy is transferred to the smaller mesoscale eld through the geostrophic instability processes. The mesoscale eld appears not to have accelerated appreciably over the last several decades, so we can assume that the mesoscale loses energy at roughly the same rate it receives energy. Interestingly, how the mesoscale loses energy is not quite clear. We have been exploring...
Show moreEnergy is introduced into the oceans primarily at large scales by means of wind, tides and surface buoyancy forcing. This energy is transferred to the smaller mesoscale eld through the geostrophic instability processes. The mesoscale eld appears not to have accelerated appreciably over the last several decades, so we can assume that the mesoscale loses energy at roughly the same rate it receives energy. Interestingly, how the mesoscale loses energy is not quite clear. We have been exploring topographic interaction as a pathway by which the mesoscale may lose energy to unbalanced forward cascading flows. To demonstrate this phenomenon, an approximate model theory is developed which consists of solving a reduced set of the momentum equations in density coordinates for any topographic conguration. The equations are solved using a high order spectral element technique and the results are similar to already published MITgcm simulations.
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Date Issued: 2017
Identifier: FSU_FALL2017_Bishnu_fsu_0071N_14263
Format: Thesis

Title: Fossil Excavation, Museums, and Wyoming: American Paleontology, 1870-1915.
Creator: Cameron, Marlena Briane, Doel, Ronald Edmund, Ruse, Michael, Buhrman, Kristina Mairi, Varry, Sandra, Florida State University, College of Arts and Sciences, Program in History...
Show moreCameron, Marlena Briane, Doel, Ronald Edmund, Ruse, Michael, Buhrman, Kristina Mairi, Varry, Sandra, Florida State University, College of Arts and Sciences, Program in History and Philosophy of Science
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Abstract/Description: Displays of dinosaurs have become a staple of modern natural history museums, but these did not emerge until the turn of the twentieth century. Through the work of Edward Drinker Cope and Othniel Charles Marsh in this field (despite their intense rivalry), paleontology grew as a discipline and, after losing federal funding, found a new home in museums and universities. Recognizing the potential of large dinosaurs for display and education, major natural history museums such as the American...
Show moreDisplays of dinosaurs have become a staple of modern natural history museums, but these did not emerge until the turn of the twentieth century. Through the work of Edward Drinker Cope and Othniel Charles Marsh in this field (despite their intense rivalry), paleontology grew as a discipline and, after losing federal funding, found a new home in museums and universities. Recognizing the potential of large dinosaurs for display and education, major natural history museums such as the American Museum of Natural History in New York under Henry Osborn began competing for their own specimens. Much work has been done on the efforts of these emerging large museums. Smaller museums such as the University of Wyoming Museum, however, have been much less studied. Through its proximity to immense, rich fossil fields, the university became directly connected to the major events shaping paleontology at the time. Yet differences in the pedagogy and intentions behind its formation—a sense of state pride rather than the concerns of wealthy, elite sponsors—served to set it apart from larger, more well-known institutions.
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Date Issued: 2017
Identifier: FSU_FALL2017_Cameron_fsu_0071N_14117
Format: Thesis

Title: Belief Systems and Executive Functioning.
Creator: Berry, Cassie Stutts, Kaschak, Michael P., Sunderman, Gretchen L., Boot, Walter Richard, Kelley, Colleen M., Conway, Paul, Florida State University, College of Arts and Sciences...
Show moreBerry, Cassie Stutts, Kaschak, Michael P., Sunderman, Gretchen L., Boot, Walter Richard, Kelley, Colleen M., Conway, Paul, Florida State University, College of Arts and Sciences, Department of Psychology
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Abstract/Description: Perceiving our world is an active process. We actively explore and investigate the environment rather than passively registering the objects and events we encounter. Our perception and attention reflect our moods, expectations, and beliefs. Recent evidence supporting this approach comes from studies that focus on the impact of individual differences on human perception and attention. Characteristics about the world we live in, like culture or religion, may drive these differences in...
Show morePerceiving our world is an active process. We actively explore and investigate the environment rather than passively registering the objects and events we encounter. Our perception and attention reflect our moods, expectations, and beliefs. Recent evidence supporting this approach comes from studies that focus on the impact of individual differences on human perception and attention. Characteristics about the world we live in, like culture or religion, may drive these differences in perception and attention. One of the ways this has been looked at is by examining executive functioning. Inhibitory control, the ignoring of irrelevant information, is an important component of executive functioning. The Simon, Flanker, and Stroop tasks are all common measures of inhibitory control. They all require to some degree the inhibition of irrelevant information when selecting an appropriate response to stimuli. Several studies have reported a bilingual advantage on these tasks. Previous research has indicated differences in cognitive functioning for those of different political beliefs. Differences are seen in perception of multi-level stimuli in people of different cultures and religions and for people with different political leanings. Previous research has found similar differences in performance on a measure of executive functioning for people of different religions. The expected effects for the Simon and Flanker task were found in this sample. Differences in the size of the Simon and Flanker effect were not found in this sample for those of different religious beliefs or political beliefs
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Date Issued: 2017
Identifier: FSU_FALL2017_Berry_fsu_0071E_14233
Format: Thesis

Title: Understanding Magnetic Exchange Behavior in Core@Shell Nanoparticles.
Creator: Carnevale, David J. (David John), Shatruk, Mykhailo, Strouse, Geoffrey F., Xiong, Peng, Schlenoff, Joseph B., Florida State University, College of Arts and Sciences, Department...
Show moreCarnevale, David J. (David John), Shatruk, Mykhailo, Strouse, Geoffrey F., Xiong, Peng, Schlenoff, Joseph B., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
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Abstract/Description: As green technology advances, the need for cheaper, stronger permanent magnets becomes more and more vital everyday. Electric motors, like those used in wind turbines and electric cars, rely heavily on Dy doped Nd2Fe14B in order to achieve the required efficiencies to be successful, however both Nd and Dy are expensive rare-earth elements that the field is trying to move away from relying on. In order to approach this issue, many are trying to combine these powerful permanent magnets with...
Show moreAs green technology advances, the need for cheaper, stronger permanent magnets becomes more and more vital everyday. Electric motors, like those used in wind turbines and electric cars, rely heavily on Dy doped Nd2Fe14B in order to achieve the required efficiencies to be successful, however both Nd and Dy are expensive rare-earth elements that the field is trying to move away from relying on. In order to approach this issue, many are trying to combine these powerful permanent magnets with cheaper and more abundant soft magnetic materials in order to create exchange-spring magnets. While exchange coupling behavior has been studied for several decades now, there are major issues with controlling the uniformity in the generated materials leading to a limited understanding of the properties of these assemblies. In order to address both of these issues at the same time, we devised an approach to create a hard magnetic nanoparticle of fcc-FePt, which was then shelled with the soft magnet Co. In order to gain the desired control of the final core@shell particles, a mix and round bottom and microwave heating was utilized, the synthetic details of which are laid out in Chapter 2. Chapter 3 lays out the results from applying a layer-by-layer shell of Co onto a constant 5 nm FePt particle. From this shelling, the transition from hard-exchange to exchange-spring to decoupling of the core@shell system can be observed. The limit of these regions were found to be very small, with the hard-exchange regime only being in the case of shell sizes smaller than 1.4 nm and decoupling occurring in the materials with >2nm of Co shelled on. This limited range is due to cobalt’s short range coupling, which can not support strong coupling beyond 3-4 layers of Co.
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Date Issued: 2017
Identifier: FSU_FALL2017_Carnevale_fsu_0071E_14044
Format: Thesis

Title: Quantum Chemical Methods and Algorithms for Ground and Excited Electronic States.
Creator: Nascimento, Daniel R. (Daniel Ricardo), DePrince, A. Eugene (Albert Eugene), Shanbhag, Sachin, Dalal, Naresh S., Steinbock, Oliver, Florida State University, College of Arts and...
Show moreNascimento, Daniel R. (Daniel Ricardo), DePrince, A. Eugene (Albert Eugene), Shanbhag, Sachin, Dalal, Naresh S., Steinbock, Oliver, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
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Abstract/Description: In this dissertation, we address some of the needs faced in the development of modern ab initio quantum chemical methods to compute high-accuracy ground and excited electronic states. Chapters 1 and 2 should be seen as introductory Chapters, where the mathematical foundations of modern electronic structure theory necessary to understand this work are laid down. Chapters 3 and 4 covers the development of methods and algorithms relevant to ground state computations. We propose a semi-definite...
Show moreIn this dissertation, we address some of the needs faced in the development of modern ab initio quantum chemical methods to compute high-accuracy ground and excited electronic states. Chapters 1 and 2 should be seen as introductory Chapters, where the mathematical foundations of modern electronic structure theory necessary to understand this work are laid down. Chapters 3 and 4 covers the development of methods and algorithms relevant to ground state computations. We propose a semi-definite-based algorithm to compute ground-state Hartree-Fock energies and wave functions, that can be easily extended to Kohn-Sham density functional theory. We also propose a parametrized coupled-pair functional to compute accurate non-covalent molecular interaction energies. Chapters 3 through 7 cover methods relevant to excited state computations. We propose an explicitly time-dependent coupled-cluster framework rooted on the equation-of-motion formalism to compute linear absorption spectra of molecular systems. The method is further expanded by recasting a linear absorption line shape function in terms of Pad ́e approximants. The expanded method is shown to be an efficient tool for the simulation of near-edge X-ray absorption fine structure. Finally, we propose a time-dependent Hartree-Fock method within the framework of cavity quantum-electrodynamics that allows us to simulate the interaction of molecular systems with quantized radiation fields, such as those found on plasmonic nanoparticles and nano cavities.
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Date Issued: 2017
Identifier: FSU_FALL2017_Nascimento_fsu_0071E_14251
Format: Thesis

Title: Microfluidic Methods for the Study of Biological Dynamics.
Creator: Mukhitov, Nikita, Bhide, Pradeep, Marshall, Alan G. (Alan George), Bleiholder, Christian, Florida State University, College of Arts and Sciences, Department of Chemistry and...
Show moreMukhitov, Nikita, Bhide, Pradeep, Marshall, Alan G. (Alan George), Bleiholder, Christian, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
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Abstract/Description: The work in this dissertation presents microfluidic methods developed for the study of biological dynamics. The requirements for the methods development was to create approaches with the ability to perform dynamic cell stimulation, measurement, and sample preparation. The methods presented herein were initially developed for the study of pancreatic islet biology but are expected to be translatable to other applications. In another study, a method to interface transmission electron microscopy ...
Show moreThe work in this dissertation presents microfluidic methods developed for the study of biological dynamics. The requirements for the methods development was to create approaches with the ability to perform dynamic cell stimulation, measurement, and sample preparation. The methods presented herein were initially developed for the study of pancreatic islet biology but are expected to be translatable to other applications. In another study, a method to interface transmission electron microscopy (TEM) with microfluidics methods was developed. The primary biological topic of interest investigated was the mechanisms of inter-islet synchronization. To test this, a microfluidic device fabricated from poly(dimethylsiloxane) (PDMS) was used to culture and stimulate pancreatic islets. Intracellular calcium ([Ca2+]i) imaging was performed with a fluorescent indicator, Fura-2-acetoxymethyl ester (Fura-2 AM). Under constant glucose (11 mM), islets demonstrated asynchronous and heterogeneous [Ca2+]i oscillations that drifted in period. However, when exposed to a glucose wave (11+/- 1 mM, 5 min period) islets were entrained to a common and consistent [Ca2+]i oscillation mode. The effect of islet entrainment on cellular function was investigated by measuring gene expression levels with microarray profiling. Calcium-dependent genes were found to be differentially expressed. Furthermore, it was speculated that islet entrained produced a beneficial effect on cell function and upkeep. While [Ca2+]i imaging is an acceptable proxy measurement for insulin, it is not a viable reporter for other islet peptides and direct measurement is desired. Electrophoretic affinity assays can be performed on a microfluidic device in a serial manner to measure peptide release from an on-chip cell culture in near real-time. Successful analysis of electrophoretic affinity assays depends strongly on the preservation of the affinity complex during separations. Elevated separation temperatures due to Joule heating promotes complex dissociation leading to a reduction in sensitivity. To address this limitation, a method to cool a glass microfluidic chip for performing an affinity assay for insulin was achieved by a Peltier cooler localized over the separation channel. The Peltier cooler allowed for rapid stabilization of temperatures, with 21 °C the lowest temperature that was possible to use without producing detrimental thermal gradients throughout the device. Kinetic capillary electrophoresis analysis was utilized as a diagnostic of the affinity assay and indicated that optimal conditions were at the highest attainable separation voltage, 6 kV, and the lowest separation temperature, 21 °C, leading to 3.4% dissociation of the complex peak during the separation. These optimum conditions were used to generate a calibration curve and produced 1 nM limits of detection (LOD), representing a 10-fold improvement over non-thermostated conditions. To date, most approaches for measurement of rapid changes in insulin levels rely on separations, making the assays difficult to translate to non-specialist laboratories. To enable rapid measurements of secretion dynamics from a single islet in a manner that will be more suitable for transfer to non-specialized laboratories, a microfluidic online fluorescence anisotropy immunoassay was developed. A single islet was housed inside a microfluidic chamber and stimulated with varying glucose levels from a gravity-based perfusion system. The total effluent of the islet chamber containing the islet secretions was mixed with gravity-driven solutions of insulin antibody and cyanine-5 (Cy5) labeled insulin. After mixing was complete, a linearly polarized 635 nm laser was used to excite the immunoassay mixture and the emission was split into parallel and perpendicular components for determination of anisotropy. Key factors for reproducible anisotropy measurements, including temperature homogeneity and flow rate stability were optimized, which resulted in a 4 nM LOD for insulin with <1% RSD of anisotropy values. The capability of this system for measuring insulin secretion from single islets was shown by stimulating an islet with varying glucose levels. As the entire analysis is performed optically, this system should be readily transferable to other laboratories. To increase the number of analytes that can be simultaneously monitored by a fluorescence anisotropy immunoassay, frequency encoding was introduced. As a demonstration of the method, simultaneous competitive immunoassays for insulin and glucagon were performed by measuring the ratio of bound and free Cy5-insulin and fluorescein isothiocyanate (FITC)-glucagon in the presence of their respective antibodies. A vertically polarized 635 nm laser was pulsed at 73 Hz and used to excite Cy5-insulin, while a vertically polarized 488 nm laser pulsed at 137 Hz excited FITC-glucagon. The total emission was split into parallel and perpendicular polarizations and collected onto separate photomultiplier tubes. The signals from each channel were demodulated using a fast Fourier transform, resolving the contributions from each fluorophore. Anisotropy calculations were carried out using the magnitude of the peaks in the frequency domain. The method produced the expected shape of the calibration curves with LOD of 0.6 and 5 nM for insulin and glucagon, respectively. This methodology could readily be expanded to other biological systems and further multiplexed to monitor increased numbers of analytes. In another study, a microfluidic platform was developed to prepare negatively stained grids for use in TEM. The microfluidic device is composed of glass etched with readily fabricated features that facilitate the extraction of the grid post-staining and maintains the integrity of the sample. Utilization of this device simultaneously reduced environmental contamination on the grids and improved the homogeneity of the heavy metal stain needed to enhance visualization of biological specimens as compared to conventionally prepared TEM grids. This easy-to-use TEM grid preparation device provides the basis for future developments of systems with more integrated features, which will allow for high-throughput and dynamic structural biology studies.
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Date Issued: 2017
Identifier: FSU_FALL2017_Mukhitov_fsu_0071E_14138
Format: Thesis

Title: Tuning the Emission and Quantum Yield of Gold and Silver Nanoclusters through Ligand Design and Doping.
Creator: Mishra, Dinesh, Mattoussi, Hedi, Xiong, Peng, Alabugin, Igor V., Shatruk, Mykhailo, Strouse, Geoffrey F., Florida State University, College of Arts and Sciences, Department of...
Show moreMishra, Dinesh, Mattoussi, Hedi, Xiong, Peng, Alabugin, Igor V., Shatruk, Mykhailo, Strouse, Geoffrey F., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
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Abstract/Description: Nanoparticles have been extensively studied in the past few decades due to the possibilities they offer in applications ranging from medicine to energy generation. A new class of ultra-small noble metal nanoparticles consisting of tens to hundreds of atoms, commonly known as clusters or nanoclusters, have drawn interest of the research community recently due to their unique optical, electronic and structural properties. Over the past few years, advances have been made in the synthesis of...
Show moreNanoparticles have been extensively studied in the past few decades due to the possibilities they offer in applications ranging from medicine to energy generation. A new class of ultra-small noble metal nanoparticles consisting of tens to hundreds of atoms, commonly known as clusters or nanoclusters, have drawn interest of the research community recently due to their unique optical, electronic and structural properties. Over the past few years, advances have been made in the synthesis of atomically precise noble metal clusters (for example, silver and gold) with distinct optical properties. Their ultra-small size distinguishes them from conventional plasmonic nanoparticles and the properties are very sensitive to the slight variation in the compositon of the cluster, i.e. the number of the metal atoms and/or the nature of the ligands. These clusters are interesting because of their potential applications in field such as sensing, imaging, catalysis, clean energy, photonics, etc. as well as they provide fundamental insight into the evolution of the optical and electronic properties of these clusters. In this project, we explored the strategies to synthesize luminescent metallic clusters of gold and silver and to promote their solubility and stability in aqueous and biological medium. We focused particularly on the thiolate protected clusters due to the higher affinity of gold and silver to sulfur. Lipoic acid (Thioctic acid) is a bio-molecule with a cyclic disulfide ring, which also acts as a chelating ligand. Due to the higher binding affinity of the cyclic disulfide ring to nanocrystal surface, lipoic acid and chemically modified lipoic acid molecules have been widely reported for the synthesis and functionalization of inorganic nanocrystals. Here, we describe the use of bidentate lipoic acid ligands in the one phase growth of luminescent gold and silver nanoclusters. In addition, we have synthesized a new set of monothiol ligands containing PEG and zwitterion for the functionalization of fluorescent clusters. Chapter 1 introduces the fundamental properties of metallic clusters and the origin of these properties from electronic and structural point of view. The optical properties of ultra-small nanocrystals (<2 nm) in comparison to the plasmonic particles is described. In addition, the variation of optical and structural properties from one metal to another as well as one ligand to another is also compared. Chapter 2 describes the synthesis of ultra-small size gold clusters with different optical emission (ranging from blue to red) using photo-activated LA-PEG ligands. The influence of various factors on the growth of the clusters is also studied. Optical properties of the clusters were studied by UV-visible absorption, PL emission and excitation and time resolved fluorescence spectroscopy. XPS and DOSY NMR were used to characterize the oxidation states and sizes of these clusters. The photo-chemical transformation of LA-PEG ligands to thiols and the effect of various experimental parameters such as solvent, oxygen, ligand functional group and effect of acid are described in chapter 3. Thiol yield percentage was quantified using ellman assay. Chapter 4 describes the one phase aqueous synthesis of Ag29 clusters capped with bidentate dihydrolipoic acid (DHLA). We also describe the drastic enhancement of the PL intensity upon gold doping of the Ag29 clusters. Optical properties along with the size characterization by electrospray ionization mass spectrometry is also described. We further describe the growth of these clusters using DHLA-PEG molecules. Chapter 5 describes the synthesis of highly fluorescent Au25-xAgx clusters stabilized with two types of ligands (triphenylphosphine and thiols). We designed a set of monothiolate ligands appended with PEG and zwitterionic moieties. This approach allows to prepare water soluble and stable metallic clusters with enhanced photoluminescence and well defined optical properties. Chapter 6 is the overall summary of our findings and prospects and outlook.
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Date Issued: 2017
Identifier: FSU_FALL2017_Mishra_fsu_0071E_14122
Format: Thesis

Title: Improving the Effectiveness of Performance Analysis for HPC by Using Appropriate Modeling and Simulation Schemes.
Creator: Tong, Zhou, Yuan, Xin, Ke, Fengfeng, Zhang, Zhenghao, Haiduc, Sonia, Pakin, Scott D., Florida State University, College of Arts and Sciences, Department of Computer Science
Abstract/Description: Performance modeling and simulation of parallel applications are critical performance analysis techniques in High Performance Computing (HPC). Efficient and accurate performance modeling and simulation can aid the tuning and optimization of current systems as well as the design of future HPC systems. As the HPC applications and systems increase in size, efficient and accurate performance modeling and simulation of parallel applications is becoming increasingly challenging. In general,...
Show morePerformance modeling and simulation of parallel applications are critical performance analysis techniques in High Performance Computing (HPC). Efficient and accurate performance modeling and simulation can aid the tuning and optimization of current systems as well as the design of future HPC systems. As the HPC applications and systems increase in size, efficient and accurate performance modeling and simulation of parallel applications is becoming increasingly challenging. In general, simulation yields higher accuracy at the cost of high simulation time in comparison to modeling. This dissertation aims at developing effective performance analysis techniques for the next generation HPC systems. Since modeling is often orders of magnitude faster than simulation, the idea is to separate HPC applications into two types: 1) the ones that modeling can produce similar performance results as simulation and 2) the ones that simulation can result in more meaningful information about the application performance than modeling. By using modeling for the first type of applications and simulation for the rest of applications, the efficiency of performance analysis can be significantly improved. The contribution of this thesis is three-fold. First, a comprehensive study of the performance and accuracy trade-offs between modeling and simulation on a wide range of HPC applications is performed. The results indicate that for the majority of HPC applications, modeling and simulation yield similar performance results. This lays the foundation for improving performance analysis on HPC systems by selecting between modeling and simulation on each application. Second, a scalable and fast classification techniques (MFACT) are developed based on the Lamport's logical clock that can provide fast diagnosis of MPI application performance bottleneck and assist in the processing of application tuning and optimization on current and future HPC systems. MFACT also classifies HPC applications into bandwidth-bound, latency-bound, communication-bound, and computation-bound. Third, built-upon MFACT, for a given system configuration, statistical methods are introduced to classify HPC applications into the two types: the ones that needs simulation and the ones that modeling is sufficient. The classification techniques and tools enable effective performance analysis for future HPC systems and applications without losing accuracy.
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Date Issued: 2017
Identifier: FSU_FALL2017_Tong_fsu_0071E_14074
Format: Thesis

Title: Philosophical, Historical, and Empirical Investigations into the Concept of Biological Fitness.
Creator: Takacs, Peter, Ruse, Michael, Travis, Joseph, Bishop, Michael A., Justus, James, Florida State University, College of Arts and Sciences, Department of Philosophy
Abstract/Description: While undeniably one of the central explanatory concepts in biology, fitness is deployed in an ambiguous or even inconsistent manner by evolutionary biologists as well as philosophers. This sort of foundational confusion is a plea for conceptual clarity and has, thereby, presented a wonderful opportunity for philosophers of science to ply their trade. After engaging with the topic, however, several influential philosophers of science (e.g., Mohan Matthen, Dennis Walsh, and Andre Ariew) and...
Show moreWhile undeniably one of the central explanatory concepts in biology, fitness is deployed in an ambiguous or even inconsistent manner by evolutionary biologists as well as philosophers. This sort of foundational confusion is a plea for conceptual clarity and has, thereby, presented a wonderful opportunity for philosophers of science to ply their trade. After engaging with the topic, however, several influential philosophers of science (e.g., Mohan Matthen, Dennis Walsh, and Andre Ariew) and biologists (Richard Lewontin and Massimo Pigliucci) have reached the conclusion that biological fitness is not in fact the cause of natural selection but instead a mere statistical artifact or redescription of systematic transgenerational change. It is, as they see matters, a label best reserved for abstract trait types rather than the organisms that bear such traits. This poses a serious challenge to the working intuitions of most biologists and many philosophers of biology. Moreover, it is but one of many challenges to the explanatory and ontological primacy of natural selection in recent memory. For at least three decades, some practitioners in the burgeoning subdiscipline of evolutionary developmental biology have been outspoken in insisting that the tools of population biology are insufficient for describing or explaining observations of adaptive evolutionary change both past and present. In this dissertation, I examine these recent challenges to orthodox conceptions of fitness and natural selection, as well as the rejoinders given in defense. Ultimately, I defend a conception of fitness as a probabilistic dispositional property (i.e., a propensity) of token organisms that causes natural selection.
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Date Issued: 2017
Identifier: FSU_FALL2017_Takacs_fsu_0071E_14240
Format: Thesis

Title: Modernist Empathy in American Litearture: William Faulkner, Nathanael West, and Richard Wright.
Creator: Tabata, Kentaro, Berry, R. M., Wakamiya, Lisa Ryoko, Epstein, Andrew, Kilgore, John Mac, Florida State University, College of Arts and Sciences, Department of English
Abstract/Description: In this dissertation that discusses the American novels by William Faulkner, Nathanael West, and Richard Wright, I delineate the concept of modernist empathy as a radical urge for intersubjective immediacy, while adjusting the concept of empathy as each situation requires instead of squeezing various manifestations of empathy into a single, standardized definition. I observe how those writers struggle to represent modernist empathy by differentiating it from its similar psychological...
Show moreIn this dissertation that discusses the American novels by William Faulkner, Nathanael West, and Richard Wright, I delineate the concept of modernist empathy as a radical urge for intersubjective immediacy, while adjusting the concept of empathy as each situation requires instead of squeezing various manifestations of empathy into a single, standardized definition. I observe how those writers struggle to represent modernist empathy by differentiating it from its similar psychological phenomena, especially sympathy. Instead of establishing empathy’s predominance over sympathy, however, I pay detailed attention to the constantly oscillating dynamic between a modernist urge for empathic immediacy and a realistic compromise of sympathetic distancing, thus revealing empathy’s instability and ambiguity. After briefly overviewing Amy Coplan’s conceptualization of empathy and sketching three categories of narrative empathy in the introduction, I have explained the concept of modernist empathy in the first chapter. In doing so, I first examine the discourse that surrounded the concept of empathy at the time, contrasting modernist empathy with its sisterly concept of sympathy. Then, since empathy and sympathy do not always form a clear dichotomy, I have argued that modernist empathy should be captured in the process of the oscillating dynamic between modernist urge for empathy and sympathetic compromise of distancing. In the second chapter, I have discussed how modernist empathy is manifested in William Faulkner’s The Sound and the Fury according to the three categories of narrative empathy. First, I have analyzed the novel’s experimental narrative in terms of readerly empathy. Then, I have discussed the novel’s empathic and anti-empathic characters as manifestations of represented empathy. Finally, I have examined Faulkner’s writerly empathy, and I have observed how he embraces the ultimate instability of modernist empathy. In the third chapter, by considering Nathanael West as a late modernist, I have argued that his novels are critiques of modernist empathy. In the analysis of his first novel, The Dream Life of Balso Snell, I have revealed West’s dichotomy between intellectual distancing and emotional involvement. Then, I have attempted to depict how West dramatizes his protagonists’ failures of empathy in Miss Lonelyhearts and The Day of the Locust. In the process, I critique Martha Nussbaum’s theory of compassion in relation to empathy. I also consider the relationship of empathy to the advent of the anonymous mass in the 1930s and observed West’s critique of empathy at the age of mass culture. The focus of the final chapter is about the writerly design of the strategic use of empathy in Richard Wright’s Native Son. After reviewing the past literary criticism of the novel’s empathy, I have discussed how the novel is strategized to establish an intimate readerly empathy with Bigger Thomas. At the end of the argument, I examine the author’s strategic design of empathy and its relation to racial politics.
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Date Issued: 2017
Identifier: FSU_FALL2017_Tabata_fsu_0071E_14190
Format: Thesis

Title: Dynamics-Guided Analysis of Tropical Waves.
Creator: Sun, Jie, Wu, Zhaohua, She, Yiyuan, Bourassa, Mark Allan, Cai, Ming, Misra, Vasubandhu, Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and...
Show moreSun, Jie, Wu, Zhaohua, She, Yiyuan, Bourassa, Mark Allan, Cai, Ming, Misra, Vasubandhu, Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
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Abstract/Description: Tropical waves are important tropical and global weather/climate systems as well as carriers for redistributing global energy. For decades, a multitude of tropical wave theories that attempt to explain the origins and maintenance mechanisms of tropical waves and the interactions between them and other tropical systems have been put forth by scientists. Partly due to the lack of effective analysis tools, observational studies of tropical waves have not been comprehensive enough, leaving many...
Show moreTropical waves are important tropical and global weather/climate systems as well as carriers for redistributing global energy. For decades, a multitude of tropical wave theories that attempt to explain the origins and maintenance mechanisms of tropical waves and the interactions between them and other tropical systems have been put forth by scientists. Partly due to the lack of effective analysis tools, observational studies of tropical waves have not been comprehensive enough, leaving many of the proposed theories unverified. For example, Fourier spectrum analysis based methods can hardly be used to obtain the accurate climatology of tropical waves because of the impacts of locality. This study serves two purposes: (1) To introduce and develop novel dynamics-based effective methods and to tailor them for isolating spatiotemporally local tropical waves of different spatiotemporal scales; and (2) To shed new insights into the climatological features of tropical waves, such as life cycles, their interactions with other tropical phenomena, and their dynamical implications. To accomplish the first goal, we introduce the multi-dimensional ensemble mode decomposition (MEEMD) method to decompose different meteorological variables. This method is combined with our newly developed optimization methods based on tropical wave theory in this study to form a dynamics based tropical wave diagnosis package. The capability of the new package is validated using both synthetic data and observational data. It is demonstrated that our package has high capability of separating tropical waves of different spatiotemporal scales as well as of different types. With the readiness of the above package, we systematically analyzed characteristic of tropical waves of different types, with emphases being placed on the spatiotemporal structures and their life cycle. It is revealed that all types of tropical waves have significantly different climatological characteristics, from wavenumbers and wave frequencies to their propagating properties. It is revealed that that upper and lower tropospheric tropical waves have distinguishable dynamic characteristics, too different for researchers to adopt a first baroclinic mode structure in the vertical to understand the origin and destiny of various tropical waves. We also quantify the modulation characteristics of high frequency tropical waves by intraseasonal oscillations.
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Date Issued: 2017
Identifier: FSU_FALL2017_Sun_fsu_0071E_14169
Format: Thesis

Title: Experience Changes Neuronal Intrinsic Physiology.
Creator: Ross, Matthew T., Hyson, Richard Lee, Morris, Richard Jack, Johnson, Frank, Bertram, R. (Richard), Kaschak, Michael P., Florida State University, College of Arts and Sciences,...
Show moreRoss, Matthew T., Hyson, Richard Lee, Morris, Richard Jack, Johnson, Frank, Bertram, R. (Richard), Kaschak, Michael P., Florida State University, College of Arts and Sciences, Department of Psychology
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Abstract/Description: The process of learning well-coordinated motor sequences is an essential aspect of human behavior. Learning to speak, play an instrument, or swing a baseball bat requires the brain to encode a very specific sequence of motor activity. It is understood at the descriptive level of analysis the environmental/experiential factors that contribute to learned motor sequences, but there is limited understanding of the neural modifications underlying such learning. This dissertation explores how...
Show moreThe process of learning well-coordinated motor sequences is an essential aspect of human behavior. Learning to speak, play an instrument, or swing a baseball bat requires the brain to encode a very specific sequence of motor activity. It is understood at the descriptive level of analysis the environmental/experiential factors that contribute to learned motor sequences, but there is limited understanding of the neural modifications underlying such learning. This dissertation explores how auditory experience shapes the intrinsic physiology of premotor neurons during the process of learning vocal patterns. Understanding these neural modifications could help in identifying ways to improve learning and identify processes that may account for learning disabilities. The hypothesis tested in this dissertation is that learning involves plasticity of the intrinsic properties of neurons. This is tested by using in vitro patch clamp electrophysiology to study the intrinsic physiology of the premotor area HVC, a brain area responsible for the vocal timing of song in zebra finches. The first set of experiments test whether the intrinsic physiology of HVC changes over song learning and development. The results show that there are systematic changes in projection neuron physiology as juvenile finches learn to sing. Biophysical models were made to predict the changes in ion channel expression that underlie the change in physiology. Some observations included alterations in the response of HVCX neurons to hyperpolarizing current pulses, including model-predicted changes in the Ih current and the T-type Ca2+ current. Additional changes included a shift in the resting potential of HVCRA neurons. The second set of experiments tests the prediction that auditory experience drives the observed changes in intrinsic physiology. The results show that tutor-deprivation has a direct effect on the intrinsic physiology of HVC projection neurons. The results also show that limited tutor exposure can reverse the change in physiology that resulted from tutor deprivation in a dose dependent fasion. These findings suggest that vocal-motor learning involves not only the alteration of synaptic weighting between neurons, but also changes in the intrinsic physiology of the component neurons in the circuit. Consequently, models of vocal learning should account for these intrinsic changes along with changes in synaptic connectivity. More broadly, models of learning and memory should consider intrinsic plasticity of neurons as a possible contributor to how the nervous system encodes new information or novel behaviors.
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Date Issued: 2017
Identifier: FSU_FALL2017_Ross_fsu_0071E_14195
Format: Thesis

Title: The Impact of Tropical Cyclones on Upper Atmospheric Chemistry Using a High-Resolution Chemical Transport Model and Aircraft Observations.
Creator: Preston, Aaron David, Fuelberg, Henry E., Van Winkle, David H., Barth, Mary, Hart, Robert E. (Robert Edward), Sura, Philip, Liu, Guosheng, Florida State University, College of...
Show morePreston, Aaron David, Fuelberg, Henry E., Van Winkle, David H., Barth, Mary, Hart, Robert E. (Robert Edward), Sura, Philip, Liu, Guosheng, Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
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Abstract/Description: This research focuses on the transport of chemical species to the upper troposphere/lower stratosphere (UTLS) by tropical cyclones (TCs). Species such as carbon monoxide, nitrogen oxides, and ozone have been found to exert a greater influence on climate change at these high altitudes than if remaining near the surface. Typhoon Mireille (1991) is examined in the western North Pacific (WNP) Ocean basin using in situ aircraft-derived chemical data from NASA's Pacific Exploratory Mission-West A...
Show moreThis research focuses on the transport of chemical species to the upper troposphere/lower stratosphere (UTLS) by tropical cyclones (TCs). Species such as carbon monoxide, nitrogen oxides, and ozone have been found to exert a greater influence on climate change at these high altitudes than if remaining near the surface. Typhoon Mireille (1991) is examined in the western North Pacific (WNP) Ocean basin using in situ aircraft-derived chemical data from NASA's Pacific Exploratory Mission-West A field project. The Weather Research and Forecasting (WRF) model was used with chemistry (WRF-Chem) at an innermost grid spacing of 3 km to explicitly resolve the convection being studied. Results show that pollution from distant sources is ingested by Mireille and subsequently lofted by eyewall convection to the UTLS, enhancing concentrations in this region. Flux calculations suggest that a strong TC, such as Mireille, can impact UTLS chemistry as much as a continental middle latitude cyclone. Furthermore, overshooting cells in Mireille produced chemical flux density values at the tropopause level as much as 10-20 times greater than that of the TC as a whole. Thus, although the overshooting tops comprise only a small area of the total TC, they transport large quantities of gaseous species to the UTLS because of their very strong updrafts. Results also suggest that millions of cars and/or several power plants would need to be hypothetically placed in the upper troposphere to have the same impact on chemical concentrations as Mireille. This demonstrates the transport strength of the TC as a whole. Improved understanding of atmospheric chemistry in the WNP basin is important, especially in the context of increasing Asian emissions and a changing climate. Furthermore, since it has been hypothesized that global warming will lead to more intense storms, it is important to understand TCs’ role in chemical transport.
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Date Issued: 2017
Identifier: FSU_FALL2017_Preston_fsu_0071E_14129
Format: Thesis

Title: Applications of Alkynogenic Fragmentation Products Derived from Vinylogous Acyl Triflates.
Creator: Ramsubhag, Ron Robert, Fajer, Piotr G., Saltiel, Jack, Zhu, Lei, Florida State University, College of Arts and Sciences, Department of Chemical and Biomedical Engineering
Abstract/Description: Carbon-carbon bond formation is the foundation to synthesizing complex molecules and has gathered the attention of many synthetic chemists. One must keep in mind that these reactions are dependent on materials for a specific agenda when tackling a structural framework, which may require additional steps to create, and at times, are difficult to prepare. As significant as C-C bond formation reactions are, these minor setbacks may draw caution when synthesizing a complicated molecule whose...
Show moreCarbon-carbon bond formation is the foundation to synthesizing complex molecules and has gathered the attention of many synthetic chemists. One must keep in mind that these reactions are dependent on materials for a specific agenda when tackling a structural framework, which may require additional steps to create, and at times, are difficult to prepare. As significant as C-C bond formation reactions are, these minor setbacks may draw caution when synthesizing a complicated molecule whose structural framework cannot be easily accessed by the unity of two fragments. On the other hand, the less familiar C-C bond cleavage reactions have, over time, demonstrated the potential to generate unique structural building blocks that can be used to overcome certain obstacles that other synthetic methods cannot provide. Here, we will be focusing on concerted anionic five-center fragmentation reactions using vinylogous acyl triflates. The generated alkynogenic fragments will then be used in different applications. We will begin by looking at chemoselective “click” reactions. The strained-promoted alkyne is synthesized by a tandem intramolecular nucleophilic addition / fragmentation. The expanded ring will contain a strained cycloalkyne which will later be tethered to a terminal alkyne. The diyne will be used to provide an example of a “dual-click” coupling via SPAAC or CuAAC in either sequential order. Next, we will expand the tandem fragmentation / olefination methodology developed in this work to include dienynes. The dienyne provides the structural backbone needed to produce neopentylene indanes. This methodology is used to design new ibuprofen derivatives that demonstrate rigidity and increase hydrophobicity to modulate the molecular pharmacology of ibuprofen.
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Date Issued: 2017
Identifier: FSU_FALL2017_Ramsubhag_fsu_0071E_14133
Format: Thesis

Title: A Comparative Study between a Single Sorption Constant Model and a Humic Ion Binding Model.
Creator: Pham, Serena Otsuka, Ye, Ming, Shanbhag, Sachin, Huang, Chen, Florida State University, College of Arts and Sciences, Department of Scientific Computing
Abstract/Description: Software packages that model geochemical speciation and complexation are useful for predicting how different materials such as heavy metals and organic matter interact with the environment. The East Fork Poplar Creek (EFPC) in Oak Ridge, Tennessee suffers from extensive mercury pollution as a result of post-WWII activities to develop thermonuclear weapons. A current model that predicts the speciation of mercury and methylmercury species treats dissolved organic matter (DOM) as a single entity...
Show moreSoftware packages that model geochemical speciation and complexation are useful for predicting how different materials such as heavy metals and organic matter interact with the environment. The East Fork Poplar Creek (EFPC) in Oak Ridge, Tennessee suffers from extensive mercury pollution as a result of post-WWII activities to develop thermonuclear weapons. A current model that predicts the speciation of mercury and methylmercury species treats dissolved organic matter (DOM) as a single entity instead of a multidimensional and multisite molecule. The Humic-Ion Binding Model VII is a discrete multisite model implemented by default in the WHAM7 software that represents binding behavior between protons, metal cations, and humic substances. Implementing Model VII into the current EFPC model using the PHREEQC speciation program can predict site interactions of organic matter with mercury and methylmercury. Adding surface complexation to the model shows a substantial increase in the amount of methylmercury bound to DOM compared to the original model. Thus, when appropriate, employing a surface complexation model in geochemical simulations should be considered.
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Date Issued: 2017
Identifier: FSU_FALL2017_Pham_fsu_0071N_14265
Format: Thesis

Title: Making Material Simulation Faster: Coarse Graining, Bridging and Bootstrapping.
Creator: Crysup, Benjamin Rosser, Shanbhag, Sachin, Rikvold, Per Arne, Huang, Chen, Mendoza-Cortes, Jose L., Slice, Dennis E., Florida State University, College of Arts and Sciences,...
Show moreCrysup, Benjamin Rosser, Shanbhag, Sachin, Rikvold, Per Arne, Huang, Chen, Mendoza-Cortes, Jose L., Slice, Dennis E., Florida State University, College of Arts and Sciences, Department of Scientific Computing
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Abstract/Description: Nanoparticles with a solid, inorganic core surrounded by long chain organic ligands have many useful properties and applications. A feature of these materials is that their properties can be tuned to an application: this makes preliminary simulations appealing (to cut down on the possibility space before going into the lab). However, from a simulation perspective, nanoparticles are big and expensive to simulate at the atomic level. There exist a collection of methods to take gross structural...
Show moreNanoparticles with a solid, inorganic core surrounded by long chain organic ligands have many useful properties and applications. A feature of these materials is that their properties can be tuned to an application: this makes preliminary simulations appealing (to cut down on the possibility space before going into the lab). However, from a simulation perspective, nanoparticles are big and expensive to simulate at the atomic level. There exist a collection of methods to take gross structural information and produce a potential fit for simulations at the molecular level. In this work, five such methods (and a few alterations to those methods) were performed on a series of increasingly large molecules to see how they perform at the most aggressive level of coarse graining. The methods were compared based on how well they reproduced structural information about the molecules, and on how much they sped up the dynamics of those systems. In order to make meaningful comparisons between these results, the uncertainty in the results needs to be known. Since large simulations are involved, running multiple simulations is expensive. However, Shanbhag (Shanbhag, 2013) recently proposed a method to obtain the uncertainty in diffusion coefficients obtained from a molecular dynamics simulation (via bootstrapping the atomic trajectories to generate estimates). This method was originally tested only on a simple system, so its validity on more complicated systems needed to be verified. This work tested the validity of this method by running two hundred Lennard-Jones simulations, performing bootstrapping on each, and finding the percentage of bootstrap results that failed to capture the overall mean. This was repeated under different conditions and potentials to determine exactly when and how poorly this method fails. After running the bootstrapping comparisons, it was found that simulations start out with a certain level of underestimation: the exact amount depends on how strongly the particles are interacting. If using unweighted least squares regression on the mean squared displacement, the amount of underestimation approaches a minimum once the simulation has run long enough for the particles to traverse the simulation box. Other methods that put emphasis on short time data do not recover gracefully from the initial effects of correlation. Armed with the ability to get a measure of the uncertainty, the effects of coarse graining were studied. It was found that Inverse Boltzmann best reproduced structural information, at the cost of added computation. Of the computationally cheap methods, Hypernetted chain tended to perform the best for reproducing structural information, while the potential of mean force and force averaging were typically among the worst. When it comes to transferability, for the pure methods force averaging was fairly transferable, Hypernetted chain less so, with Inverse Boltzmann suffering from overfitting (though this problem is improved by calculating a bridge function). While it was expected that coarse graining would speed up dynamics, it was hoped the speedup would be consistent: it was not.
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Date Issued: 2017
Identifier: FSU_FALL2017_Crysup_fsu_0071E_14203
Format: Thesis

Title: The Effects of Military Service Experience on Psychiatric Symptoms among U.S. Firefighters.
Creator: Gai, Anna R., Joiner, Thomas, Ganley, Colleen M., Franklin, Joseph, Florida State University, College of Arts and Sciences, Department of Psychology
Abstract/Description: Individuals employed in first responder professions are at risk for the development of psychiatric symptoms. Two of these professions, firefighting and military service, demonstrate a strong overlap of employees. Prior research has demonstrated increased prevalence rates of psychiatric symptoms, including suicide-related behaviors among firefighters. Subpopulations within this occupation provide an opportunity to inform tailored prevention and intervention tactics. One such subpopulation are...
Show moreIndividuals employed in first responder professions are at risk for the development of psychiatric symptoms. Two of these professions, firefighting and military service, demonstrate a strong overlap of employees. Prior research has demonstrated increased prevalence rates of psychiatric symptoms, including suicide-related behaviors among firefighters. Subpopulations within this occupation provide an opportunity to inform tailored prevention and intervention tactics. One such subpopulation are firefighters with military service history (concurrent and prior). The current study looks to investigate psychiatric symptom differences between firefighters with and without military service history. We hypothesized an additive effect of military service, such that firefighters with a history of military service will be at increased risk for various psychiatric symptoms compared to their civilian-only counterparts. In addition, potential theoretically-based explanatory constructs will be used to investigate mechanisms of significant relationships between military service and psychiatric outcomes. Results did not support an additive effect of military service history within the firefighting profession, as firefighters with military service history were not more likely to endorse various psychiatric symptoms. Military service history was found to be significantly related to career NSSI, such that firefighters with a history of military service were 2.52 times more likely to report a career history of NSSI. Emotion dysregulation did not explain this relationship. Further investigation into the type of military service history suggests firefighters who are also reservists in the armed forces are at particular risk for suicide-related behaviors. Compared to civilian-only firefighters, firefighters with a history of active duty service and national guard service also demonstrated increased risk for suicide-related behaviors. The present study’s results indicate the type of military service, rather than military service in general, is particularly relevant for suicide-related behaviors within a firefighter population. Future directions for further investigation into this unique population are discussed.
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Date Issued: 2017
Identifier: FSU_FALL2017_Gai_fsu_0071N_14210
Format: Thesis

Title: Assessing the Clinical Utility of Non-Invasive Brain Stimulation in the Treatment of Anxious Arousal and Sensory Hypersensitivity: A Targeted Transcranial Alternating Current Stimulation Study.
Creator: Clancy, Kevin J., Li, Wen, Sachs-Ericsson, Natalie J., Eckel, Lisa A., Florida State University, College of Arts and Sciences, Department of Psychology
Abstract/Description: The ability of transcranial alternating current stimulation (tACS) to augment underlying rhythmic fluctuations of neuronal activity provides meaningful implications in the treatment of neuropsychiatric disorders characterized by aberrations in neural oscillations. However, in evaluating its clinical utility, evidence is lacking for the efficacy of tACS to induce long-term (> 24 hours) plastic changes that translate to lasting behavioral outcomes. Here, we repeatedly administered alpha...
Show moreThe ability of transcranial alternating current stimulation (tACS) to augment underlying rhythmic fluctuations of neuronal activity provides meaningful implications in the treatment of neuropsychiatric disorders characterized by aberrations in neural oscillations. However, in evaluating its clinical utility, evidence is lacking for the efficacy of tACS to induce long-term (> 24 hours) plastic changes that translate to lasting behavioral outcomes. Here, we repeatedly administered alpha-frequency tACS across 4 consecutive days in 38 healthy adults to evaluate lasting changes in local alpha power and directed connectivity as well as clinically-relevant indices of anxious arousal and affective sensory processing. Replicating previous findings, participants who received active stimulation (vs. a sham control group) demonstrated transient increases in resting occipito-parietal alpha power that lasted 30 minutes post-stimulation, reflecting acute entrainment to the exogenous electrical stimulation. However, these effects were short-term, returning to baseline levels 24 hours after stimulation. Conversely, long-term increases in intrinsic posteriorfrontal alpha-frequency connectivity emerged and persisted across all 4 days, reflecting plastic-changes in directed cortico-cortical networks. These lasting connectivity changes were paralleled by sustained decreases in anxious arousal and increases in perceived pleasantness of auditory stimuli. These findings suggest that while local oscillatory activity may be constrained by a self-sustaining thalamo-cortical loop that restores cortical oscillations to baseline, long-range oscillatory connectivity may strengthen over time through plastic synaptic changes in intrinsic cortico-cortical networks. The lasting augmentation of this inter-areal oscillatory network via tACS provides meaningful implications in an array of affective and cognitive processes that are orchestrated through the integrity of these global networks. This provides novel extensions of tACS applications, shifting neuromodulatory targets from local oscillations to global oscillatory networks to progress the clinical utility of this technology.
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Date Issued: 2017
Identifier: FSU_FALL2017_Clancy_fsu_0071N_14146
Format: Thesis

Title: Low-Rank Riemannian Optimization Approach to the Role Extraction Problem.
Creator: Marchand, Melissa Sue, Gallivan, Kyle A., Dooren, Paul van, Erlebacher, Gordon, Sussman, Mark, Florida State University, College of Arts and Sciences, Department of Mathematics
Abstract/Description: This dissertation uses Riemannian optimization theory to increase our understanding of the role extraction problem and algorithms. Recent ideas of using the low-rank projection of the neighborhood pattern similarity measure and our theoretical analysis of the relationship between the rank of the similarity measure and the number of roles in the graph motivates our proposal to use Riemannian optimization to compute a low-rank approximation of the similarity measure. We propose two indirect...
Show moreThis dissertation uses Riemannian optimization theory to increase our understanding of the role extraction problem and algorithms. Recent ideas of using the low-rank projection of the neighborhood pattern similarity measure and our theoretical analysis of the relationship between the rank of the similarity measure and the number of roles in the graph motivates our proposal to use Riemannian optimization to compute a low-rank approximation of the similarity measure. We propose two indirect approaches to use to solve the role extraction problem. The first uses the standard two-phase process. For the first phase, we propose using Riemannian optimization to compute a low-rank approximation of the similarity of the graph, and for the second phase using k-means clustering on the low-rank factor of the similarity matrix to extract the role partition of the graph. This approach is designed to be efficient in time and space complexity while still being able to extract good quality role partitions. We use basic experiments and applications to illustrate the time, robustness, and quality of our two-phase indirect role extraction approach. The second indirect approach we propose combines the two phases of our first approach into a one-phase approach that iteratively approximates the low-rank similarity matrix, extracts the role partition of the graph, and updates the rank of the similarity matrix. We show that the use of Riemannian rank-adaptive techniques when computing the low-rank similarity matrix improves robustness of the clustering algorithm.
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Date Issued: 2017
Identifier: FSU_FALL2017_Marchand_fsu_0071E_14046
Format: Thesis

Title: The Psychometric Properties of the Barkley Adult ADHD Rating Scale—IV (BAARS-IV) in a College Sample.
Creator: Lynch, Rebecca, Kistner, Janet, Paek, Insu, Hart, Sara, Kofler, Michael J., Schatschneider, Christopher, Florida State University, College of Arts and Sciences, Department of...
Show moreLynch, Rebecca, Kistner, Janet, Paek, Insu, Hart, Sara, Kofler, Michael J., Schatschneider, Christopher, Florida State University, College of Arts and Sciences, Department of Psychology
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Abstract/Description: Attention-Deficit/Hyperactivity Disorder (ADHD) is a chronic disorder associated with long-term impairment across multiple life domains, including academic, occupational, social, and psychological (Barkley, Murphy, & Kwasnik, 1996; Harpin, 2005; Wilens, Biederman, & Spencer, 2002). Increasing numbers of college students are presenting to health centers and counseling programs with complaints of inattention, distractibility, and restlessness, underscoring the critical need for reliable and...
Show moreAttention-Deficit/Hyperactivity Disorder (ADHD) is a chronic disorder associated with long-term impairment across multiple life domains, including academic, occupational, social, and psychological (Barkley, Murphy, & Kwasnik, 1996; Harpin, 2005; Wilens, Biederman, & Spencer, 2002). Increasing numbers of college students are presenting to health centers and counseling programs with complaints of inattention, distractibility, and restlessness, underscoring the critical need for reliable and valid methods for evaluating ADHD in this age group (e.g., U.S. Government Accountability Office [GAO], 2009). There is a growing body of research suggesting that the Barkley Adult ADHD Rating Scale—IV (BAARS-IV; Barkley, 2011) is a reliable tool for assessing ADHD in adults (e.g., Becker, Marshall, & McBurnett, 2014), yet there are a number of limitations and omissions in existing data. The current study investigated the psychometric properties of the BAARS-IV in a clinic-referred sample of 607 college students between the ages of 18 and 25. First, the factor structure of ADHD was examined by comparing traditional two-factor and three-factor models of ADHD with bifactor models of ADHD using confirmatory factor analyses (CFA). The correlated three-factor model consisting of separate dimensions of inattention, hyperactivity, and impulsivity was considered the best representation of the ADHD constructs for this sample. Next, a multidimensional graded response model (GRM) based on item response theory (IRT) was applied to the data. The results of the GRM indicated that most items of the BAARS-IV showed adequate discrimination of their respective latent traits (i.e., Inattention, Hyperactivity, and Impulsivity) and functioned best when measuring participants with average levels of the latent traits. Of the 18 items, only seven items measure sub-clinical levels of their respective latent trait; however, two of these items provided relatively less information. The remaining five items (one hyperactivity and four impulsivity) had good discrimination and difficulty parameters, providing useful information at sub-clinical levels of the latent traits. The final aim of this study was to examine the items for potential differential item functioning (DIF) by gender and to estimate the size and impacts of detected DIF. The results revealed significant DIF for two inattention items, two hyperactivity items, and one impulsivity item. The findings from the current study suggest that some items of the BAARS-IV may have more clinical utility than the others in the assessment of ADHD in college students.
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Date Issued: 2017
Identifier: FSU_FALL2017_Lynch_fsu_0071E_14070
Format: Thesis

Title: Mathematical Modeling of Biofilms with Applications.
Creator: Li, Jian, Cogan, Nicholas G., Chicken, Eric, Gallivan, Kyle A., Hurdal, Monica K., Florida State University, College of Arts and Sciences, Department of Mathematics
Abstract/Description: Biofilms are thin layers of microorganisms in which cells adhere to each other and stick to a surface. They are resistant to antibiotics and disinfectants due to the protection from extracellular polymeric substance (EPS), which is a gel like self-produced matrix, consists of polysaccharide, proteins and nucleic acids. Biofilms play significant roles in many applications. In this document, we provide analysis about effects and influences of biofilms in microfiltration and dental plaque...
Show moreBiofilms are thin layers of microorganisms in which cells adhere to each other and stick to a surface. They are resistant to antibiotics and disinfectants due to the protection from extracellular polymeric substance (EPS), which is a gel like self-produced matrix, consists of polysaccharide, proteins and nucleic acids. Biofilms play significant roles in many applications. In this document, we provide analysis about effects and influences of biofilms in microfiltration and dental plaque removing process. Differential equations are used for modelling the microfiltration process and the optimal control method is applied to analyze the efficiency of the filtration. The multiphase fluid system is introduced to describe the dental plaque removing process and results are obtained by numerical schemes.
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Date Issued: 2017
Identifier: FSU_FALL2017_Li_fsu_0071E_13839
Format: Thesis

Title: Bayesian Modeling and Variable Selection for Complex Data.
Creator: Li, Hanning, Pati, Debdeep, Huffer, Fred W. (Fred William), Kercheval, Alec N., Sinha, Debajyoti, Bradley, Jonathan R., Florida State University, College of Arts and Sciences,...
Show moreLi, Hanning, Pati, Debdeep, Huffer, Fred W. (Fred William), Kercheval, Alec N., Sinha, Debajyoti, Bradley, Jonathan R., Florida State University, College of Arts and Sciences, Department of Statistics
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Abstract/Description: As we routinely encounter high-throughput datasets in complex biological and environment research, developing novel models and methods for variable selection has received widespread attention. In this dissertation, we addressed a few key challenges in Bayesian modeling and variable selection for high-dimensional data with complex spatial structures. a) Most Bayesian variable selection methods are restricted to mixture priors having separate components for characterizing the signal and the...
Show moreAs we routinely encounter high-throughput datasets in complex biological and environment research, developing novel models and methods for variable selection has received widespread attention. In this dissertation, we addressed a few key challenges in Bayesian modeling and variable selection for high-dimensional data with complex spatial structures. a) Most Bayesian variable selection methods are restricted to mixture priors having separate components for characterizing the signal and the noise. However, such priors encounter computational issues in high dimensions. This has motivated continuous shrinkage priors, resembling the two-component priors facilitating computation and interpretability. While such priors are widely used for estimating high-dimensional sparse vectors, selecting a subset of variables remains a daunting task. b) Spatial/spatial-temporal data sets with complex structures are nowadays commonly encountered in various scientific research fields ranging from atmospheric sciences, forestry, environmental science, biological science, and social science. Selecting important spatial variables that have significant influences on occurrences of events is undoubtedly necessary and essential for providing insights to researchers. Self-excitation, which is a feature that occurrence of an event increases the likelihood of more occurrences of the same type of events nearby in time and space, can be found in many natural/social events. Research on modeling data with self-excitation feature has increasingly drawn interests recently. However, existing literature on self-exciting models with inclusion of high-dimensional spatial covariates is still underdeveloped. c) Gaussian Process is among the most powerful model frames for spatial data. Its major bottleneck is the computational complexity which stems from inversion of dense matrices associated with a Gaussian process covariance. Hierarchical divide-conquer Gaussian Process models have been investigated for ultra large data sets. However, computation associated with scaling the distributing computing algorithm to handle a large number of sub-groups poses a serious bottleneck. In chapter 2 of this dissertation, we propose a general approach for variable selection with shrinkage priors. The presence of very few tuning parameters makes our method attractive in comparison to ad hoc thresholding approaches. The applicability of the approach is not limited to continuous shrinkage priors, but can be used along with any shrinkage prior. Theoretical properties for near-collinear design matrices are investigated and the method is shown to have good performance in a wide range of synthetic data examples and in a real data example on selecting genes affecting survival due to lymphoma. In Chapter 3 of this dissertation, we propose a new self-exciting model that allows the inclusion of spatial covariates. We develop algorithms which are effective in obtaining accurate estimation and variable selection results in a variety of synthetic data examples. Our proposed model is applied on Chicago crime data where the influence of various spatial features is investigated. In Chapter 4, we focus on a hierarchical Gaussian Process regression model for ultra-high dimensional spatial datasets. By evaluating the latent Gaussian process on a regular grid, we propose an efficient computational algorithm through circulant embedding. The latent Gaussian process borrows information across multiple sub-groups, thereby obtaining a more accurate prediction. The hierarchical model and our proposed algorithm are studied through simulation examples.
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Date Issued: 2017
Identifier: FSU_FALL2017_Li_fsu_0071E_14159
Format: Thesis

Title: Nationalism, Modernization and the "Woman Question" in the Late Ottoman Empire and the Early Turkish Republic from the Perspective of the "Ideal/New Turkish Women".
Creator: Sonmez Poyraz, Sebahat, Garretson, Peter P., Johnson, David F. (David Frame), Hanley, Will, Dupuigrenet Desroussilles, François, Florida State University, College of Arts and...
Show moreSonmez Poyraz, Sebahat, Garretson, Peter P., Johnson, David F. (David Frame), Hanley, Will, Dupuigrenet Desroussilles, François, Florida State University, College of Arts and Sciences, Program in Interdisciplinary Humanities
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Abstract/Description: The purpose of this dissertation is to explore the complex and multidimensional relationship of women to the idea of nations and nationalism. In particular, it seeks answers to the following questions: What did nationalism mean to women? How did they imagine the nation? How did they respond to the gendered nationalist discourses? How did they exercise their agency as social actors in the nation building project? With an inquiry of such questions, this study challenges the perception of the ...
Show moreThe purpose of this dissertation is to explore the complex and multidimensional relationship of women to the idea of nations and nationalism. In particular, it seeks answers to the following questions: What did nationalism mean to women? How did they imagine the nation? How did they respond to the gendered nationalist discourses? How did they exercise their agency as social actors in the nation building project? With an inquiry of such questions, this study challenges the perception of the “woman question” as “a struggle in which male protagonists engaged each other while women remained surprisingly passive onlookers.” This study rather explores the dialectical relationship between woman-as-objects, who have been discussed and portrayed as a static, homogenous form within nationalist discourses, and woman-as-subjects who actively participated in constructing and/or contesting nationalist discourses while tracing the continuities and discontinues in nationalist discourse. In other words, this study lets female intellectuals speak in their own terms and in their historical contexts. In order to do so, this study concentrates on two pioneer female intellectuals who were actively involved in constructing national identity in the late Ottoman Empire and the early Turkish Republic: Halide Edib [Adıvar] (1884-1964), a novelist, an activist, and an ardent nationalist who also took part in the Turkish War of Independence (1919-1923), and Ayşe Afet [İnan] (1908-1985), one of the adopted daughters of Mustafa Kemal Atatürk, the first female historian of the Turkish Republic, and the ideologue of Kemalist master narrative.
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Date Issued: 2017
Identifier: FSU_FALL2017_SonmezPoyraz_fsu_0071E_13846
Format: Thesis

Title: Third Order A-Hypergeometric Functions.
Creator: Xu, Wen, Hoeij, Mark van, Reina, Laura, Agashe, Amod S. (Amod Sadanand), Aldrovandi, Ettore, Aluffi, Paolo, Florida State University, College of Arts and Sciences, Department of...
Show moreXu, Wen, Hoeij, Mark van, Reina, Laura, Agashe, Amod S. (Amod Sadanand), Aldrovandi, Ettore, Aluffi, Paolo, Florida State University, College of Arts and Sciences, Department of Mathematics
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Abstract/Description: To solve globally bounded order $3$ linear differential equations with rational function coefficients, this thesis introduces a partial $_3F_2$-solver (Section~\ref{3F2 type solution}) and $F_1$-solver (Chapter~\ref{F1 solver}), where $_3F_2$ is the hypergeometric function $_3F_2(a_1,a_2,a_3;b_1,b_2\,|\,x)$ and $F_1$ is the Appell's $F_1(a,b_1,b_2,c\,|\,x,y).$ To investigate the relations among order $3$ multivariate hypergeometric functions, this thesis presents two multivariate tools:...
Show moreTo solve globally bounded order $3$ linear differential equations with rational function coefficients, this thesis introduces a partial $_3F_2$-solver (Section~\ref{3F2 type solution}) and $F_1$-solver (Chapter~\ref{F1 solver}), where $_3F_2$ is the hypergeometric function $_3F_2(a_1,a_2,a_3;b_1,b_2\,|\,x)$ and $F_1$ is the Appell's $F_1(a,b_1,b_2,c\,|\,x,y).$ To investigate the relations among order $3$ multivariate hypergeometric functions, this thesis presents two multivariate tools: compute homomorphisms (Algorithm~\ref{hom}) of two $D$-modules, where $D$ is a multivariate differential ring, and compute projective homomorphisms (Algorithm~\ref{algo ProjHom}) using the tensor product module and Algorithm~\ref{hom}. As an application, all irreducible order $2$ subsystems from reducible order $3$ systems turn out to come from Gauss hypergeometric function $_2F_1(a,b;c\,|\,x)$ (Chapter~\ref{chapter applications}).
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Date Issued: 2017
Identifier: FSU_FALL2017_XU_fsu_0071E_14234
Format: Thesis

Title: Fate of the Mesophotic Coral Ecosystem (MCE) in the Northeastern Gulf of Mexico after the Deepwater Horizon Incident: Impacts, Restoration, Conservation, and Hazards.
Creator: Silva-Aguilera, Mauricio G., MacDonald, Ian R. (Ian Rosman), Wulff, Janie L., Huettel, Markus, Baco-Taylor, Amy R. (Amy Rose), Fuentes, Mariana, Florida State University,...
Show moreSilva-Aguilera, Mauricio G., MacDonald, Ian R. (Ian Rosman), Wulff, Janie L., Huettel, Markus, Baco-Taylor, Amy R. (Amy Rose), Fuentes, Mariana, Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
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Abstract/Description: The Gulf of Mexico, one of the most geomorphologically complex oceanic basin, is also one of the most prolific hydrocarbon reserves in the world. It hosts a varied range of marine communities from shallow reefs and estuarine communities in coastal areas, to deep-sea and chemosynthetic communities in greater depths. In some particular areas in water depth between 50 to 120 m are hosted the mesophotic reef ecosystem, also known as the twilight communities, where sunlight is almost extinguished...
Show moreThe Gulf of Mexico, one of the most geomorphologically complex oceanic basin, is also one of the most prolific hydrocarbon reserves in the world. It hosts a varied range of marine communities from shallow reefs and estuarine communities in coastal areas, to deep-sea and chemosynthetic communities in greater depths. In some particular areas in water depth between 50 to 120 m are hosted the mesophotic reef ecosystem, also known as the twilight communities, where sunlight is almost extinguished but still enough to support some photosynthesis. Mesophotic ecosystems are mainly characterized by the presence of both light dependent and independent corals, which are the bioengineering support from a vast variety of invertebrate and vertebrate that compound the mesophotic coral ecosystem. One of these mesophotic coral ecosystem, the Pinnacle Reef Trend, was under the influence of floating oil after the Deepwater Horizon incident released more than 4.1 million barrels of crude oil and 500 T of gas to the environment. Visible injuries in over 400 octocoral and antipatharian colonies were quantified in the aftermath of the DWH oil discharge. Observations were made in September 2011 at water depths of about 65 to 75 m in the Pinnacle Reefs area offshore of Mississippi and Alabama, Gulf of Mexico, using a digital macro camera deployed from an ROV to examine the coral populations of two principal sites: Alabama Alps Reef (AAR) and Roughtongue Reef (RTR). Observed taxa (identifications provisional), listed in order of injury frequency, included the following: Hypnogorgia pendula (Duchassaing & Michelotti, 1864), Bebryce spp., Thesea nivea (Deichmann, 1936), Swiftia exserta (Ellis & Solander, 1786), Antipathes atlantica (Gray, 1857), Stichopathes sp., and Ellisella barbadensis (Duchassaing & Michelotti, 1864). The most conspicuous injuries observed were a biofilm, often with a clumped or flake-like appearance, that covered sea-fan branches. Extreme injuries were characterized by bare skeleton, broken, and missing branches. Comparing the 2011 results to previous photo surveys in the same study sites between 1997 and 1999, we found, in 2011, significantly elevated occurrences of injury covering more than 10% of colony area among taxa with growth forms > 0.5 m. We hypothesize that Tropical Storm Bonnie facilitated and accelerated the mixing process of dispersant-treated hydrocarbons into the water column, resulting in harmful contact with coral colonies at mesophotic depths. Analysis of sediment PAH concentrations at AAR and RTR found levels elevated above pre-DWH discharge values, but orders of magnitude below toxicity thresholds established for fauna in estuarine sediments. The PAH concentrations measured in octocoral and echinoderm tissue samples from AAR and RTR were low compared to detection thresholds (10 - 100 ppb). Our findings indicate that coral injuries observed in 2011 resulted from an acute, isolated event rather than ongoing natural processes. Maximum Entropy Modeling was applied to predict the spatial extent of mesophotic azooxanthellate octocorals and antipatharians within the mesophotic area located between Mississippi (Pinnacle Trend Area) and the mid continental shelf and upper slope of Florida, eastern Gulf of Mexico. Habitat prediction models were generated using geo-referenced, coral-presence records obtained by compiling photographic samples with co-located geophysical data, oceanographic variables, and atmospheric variables. Resulting models were used to predict the extent of suitable habitat in the study area. An independent set of presence-records was used to test the model performance. Results (general and by taxon) predict that suitable areas for MCE exceed 400 km2, which occur along carbonate mounds and paleo-shoreline ridges (hard substrata and high ruggedness) with lower amounts of fine sediments and surrounding waters rich in CDOM and upwelling currents (w). The model results significantly exceeded (>0.5) random output and predicted that ruggedness and CDOM are the most important variables associated with coral habitat. Areas of hard substrate within the study area that were not identified as coral habitat by the model suggest that mesophotic sea fans and sea whips depend as much on the chemical and physical conditions (e.g. currents that transport oxygen and food) as on hard substrata for settlement. Finally, three submarine channels that incise into the continental slope in Northeastern Gulf of Mexico have been identified and described. The slope-source channels, seemingly formed after a mass wasting events, are 65 km long and 2.5 km width on average. They show a transition of their transversal profile from V-shape in the head to U-shape in the toe, high sinuosity in the upper ¾ of the channel, showing accumulation of sediments in the turn-sections of the channels, and accumulation of sediment on the walls due to collapsing of unconsolidated sediments. Sedimentary facies obtained by sediment cores show the evidence of disturbed interval of sedimentation and erosion, with erratic periods of laminar sedimentation, erosion, turbidities, disturbed by coarse fractions of sediment. C14 dating of sediments cores from the inside of the channel suggest that hydrodynamic erosion is continuously occurring inside the channel, exposing older sediments to the surface. However, we do not discard the possibility that mass wasting processes are still occurring in the area. The presence of coarse sediment fractions typically found in the continental shelf, beside the occurrence of turbidite homogenous fractions demonstrate that sediment wasting from the upper slope could be still occur. This could lead to a potential disaster in the area because of the presence of oil industry structures. Massive turbidity flows and submarine slumps have been described to occur in this area and other places
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Date Issued: 2017
Identifier: FSU_FALL2017_Silva_fsu_0071E_14250
Format: Thesis

Title: Coupling Ocean Currents and Waves with Wind Stress over the Gulf Stream.
Creator: Shi, Qi, Bourassa, Mark Allan, Yuan, Xin, Dewar, William K., Chagnon, Jeffery M., Holmes, Christopher D., Florida State University, College of Arts and Sciences, Department of...
Show moreShi, Qi, Bourassa, Mark Allan, Yuan, Xin, Dewar, William K., Chagnon, Jeffery M., Holmes, Christopher D., Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
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Abstract/Description: The exchange of momentum, heat, moisture, and gas across the air-sea interface plays a crucial role in atmospheric and oceanic circulations on variety of spatial and temporal scales. That is why improved understanding and realistic simulations of air-sea flux are critical to advancing oceanic and atmospheric prediction capabilities. This study provides the first detailed analysis of oceanic and atmospheric responses to the current-stress, wave-stress, and wave-current-stress interaction at...
Show moreThe exchange of momentum, heat, moisture, and gas across the air-sea interface plays a crucial role in atmospheric and oceanic circulations on variety of spatial and temporal scales. That is why improved understanding and realistic simulations of air-sea flux are critical to advancing oceanic and atmospheric prediction capabilities. This study provides the first detailed analysis of oceanic and atmospheric responses to the current-stress, wave-stress, and wave-current-stress interaction at the Gulf Stream using a high-resolution three-way coupled regional modeling system. This modeling system allows for the exchange of data fields between the atmospheric model—Weather Research and Forecasting (WRF), the ocean model—Regional Ocean Modeling System (ROMS), and the wave model—Simulating Waves Nearshore (SWAN) through the Model Coupling Toolkit (MCT). We perform four one-month simulations for October 2012, a time period when the impact of wind and waves is relatively large. The four experiments differ in how wind shear and surface roughness length are calculated in the bulk flux parameterization: 1) The control experiment calculates the surface roughness length by using the surface wind only (no shear from currents). 2) The current experiment interactively takes into account surface currents in the wind shear. 3) The wave experiment explicitly includes the sea-state parameters in calculating the roughness length. 4) The current-wave experiment computes the surface roughness by taking into account the current-induced shear and sea state simultaneously. In general, our results highlight the substantial impact of coupling currents/waves with wind stress on the air-sea flux exchange and ocean upwelling over the Gulf Stream. Two-way coupling of waves and wind stress causes wind stress (30-day averaged) increase up to 12% in 95th percentile of the model domain, and increases greater than 5% are found in 50% of the model domain. For two-way coupling of surface currents and wind stress, both positive and negative changes in wind stress (greater than 5%) are found at the Gulf Stream, with only small changes elsewhere. The pattern of wind stress change in the wave-current-stress coupling experiment is similar to that in the current-stress coupling experiment, with over 15% increase of wind stress at the Gulf Stream. The current impact on wind stress cancels out the wave impact outside of the Gulf Stream in the wave-current-stress experiment. Coupling currents/waves with wind stress also change the wind stress curl, which impacts the response patterns of upwelling and downwelling in the upper ocean. Changes in wind stress and its curl due to coupling processes lead to changes in SST and ocean current in the Gulf Stream. Considerable SST change (in excess of 1 oC) and ocean current change (in excess of 0.2 m/s) are collocated near the SST front region in the shape of warm/cold core eddies in all coupling configurations. We perform a mixed layer heat budget analysis to investigate the physical processes happening in the ocean mixed layer and their contribution to the SST changes. Substantial latent heat flux changes exceeding 20 W/m2 and sensible heat flux changes exceeding 5 W/m2 are found over the Gulf Stream in all coupled configurations. Sensitivity test shows that SST-induced differences of air-sea temperature and humidity are major contributors to the LHF and SEN changes. The coupling processes also change the surface wind convergence, which further impacts precipitation.
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Date Issued: 2017
Identifier: FSU_FALL2017_Shi_fsu_0071E_14148
Format: Thesis

Title: Non-Aqueous Transuranic Coordination Complexes.
Creator: Galley, Shane S., Dobrosavljević, Vladimir, Hanson, Kenneth G., Shatruk, Mykhailo, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Abstract/Description: As of 2014, there is an expected 69,000 metric tons of nuclear waste sitting in storage in the U.S. Little efforts have been made to deal with the radiotoxicity of the spent nuclear fuel (SNF). The problem arises from the complex mixture of the SNF and highly radioactive actinides. Due to the high radioactivity of the minor actinides (Pu-Cm), there is a lack of understanding the fundamental chemistry of the actinides. The focus of this work is to prepare coordination complexes that can be...
Show moreAs of 2014, there is an expected 69,000 metric tons of nuclear waste sitting in storage in the U.S. Little efforts have been made to deal with the radiotoxicity of the spent nuclear fuel (SNF). The problem arises from the complex mixture of the SNF and highly radioactive actinides. Due to the high radioactivity of the minor actinides (Pu-Cm), there is a lack of understanding the fundamental chemistry of the actinides. The focus of this work is to prepare coordination complexes that can be used as probes for elucidating changes in the structure and bonding across the actinides series Most coordination chemistry that has been studied with the actinide series has only utilized ligands stable to oxygen and moisture due to the difficulties of handling the transuranium actinides. The chemistry of non-aqueous ranium has made great progress, while, the non-aqueous chemistry of the transuranic elements is relatively unexplored and offers a wider platform for exploring methods of deducing electronic structure and information about the actinide-ligand bond. Such information can be very useful for discovering trends in the whole series. The beginning chapters focus on simple coordination compounds using soft N and S donor ligands for complexing Am-Cf. Since very little structure data is known for these elements and softer donor ligands have shown to have a preference over trivalent actinides than lanthanides, we focus on these systems to understand the trends in bonding across the 5f series. Chapter 4 focus on a series (U-Cf) of complexes using the redox active ligand 2,4,6,8-tetrakis(tert-butyl)-9-hydroxyphenoxanone (HDOPO) were synthesized in non-aqueous conditions under an inert atmosphere and have been fully characterized by X-ray, optical, magnetic, and computational techniques. Spectroscopic data reveals the An(DOPO)3 complexes of the earlier actinides being the tetravalent state, in contrast to the later actinides, they are in the trivalent state. Furthermore, the Cf(III) complex disrupts the tris-chelate trend due to radiolysis. It is also shown that the ligand undergoes redox transitions to stabilize the higher oxidation states of the earlier actinides. The results will help contribute toward gaining foundational knowledge of structure and bonding in non-aqueous transuranic chemistry as well as give insight into the participation of f-orbitals in bonding. The ending chapters are out of the scope of non-aqueous chemistry but projects that pertain to the nature of the actinide series. As the first focuses on the effects of radiolysis. As we go to the heavier actinides, radiolysis affects the crystallization of our targeted products. In this case, an aged thorium source produces peroxide over time changing the result of the product. Lastly, is an example of driven degeneracy covalency in an americium chromate system. It was thought the later actinides tend to be more ionic, however we are finding small amount of covalent character partakes in the bonding. Collectively, this body of work primary focus is elucidating the structure and bonding of the f-elements through coordination complexes utilizing various techniques.
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Date Issued: 2017
Identifier: FSU_FALL2017_Galley_fsu_0071E_14279
Format: Thesis

Title: Spatial Statistics and Its Applications in Biostatistics and Environmental Statistics.
Creator: Hu, Guanyu, Huffer, Fred W. (Fred William), Paek, Insu, Sinha, Debajyoti, Slate, Elizabeth H., Bradley, Jonathan R., Florida State University, College of Arts and Sciences,...
Show moreHu, Guanyu, Huffer, Fred W. (Fred William), Paek, Insu, Sinha, Debajyoti, Slate, Elizabeth H., Bradley, Jonathan R., Florida State University, College of Arts and Sciences, Department of Statistics
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Abstract/Description: This dissertation presents some topics in spatial statistics and their application in biostatistics and environmental statistics. The field of spatial statistics is an energetic area in statistics. In Chapter 2 and Chapter 3, the goal is to build subregion models under the assumption that the responses or the parameters are spatially correlated. For regression models, considering spatially varying coecients is a reasonable way to build subregion models. There are two different techniques for...
Show moreThis dissertation presents some topics in spatial statistics and their application in biostatistics and environmental statistics. The field of spatial statistics is an energetic area in statistics. In Chapter 2 and Chapter 3, the goal is to build subregion models under the assumption that the responses or the parameters are spatially correlated. For regression models, considering spatially varying coecients is a reasonable way to build subregion models. There are two different techniques for exploring spatially varying coecients. One is geographically weighted regression (Brunsdon et al. 1998). The other is a spatially varying coecients model which assumes a stationary Gaussian process for the regression coecients (Gelfand et al. 2003). Based on the ideas of these two techniques, we introduce techniques for exploring subregion models in survival analysis which is an important area of biostatistics. In Chapter 2, we introduce modied versions of the Kaplan-Meier and Nelson-Aalen estimators which incorporate geographical weighting. We use ideas from counting process theory to obtain these modied estimators, to derive variance estimates, and to develop associated hypothesis tests. In Chapter 3, we introduce a Bayesian parametric accelerated failure time model with spatially varying coefficients. These two techniques can explore subregion models in survival analysis using both nonparametric and parametric approaches. In Chapter 4, we introduce Bayesian parametric covariance regression analysis for a response vector. The proposed method denes a regression model between the covariance matrix of a p-dimensional response vector and auxiliary variables. We propose a constrained Metropolis-Hastings algorithm to get the estimates. Simulation results are presented to show performance of both regression and covariance matrix estimates. Furthermore, we have a more realistic simulation experiment in which our Bayesian approach has better performance than the MLE. Finally, we illustrate the usefulness of our model by applying it to the Google Flu data. In Chapter 5, we give a brief summary of future work.
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Date Issued: 2017
Identifier: FSU_FALL2017_Hu_fsu_0071E_14205
Format: Thesis

Title: The One-and Two-Sample Problem for Data on Hilbert Manifolds with Applications to Shape Analysis.
Creator: Qiu, Mingfei, Patrangenaru, Victor, Liu, Xiuwen, Slate, Elizabeth H., Barbu, Adrian G. (Adrian Gheorghe), Clickner, Robert Paul, Paige, Robert, Florida State University, College...
Show moreQiu, Mingfei, Patrangenaru, Victor, Liu, Xiuwen, Slate, Elizabeth H., Barbu, Adrian G. (Adrian Gheorghe), Clickner, Robert Paul, Paige, Robert, Florida State University, College of Arts and Sciences, Department of Statistics
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Abstract/Description: This dissertation is concerned with high level imaging analysis. In particular, our focus is on extracting the projective shape information or the similarity shape from digital camera images or Magnetic Resonance Imaging(MRI). The approach is statistical without making any assumptions about the distributions of the random object under investigation. The data is organized as points on a Hilbert manifold. In the case of projective shapes of finite dimensional configuration of points, we...
Show moreThis dissertation is concerned with high level imaging analysis. In particular, our focus is on extracting the projective shape information or the similarity shape from digital camera images or Magnetic Resonance Imaging(MRI). The approach is statistical without making any assumptions about the distributions of the random object under investigation. The data is organized as points on a Hilbert manifold. In the case of projective shapes of finite dimensional configuration of points, we consider testing a one-sample null hypothesis, while in the infinite dimensional case, we considered a neighborhood hypothesis testing methods. For 3D scenes, we retrieve the 3D projective shape, and use the Lie group structure of the projective shape space. We test the equality of two extrinsic means, by introducing the mean projective shape change. For 2D MRI of midsections of Corpus Callosum contours, we use an automatic matching technique that is necessary in pursuing a one-sample neighborhood hypothesis testing for the similarity shapes. We conclude that the mean similarity shape of the Corpus Callosum of average individuals is very far from the shape of Albert Einstein's, which may explain his geniality. Another application of our Hilbert manifold methodology is two-sample testing problem for Veronese-Whitney means of projective shapes of 3D contours. Particularly, our data consisting comparing 3D projective shapes of contours of leaves from the same tree species.
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Date Issued: 2015
Identifier: FSU_2015fall_Qiu_fsu_0071E_12922
Format: Thesis

Title: Volume Pulsation of Small Gas Bubbles in the Surface Layer of Coastal Sands Caused by Surface Gravity Waves.
Creator: Russell, Lee, Huettel, Markus, Wulff, Jeanette L., MacDonald, Ian R. (Ian Rosman), Chanton, Jeffrey P., Dewar, William, Florida State University, College of Arts and Sciences,...
Show moreRussell, Lee, Huettel, Markus, Wulff, Jeanette L., MacDonald, Ian R. (Ian Rosman), Chanton, Jeffrey P., Dewar, William, Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
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Abstract/Description: In the uppermost millimeters of shallow submerged coastal sediments, photosynthesis by microalgae and cyanobacteria during daylight hours can cause oxygen supersaturation of sediment porewater, leading to bubble formation. In shallow water depths, the seabed is affected by the pressure maximum beneath the wave crest and pressure minimum beneath the wave trough. While the photosynthetically-generated gas bubbles persist within the surface layer highly permeable sand sediments, they may be...
Show moreIn the uppermost millimeters of shallow submerged coastal sediments, photosynthesis by microalgae and cyanobacteria during daylight hours can cause oxygen supersaturation of sediment porewater, leading to bubble formation. In shallow water depths, the seabed is affected by the pressure maximum beneath the wave crest and pressure minimum beneath the wave trough. While the photosynthetically-generated gas bubbles persist within the surface layer highly permeable sand sediments, they may be exposed to pressure pulsations caused by tides and passing surface gravity waves, because pressure is not significantly attenuated in the upper few centimeters of permeable sediments. The question arises, whether the tens of thousands of millimeter-size bubbles that are produced on sunny days in each square meter of nearshore sands respond to these pressure oscillations and if so, what consequences these responses may have. The main goals of the research thus were the demonstration of the bubble pulsation within the sediment and the quantification of the pore water flow, associated interfacial solute flux, and sand grain movement caused by the pulsation. The central working hypotheses tested in this research were: 1) Millimeter-size photosynthetic gas bubbles buried in the surface layer of submerged permeable coastal sands respond to passing surface gravity waves by volume changes leading to bubble volume pulsation. 2) This bubble volume pulsation causes pore water flows and thereby exchange across the sediment-water interface and an increase of the net solute flux from the sediment. 3) The bubble volume pulsation causes sand grain movement and thereby local sediment compaction, alteration of sediment surface topography and vertical transport of substances attached to the sand grains. These three working hypotheses were addressed in Thesis chapters 1, 2 and 3, respectively. In-situ video observations with a buried camera showed that the bubbles (1-3 mm diameter) buried in the surface layer ([less than] 10 cm) of nearshore sand respond to passing waves by volume pulsation and allowed estimation of the oscillating volume change of the bubbles visible in the sediment-cross section. These observations revealed bubble volume oscillation with compressions of 7.4% caused by ~1 meter water waves producing a temporary 10 kPa pressure increase. Laboratory measurements in a custom-built pressure tank confirmed the in-situ observations: Bubbles with 1.24 mm to 2.12 mm diameter (1 mm3 to 5 mm3), embedded in transparent Nafion[TM] sand sediment, at 1 m water depth were compressed by 8.7 ± 1.3 % of their volume when exposed to the same pressure increase of 10 kPa as produced by a 1 meter water wave. With an observed abundance of 50,000 bubbles m-2 in sandy Gulf of Mexico sediments, the pulsation of bubbles with 2 mm diameter produced by the passing of thirty 1 m-waves per minute (8.3% compression) could pump 31.3 L m-2 h-1 (or 750 L m-2 d-1) of water across the sediment-water interface. Once it was established that surface layer bubbles pulsate due to pressure oscillations associated with passing surface gravity waves at a rate consistent with Boyle's Law, the effect of pulsating bubbles on pore water movement and grain movement was investigated. Fluorescein dye tracer experiments conducted at the same wave frequency (0.5 Hz) and wave height (75-100 cm) showed a linear correlation (R2 = 0.99) between interstitial gas bubble volume and interfacial tracer flux. The pulsation of 200 five-microliter bubbles embedded in the top 2 cm of a 10 cm (L) x 10 (W) x 45 cm (D) wet sediment core (bubbles occupied 0.5% of the volume of the 2 cm thick upper sediment layer) increased interfacial flux initially (first 7 min) by a factor of 17 compared to the control experiment, where tracer transport was limited to molecular diffusion and some tracer release caused by the setup of the experiment. The increase of flux caused by the bubbles is produced by the oscillating water flow across the sediment-water interface that pushes pore water out of the sediment that then is mixed into the overlying water through dispersion and turbulence. At an observed in-situ abundance of 50,000 bubbles m-2, bubble pulsation can be estimated to increase solute transport across the highly-active sediment-water interface by a factor of 30 when compared to molecular diffusion. Over time, the intermittent movement of sand grains driven by the pulsating bubbles resulted in a tighter packing of the sand, with a decrease in pore space, and an overall downward migration of grains above and around the buried bubbles. Particle Image Velocimetry showed that the cross-sectional area around the bubble, in which grains were moved by its pulsation, decayed exponentially over time. In the natural environment, decompaction of the sediment surface layer by bioturbation and sediment resuspension by bottom currents counteracts the compaction caused by the bubble pulsation, resulting in a continuous cycle of compaction/de-compaction that keeps a substantial fraction of the grains in the surface layer moving. With observed in-situ abundances of 50,000 bubbles m-2 and an average bubble volume of 5 mm3, approximately 5,000 cm3 m-2 or 50% of the grains in the top 1 cm of the sand bed are moved by the pulsation of buried gas bubbles every hour. The movement and net downward migration of surface layer sand grains towards pulsating bubbles has broad implications for sediment physical characteristics, sediment geochemistry and pore water flow.
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Date Issued: 2015
Identifier: FSU_2015fall_Russell_fsu_0071E_12931
Format: Thesis

Title: Structural Evolution of Ad Damm Shear Zone, Western Saudi Arabian Margin and Its Relation to Red Sea Rift System.
Creator: Samkari, Abdulaziz, Farris, David W., Tull, James F., Odom, A. L. (A. Leroy), Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric...
Show moreSamkari, Abdulaziz, Farris, David W., Tull, James F., Odom, A. L. (A. Leroy), Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
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Abstract/Description: This project seeks to determine how the opening of the Red Sea rift was influenced by pre-existing tectonic features and to place constraints on the structural evolution of the western Saudi Arabia margin. In detail, we investigate whether or not the Ad Damm Shear Zone (ADSZ) was solely a Neoproterozoic structure or if it has been reactivated during the Cenozoic. The Ad Damm shear zone is a major mylonitic right-lateral structure that bounds the Jeddah terrane to the north from the Asir...
Show moreThis project seeks to determine how the opening of the Red Sea rift was influenced by pre-existing tectonic features and to place constraints on the structural evolution of the western Saudi Arabia margin. In detail, we investigate whether or not the Ad Damm Shear Zone (ADSZ) was solely a Neoproterozoic structure or if it has been reactivated during the Cenozoic. The Ad Damm shear zone is a major mylonitic right-lateral structure that bounds the Jeddah terrane to the north from the Asir terrane to the south. South of the ADSZ, the Red Sea rift exhibits well-developed linear magnetic anomalies, but north of it, they are not present. On land, the ADSZ bounds a large topographic escarpment perpendicular to the rift margin, with higher elevations to the south. In addition, recent studies show active seismicity within the Jeddah terrane bounded by the ADSZ. These observations collectively suggest some type of tectonic reactivation. Four techniques were used to test this hypothesis: field mapping, satellite image processing (ASTER, SPOT-5), microstructural studies, and whole rock geochemistry. Field observations show various meta-plutonic and volcanic rocks that range in age from 800-540 Ma. North of the ADSZ, Jeddah terrane is characterized by heterogeneous magmatism with extensive meta-basalt intruded by silicic plutons of varying size. South of the ADSZ, Asir terrane is characterized by larger-scale granitic batholiths. In addition, a large synform, likely a km-scale drag fold, is present along the northern edge of the ADSZ. Felsic dikes intrude a package of metabasalt and are folded in the synform. A younger generation of Eocene to Miocene basaltic dikes cut the mylonitic shear zone at a high angle. Petrographic analyses of mylonitic rocks indicate dynamic recrystallization and grain size reduction suggesting high-temperature recrystallization. Field observations also found a lack of low temperature fault zone rocks (e.g. gouge) except for isolated brittle slickensides. Spider diagram of Jeddah, Asir terranes, and ADSZ rocks are characterized by arc-related signature, which related to the amalgamation of Jeddah and asir terranes and defined ADSZ as Neoproterozoic structure. In contrast, Eocen-Miocene Basaltic dikes and southern basaltic flow are represented by rift-related signature, which is associated with development of Red Sea rift system. However, differences in the crustal characteristics of Asir and Jeddah terranes still influence the ongoing tectonic evolution of the Red Sea rift.
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Date Issued: 2015
Identifier: FSU_2015fall_SAMKARI_fsu_0071N_12958
Format: Thesis

Title: Cell Adhesion and Motility on Biocompatible Polyelectrolyte Multilayers.
Creator: Martinez, Jessica Susanne, Keller, Thomas C. S., Schlenoff, Joseph B., Keller, Laura R., Ma, Teng, Lenhert, Steven, Florida State University, College of Arts and Sciences,...
Show moreMartinez, Jessica Susanne, Keller, Thomas C. S., Schlenoff, Joseph B., Keller, Laura R., Ma, Teng, Lenhert, Steven, Florida State University, College of Arts and Sciences, Department of Biological Science
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Abstract/Description: To improve the design of prostheses surfaces, our research group investigates how biocompatible polyelectrolyte multilayers (PEMUs) can be constructed to serve as coatings for biomedical implants, providing a versatile, inexpensive, and potentially efficient solution to create anti-bacterial, anti-inflammatory, and biologically selective surfaces. More specifically, this dissertation research investigates how individual cells and cell sheets adhere and migrate on PEMUs constructed to have...
Show moreTo improve the design of prostheses surfaces, our research group investigates how biocompatible polyelectrolyte multilayers (PEMUs) can be constructed to serve as coatings for biomedical implants, providing a versatile, inexpensive, and potentially efficient solution to create anti-bacterial, anti-inflammatory, and biologically selective surfaces. More specifically, this dissertation research investigates how individual cells and cell sheets adhere and migrate on PEMUs constructed to have uniform and gradients of modulus and how individual cells and gram negative bacteria, Escherichia coli, adhere to PEMUs constructed to have an anti-adhesive surface chemistry. In this investigation, PAH/PAA PEMUs are shown to be biocompatible compared to the soluble polycation PAH at concentrations above 0.1mM. Soluble PAH concentrations at 1 and 10mM cause irreversible damage to the plasma membrane of smooth muscle, A7r5, and bone, U2OS, cells. Additionally, adhesive and motile responses of cells are dependent on PEMU surface chemistry. Cells on PEMUs terminated with the polycation PAH relocalize their focal adhesions to their cell periphery and are highly motile compared to cells cultured on PAA terminated PEMUs and uncoated glass coverslips. To investigate effects of PEMU modulus on cell adhesion and motility, PEMUs were made with the polyanion PAA (poly(acrylic acid)) modified with a photosensitive 4-(2-Hydroxyethoxy) benzophenone (PAABp) and the polycation PAH (poly(allylamine hydrochloride)). UV irradiating PAH/ PAABp PEMUs forms covalent bonds between PE layers and consequently increases its Young's Elastic Modulus, while retaining innate surface chemistry. Individual cells and cell sheets detect differences in PEMU modulus and respond by varying morphology and behavior. These PAH/PAABp PEMUs modulate the adhesion, spreading, and migration of individual cells, specifically smooth muscle, bone, and fibroblast cells. PAABp containing PEMUs were constructed to have either a shallow (~5MPa mm-1) or a steep (~50MPa mm-1) modulus gradient. Only smooth muscle cells durotax along steep modulus gradients toward increasing modulus and orient toward increasing modulus on shallow modulus gradients. In contrast, bone cells discriminately adhere to the stiffest region of both steep and shallow modulus gradients and fibroblasts show no difference in behavior along any region of the gradients. Epithelial sheets, isolated as primary explants of fish epithelial tissue from the scales of fish Poecilia sphenops (Black Molly) and Carassius auratus (Comet Goldfish), orient toward increasing modulus on steep modulus gradient. Cell sheets collectively durotax near the ~90MPa region of the gradient toward increasing modulus. Surfaces with substantial zwitterionic functionality (possessing a net neutral surface charge due to equal contribution of both positive and negative charges in polymer side groups) have been shown to effectively prevent cell and protein attachment. PEMUs built with PAH (poly(allylamine hydrochloride)) and PAA (poly(acrylic acid)) containing the AEDAPS zwitterionic group 3-(2-(acrylamido)-ethyldimethyl ammonio) propane sulfonate (PAH/PAA-co-AEDAPS PEMUs) and a new benzophenone crosslinker to stiffen the thin film were shown to prevent rat aortic smooth muscle (A7r5) and mouse fibroblast (3T3) cells attachment, but failed to prevent irreversible attachment of biofilm-forming gram-negative bacteria Escherichia coli, strain ATCC-8739. AEDAPS containing PEMUs are hydrophilic and have increased nanoroughness of ~10nm. 'Super soaking' AEDAPS PEMUs incorporates more zwitterions into the PEMU and significantly maximizes the surface presentation of PAA-co-AEDAPS, which promotes early attachment of bacteria, but eventually, causes a gradual decrease in bacteria attachment with increasing incubation time. This investigation provides further insight into the possible application of PEMUs as bioselective thin film coatings, which may have potential for use in biomedical applications.
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Date Issued: 2015
Identifier: FSU_2015fall_Martinez_fsu_0071E_12894
Format: Thesis

Title: Game Based Visual-to-Auditory Sensory Substitution Training.
Creator: Marshall, Justin B., Tyson, Gary Scott, Erlebacher, Gordon, Liu, Xiuwen, Ackerman, Margareta, Florida State University, College of Arts and Sciences, Department of Computer Science
Abstract/Description: There has been a great deal of research devoted to computer vision related assistive technologies. Unfortunately, this area of research has not produced many usable solutions. The long cane and the guard dog are still far more useful than most of these devices. Through the push for advanced mobile and gaming systems, new low-cost solutions have become available for building innovative and creative assistive technologies. These technologies have been used for sensory substitution projects that...
Show moreThere has been a great deal of research devoted to computer vision related assistive technologies. Unfortunately, this area of research has not produced many usable solutions. The long cane and the guard dog are still far more useful than most of these devices. Through the push for advanced mobile and gaming systems, new low-cost solutions have become available for building innovative and creative assistive technologies. These technologies have been used for sensory substitution projects that attempt to convert vision into either auditory or tactile stimuli. These projects have reported some degree of measurable success. Most of these projects focused on converting either image brightness or depth into auditory signals. This research was devoted to the design and creation of a video game simulator that was capable of performing research and training for these sensory substitution concepts that converts vision into auditory stimuli. The simulator was used to perform direct comparisons between some of the popular sensory substitution techniques as well as exploring new concepts for conversion. This research of 42 participants tested different techniques for image simplification and discovered that using depth-to-tone sensory substitution may be more usable than brightness-to-tone simulation. The study has shown that using 3D game simulators can be used in lieu of building costly prototypes for testing new sensory substitution concepts.
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Date Issued: 2015
Identifier: FSU_2015fall_Marshall_fsu_0071E_12749
Format: Thesis

Title: Coulomb Pseudogaps and Their Role at Metal-Insulator Transitions.
Creator: Mahmoudian, Samiyeh, Dobrosavljević, Vladimir, Dalal, Naresh S., Balicas, Luis, Manousakis, Efstratios, Capstick, Simon, Florida State University, College of Arts and Sciences,...
Show moreMahmoudian, Samiyeh, Dobrosavljević, Vladimir, Dalal, Naresh S., Balicas, Luis, Manousakis, Efstratios, Capstick, Simon, Florida State University, College of Arts and Sciences, Department of Physics
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Abstract/Description: We investigate various fundamental aspects of the metal insulator transition (MIT) by employing several theoretical approaches. Describing the novel features of interacting electronic systems remains one of the principle challenges to theoretical condensed matter physics. Therefore, any effort to provide a deep insight into understanding the nature of MITs opens a new avenue for development of modern technology. First, we present a complete analytical and numerical solution of the Typical...
Show moreWe investigate various fundamental aspects of the metal insulator transition (MIT) by employing several theoretical approaches. Describing the novel features of interacting electronic systems remains one of the principle challenges to theoretical condensed matter physics. Therefore, any effort to provide a deep insight into understanding the nature of MITs opens a new avenue for development of modern technology. First, we present a complete analytical and numerical solution of the Typical Medium Theory (TMT) for the metal-insulator transition. In this theory, we self-consistently calculate the typical amplitude of the electron wave-functions, representing the conceptually simplest order-parameter for the Anderson transition. We classify all possible universality classes for the critical behavior, that can be found within such a mean-field approach. This provides insights into how interaction-induced renormalizations of the disorder potential may produce qualitative modifications of critical behavior. We also formulate a simple description of the leading critical behavior of varies quantities, and then obtain an effective Landau theory for Anderson localization. We also develop an efficient numerical algorithm, "Cluster Typical Medium Theory" (CTMT) to capture both non-local effects and localization in disordered electronic systems. Our formalism utilizes the momentum-resolved typical density of states to characterize the localization transition. We apply this approach to the Anderson model of localization in one and two-dimensions. In one dimension, we find that the critical disorder strength scales inversely with the linear cluster size with a power-law, W[subscript c] ∼ (1/L[subscript c])[superscript 1/v]; whereas in two dimensions, the critical disorder strength decreases logarithmically with the linear cluster size. Our results are in agreement with the one-parameter scaling theory. Furthermore, we show how spatial correlations can also be captured analytically within such a self-consistent theory, by utilizing the standard Landau method of allowing for (slow) spatial fluctuations of the order parameter, and performing an appropriate gradient expansion. Our theoretical results provide insight into recent STM experiments, which were used to visualize the spatially fluctuating electronic wave functions near the metal insulator transition in Ga[subscript 1-x]Mn[subscript x]As.$ We show that, within our theory, all features of the experiment can be accounted for by considering a model of disorder renormalized by long-range Coulomb interactions. This includes the pseudogap formation, the C(R) ∼ 1/R form of the LDOS autocorrelations function, and the ζ ∼ 1/E energy dependence of the correlation length at criticality. In the second part of my Thesis, we show that introducing long-range Coulomb interactions immediately lifts the massive ground state degeneracy induced by geometric frustration for electrons on quarter-filled triangular lattices in the classical limit. Important consequences include the stabilization of a stripe-ordered crystalline (global) ground state, but also the emergence of very many low-lying metastable states with amorphous "stripe-glass" spatial structures. Melting of the stripe order thus leads to a frustrated Coulomb liquid at intermediate temperatures, showing remarkably slow (viscous) dynamics, with very long relaxation times growing in Arrhenius fashion upon cooling, as typical of strong glass formers. On shorter time scales, the system falls out of equilibrium and displays the aging phenomena characteristic of supercooled liquids above the glass transition. Our results show remarkable similarity with the recent observations of charge-glass behavior in ultra-clean triangular organic materials of the θ-(BEDT-TTF)₂ family.
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Date Issued: 2015
Identifier: FSU_2015fall_Mahmoudian_fsu_0071E_12817
Format: Thesis

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