Current Search: Shanbhag, Sachin (x)
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 Title
 Nonmonotonic Dnalengthdependent Mobility In Pluronic Gels.
 Creator

You, Seungyong, Wei, Ling, Shanbhag, Sachin, Van Winkle, David H.
 Abstract/Description

Twodimensional electrophoresis was used to analyze the mobility of DNA fragments in micellar gels of pluronic F127 (EO100PO70EO100) and pluronic P123 (EO20PO70EO20). The 203500 base pair DNA fragments were separated by size first in agarose gels, and then in pluronic gels at room temperature. In agarose gels, the DNA mobility decreases monotonically with increasing DNA length. In pluronic gels, however, the mobility varies nonmonotonically according to fragment lengths that are strongly...
Show moreTwodimensional electrophoresis was used to analyze the mobility of DNA fragments in micellar gels of pluronic F127 (EO100PO70EO100) and pluronic P123 (EO20PO70EO20). The 203500 base pair DNA fragments were separated by size first in agarose gels, and then in pluronic gels at room temperature. In agarose gels, the DNA mobility decreases monotonically with increasing DNA length. In pluronic gels, however, the mobility varies nonmonotonically according to fragment lengths that are strongly correlated with the diameter of the spherical micelles. Brownian dynamics (BD) simulations with shortranged intraDNA hydrodynamic interactions were performed to numerically calculate the lengthdependent mobility in pluronic lattices. The rising and falling trends, as well as the oscillations of mobility, were captured by the coarsegrained BD simulations. Molecular dynamics simulations in pluronic F127, with explicitly modeled micelle coronas, justified that the hydrodynamic interactions mediated by the complex fluid of hydrated poly(ethylene oxide) are a possible reason for the initial rise of mobility with DNA length.
Show less  Date Issued
 20170407
 Identifier
 FSU_libsubv1_wos_000399393400005, 10.1103/PhysRevE.95.042602
 Format
 Citation
 Title
 Solution of the NavierStokes Equations by the Finite Element Method Using Reduced Order Modeling.
 Creator

Forinash, Nick, Peterson, Janet, Plewa, Tomasz, Shanbhag, Sachin, Department of Scientific Computing, Florida State University
 Abstract/Description

Reduced Order Models (ROM) provide a lowdimensional alternative form of a system of differential equations. Such a form permits faster computation of solutions. In this paper, Poisson's Equation in two dimensions, the Heat Equation in one dimension, and a Nonlinear ReactionDiffusion equation in one dimension are solved using the Galerkin formulation of the Finite Element Method (FEM) in conjunction with Newton's Method. Reduced Order Modeling (ROM) by Proper Orthogonal Decomposition (POD)...
Show moreReduced Order Models (ROM) provide a lowdimensional alternative form of a system of differential equations. Such a form permits faster computation of solutions. In this paper, Poisson's Equation in two dimensions, the Heat Equation in one dimension, and a Nonlinear ReactionDiffusion equation in one dimension are solved using the Galerkin formulation of the Finite Element Method (FEM) in conjunction with Newton's Method. Reduced Order Modeling (ROM) by Proper Orthogonal Decomposition (POD) is then used to accelerate the solution of successive linear systems required by Newton's Method. This is done to show the viability of the method on a simple problem. The NavierStokes (NS) Equations are introduced and solved by FEM. A ROM using both POD and clustering by Centroidal Voronoi Tesselation (CVT) are then used to solve the NS equations, and the results are compared with the FEM solution. The specific NS problem we consider has inhomogeneous Dirichlet boundary conditions and the treatment of the boundary conditions is explained. The resulting decrease in computation time required for solving the various equations are compared with ROM methods.
Show less  Date Issued
 2012
 Identifier
 FSU_migr_etd5352
 Format
 Thesis
 Title
 Generalizes Procrustes Surface Analysis: A LandmarkFree Approach to Superimposition and Shape Analysis.
 Creator

Pomidor, Benjamin, Slice, Dennis, Beerli, Peter, Shanbhag, Sachin, Department of Scientific Computing, Florida State University
 Abstract/Description

The tools and techniques used in shape analysis have constantly evolved, but their objective remains fixed: to quantify the differences in shape between two objects in a consistent and meaningful manner. The handmeasurements of calipers and protractors of the past have yielded to laser scanners and landmarkplacement software, but the process still involves transforming an object's physical shape into a concise set of numerical data that can be readily analyzed by mathematical means [Rohlf...
Show moreThe tools and techniques used in shape analysis have constantly evolved, but their objective remains fixed: to quantify the differences in shape between two objects in a consistent and meaningful manner. The handmeasurements of calipers and protractors of the past have yielded to laser scanners and landmarkplacement software, but the process still involves transforming an object's physical shape into a concise set of numerical data that can be readily analyzed by mathematical means [Rohlf 1993]. In this paper, we present a new method to perform this transformation by taking full advantage of today's highpower computers and highresolution scanning technology. This method uses surface scans to calculate a shapedifference metric and perform superimposition rather than relying on carefully (and tediously) placed manual landmarks. This is accomplished by building upon and extending the Iterative Closest Point algorithm. We also examine some new ways this data may be used; we can, for example, calculate an averaged surface directly and visualize pointwise shape information over this surface. Finally, we demonstrate the use of this method on a set of primate skulls and compare the results of the new methodology with traditional geometric morphometric analysis.
Show less  Date Issued
 2013
 Identifier
 FSU_migr_etd8714
 Format
 Thesis
 Title
 Na+ during Dhpg Application Plays a Critical Role in DHPGInduced Inhibition of NMDA ChannelMediated Synaptic Responses in CA1 Neurons.
 Creator

Zhong, Peng, Chen, ChiKai (Kevin), Yu, XianMin, Shanbhag, Sachin, Department of Chemical and Biomedical Engineering, Florida State University
 Abstract/Description

Receptor trafficking such as endocytosis may decrease the number of surface receptors and hence downregulate receptormediated functions. Previous studies showed that dynamic endocytosis of Nmethyldaspartate receptor/channels (NMDARs) inhibits the gating of remaining surface NMDARs characterized by a reduction in channel open duration. Surprisingly, the blockade of Na+ influx prevents the gating downregulation of remaining surface NMDARs induced by NMDAR endocytosis. More importantly, if...
Show moreReceptor trafficking such as endocytosis may decrease the number of surface receptors and hence downregulate receptormediated functions. Previous studies showed that dynamic endocytosis of Nmethyldaspartate receptor/channels (NMDARs) inhibits the gating of remaining surface NMDARs characterized by a reduction in channel open duration. Surprisingly, the blockade of Na+ influx prevents the gating downregulation of remaining surface NMDARs induced by NMDAR endocytosis. More importantly, if this gating downregulation is prevented, NMDA channel endocytosis produces no change in NMDA channelmediated wholecell and synaptic responses. Here, I report that blocking Na+ influx only during (R,S)3,5dihydroxyphenylglycine (DHPG) application, which induces NMDA channel endocytosis, could effectively block the downregulation of NMDA channelmediated excitatory postsynaptic currents (EPSCs) induced by NMDA channel endocytosis in adult CA1 neurons. This finding provided the first evidence confirming that the Na+ influx blockade during DHPG application sufficiently prevents DHPGinduced downregulation of NMDA channelmediated synaptic responses in CA1 neurons.
Show less  Date Issued
 2008
 Identifier
 FSU_migr_etd0522
 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 decisionmaking 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 ArcGISbased 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 steadystate, onedimensional 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 MainSouth 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 sitespecific 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 MainSouth 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 MainSouth 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 MainSouth Canal area. (6) The flow model calibration in the City of Sebastian area is not as satisfactory as in the MainSouth 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 ongoing Basin Management Action Plan. More efforts, such as investigating the soil condition (e.g. microbacteria 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.
Show less  Date Issued
 2017
 Identifier
 FSU_FALL2017_Lei_fsu_0071N_14260
 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 postWWII 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 postWWII 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 HumicIon 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.
Show less  Date Issued
 2017
 Identifier
 FSU_FALL2017_Pham_fsu_0071N_14265
 Format
 Thesis
 Title
 Morphometric Analysis of Shape Differences in Windover and Point Hope Archaic Human Mandibles.
 Creator

Boren, Seth B., Slice, Dennis E., Shanbhag, Sachin, Beerli, Peter, Florida State University, College of Arts and Sciences, Department of Scientific Computing
 Abstract/Description

The mandible can provide valuable information on both the life history and genetic makeup of Archaic human populations. If two genetically separated Homo sapiens populations practice differing dietary behaviors, one may expect to see significant variation in mandibular morphology. The following analysis tests two hypotheses: (1) that there are significant differences in morphology in mandibular shape between the sexes amongst Archaic North American H. sapiens and (2) that there is a...
Show moreThe mandible can provide valuable information on both the life history and genetic makeup of Archaic human populations. If two genetically separated Homo sapiens populations practice differing dietary behaviors, one may expect to see significant variation in mandibular morphology. The following analysis tests two hypotheses: (1) that there are significant differences in morphology in mandibular shape between the sexes amongst Archaic North American H. sapiens and (2) that there is a significant difference in variance in mandibular shape between Archaic Floridian and Alaskan H. sapiens. The Archaic Floridian H. sapiens are taken from the Windover burial site and the Alaskan H. sapiens are taken from the Point Hope burial site. A sample made from mandible specimens taken from both populations is subjected to Principal Component Analyses (PCA). The component scores from the PCAs are subjected to both a Multivariate Analysis of Covariance (MANCOVA) and general Multivariate Analysis of Variance (MANOVA) to determine whether significant differences in variance exist between the sexes and the populations. The MANCOVA found that there were no significant interactions between the PC scores between populations, sexes, or size. Significant differences in variance were found between males and females and between the Windover and Point Hope populations. Differences in variance observed between the populations are suspected to be due to differences in subsistence strategies. Differences in variance between the sexes are suspected to be genetic in origin.
Show less  Date Issued
 2017
 Identifier
 FSU_FALL2017_Boren_fsu_0071N_14264
 Format
 Thesis
 Title
 A GISBased Model for Estimating Nitrate Fate and Transport from Septic Systems in Surficial Aquifers.
 Creator

Rios, J. Fernando, Ye, Ming, Peterson, Janet, Shanbhag, Sachin, Wilgenbusch, James, Department of Scientific Computing, Florida State University
 Abstract/Description

Estimating groundwater nitrate fate and transport is an important task in water resources and environmental management because excess nitrate loads may have negative impacts on human and environmental health. This work discusses the development of a simplified nitrate transport model and its implementation as a geographic information system (GIS)based screening tool, whose purpose is to estimate nitrate loads to surface water bodies from onsite wastewatertreatment systems (OWTS). Key...
Show moreEstimating groundwater nitrate fate and transport is an important task in water resources and environmental management because excess nitrate loads may have negative impacts on human and environmental health. This work discusses the development of a simplified nitrate transport model and its implementation as a geographic information system (GIS)based screening tool, whose purpose is to estimate nitrate loads to surface water bodies from onsite wastewatertreatment systems (OWTS). Key features of this project are the reduced data demands due to the use of a simplified model, as well as ease of use compared to traditional groundwater flow and transport models, achieved by embedding the model within a GIS. The simplified conceptual model consists of a simplified groundwater flow model in the surficial aquifer, and a simplified transport model that makes use of an analytical solution to the advectiondispersion equation, used for determining nitrate fate and transport. Denitrification is modeled using first order decay in the analytical solution with the decay constant obtained from literature and/or sitespecific data. The groundwater flow model uses readily available topographic data to approximate the hydraulic gradient, which is then used to calculate seepage velocity magnitude and direction. The flow model is evaluated by comparing the results to a previous numerical modeling study of the U.S. Naval Air Station, Jacksonville (NAS) performed by the USGS. The results show that for areas in the vicinity of the NAS, the model is capable of predicting groundwater travel times from a source to a surface water body to within ±20 years of the USGS model, 75% of the time. The transport model uses an analytical solution based on the one by Domenico and Robbins (1985), the results of which are then further processed so that they may be applied to more general, realworld scenarios. The solution, as well as the processing steps are tested using artificially constructed scenarios, each meant to evaluate a certain aspect of the solution. For comparison purposes, each scenario is solved using a well known numerical contaminant transport model. The results show that the analytical solution provides a reasonable approximation to the numerical result. However, it generally underestimates the concentration distribution to varying degrees depending on choice of parameters, especially along the plume centerline. These results are in agreement with previous studies (Srinivasan et al., 2007; West et al., 2007). The adaptation of the analytical solution to more realistic scenarios results in an adequate approximation to the numerically calculated plume, except in areas near the advection front, where the model produces a plume whose shape differs noticeably from the numerical solution. Load calculations are carried out using a mass balance approach where the system is considered to be in the steady state. The steadystate condition allows for a load estimate by subtracting the mass removal rate due to denitrification from the input mass rate. The input mass rate is calculated by taking into account advection and dispersion while the mass removal rate due to denitrification is calculated from the definition of a first order reaction. Comparison with the synthetic scenarios of the transport model shows that for the test cases, when decay rates are low, the model agrees well with the load calculation from the numerical model. As decay rates increase and the plume becomes shorter, the input load is overestimated by about 9% in the test cases and the mass removed due to denitrification is underestimated by 30% in the worst case. These results are likely due to the underestimation of concentration values by the analytical solution of the transport model.
Show less  Date Issued
 2010
 Identifier
 FSU_migr_etd1851
 Format
 Thesis
 Title
 NMR Characterization and Isothermal Crystallization of Random IsoPropylene Copolymers with Ethylene and 1Octene Counits.
 Creator

Chiari, Ysela L., Alamo, Rufina G., Chella, Ravindran, Shanbhag, Sachin, Department of Chemical and Biomedical Engineering, Florida State University
 Abstract/Description

Propylene ethylene and 1octene copolymers synthesized with the same type of metallocene catalyst were analyzed using 13C solution NMR to determine the microstructure (tacticity, regioregularity, and concentration of comonomer) and the comonomer sequence distribution. The peak assignments followed published literature. Propylene ethylene copolymers (PE) show a comonomer content ranging from 7.5 up to 20.8 mol %, and constant stereo and regio defects of 1.3 0.40 mol % and 1.0 0.1 mol %...
Show morePropylene ethylene and 1octene copolymers synthesized with the same type of metallocene catalyst were analyzed using 13C solution NMR to determine the microstructure (tacticity, regioregularity, and concentration of comonomer) and the comonomer sequence distribution. The peak assignments followed published literature. Propylene ethylene copolymers (PE) show a comonomer content ranging from 7.5 up to 20.8 mol %, and constant stereo and regio defects of 1.3 0.40 mol % and 1.0 0.1 mol % respectively. The propylene 1octene copolymers (PO) have a comonomer content ranging from 5.9 to 14.9 mol % while the stereo and regio defects, also constant in this series, are 2.4 0.3 mol % and 0.4 0.1 mol % respectively. A triad distribution analysis of the NMR resonances of sequences pertaining to the comonomer followed the predictions from Bernoullian and first order Markovian distributions for all copolymers. The product of the reactivity ratio was consistent with a random distribution for all copolymers of the series. A very strong effect of molecular weight on the crystallization kinetics of two PE copolymers with similar ethylene content (~20 mol %) and different molar mass is associated with slow segmental dynamics in a crystallization temperature range near Tg. Isothermally crystallized copolymers display two melting peaks. The intensity of the low melting or aging peak increases with increasing aging time and crystallization temperature. Aging at temperatures above and below the maximum of the crystallization rates yielded a changeover in the contribution to the total heat of fusion of the low melting peak from 4.3% (smallest contribution) to 93% (largest contribution). The two melting peaks are attributed to two populations of crystals formed by a mechanism of sequence selection during isothermal crystallization.
Show less  Date Issued
 2007
 Identifier
 FSU_migr_etd3820
 Format
 Thesis
 Title
 Integrating TwoWay Interaction Between Fluids and Rigid Bodies in the RealTime Particle Systems Library.
 Creator

Young, Andrew S., Erlebacher, Gordon, Plewa, Tomasz, Shanbhag, Sachin, Department of Scientific Computing, Florida State University
 Abstract/Description

In the last 15 years, Video games have become a dominate form of entertainment. The popularity of video games means children are spending more of their free time play video games. Usually, the time spent on homework or studying is decreased to allow for the extended time spent on video games. In an effort to solve the problem, researchers have begun creating educational video games. Some studies have shown a significant increase in learning ability from video games or other interactive...
Show moreIn the last 15 years, Video games have become a dominate form of entertainment. The popularity of video games means children are spending more of their free time play video games. Usually, the time spent on homework or studying is decreased to allow for the extended time spent on video games. In an effort to solve the problem, researchers have begun creating educational video games. Some studies have shown a significant increase in learning ability from video games or other interactive instruction. Educational games can be used in conjunction with formal educational methods to improve the retention among students. To facilitate the creation of games for science education, the RTPS library was created by Ian Johnson to simulate fluid dynamics in realtime. This thesis seeks to extend the RTPS library, to provide more realistic simulations. Rigid body dynamics have been added to the simulation framework. In addition, a twoway coupling between the rigid bodies and fluids have been implemented. Another contribution to the library, was the addition of fluid surface rendering to provide a more realistic looking simulation. Finally, a Qt interface was added to allow for modification of simulation parameters in realtime. In order to perform these simulations in realtime one must have a significant amount of computational power. Though processing power has seen consistent growth for many years, the demands for higher performance desktops grew faster than CPUs could satisfy. In 2006, general purpose graphics processing(GPGPU) was introduced with the CUDA programming language. This new language allowed developers access to an incredible amount of processing power. Some researchers were reporting up to 10 times speedups over a CPU. With this power, one can perform simulations on their desktop computers that were previously only feasible on super computers. GPGPU technology is utilized in this thesis to enable realtime simulations.
Show less  Date Issued
 2012
 Identifier
 FSU_migr_etd5463
 Format
 Thesis
 Title
 Phase Field Modeling of Microstructure Evolution in Thermal Barrier Coating Systems.
 Creator

Ahmed, Karim, ElAzab, Anter, MeyerBaese, Anke, Shanbhag, Sachin, Wang, Xiaoqiang, Program in Materials Science, Florida State University
 Abstract/Description

The development of robust thermal barrier coating (TBC) systems is crucial in many hightemperature applications. The performance of a TBC system is significantly limited by microstructural evolution mechanisms, such as sintering at elevated temperatures. Sintering reduces the porosity of TBC and makes it denser which eventually increases the thermal conductivity and reduces the strain compliance of TBC. Understanding how sintering proceeds in TBC systems is thus important in improving the...
Show moreThe development of robust thermal barrier coating (TBC) systems is crucial in many hightemperature applications. The performance of a TBC system is significantly limited by microstructural evolution mechanisms, such as sintering at elevated temperatures. Sintering reduces the porosity of TBC and makes it denser which eventually increases the thermal conductivity and reduces the strain compliance of TBC. Understanding how sintering proceeds in TBC systems is thus important in improving the design of such systems. An elaborate phase field model was developed in order to understand the sintering behavior of columnar TBC structure. The model takes into account different sintering mechanisms, such as volume diffusion, grain boundary diffusion, surface diffusion, and grain boundary migration, coupled with elastic strain arising from the thermal expansion mismatch in thermal barrier coating system. Direct relations between model parameters and material properties were established. Such relations facilitate quantitative studies of the sintering process in any material of interest. The model successfully demonstrates a strong dependence of the sintering process in TBC on the initial morphology and dimensions of coatings, strain, and temperature.
Show less  Date Issued
 2011
 Identifier
 FSU_migr_etd4684
 Format
 Thesis
 Title
 A Computational Method for AgeatDeath Estimation Based on the Pubic Symphysis.
 Creator

Stoyanova, Detelina, Slice, Dennis, Burkardt, John, Ye, Ming, Shanbhag, Sachin, Department of Scientific Computing, Florida State University
 Abstract/Description

A significant component of forensic science is analyzing bones to assess the age at death of an individual. Forensic anthropologists often include the pubic symphysis in such studies. Subjective methods, such as the SucheyBrooks method, are currently used to analyze the pubic symphysis. This thesis examines a more objective, quantitative method. The method analyzes 3D surface scans of the pubic symphysis and implements a thin plate spline algorithm which models the bending of a flat plane to...
Show moreA significant component of forensic science is analyzing bones to assess the age at death of an individual. Forensic anthropologists often include the pubic symphysis in such studies. Subjective methods, such as the SucheyBrooks method, are currently used to analyze the pubic symphysis. This thesis examines a more objective, quantitative method. The method analyzes 3D surface scans of the pubic symphysis and implements a thin plate spline algorithm which models the bending of a flat plane to approximately match the surface of the bone. The algorithm minimizes the bending energy required for this transformation. Results presented here show that there is a correlation between the minimum bending energy and the age at death of the individual. The method could be useful to medicolegal practitioners.
Show less  Date Issued
 2012
 Identifier
 FSU_migr_etd7010
 Format
 Thesis
 Title
 Reduced Order Modeling of Reactive Transport in a Column Using Proper Orthogonal Decomposition.
 Creator

McLaughlin, Benjamin R. S., Peterson, Janet, Ye, Ming, Shanbhag, Sachin, Department of Scientific Computing, Florida State University
 Abstract/Description

Estimating parameters for reactive contaminant transport models can be a very computationally intensive. Typically this involves solving a forward problem many times, with many degrees of freedom that must be computed each time. We show that reduced order modeling (ROM) by proper orthogonal decomposition (POD) can be used to approximate the solution to the forward model using many fewer degrees of freedom. We provide background on the finite element method and reduced order modeling in one...
Show moreEstimating parameters for reactive contaminant transport models can be a very computationally intensive. Typically this involves solving a forward problem many times, with many degrees of freedom that must be computed each time. We show that reduced order modeling (ROM) by proper orthogonal decomposition (POD) can be used to approximate the solution to the forward model using many fewer degrees of freedom. We provide background on the finite element method and reduced order modeling in one spatial dimension, and apply both methods to a system of linear uncoupled timedependent equations simulating reactive transport in a column. By comparing the reduced order and finite element approximations, we demonstrate that the reduced model, while having many fewer degrees of freedom to compute, gives a good approximation of the highdimensional (finite element) model. Our results indicate that one may substitute a reduced model in place of a highdimensional model to solve the forward problem in parameter estimation with many fewer degrees of freedom.
Show less  Date Issued
 2011
 Identifier
 FSU_migr_etd5030
 Format
 Thesis
 Title
 High Temperature Polyimide/Carbon Fiber/Carbon Nanotubes Multiscale Composites: Processing, Cure Kinetics and Multifunctionality.
 Creator

Fu, Xiang, Zhang, Chuck, Liu, Tao, Shanbhag, Sachin, Liang, Zhiyong, Department of Industrial and Manufacturing Engineering, Florida State University
 Abstract/Description

The discovery of carbon nanotubes (CNTs) by Iijima in 1991 has initiated a great deal of scientific research on exploring their unique properties and potential applications. One of the promising applications is integrating CNTs into polymer or polymer/fiber composites to form nanocomposite or multiscale composites. High temperature polymer composites are required for use in structural components in advanced high speed aircraft, weapon systems and space vehicles. Motivated by the potential of...
Show moreThe discovery of carbon nanotubes (CNTs) by Iijima in 1991 has initiated a great deal of scientific research on exploring their unique properties and potential applications. One of the promising applications is integrating CNTs into polymer or polymer/fiber composites to form nanocomposite or multiscale composites. High temperature polymer composites are required for use in structural components in advanced high speed aircraft, weapon systems and space vehicles. Motivated by the potential of significantly improving thermal, electrical, mechanical and properties and fire retardancy of polymer matrix composites at relatively low concentration, this research focuses on integrating CNTs into high temperature fiberreinforced composites aiming at matrix enhancement at the interfiber level, zdirection reinforcement and multifunctionality such as thermal and electrical conductivity, fire retardancy or resistance. High temperature vacuumassisted resin transfer molding was designed and successfully demonstrated with inplane and throughthickness resin flow methods. Polyimide based PETI330/carbon fabric T65035 laminates were manufactured with fiber volume fraction of ~60% and void contents of 34%. The tensile strengths of PETI330/T65035 laminates fabricated by inplane and throughthickness processes are 834 and 799 MPa, respectively. Short beam strengths of the laminates via both processes are 43 and 52 MPa, which are ~77% and ~93% of that processed via RTM using an injection pressure of 2.75 MPa. CNT/carbon fiber/PETI330 multiscale composites were fabricated using prepregassisted RTM process. Homogeneous dispersion of CNTs in the PETI330 matrix were achieved using the solution processing method. Using this method, multiscale composite laminates with various concentrations of CNTs were manufactured. Comprehensive characterizations were carried out to investigate the thermal stability, thermal mechanical properties, microstructure and morphologies of the CNT/PETI330/T650 multiscale composite laminates. As a result, we found that: (1) the incorporation of small amounts of CNTs can significantly improve the hightemperature thermal mechanical properties of the PETI330 resin; (2) after postcuring the room temperature storage modulus of 1 wt% CNT/PETI330/T650 composite increased from ~60 GPa to ~71GPa, the glass transition temperature increased from 331°C to 350°C; (3) the existence of CNT induces hindered cure kinetics of PETI330. Multiscale composites were also fabricated using buckypapers made of mixed SWNTs/MWNTs integrated onto polyimide/carbon fibre composite surface and their fire retardancy was characterized. Compared to the control sample (CP), buckypaper incorporated sample produced further delayed ignition, 40% lower peak heat release rate, 26% lower heat release, 82% less smoke release and 33% less mass loss. Further, buckypaper effectively increases the thermal conductivity of PETI330/carbon fiber composite; the thermal conductivity improves 13% at 25°C and 27% at 300°C. The buckypaper is more efficient as fire retardant in polyimide/carbon fiber composites than direct mixing CNTs into polymer matrix. The effect of CNTs on the cure kinetics of imide oligomer was studied using differential scanning calorimetry. During isothermal cure, the neat resin begins to cure first. As the reaction proceeds, the enthalpy of reaction decreases for the nanocomposites. As the samples vitrify and the reaction is completed, the neat PETI330 vitrifies faster than the 1% CNT/PETI330 nanocomposite sample. The adding of 1 wt% CNTs caused lower enthalpy, slightly lower activation energy. The cure kinetics of neat PETI330 and the PETI330/CNT systems can be modeled as firstorder reactions, meaning the reactions are mainly ethynylethynyl addition polymerization to form carboncarbon double bonds. Comparison of the activation energies, rate constant and cure times suggests that the cure mechanisms of the neat PETI330 resin and CNTs embedded nanocomposites are similar. Last but not least, the molecular models of the PETI330 imide oligomer and CNTs were constructed. Molecular dynamics simulations showed that molecular interaction energy of imide/ CNT system is 37.5 kcal/mol. The major contributor of the interactions between CNT and the imide oligomer is van de Waals energy which is due to the ÆÃ stacking effect between similar molecular structure of CNT surface and the phenyl rings in the backbone and sidegroups. The attractive energy between CNT and imide oligomer can explain why the glass transition temperature shifts toward higher temperature in multiscale composites manufactured in this study.
Show less  Date Issued
 2010
 Identifier
 FSU_migr_etd4388
 Format
 Thesis
 Title
 ProcessingStructureProperty Relationships of Carbon Nanotube and Nanoplatelet Enabled Piezoresistive Sensors.
 Creator

Luo, Sida, Liu, Tao, Brooks, James, Zhang, Chuck, Zhang, Mei, Shanbhag, Sachin, Department of Industrial and Manufacturing Engineering, Florida State University
 Abstract/Description

Individual carbon nanotubes (CNTs) possess excellent piezoresistive performance, which is manifested by the significant electrical resistance change when subject to mechanical deformation. In comparison to individual CNTs, the CNT thin films, formed by a random assembly of individual tubes or bundles, show much lower piezoresistive sensitivity. Given the progress made to date in developing CNT ensemble basedpiezoresistive sensors, the related piezoresistive mechanism(s) are still not well...
Show moreIndividual carbon nanotubes (CNTs) possess excellent piezoresistive performance, which is manifested by the significant electrical resistance change when subject to mechanical deformation. In comparison to individual CNTs, the CNT thin films, formed by a random assembly of individual tubes or bundles, show much lower piezoresistive sensitivity. Given the progress made to date in developing CNT ensemble basedpiezoresistive sensors, the related piezoresistive mechanism(s) are still not well understood. The crucial step to obtain a better understanding of this issue is to study the effects of CNT structure in the dispersion on the piezoresistivity of CNT ensemble basedpiezoresistive sensors. To reach this goal, my Ph.D. research first focuses on establishing the processingstructureproperty relationship of SWCNT thin film piezoresistive sensors. The key accomplishment contains: 1) developing the combined preparative ultracentrifuge method (PUM) and dynamic light scattering (DLS) method to quantitatively characterized SWCNT particle size in dispersions under various sonication conditions; 2) designing combined ultrasonication and microfluidization processing protocol for high throughput and largescale production of high quality SWCNT dispersions; 3) fabricating varied SWCNT thin film piezoresistive sensors through spray coating technique and immersiondrying posttreatment; and 4) investigating the effect of microstructures of SWCNTs on piezoresistivity of SWCNT thin film sensors. This experimental methodology for quantitative and systematic investigation of the processingstructureproperty relationships provides a means for the performance optimization of CNT ensemble based piezoresistive sensors. As a start to understand the piezoresistive mechanism, the second focus of my Ph.D. research is studying charge transport behaviors in SWCNT thin films. It was found that the temperaturedependent sheet resistance of SWCNT thin films could be explained by a 3D variable range hopping (3DVRH) model. More importantly, a strong correlation between the length of SWCNTs and the VRH parameter T0, indicating the degree of disorder of the electronic system, has been identified. With the structure dependent transport mechanism study, a very interesting topic  how T0 changes when SWCNT thin film is under a mechanical deformation, would be helpful for better understanding the piezoresistive mechanism of SWCNT thin film sensors. As demonstrated in transport mechanism study, SWCNT thin film exhibits a negative temperature coefficient (NTC) of resistance. In contrast, another family of carbon nanomaterials, graphite nanoplatelets (GNPs), shows positive temperature coefficient (PTC) of resistance, attributed to their metallic nature. Therefore, upon a wise selection of mass ratio of SWCNTs to GNPs for fabrication of hybrid SWCNT/GNP thin film piezoresistive sensors, a near zero temperature coefficients of resistance in a broad temperature range has been achieved. This unique selftemperature compensation feature along with the high sensitivity of SWCNT/GNP hybrid sensors provides them a vantage for readily and accurately measuring the strain/stress levels in different conditions. With the unique features of SWCNT/GNP hybrid thin film sensors, my future work will focus on application exploration on SWCNT/GNP thin film sensor based devices. For example, we have demonstrated that it is potential for manmachine interaction and body monitoring when coating the hybrid sensor on highly stretchable nitrile glove. The structure health monitoring (SHM) of composite materials could also be realized by coating the thin film sensor on a glass fiber surface and then embedding the fiber sensor in composite structure.
Show less  Date Issued
 2013
 Identifier
 FSU_migr_etd7478
 Format
 Thesis
 Title
 Peridynamic Modeling and Simulation of PolymerNanotube Composites.
 Creator

Henke, Steven F., Shanbhag, Sachin, Okoli, Okenwa, Erlebacher, Gordon, Plewa, Tomasz, Oates, William, Department of Scientific Computing, Florida State University
 Abstract/Description

In this document, we develop and demonstrate a framework for simulating the mechanics of polymer materials that are reinforced by carbon nanotubes. Our model utilizes peridynamic theory to describe the mechanical response of the polymer and polymernanotube interfaces. We benefit from the continuum formulation used in peridynamics because (1) it allows the polymer material to be coarsegrained to the scale of the reinforcing nanofibers, and (2) failure via nanotube pullout and matrix tearing...
Show moreIn this document, we develop and demonstrate a framework for simulating the mechanics of polymer materials that are reinforced by carbon nanotubes. Our model utilizes peridynamic theory to describe the mechanical response of the polymer and polymernanotube interfaces. We benefit from the continuum formulation used in peridynamics because (1) it allows the polymer material to be coarsegrained to the scale of the reinforcing nanofibers, and (2) failure via nanotube pullout and matrix tearing are possible based on energetic considerations alone (i.e. without special treatment). To reduce the degrees of freedom that must be simulated, the reinforcement effect of the nanotubes is represented by a mesoscale beadspring model. This approach permits the arbitrary placement of reinforcement ''strands'' in the problem domain and motivates the need for irregular quadrature point distributions, which have not yet been explored in the peridynamic setting. We address this matter in detail and report on aspects of mesh sensitivity that we uncovered in peridynamic simulations. Using a manufactured solution, we study the effects of quadrature point placement on the accuracy of the solution scheme in one and two dimensions. We demonstrate that square grids and the generator points of a centroidal Voronoi tessellation (CVT) support solutions of similar accuracy, but CVT grids have desirable characteristics that may justify the additional computational cost required for their construction. Impact simulations provide evidence that CVT grids support fracture patterns that resemble those obtained on higher resolution cubic Cartesian grids with a reduced computational burden. With the efficacy of irregular meshing schemes established, we exercise our model by dynamically stretching a cylindrical specimen composed of the polymernanotube composite. We vary the number of reinforcements, alignment of the filler, and the properties of the polymernanotube interface. Our results suggest that enhanced reinforcement requires an interfacial stiffness that exceeds that of the neat polymer. We confirm that the reinforcement is most effective when a nanofiber is aligned with the applied deformation, least effective when a nanofiber is aligned transverse to the applied deformation, and achieves intermediate values for other orientations. Sample configurations containing two fibers are also investigated.
Show less  Date Issued
 2013
 Identifier
 FSU_migr_etd8566
 Format
 Thesis
 Title
 Bayesian Neural Networks in DataIntensive High Energy Physics Applications.
 Creator

Perry, Michelle, MeyerBaese, Anke, Prosper, Harrison, Piekarewicz, Jorge, Shanbhag, Sachin, Beerli, Peter, Department of Scientific Computing, Florida State University
 Abstract/Description

This dissertation studies a graphical processing unit (GPU) construction of Bayesian neural networks (BNNs) using large training data sets. The goal is to create a program for the mapping of phenomenological Minimal Supersymmetric Standard Model (pMSSM) parameters to their predictions. This would allow for a more robust method of studying the Minimal Supersymmetric Standard Model, which is of much interest at the Large Hadron Collider (LHC) experiment CERN. A systematic study of the speedup...
Show moreThis dissertation studies a graphical processing unit (GPU) construction of Bayesian neural networks (BNNs) using large training data sets. The goal is to create a program for the mapping of phenomenological Minimal Supersymmetric Standard Model (pMSSM) parameters to their predictions. This would allow for a more robust method of studying the Minimal Supersymmetric Standard Model, which is of much interest at the Large Hadron Collider (LHC) experiment CERN. A systematic study of the speedup achieved in the GPU application compared to a Central Processing Unit (CPU) implementation are presented.
Show less  Date Issued
 2014
 Identifier
 FSU_migr_etd8867
 Format
 Thesis
 Title
 A Study of Shock Formation and Propagation in the ColdIon Model.
 Creator

Cheung, James, Gunzburger, Max D., Peterson, Janet S., Shanbhag, Sachin, Florida State University, College of Arts and Sciences, Department of Scientific Computing
 Abstract/Description

The central purpose of this thesis is to explore the behavior of the numerical solution of the Cold Ion model with shock forming conditions in one and two dimensions. In the one dimensional case, a comparison between the numerical solution of the Vlasov equation is made. It is observed that the ColdIon model is no longer representative of the coldion limit of the VlasovPoisson equation when a spike forms in the solution. It was found that the lack of a spike in the solution of the Cold...
Show moreThe central purpose of this thesis is to explore the behavior of the numerical solution of the Cold Ion model with shock forming conditions in one and two dimensions. In the one dimensional case, a comparison between the numerical solution of the Vlasov equation is made. It is observed that the ColdIon model is no longer representative of the coldion limit of the VlasovPoisson equation when a spike forms in the solution. It was found that the lack of a spike in the solution of the ColdIon model does not necessarily mean that a bifurcation has not formed in the solution of the VlasovPoisson equation. It was also determined that the spike present in the solution of the one dimensional problem appears again in the two dimensional simulation. The findings presented in this thesis opens up the question of determining which initial and boundary conditions of the ColdIon model causes a shock to form in the solution.
Show less  Date Issued
 2014
 Identifier
 FSU_migr_etd9158
 Format
 Thesis
 Title
 Snynthesis and Magnetization of BaLn₂O₄ (Ln = Lanthanide).
 Creator

Lundberg, Matthew, Siegrist, Theo M., Latturner, Susan, Shanbhag, Sachin, Florida State University, The Graduate School, Program in Materials Science
 Abstract/Description

The BaLn(sub)2(/sub)O(sub)4(/sub) family has been synthesized successfully as single crystals by the fluxgrowth method. The phases crystallize in the CaV(sub)2(/sub)O(sub)4(/sub) structure prototype in space group Pnma (# 62). The structure has been studied using singlecrystal xray diffraction, and stoichiometry confirmed with EDS, and the unit cell parameters and atomic positions have been determined for the whole lanthanide series (with the exception of the Lu compound). The effects of...
Show moreThe BaLn(sub)2(/sub)O(sub)4(/sub) family has been synthesized successfully as single crystals by the fluxgrowth method. The phases crystallize in the CaV(sub)2(/sub)O(sub)4(/sub) structure prototype in space group Pnma (# 62). The structure has been studied using singlecrystal xray diffraction, and stoichiometry confirmed with EDS, and the unit cell parameters and atomic positions have been determined for the whole lanthanide series (with the exception of the Lu compound). The effects of the lanthanide ionic radius on the atomic positions in the unit cell has been studied in terms of fractional atomic coordinates, bond lengths and angles, and bond valence sums. Magnetic measurements have been performed on the series with the exception of the La, Eu, and Lu members in the form of susceptibility versus temperature. The crystals all show signs of geometric antiferromagnetic frustration with the Néel temperatures significantly below the temperature predicted by the Weiss constant. Additionally some members of the family, namely BaCe(sub)2(/sub)O(sub)4(/sub), BaNd(sub)2(/sub)O(sub)4(/sub), BaPr(sub)2(/sub)O(sub)4(/sub), BaSm(sub)2(/sub)O(sub)4(/sub), BaTb(sub)2(/sub)O(sub)4(/sub), and BaYb(sub)2(/sub)O(sub)4(/sub) show significant crystal field splitting, that causes deviation from CurrieWeiss behavior
Show less  Date Issued
 2014
 Identifier
 FSU_migr_etd9212
 Format
 Thesis
 Title
 IrradiationInduced Composition Patterns and Segregation in Binary Solid Solutions.
 Creator

Dubey, Santosh, Azab, Anter El, Rikvold, Per Arne, Shanbhag, Sachin, Erlebacher, Gordon, Plewa, Tomasz, Department of Scientific Computing, Florida State University
 Abstract/Description

A theoreticalcomputational model is developed to study irradiationinduced composition patterns and segregation in binary solid solutions under irradiation, which is motivated by the fact that such composition changes alter a wide range of metallurgical properties of structural alloys used in the nuclear industry. For a binary alloy system, the model is based on a coupled, nonlinear set of reactiondiffusion equations for six defect and atomic species, which include vacancies, three...
Show moreA theoreticalcomputational model is developed to study irradiationinduced composition patterns and segregation in binary solid solutions under irradiation, which is motivated by the fact that such composition changes alter a wide range of metallurgical properties of structural alloys used in the nuclear industry. For a binary alloy system, the model is based on a coupled, nonlinear set of reactiondiffusion equations for six defect and atomic species, which include vacancies, three interstitial dumbbell configurations, and the two alloy elements. Two sets of boundary conditions have been considered: periodic boundary conditions, which are used to investigate composition patterning in bulk alloys under irradiation, and reaction boundary conditions to study the radiationinduced segregation at surfaces. Reactions are considered to be either between defects, which is called recombination, or between defects and alloying elements, which result in change in the interstitial dumbbell type. Long range diffusion of all the species is considered to happen by vacancy and interstitialcy mechanisms. As such, diffusion of the alloy elements is coupled to the diffusion of vacancies and interstitials. Defect generation is considered to be associated with collision cascade events that occur randomly in space and time. Each event brings about a change in the local concentration of all the species over the mesoscale material volume affected by the cascade. Stifflystable Gear's method has been implemented to solve the reactiondiffusion model numerically. Gear's method is a variant of higher order implicit linear multistep method, implemented in predictorcorrector fashion. The resulting model has been tested with a miscible CuAu solid solution. For this alloy, and in the absence of boundaries, steady state composition patterns of several nanometers have been observed. Fourier space properties of these patterns have been found to depend on irradiationspecific control parameters, temperature, and initial state of the alloy. Linear stability analysis of the set of reactiondiffusion equations confirms the findings of the numerical simulations. In the presence of boundaries, radiationinduced segregation of alloying species has been observed near in the boundary layer: enrichment of faster diffusing species and depletion of slower diffusing species. Radiationinduced segregation has also been found to depend upon irradiationspecific control parameters and temperature. The results show that the degree of segregation is spatially nonuniform and hence it should be studied in higher dimensions. Proper formulation of the boundary conditions showed that segregation of the alloy elements to the boundary is coupled to the boundary motion. With both patterning and segregation investigations, the irradiated sample has been found to recover its uniform state with time when irradiation is turned off. The inference drawn out from this observation is that in miscible solid solutions irradiationinduced composition patterning and radiationinduced segregation are not realizable in the absence of irradiation.
Show less  Date Issued
 2012
 Identifier
 FSU_migr_etd5601
 Format
 Thesis
 Title
 SolidState NMR Evaluation of Molecular Structural Engineering for Controlled Peptide SelfAssembly.
 Creator

Leonard, Sarah, Paravastu, Anant, Shanbhag, Sachin, Alamo, Rufina, Li, Yan, Department of Chemical and Biomedical Engineering, Florida State University
 Abstract/Description

This works provides atomic level molecular information regarding the selfassembled states of several designer nanofibers; nanofibers that have demonstrated utility in the fields of drug delivery and tissue engineering. The first selfassembling nanofiber of interest is MAX8. As the 8th iteration in the MAX peptide family, originally designed by Drs. Schneider and Pochan, MAX8 is believed to possess several unique properties making it particularly advantageous for medical applications: 1) a...
Show moreThis works provides atomic level molecular information regarding the selfassembled states of several designer nanofibers; nanofibers that have demonstrated utility in the fields of drug delivery and tissue engineering. The first selfassembling nanofiber of interest is MAX8. As the 8th iteration in the MAX peptide family, originally designed by Drs. Schneider and Pochan, MAX8 is believed to possess several unique properties making it particularly advantageous for medical applications: 1) a stimuli sensitive selfassembly mechanism, 2) a βsheet rich hydrogel structure, and 3) shearthinning characteristics followed by poststress recovery of mechanical properties. The second selfassembling nanofiber of interest is SAF. Originally designed by Dr. Woolfson, SAF is another example of a unique de novo designed peptide possessing several advantageous features: 1) SAF only selfassembles when complementary peptides are mixed, 2) it forms an αhelical rich nanofiber structure, and 3) the sequence can be modified at the amino acid level to produce selfassembling hydrogels. Though several design principles are utilized to produce functional nanofibers likely to adopt specific threedimensional structures, the structural characterization techniques employed, such as TEM, FTIR, and CD, are best suited to bulk measurements of secondary structure; there still remains a lack of atomiclevel measurements regarding the final nanofiber structures of both MAX8 and SAF. Here, solidstate NMR is utilized to obtain atomiclevel constraints in order to probe the selfassembled nanofiber structures of MAX8 and SAF peptides. Selfassembled MAX8 hydrogels were prepared according to established protocols in the literature and TEM was used to confirm nanofiber formation. Solidstate NMR techniques were used to probe the molecular structure of isotopically labeled samples. Specifically, CPMAS measurements were conducted on unlabeled peptides and fpRFDR measurements were conducted on uniformly 13C, 15Nlabeled samples to obtain precise chemical shift information, confirming the presence of linear βstrand secondary structure. DARR measurements were performed on uniformly 13C, 15Nlabeled samples to probe for contacts between spatially close yet sequentially distant atomic sites, indicating a contact between the V3 and K17 residues within a selfassembled nanofiber network. PITHIRDSCT 13C13C dipolar recoupling solidstate NMR measurements were used to probe for spatial proximity between singly or doubly 13Clabeled samples. Combined, the PITHIRDSCT measurements for several selectively labeled samples indicated that the spatial proximity between the V3 and V18 carbonyl sites was intramolecular, providing atomiclevel proof of a closed βhairpin in the selfassembled MAX8 nanofiber structure. Nuclear spin simulations were conducted to computationally predict PITHIRDSCT results, and deviation from experimental data indicates that approximately 70% of MAX8 monomers are in a closedhinge configuration. Additional MAX8 nanofiber samples were synthesized to probe the arrangement of βstrands into βsheets. PITHIRDSCT experiments were conducted on a singly 13Clabeled sample at the V5 carbonyl site. Weak dipolar couplings were observed, consistent with syn βsheets where βhairpins align along the same edge of the nanofiber axis. REDOR solidstate NMR measurements, coupled with nuclear spin simulations, were used to evaluate the distances between isotopically labeled 13C and 13N sites within MAX8 nanofiber networks. Two sample were studied; both samples had 50% of the molecules labeled on the V16 nitrogen with the remaining 50% of the molecules labeled on either the V5 carbonyl carbon or the V3 carbonyl carbon. The experimental curve for the V5 sample was weaker than predicted by nuclear spin simulations for syn βsheets while the experimental curve for the V3 sample was stronger than predicted by nuclear spin simulations for syn βsheets. In both cases, the experimental curves were significantly stronger than would be expected for anti βsheets. These results suggest that MAX8 nanofibers are polymorphic with approximately half of the molecules adopting the syn configuration with the other half adopting a syn configuration with a registry shift of 2. 2D DARR experiments were conducted on a sample uniformly labeled at the V3, T12, and K17 residues as well as a mixed sample having 50% of the molecules labeled at V3, T12, and K17 and the remaining 50% of the molecules labeled at V9. When these two samples are compared, the signal intensity for the interresidue crosspeak between the V3 Cα and K17 Cα for the mixed sample is attenuated by an additional 30% after normalizing to intraresidue crosspeak intensity. This attenuation suggests an intermolecular component to the interaction, consistent with syn βsheets. 2D DARR results also indicate that the nanofibers are not in the synantiparallel or anti configuration due to a lack of V3/T12 crosspeaks. Estimations of signaltonoise for this crosspeak, based on the observed strength of the V3/K17 crosspeak, suggest that the signaltonoise attained would be sufficient to clearly discern these crosspeaks. The level of signaltonoise, howeer, would not be sufficient to observe the expected crosspeaks between the V9 and T12 residues for a synparallel nanofiber. As a highly redundant sequence, it is not possible to develop a labeling scheme for solidstate NMR that would provide a positive contact for the synparallel configuration. Despite this, collective evidence strongly points toward this configuration as the dominate nanofiber structure within selfassembled MAX8 nanofibers. For this reason, we propose a molecular model that is a mixture of inregister syn βsheets and syn βsheets with a registry shift of 2. These βsheets stack to form synparallel nanofibers with all βhairpins aligned along the same edge of the fiber axis. Selfassembled SAFAAQ nanofiber networks were also produced according to the established protocols from the literature. TEM was used to verify the successful reproduction of hSAFAAQ nanofibers. Contrary to several other SAF sequences, hSAFAAQp1 fibers were observed by TEM. Circular dichroism experiments were conducted on hSAFAAQ individual components and mixed components. All three samples (hSAFAAQp1, hSAFAAQp2, and hSAFAAQ) exhibited some degree of αhelical secondary structure. The circular dichroism data is supported by CPMAS NMR results suggesting that the secondary structure of hSAFAAQ does not change upon mixture of the individual components. The 2D NMR experiments fpRFDR and DARR were conducted on labeled hSAFAAQ nanofibers to determine precise chemical shift information, evaluate secondary structure at the atomic level, and constrain the molecular organization of hSAFAAQ molecules within selfassembled nanofibers. Peak positions obtained from fpRFDR NMR experiments conducted on a uniformally 13C, 15Nlabeled nanofiber sample are correlated with αhelical secondary structure for all relevant 13Clabeled sites (K6 and L12 on hSAFAAQp1 and A4, E15, and I23 on hSAFAAQp2). DARR solidstate NMR measurements were conducted to probe for contacts between L12 residues on hSAFAAQp1 and I23 residues on hSAFAAQp2; this contact is predicted to occur only upon formation of a staggered heterodimer. DARR results clearly exhibit crosspeaks between these residues suggesting that the dominant structure within selfassembled hSAFAAQ nanofibers is a staggered heterodimer, verifying the structure proposed by Dr. Woolfson.
Show less  Date Issued
 2014
 Identifier
 FSU_migr_etd9029
 Format
 Thesis
 Title
 Characterization of MetalloceneCatalyzed Polyethylenes from Rheological Measurements Using a Bayesian Formulation.
 Creator

Takeh, Arsia, Shanbhag, Sachin, ElAzab, Anter, Beerli, Peter, Department of Scientific Computing, Florida State University
 Abstract/Description

Longchain branching affects the rheological properties of the polyethylenes strongly. Branching structure  density of branch points, branch length, and the locations of the branches  is complicated, therefore, without controlled branching structure it is almost impossible to study the effect of longchain branching on the rheological properties. Singlesite catalysts now make it possible to prepare samples in which the molecular weight distribution is relatively narrow and quite...
Show moreLongchain branching affects the rheological properties of the polyethylenes strongly. Branching structure  density of branch points, branch length, and the locations of the branches  is complicated, therefore, without controlled branching structure it is almost impossible to study the effect of longchain branching on the rheological properties. Singlesite catalysts now make it possible to prepare samples in which the molecular weight distribution is relatively narrow and quite reproducible. In addition, a particular type of singlesite catalyst, the constrained geometry catalyst, makes it possible to introduce low and wellcontrolled levels of long chain branching while keeping the molecular weight distribution narrow. Linear viscoelastic properties (LVE) of rheological properties contain a rich amount of data regarding molecular structure of the polymers. A computational algorithm that seeks to invert the linear viscoelastic spectrum of singlesite metallocenecatalyzed polyethylenes is presented in this work. The algorithm uses a general linear rheological model of branched polymers as its underlying engine, and is based on a Bayesian formulation that transforms the inverse problem into a sampling problem. Given experimental rheological data on unknown singlesite metallocenecatalyzed polyethylenes, it is able to quantitatively describe the range of values of weightaveraged molecular weight, MW, and average branching density, bm, consistent with the data. The algorithm uses a Markovchain Monte Carlo method to simulate the sampling problem. If, and when information about the molecular weight is available through supplementary experiments, such as chromatography or light scattering, it can easily be incorporated into the algorithm, as demonstrated.
Show less  Date Issued
 2011
 Identifier
 FSU_migr_etd1729
 Format
 Thesis
 Title
 The Dynamics of DNA Electrophoresis in Lyotropic Polymer Liquid Crystals.
 Creator

You, Seungyong, Van Winkle, David H., Shanbhag, Sachin, Brooks, James, Manousakis, Efstratios, Wiedenhover, Ingo, Department of Physics, Florida State University
 Abstract/Description

Electrophoresis is one of the most powerful tools used to separate biological molecules by size in a supporting medium under the influence of an electric field. Pluronic F127 gel, introduced as a new sieving medium for electrophoresis in the late 1990s, has potential promise, but the transport and separation of DNA molecules in Pluronic gel are not fully understood among scientists. This dissertation research conducts three experiments to investigate the dynamics of DNA electrophoresis in...
Show moreElectrophoresis is one of the most powerful tools used to separate biological molecules by size in a supporting medium under the influence of an electric field. Pluronic F127 gel, introduced as a new sieving medium for electrophoresis in the late 1990s, has potential promise, but the transport and separation of DNA molecules in Pluronic gel are not fully understood among scientists. This dissertation research conducts three experiments to investigate the dynamics of DNA electrophoresis in Pluronic gel. First, a direct observation study examines how DNA molecules move through the Pluronic gel on a microscopic scale using fluorescence microscopy. Evidence is presented that in some cases DNA molecules electrophorese directly through gel crystallites and in other cases along grain boundaries between gel crystallites. Next, two dimensional electrophoresis is performed in order to understand the size dependence of the mobility of DNA molecules ranging from 20 bp to 3500 bp in Pluronic gels. Small DNA molecules (<125 >bp) became slower as their molecular size decreased, while large DNA molecules (>175 bp) became exponentially slower as their molecular size increased. DNA molecules of intermediate sizes showed a sinusoidal pattern in their mobility. Based on the experimental results, we developed a phenomenological model to fit the size dependence of the DNA mobility, and discussed the separation mechanisms of the DNA molecules in the Pluronic gels. In the final experiment, DNA molecules of the same length, which moved together and formed a single band in the agarose gel, were split into two bands in the Pluronic gel. This indicates that the Pluronic gel is possibly able to separate the DNA molecules according to their sequence. We expect that this study will contribute to an enhanced understanding of the dynamics of DNA molecules in Pluronic gel and facilitation of Pluronic gel as an alternative sieving medium for electrophoresis in the fields of molecular biology and biotechnology.
Show less  Date Issued
 2009
 Identifier
 FSU_migr_etd0863
 Format
 Thesis
 Title
 Inverse Problems in Polymer Characterization.
 Creator

Takeh, Arsia, Shanbhag, Sachin, Oates, William, MeyerBaese, Anke, Beerli, Peter, Wilgenbusch, Jim, Department of Scientific Computing, Florida State University
 Abstract/Description

This work implements inverse methods in various polymer characterization problems. In the first topic, a new approach is proposed to infer the comonomer content using Crystaf method considering and quantifying the associated uncertainty. In the second topic, a comparison is carried out between various rheological probes (methods) to determine their sensitivity in longchain branching (LCB) detection and measurement. In the last topic, an opensource software is implemented to infer continuous...
Show moreThis work implements inverse methods in various polymer characterization problems. In the first topic, a new approach is proposed to infer the comonomer content using Crystaf method considering and quantifying the associated uncertainty. In the second topic, a comparison is carried out between various rheological probes (methods) to determine their sensitivity in longchain branching (LCB) detection and measurement. In the last topic, an opensource software is implemented to infer continuous and discrete relaxation modulus.
Show less  Date Issued
 2014
 Identifier
 FSU_migr_etd9104
 Format
 Thesis
 Title
 Peridynamic Multiscale Models for the Mechanics of Materials: Constitutive Relations, Upscaling from Atomistic Systems, and Interface Problems.
 Creator

Seleson, Pablo D, Gunzburger, Max, Rikvold, Per Arne, ElAzab, Anter, Peterson, Janet, Shanbhag, Sachin, Lehoucq, Richard B., Parks, Michael L., Department of Scientific...
Show moreSeleson, Pablo D, Gunzburger, Max, Rikvold, Per Arne, ElAzab, Anter, Peterson, Janet, Shanbhag, Sachin, Lehoucq, Richard B., Parks, Michael L., Department of Scientific Computing, Florida State University
Show less  Abstract/Description

This dissertation focuses on the non local continuum peridynamics model for the mechanics of materials, related constitutive models, its connections to molecular dynamics and classical elasticity, and its multiscale and multimodel capabilities. A more generalized role is defined for influence functions in the statebased peridynamic model which allows for the strength of non local interactions to be modulated. This enables the connection between different peridynamic constitutive models,...
Show moreThis dissertation focuses on the non local continuum peridynamics model for the mechanics of materials, related constitutive models, its connections to molecular dynamics and classical elasticity, and its multiscale and multimodel capabilities. A more generalized role is defined for influence functions in the statebased peridynamic model which allows for the strength of non local interactions to be modulated. This enables the connection between different peridynamic constitutive models, establishing a hierarchy that reveals that some models are special cases of others. Furthermore, this allows for the modulation of the strength of non local interactions, even for a fixed radius of interactions between material points in the peridynamics model. The multiscale aspect of peridynamics is demonstrated through its connections to molecular dynamics. Using higherorder gradient models, it is shown that peridynamics can be viewed as an upscaling of molecular dynamics, preserving the relevant dynamics under appropriate choices of length scales. The statebased peridynamic model is shown to be appropriate for the description of multiscale and multimodel systems. A formulation for nonlocal interface problems involving scalar fields is presented, and derivations of non local transmission conditions are derived. Specializations that describe local, non local, and local/non local transmission conditions are considered. Moreover, the convergence of the non local transmission conditions to their classical local counterparts is shown. In all cases, results are illustrated by numerical experiments.
Show less  Date Issued
 2010
 Identifier
 FSU_migr_etd0273
 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
Show less  Abstract/Description

In this dissertation, we address some of the needs faced in the development of modern ab initio quantum chemical methods to compute highaccuracy 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 semidefinite...
Show moreIn this dissertation, we address some of the needs faced in the development of modern ab initio quantum chemical methods to compute highaccuracy 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 semidefinitebased algorithm to compute groundstate HartreeFock energies and wave functions, that can be easily extended to KohnSham density functional theory. We also propose a parametrized coupledpair functional to compute accurate noncovalent molecular interaction energies. Chapters 3 through 7 cover methods relevant to excited state computations. We propose an explicitly timedependent coupledcluster framework rooted on the equationofmotion 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 nearedge Xray absorption fine structure. Finally, we propose a timedependent HartreeFock method within the framework of cavity quantumelectrodynamics that allows us to simulate the interaction of molecular systems with quantized radiation fields, such as those found on plasmonic nanoparticles and nano cavities.
Show less  Date Issued
 2017
 Identifier
 FSU_FALL2017_Nascimento_fsu_0071E_14251
 Format
 Thesis
 Title
 Making Material Simulation Faster: Coarse Graining, Bridging and Bootstrapping.
 Creator

Crysup, Benjamin Rosser, Shanbhag, Sachin, Rikvold, Per Arne, Huang, Chen, MendozaCortes, Jose L., Slice, Dennis E., Florida State University, College of Arts and Sciences,...
Show moreCrysup, Benjamin Rosser, Shanbhag, Sachin, Rikvold, Per Arne, Huang, Chen, MendozaCortes, Jose L., Slice, Dennis E., Florida State University, College of Arts and Sciences, Department of Scientific Computing
Show less  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 LennardJones 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.
Show less  Date Issued
 2017
 Identifier
 FSU_FALL2017_Crysup_fsu_0071E_14203
 Format
 Thesis
 Title
 Piezoresistivity of Mechanically Drawn Swcnt Thin Films: Mechanism and Optimizing Principle.
 Creator

Obitayo, Waris, Liu, Tao, Shanbhag, Sachin, Zhang, Mei, Okoli, Okenwa, Oates, William S., Florida State University, College of Engineering, Department of Industrial and...
Show moreObitayo, Waris, Liu, Tao, Shanbhag, Sachin, Zhang, Mei, Okoli, Okenwa, Oates, William S., Florida State University, College of Engineering, Department of Industrial and Manufacturing Engineering
Show less  Abstract/Description

Carbon nanotubes (CNTs) are known to exhibit outstanding mechanical, electrical, thermal, and coupled electromechanical properties. CNTs can be employed towards the design of an innovative strain sensor with enhanced multifunctionality due to their load carrying capability, sensing properties, high thermal stability, and outstanding electrical conductivity. All these features indicate the prospect to use CNTs in a very wide range of applications, for instance, highly sensitive resistancetype...
Show moreCarbon nanotubes (CNTs) are known to exhibit outstanding mechanical, electrical, thermal, and coupled electromechanical properties. CNTs can be employed towards the design of an innovative strain sensor with enhanced multifunctionality due to their load carrying capability, sensing properties, high thermal stability, and outstanding electrical conductivity. All these features indicate the prospect to use CNTs in a very wide range of applications, for instance, highly sensitive resistancetype strain/force sensors, wearable electronics, flexible microelectronic devices, robotic skins, and insitu structural health monitoring. CNTbased strain sensors can be divided into two different types, the individual CNT based strain sensors and the ensemble CNTbased strain sensors e.g. CNT/polymer nanocomposites and CNT thin films. In contrast, to individual CNTbased strain sensors with very high gauge factor (GF) e.g. ~3000, the ensemble CNTbased strain sensors exhibit very low GFs e.g. for a SWCNT thin film strain sensor, GF is ~1. This research discusses the mechanisms and the optimizing principles of a SWCNT thin film piezoresistive sensor, and provide an experimental validation of the numerical/analytical investigations. The dependence of the piezoresistivity on key parameters like alignment, network density, bundle diameter (effective tunneling area), and SWCNT length is studied. The tunneling effect is significant in SWCNT thin films showing higher degrees of alignment, due to greater intertube distances between the SWCNTs as compared to random oriented SWCNT thin films. It can be concluded that SWCNT thin films featuring higher alignment would have a higher GF. On the other hand, the use of sparse network density which comprises of aligned SWCNTs can as well intensify the tunneling effect which can result to a further increase in the GF. In addition, it is wellknown that percolation is greatly influenced by the geometry of the nanotubes e.g. bundle diameter and length. A study on the influence of bundle diameter of SWCNTs on the piezoresistivity behavior of mechanically drawn SWCNT thin films showed the best performance with an improved GF of ~10 when compared to the randomly oriented SWCNT thin films with GF of ~1. The nonlinear piezoresistivity of the mechanically drawn SWCNT thin films is considered to be the main mechanism behind the high strain sensitivity. Furthermore, information about the average length and length distribution is very essential when examining the influence of individual nanotube length on the strain sensitivity. With that in mind, we use our previously developed preparative ultracentrifuge method (PUM), and our newly developed gel electrophoresis and simultaneous Raman and photolumiscence spectroscopy (GEPSRSPL) to characterize the average length and length distribution of SWCNTs respectively.
Show less  Date Issued
 2015
 Identifier
 FSU_2015fall_Obitayo_fsu_0071E_12891
 Format
 Thesis
 Title
 Parma: Applications of VectorAutoregressive Models to Biological Inference with an Emphasis on ProcrustesBased Data.
 Creator

Soda, K. James (Kenneth James), Slice, Dennis E., Beaumont, Paul M., Beerli, Peter, MeyerBaese, Anke, Shanbhag, Sachin, Florida State University, College of Arts and Sciences,...
Show moreSoda, K. James (Kenneth James), Slice, Dennis E., Beaumont, Paul M., Beerli, Peter, MeyerBaese, Anke, Shanbhag, Sachin, Florida State University, College of Arts and Sciences, Department of Scientific Computing
Show less  Abstract/Description

Many phenomena in ecology, evolution, and organismal biology relate to how a system changes through time. Unfortunately, most of the statistical methods that are common in these fields represent samples as static scalars or vectors. Since variables in temporallydynamic systems do not have stable values this representation is unideal. Differential equation and basis function representations provide alternative systems for description, but they are also not without drawbacks of their own....
Show moreMany phenomena in ecology, evolution, and organismal biology relate to how a system changes through time. Unfortunately, most of the statistical methods that are common in these fields represent samples as static scalars or vectors. Since variables in temporallydynamic systems do not have stable values this representation is unideal. Differential equation and basis function representations provide alternative systems for description, but they are also not without drawbacks of their own. Differential equations are typically outside the scope of statistical inference, and basis function representations rely on functions that solely relate to the original data in regards to qualitative appearance, not in regards to any property of the original system. In this dissertation, I propose that vector autoregressivemoving average (VARMA) and vector autoregressive (VAR) processes can represent temporallydynamic systems. Under this strategy, each sample is a time series, instead of a scalar or vector. Unlike differential equations, these representations facilitate statistical description and inference, and, unlike basis function representations, these processes directly relate to an emergent property of dynamic systems, their crosscovariance structure. In the first chapter, I describe how VAR representations for biological systems lead to both a metric for the difference between systems, the Euclidean process distance, and to a statistical test to assess whether two time series may have originated from a single VAR process, the likelihood ratio test for a common process. Using simulated time series, I demonstrate that the likelihood ratio test for a common process has a true Type I error rate that is close to the prespecified nominal error rate, regardless of the number of subseries in the system or of the order of the processes. Further, using the Euclidean process distance as a measure of difference, I establish power curves for the test using logistic regression. The test has a high probability of rejecting a false null hypothesis, even for modest differences between series. In addition, I illustrate that if two competitors follow the LotkaVolterra equations for competition with some additional white noise, the system deviates from VAR assumptions. Yet, the test can still differentiate between a simulation based on these equations in which the constraints on the system change and a simulation where the constraints do not change. Although the Type I error rate is inflated in this scenario, the degree of inflation does not appear to be larger when the system deviates more noticeably from model assumptions. In the second chapter, I investigate the likelihood ratio test for a common process's performance with shape trajectory data. Shape trajectories are an extension of geometric morphometric data in which a sample is a set of temporallyordered shapes as opposed to a single static shape. Like all geometric morphometric data, each shape in a trajectory is inherently highdimensional. Since the number of parameters in a VAR representation grows quadratically with the number of subseries, shape trajectory data will often require dimension reduction before a VAR representation can be estimated, but the effects that this reduction will have on subsequent inferences remains unclear. In this study, I simulated shape trajectories based on the movements of roundworms. I then reduced the number of variables that described each shape using principle components analysis. Based on these lower dimensional representations, I estimated the likelihood ratio test's Type I error rate and power with the simulated trajectories. In addition, I also used the same workflow on an empirical dataset of women walking (originally from Morris13) but also tried varying amounts of preprocessing before applying the workflow as well. The likelihood ratio test's Type I error rate was mildly inflated with the simulated shape trajectories but had a high probability of rejecting false null hypotheses. Without preprocessing, the likelihood ratio test for a common process had a highly inflated Type I error rate with the empirical data, but when the sampling density is lowered and the number of cycles is standardized within a comparison the degree of inflation becomes comparable to that of the simulated shape trajectories. Yet, these preprocessing steps do not appear to negatively impact the test's power. Visualization is a crucial step in geometric morphometric studies, but there are currently few, if any, methods to visualize differences in shape trajectories. To address this absence, I propose an extension to the classic vectordisplacement diagram. In this new procedure, the VAR representations for two trajectories' processes generate two simulated trajectories that share the same shocks. Then, a vectordisplacement diagram compares the simulated shapes at each time step. The set of all diagrams then illustrates the difference between the trajectories' processes. I assessed the validity of this procedure using two simulated shape trajectories, one based on the movements of roundworms and the other on the movements of earthworms. The result provided mixed results. Some diagrams do show comparisons between shapes that are similar to those in the original trajectories but others do not. Of particular note, diagrams show a bias towards whichever trajectory's process was used to generate pseudorandom shocks. This implies that the shocks to the system are just as crucial a component to a trajectory's behavior as the VAR model itself. Finally, in the third chapter I discuss a new R library to study dynamic systems and represent them as VAR and VARMA processes, iPARMA. Since certain processes can have multiple VARMA representations, the routines in this library place an emphasis on the reverse echelon format. For every process, there is only one VARMA model in reverse echelon format. The routines in iPARMA cover a diverse set of topics, but they all generally fall into one of four categories: simulation and study, model estimation, hypothesis testing, and visualization methods for shape trajectories. Within the chapter, I discuss highlights and features of key routines' algorithms, as well as how they differ from analogous routines in the R package MTS \citep{mtsCite}. In many regards, this dissertation is foundational, so it provides a number of lines for future research. One major area for further work involves alternative ways to represent a system as a VAR or VARMA process. For example, the parameter estimates in a VAR or VARMA model could depict a process as a point in parameter space. Other potentially fruitful areas include the extension of representational applications to other families of time series models, such as cointegrated models, or altering the generalized Procrustes algorithm to better suit shape trajectories. Based on these extensions, it is my hope that statistical inference based on stochastic process representations will help to progress what systems biologists are able to study and what questions they are able to answer about them.
Show less  Date Issued
 2017
 Identifier
 FSU_SUMMER2017_Soda_fsu_0071E_13917_P
 Format
 Set of related objects
 Title
 Modeling of Complex Behaviors of Submarine Debris Flows.
 Creator

Saha, Bikash C. (Bikash Chandra), Ye, Ming, Niedoroda, Alan W., Misra, Vasubandhu, Shanbhag, Sachin, Wang, Xiaoqiang, Florida State University, College of Arts and Sciences,...
Show moreSaha, Bikash C. (Bikash Chandra), Ye, Ming, Niedoroda, Alan W., Misra, Vasubandhu, Shanbhag, Sachin, Wang, Xiaoqiang, Florida State University, College of Arts and Sciences, Department of Scientific Computing
Show less  Abstract/Description

Submarine debris flows are hazards when they threaten the facilities that are built on sea floor to facilitate submarine transportation. The dynamics of submarine debris flow is simple once the debris material gets in the flow motion and that it can be represented using simple physics. A twodimensional model with twolayer Bingham fluid representations, SDFlow2D, was developed by using an Eulerian frame of reference to predict the consequences of complex submarine debris flows. The model was...
Show moreSubmarine debris flows are hazards when they threaten the facilities that are built on sea floor to facilitate submarine transportation. The dynamics of submarine debris flow is simple once the debris material gets in the flow motion and that it can be represented using simple physics. A twodimensional model with twolayer Bingham fluid representations, SDFlow2D, was developed by using an Eulerian frame of reference to predict the consequences of complex submarine debris flows. The model was viscoplastic in nature based on depthaveraged approximation to the Shallow Water Equations (SWE), and it assumes that the flow consists of a nondeforming upper layer riding on a deforming layer. The model was verified by comparing the numerical solution with experimental observations as well as with an analytical solution. The comparison shows a good agreement with analytical solution and an acceptable agreement with experimental observations. The model was found to be capable of simulating realword submarine debris flows. The consequence of bed material entrainment is worth studying as this process adds antecedent sediment to the debris flow mass that in turn increases the intensity of hazard. The modeling code SDFlow2D was enhanced by using simple physics to include the capability of computing bed material entrainment. It was assumed that no inertial force was involved in the process, and that the entrainment was instantaneous. The modified SDFlow2D was applied to two idealized cases and to a prognostic case. A total variation diminishing (TVD) scheme with flux limiter was applied with MacCormack predictorcorrector scheme to smooth out the spurious solution near the source area of debris flow. While the TVD scheme served that purpose to some extent, it was not helpful to make the model robust as the computational time was 15 times greater than that of using the code without TVD scheme. The Bayesian inverse modeling was implemented to quantify the Bingham parameters uncertainty. The technique helps find not only the most probable pair of Bingham parameters but also the distribution of the parameters by conducting a small number of model simulations. The overall outcome of the study benefits the deep sea explorers as well as the designers and planners in charge of designing the submarine structures.
Show less  Date Issued
 2017
 Identifier
 FSU_2017SP_Saha_fsu_0071E_13595
 Format
 Thesis
 Title
 ContactFree Simulations of Rigid Particle Suspensions Using Boundary Integral Equations.
 Creator

Bystricky, Lukas, Quaife, Bryan, Shanbhag, Sachin, Cogan, Nicholas G., Huang, Chen, Moore, Matthew Nicholas J., Florida State University, College of Arts and Sciences,...
Show moreBystricky, Lukas, Quaife, Bryan, Shanbhag, Sachin, Cogan, Nicholas G., Huang, Chen, Moore, Matthew Nicholas J., Florida State University, College of Arts and Sciences, Department of Scientific Computing
Show less  Abstract/Description

In many composite materials, rigid fibers are distributed throughout the material to tune the mechanical, thermal, and electric properties of the composite. The orientation and distribution of the fibers play a critical role in the properties of the composite. Many composites are processed as a liquid molten suspension of fibers and then solidified, holding the fibers in place. Once the fiber orientations are known, theoretical models exist that can predict properties of the composite...
Show moreIn many composite materials, rigid fibers are distributed throughout the material to tune the mechanical, thermal, and electric properties of the composite. The orientation and distribution of the fibers play a critical role in the properties of the composite. Many composites are processed as a liquid molten suspension of fibers and then solidified, holding the fibers in place. Once the fiber orientations are known, theoretical models exist that can predict properties of the composite.Modeling the suspended fibers in the liquid state is important because their ultimate configuration depends strongly on the flow history during the molten processing. Continuum models, such as the FolgarTucker model, predict the evolution of the fibers’ orientation in a fluid. These models are limited in several ways. First, they require empirical constants and closure relations that must be determined a priori, either by experiments or detailed computer simulations. Second, they assume that all the fibers are slender bodies of uniform length. Lastly, these methods break down for concentrated suspensions. For these reasons, it is desirable in certain situations to model the movement of individual fibers explicitly. This dissertation builds upon recent advances in boundary integral equations to develop a robust, accurate, and stable method that simulates fibers of arbitrary shape in a planar flow. In any method that explicitly models the individual fiber motion, care must be taken to ensure numerical errors do not cause the fibers to overlap. To maintain fiber separation, a repulsion force and torque are added when required. This repulsion force is free of tuning parameters and is determined by solving a sequence of linear complementarity problems to ensure that the configuration does not have any overlap between fibers. Numerical experiments demonstrate the stability of the method for concentrated suspensions.
Show less  Date Issued
 2018
 Identifier
 2018_Su_Bystricky_fsu_0071E_14725
 Format
 Thesis
 Title
 New Numerical Procedures for the Lagrangian Analysis of Hierarchical BlockStructured Reactive Flow Simulations.
 Creator

Boehner, Philip Scott, Plewa, Tomasz, Sussman, Mark, Erlebacher, Gordon, Shanbhag, Sachin, Ye, Ming, Florida State University, College of Arts and Sciences, Department of...
Show moreBoehner, Philip Scott, Plewa, Tomasz, Sussman, Mark, Erlebacher, Gordon, Shanbhag, Sachin, Ye, Ming, Florida State University, College of Arts and Sciences, Department of Scientific Computing
Show less  Abstract/Description

Chemical evolution of stellar plasma is one of the most critical components of computational models in stellar astrophysics. Nuclear abundance distributions resulting from chains of nuclear reactions serve as a key comparison tool against observations, used to further constrain models. To that end, we focus on improving the accuracy of model abundances. In most cases, abundances are obtained in the course of hydrodynamic simulations performed on Eulerian meshes. Unfortunately, those models...
Show moreChemical evolution of stellar plasma is one of the most critical components of computational models in stellar astrophysics. Nuclear abundance distributions resulting from chains of nuclear reactions serve as a key comparison tool against observations, used to further constrain models. To that end, we focus on improving the accuracy of model abundances. In most cases, abundances are obtained in the course of hydrodynamic simulations performed on Eulerian meshes. Unfortunately, those models are subject to the unphysical mixing of nuclear species due to numerical diffusion effects. For more reliable nucleosynthesis calculations, mass motions are described using passively advected Lagrangian tracer particles. These particles represent fluid elements, recording their thermodynamic histories which are subsequently used to drive detailed nucleosynthesis calculations in a postprocessing procedure performed with large number of relevant isotopes. Accuracy of nucleosynthesis calculations strongly depends on the accurate coupling between fluid represented on the Eulerian mesh and tracer particles. The coupling involves both interpolation of Eulerian data to particles as well as integrating equations of motion of particles. Both steps contribute numerical errors resulting in divergence of particle tracks from fluid streamlines. Here we propose a new particle advection scheme driven by only the hydrodynamics, replacing the interpolation step of particle motion and show preliminary results. We also introduce an interpolation method for mapping our postprocessed nucleosynthesis results back onto our Eulerian mesh. Spatial convergence studies are performed for the Eulerian hydrodynamic nucleosynthesis results and the remapped, postprocessed Lagrangian results using a reactive HawleyZabusky flow.
Show less  Date Issued
 2018
 Identifier
 2018_Su_Boehner_fsu_0071E_14773
 Format
 Thesis
 Title
 Overcoming Geometric Limitations in the Finite Element Method by Means of Polynomial Extension: Application to Second Order Elliptic Boundary Value and Interface Problems.
 Creator

Cheung, James, Gunzburger, Max D., Steinbock, Oliver, Bochev, Pavel B., Perego, Mauro, Peterson, Janet S., Shanbhag, Sachin, Florida State University, College of Arts and...
Show moreCheung, James, Gunzburger, Max D., Steinbock, Oliver, Bochev, Pavel B., Perego, Mauro, Peterson, Janet S., Shanbhag, Sachin, Florida State University, College of Arts and Sciences, Department of Scientific Computing
Show less  Abstract/Description

In this dissertation, we present a new approach for approximating the solution of second order partial differential equations and interface problems. This approach is based on the classical finite element method, where instead of using geometric manipulations to fit the discrete domain to the curved domain given by the continuous problem, we use polynomial extensions to enforce that a suitably constructed extension of the numerical solution matches the boundary condition given by the...
Show moreIn this dissertation, we present a new approach for approximating the solution of second order partial differential equations and interface problems. This approach is based on the classical finite element method, where instead of using geometric manipulations to fit the discrete domain to the curved domain given by the continuous problem, we use polynomial extensions to enforce that a suitably constructed extension of the numerical solution matches the boundary condition given by the continuous problem in the weak sense. This method is thus aptly named the Polynomial Extension Finite Element Method (PEFEM). Using this approach, we may approximate the solution of elliptic interface problems by enforcing that the extension of the solution on their respective subdomains matches weakly the continuity conditions prescribed by the continuous problem on a curved interface. This method is then called the Method of Virtual Interfaces (MVI), since, while the continuous interface exists in the context of the continuous problem, it is virtual in the context of its numerical approximation. The key benefits of this polynomial extension approach is that it is simple to implement and that it is optimally convergent with respect to the best approximation results given by interpolation. Theoretical analysis and computational results are presented.
Show less  Date Issued
 2018
 Identifier
 2018_Sp_Cheung_fsu_0071E_14328
 Format
 Thesis
 Title
 Effect of Branching Architecture on the Crystallization Behavior of Random Ethylene Copolymers.
 Creator

Vadlamudi, Madhavi, Alamo, Rufina G., Striegel, André M., Chella, Ravindran, Shanbhag, Sachin, Department of Chemical and Biomedical Engineering, Florida State University
 Abstract/Description

In the first part of this thesis, the bivariate or cross branching distribution of a filmgrade ethylene 1hexene copolymer with enhanced MD and TD Elmendorf tear (> 400 g/mil) and high dart impact, synthesized ExxonMobil Chemical Company at Bayton, TX, has been characterized through the analysis of fractions obtained by molecular weight and by 1hexene composition. The molecular weight fractions, obtained by a solventnonsolvent fractionation technique, are each mixtures of molecules with...
Show moreIn the first part of this thesis, the bivariate or cross branching distribution of a filmgrade ethylene 1hexene copolymer with enhanced MD and TD Elmendorf tear (> 400 g/mil) and high dart impact, synthesized ExxonMobil Chemical Company at Bayton, TX, has been characterized through the analysis of fractions obtained by molecular weight and by 1hexene composition. The molecular weight fractions, obtained by a solventnonsolvent fractionation technique, are each mixtures of molecules with at least two different 1hexene compositions, one component with a constant relatively high density (~ 1 mol% hexene) and a second of a lower density broadly distributed along the molecular weight fractions. The content of the low density component increases with increasing molecular weight of the fractions while the level of 1hexene decreases accordingly. The mixed compositional character of these fractions is easily inferred by their high crystallization rates and high melting and crystallization temperatures compared to the values of model random ethylene copolymers. The set of compositional fractions obtained by TREF display an increasing 1hexene concentration with increasing molecular weight, and except for the highest molecular weight components (Mw > 150,000 g/mol) their melting and crystallization behavior followed the random pattern. Higher than expected melting temperatures and a constancy of the high melting temperature peak with increasing crystallization temperature, indicate that the intrachain 1hexene distribution of the highly branched, high molecular weight fractions deviates strongly from the random behavior. These structural features and the bimodal character of the composition distribution of this resin, that contains high molecular weight chains with both low and high 1hexene contents, are correlated with the enhanced key film properties. The second part of this thesis studies the influence of long chain branched (LCB) architecture on the crystallization of polyethylene using models based on hydrogenated polybutadienes with ~ 2.1 mol% of ethyl branches randomly distributed in all chain segments. The melting behavior, overall crystallization rates measured by DCS, the crystalline phase structure determined by WAXD, RAMAN, DSC, and NMR, and super molecular and lamellar morphology measured by optical microscopy and by SAXS and TEM of the LCB PEs are studied in reference to the linear chain. At a fixed undercooling the crystallization rates of all LCB PEs are 30 to 40% lower than the rate of the linear as expected from transport limitations to the nucleation rate of the LCB systems and the interfacial free energies associated with this process are significantly higher for the LCB types compared to the linear HPBD samples. Smaller differences in the rate are found within the various LCB architectures. The components of the phase structure are controlled by the content of short chain branching with a negligible effect from the LCB architectures. For all LCB PEs the crystalline component is ~ 30% and the interphase region is ~15%. The structural parameters i.e. long range periodicity and core lamellar thickness measured by SAXS and TEM, also are primarily affected by the short chain branching content and to some extent with the introduction of LCB into linear HPBD chain, but not by the LCB type of architecture. The long range periodicity (L), core crystal thickness (lc) of the linear (un branched) are 330 ' and 266 ' respectively, whereas introduction of ~2 mol% ethyl branches in the linear chain (90 K molar mass) reduced L to 125 ' and lc to 85 '. Conversely, all the LCB types have L ~ 110 ' and lc values of ~70 '. Restrictions from the LCB melt topology cause a change from poorly organized lamellar spherulites (linear HPBD) to micelle type crystallite structures in LCB PEs. The effect of LCB architecture is mainly observed in the long range dynamics probed by the 1H NMR T2 relaxation measurements. The dynamics of the non crystalline region, or soft component where short branches and the LCB junctions are rejected, reflect the increasing constraints to motion in this region as the complexity in LCB architecture increases. The soft component displays higher T2 values (more mobility) for the 3 arm star type compared to the more complex comb type architecture at all the temperatures studied. The restrictions by the LCB architecture to longrange chain dynamics are more prominent in the molten state, with T2 values decreasing from 615 and #956;sec for the star to 537 and #956;sec for the H type and decreasing further to 454 and #956;sec for the comb type structures.
Show less  Date Issued
 2010
 Identifier
 FSU_migr_etd7242
 Format
 Thesis
 Title
 Crystallization of Precision Polyethylenes.
 Creator

Zhang, Xiaoshi, Alamo, Rufina G., Shanbhag, Sachin, Chung, Hoyong, Kennemur, Justin Glenn, Florida State University, FAMUFSU College of Engineering, Department of Chemical and...
Show moreZhang, Xiaoshi, Alamo, Rufina G., Shanbhag, Sachin, Chung, Hoyong, Kennemur, Justin Glenn, Florida State University, FAMUFSU College of Engineering, Department of Chemical and Biomedical Engineering
Show less  Abstract/Description

Polyethylenes with functional groups precisely placed on a fixed number of backbone carbons have been recently synthesized via acyclic diene metathesis (ADMET), polycondensation and ringopening metathesis polymerization (ROMP). The successful synthesis of polymers with precise branch distribution provides models to study relationship between the precise branch distribution with their crystalline properties. This work covers a comprehensive study of the crystallization of precision...
Show morePolyethylenes with functional groups precisely placed on a fixed number of backbone carbons have been recently synthesized via acyclic diene metathesis (ADMET), polycondensation and ringopening metathesis polymerization (ROMP). The successful synthesis of polymers with precise branch distribution provides models to study relationship between the precise branch distribution with their crystalline properties. This work covers a comprehensive study of the crystallization of precision polyethylenes synthesized via three different polymerization methods. ADMETsynthesized precision polyethylenes with a fluorine, chlorine or bromine atom placed on each 9th, 15th or 21st backbone carbon are investigated to test polymorphism. Studies combining Xray and FTIR have revealed major differences between the series of Fcontaining samples and those with Cl and Br. The latter undergo a drastic change in layered crystalline structure between fast (planar, Form I) and slowcrystallized samples (nonplanar, Form II) while the F series remain isomorphic. The crystallization kinetics of Cl and Br containing samples are unusual due to the presence of two inversions in the temperature coefficient of the overall crystallization rate, both related with the retardation effect of one polymorph on the development of the second. The availability of polycondensationsynthesized precision polyethylenes with acetals placed on each and every 12th, 18th, 19th, and 23rd allows models of precision polyethylenes with inchain functional groups to test polymorphism, the oddeven effect on crystallization, as well as unusual crystallization kinetics. Realtime Xray with parallel studies using DSC, FTIR, and POM revealed that all samples undergo multiple polymorphic transitions on heating. A clear difference in crystallization behavior between odd and even spaced polyacetals was also observed. Similar to halogencontaining precision polyethylenes, precision polyacetals display a sharp inversion in the rate of crystallization at temperatures where both polymorphs coexist. The effect of tacticity on crystallization kinetics was investigated using unique samples in the literature for which tacticity was wellcontrolled, ROMPsynthesized precision polyethylenes with acetoxy side groups. The higher crystallization rates observed in the isotactic sample at the same undercooling demonstrate atactic acetoxy group slows down the crystallization kinetics, regardless of the branch distribution.
Show less  Date Issued
 2018
 Identifier
 2018_Fall_Zhang_fsu_0071E_14876
 Format
 Thesis
 Title
 Towards Ubiquitous Sensing Using Commodity WiFi.
 Creator

Tan, Sheng, Yang, Jie, Shanbhag, Sachin, Wang, AnI Andy, Duan, Zhenhai, Florida State University, College of Arts and Sciences, Department of Computer Science
 Abstract/Description

Recently, the prevalence of WiFi devices and ubiquitous coverage of WiFi network provide us the opportunity to extend WiFi capabilities beyond communication, particularly in sensing the physical environment. Most existing systems that enable human sensing utilizing commodity WiFi devices are simply rely on profile training based techniques. Such techniques suffer from performance degradation when configuration changes after training. Furthermore, those systems can not work under multiuser...
Show moreRecently, the prevalence of WiFi devices and ubiquitous coverage of WiFi network provide us the opportunity to extend WiFi capabilities beyond communication, particularly in sensing the physical environment. Most existing systems that enable human sensing utilizing commodity WiFi devices are simply rely on profile training based techniques. Such techniques suffer from performance degradation when configuration changes after training. Furthermore, those systems can not work under multiuser scenarios. To overcome the limitations of existing solutions, this dissertation introduces the design and implementation of three systems. First, we propose MultiTrack, a multiuser indoor tracking and activity recognition system. It leverages multiple transmission links and all the available bandwidth at 5GHz of commodity WiFi to achieve tracking multiple users simultaneously. Second, we present WiFinger, a finegrained finger gesture recognition system, which utilizes single RF device and does not require peruser or perlocation training. Lastly, we present FruitSense, a RF based fruit ripeness level detection system that achieves environmentindependent sensing. Such system demonstrates the wireless sensing can be utilized beyond human sensing to the biosensing field.
Show less  Date Issued
 2019
 Identifier
 2019_Spring_Tan_fsu_0071E_14891
 Format
 Thesis
 Title
 Melt Structure and Crystallization of Random Ethylene Copolymers.
 Creator

Chen, Xuejian, Alamo, Rufina G., Shanbhag, Sachin, Hallinan, Daniel T., Chung, Hoyong, Florida State University, College of Engineering, Department of Chemical and Biomedical...
Show moreChen, Xuejian, Alamo, Rufina G., Shanbhag, Sachin, Hallinan, Daniel T., Chung, Hoyong, Florida State University, College of Engineering, Department of Chemical and Biomedical Engineering
Show less  Abstract/Description

Linear low density polyethylenes (LLDPEs are substantially linear polyethylenes [(C2H4)n] with randomly distributed 1alkyl short chain branches. The presence of branches on the ethylene backbone sharply reduces the crystallinity level of LLDPEs and retards the crystallization rate compared to the homopolymer. With respect the linear chain, LLDPEs are more flexible, ductile, and more transparent; hence, they are widely used for film applications. It is of great interest to find avenues to...
Show moreLinear low density polyethylenes (LLDPEs are substantially linear polyethylenes [(C2H4)n] with randomly distributed 1alkyl short chain branches. The presence of branches on the ethylene backbone sharply reduces the crystallinity level of LLDPEs and retards the crystallization rate compared to the homopolymer. With respect the linear chain, LLDPEs are more flexible, ductile, and more transparent; hence, they are widely used for film applications. It is of great interest to find avenues to increase the crystallization rate of LLPDEs, or increase production cycles, due to its huge global demand. This work covers a comprehensive study of the correlation between melt topology and phase structure with the crystallization rates of LLDPEs. Narrowly distributed random ethylene 1alkene copolymers display strong memory of crystallization in the melt, even at temperatures above their equilibrium melting point, as indicated by a sharp increase in the recrystallization temperature. Meltmemory is associated with ethylene sequences from prior crystallites that remain in close proximity forming clusters that do not dissolve till very high temperatures. The melt memory strength first increases with branch content due to a topologically more complex intercrystalline region formed by diffusing a larger number of crystalline sequences and then decreases due to depleted crystallinity level. The observed MM strength is independent of alkyl branch length up to octyl. Increasing the crystallinity level makes the intercrystalline region topologically more complex, retarding the dissolution of the clusters in the melt. The dissolution process is thermally activated and becomes extremely slow in the melt of high molar mass copolymers (> 50 kDa) with ~2.2 mol% ethyl branches. Broadly distributed random ethylene 1alkene copolymers, display a special melt memory effect: the crystallization rate increases and then decreases with lowering temperature the melt is cooled from. This inversion of the expected trend of the crystallization rate is associated with the onset of liquidliquid phase separation (LLPS) between lowly branched molecules and highly branched molecules. Upon decreasing melt temperature and crossing the binodal, the thermodynamic drive of phase separation enhances chain dynamics and accelerates dissolution of melt memory. Strong evidence of LLPS is provided in both, solid and melt states using TEM, AFM, SANS, SALS and BFOM. The inversion of crystallization rate is enhanced in systems with a broader distribution of branch content due to stronger thermodynamic drive of phase separation.
Show less  Date Issued
 2018
 Identifier
 2018_Sp_Chen_fsu_0071E_14395
 Format
 Thesis
 Title
 Semiparametric Bayesian Regression Models for Skewed Responses.
 Creator

Bhingare, Apurva Chandrashekhar, Sinha, Debajyoti, Shanbhag, Sachin, Linero, Antonio Ricardo, Bradley, Jonathan R., Pati, Debdeep, Lipsitz, Stuart, Florida State University,...
Show moreBhingare, Apurva Chandrashekhar, Sinha, Debajyoti, Shanbhag, Sachin, Linero, Antonio Ricardo, Bradley, Jonathan R., Pati, Debdeep, Lipsitz, Stuart, Florida State University, College of Arts and Sciences, Department of Statistics
Show less  Abstract/Description

It is common to encounter skewed response data in medicine, epidemiology and health care studies. Methodology needs to be devised to overcome the natural difficulties that occur in analyzing such data particularly when it is multivariate. Existing Bayesian statistical methods to deal with skewed data are mostly fully parametric. We propose novel semiparametric Bayesian methods to model an analyze such data. These methods make minimal assumptions about the true form of the distribution and...
Show moreIt is common to encounter skewed response data in medicine, epidemiology and health care studies. Methodology needs to be devised to overcome the natural difficulties that occur in analyzing such data particularly when it is multivariate. Existing Bayesian statistical methods to deal with skewed data are mostly fully parametric. We propose novel semiparametric Bayesian methods to model an analyze such data. These methods make minimal assumptions about the true form of the distribution and structure of the observed data. Through examples from real life studies, we demonstrate practical advantages of our semiparametric Bayesian methods over the existing methods. For many reallife studies with skewed multivariate responses, the level of skewness and association structure assumptions are essential for evaluating the covariate effects on the response and its predictive distribution. First, we present a novel semiparametric multivariate model class leading to a theoretically justifiable semiparametric Bayesian analysis of multivariate skewed responses. Like the multivariate Gaussian densities, this multivariate model is closed under marginalization, allows a wide class of multivariate associations, and has meaningful physical interpretations of skewness levels and covariate effects on the marginal density. Compared to existing models, our model enjoys several desirable practical properties, including Bayesian computing via available software, and assurance of consistent Bayesian estimates of parameters and the nonparametric error density under a set of plausible prior assumptions. We introduce a particular parametric version of the model as an alternative to various parametric skewsymmetric models available in the literature. We illustrate the practical advantages of our methods over existing parametric alternatives via application to a clinical study to assess periodontal disease and through a simulation study. Unlike most of the models existing in literature, this class of models advocates a latent variable approach making implementation under the Bayesian paradigm via standard software for MCMC computation like WinBUGS/JAGS straightforward. Although, JAGS and WinBUGS are flexible MCMC engines, for complex model structures they tend to be rather slow. We offer an alternative tool to implement the aforementioned parametric version of the models using PROC MCMC in SAS. Our goal is to facilitate and encourage more extensive implementation of these models. To achieve this goal, we illustrate the implementation using PROC MCMC in SAS via examples from real life and provide a full annotated SAS code. In large scale national surveys, we often come across skewed data as well as semicontinuous data, that is, data characterized by point mass at zero (degenerate) and right skewed continuous distribution on positive support. For example, in the Medical Expenditure Panel Survey (MEPS), the variable total health care expenditure (i.e., the response) for nonusers of the health care services is zero, whereas for the users it is has continuous distribution typically skewed towards the right. We provide an overview of the existing models and methods to analyze such data.
Show less  Date Issued
 2018
 Identifier
 2018_Sp_Bhingare_fsu_0071E_14468
 Format
 Thesis
 Title
 Modeling, Manufacturing, and Characterization of Nanocomposites and Multiscale Composites.
 Creator

Kim, Myungsoo, Okoli, Okenwa I., Shanbhag, Sachin, Park, YoungBin, Liang, Zhiyong, Jack, David, Department of Industrial and Manufacturing Engineering, Florida State University
 Abstract/Description

Carbon nanotubes (CNTs) have excellent mechanical, electrical, and thermal properties making them outstanding reinforcements in polymer matrix composites. In this research, the effect of CNTintegration in polymer matrices (twophase) and fiberreinforced composites (threephase) was studied theoretically and experimentally. This work sought to enhance the mechanical properties of composites by the improving dispersion of CNTs in polymers. This was achieved by optimizing the CNT/polymer...
Show moreCarbon nanotubes (CNTs) have excellent mechanical, electrical, and thermal properties making them outstanding reinforcements in polymer matrix composites. In this research, the effect of CNTintegration in polymer matrices (twophase) and fiberreinforced composites (threephase) was studied theoretically and experimentally. This work sought to enhance the mechanical properties of composites by the improving dispersion of CNTs in polymers. This was achieved by optimizing the CNT/polymer composite manufacturing process. Generally, higher sonication intensity and longer sonication time improved the mechanical properties of CNT/polymer composites through improved CNT dispersion. Simulations for CNT/polymer composites (nanocomposites) and CNT/fiber/polymer composites (multiscale composites) were successfully carried out using a new method that combines nanocomposites micromechanics and woven fiber micromechanics. With this new method, the mechanical properties, including the Young's modulus, Poisson's ratio, and shear modulus, of nanocomposites and multiscale composites were predicted in terms of CNT loading in a polymer. The relationships between the mechanical properties of the composites and aspect ratios of the CNTs were studied and, as the third part of the simulation, the mechanical properties of multiscale composites that have no CNTs in the fiber strands were compared with those of multiscale composites that have CNTs in the fiber strands. In order to compare the predicted mechanical properties obtained by the simulations, nano and multiscale composites were manufactured and characterized. Good dispersion of the CNTs and strong bonding between the CNTs and polymer matrix and fibers and matrix are necessary to improve the mechanical properties of nanocomposites and multiscale composites.
Show less  Date Issued
 2009
 Identifier
 FSU_migr_etd3069
 Format
 Thesis
 Title
 ReducedOrder Modeling of Reactive Solute Transport for AdvectionDominated Problems with Nonlinear Kinetic Reactions.
 Creator

McLaughlin, Benjamin R. S., Peterson, Janet S., Ye, Ming, Duke, D. W. (Dennis W.), Gunzburger, Max D., Shanbhag, Sachin, Florida State University, College of Arts and Sciences,...
Show moreMcLaughlin, Benjamin R. S., Peterson, Janet S., Ye, Ming, Duke, D. W. (Dennis W.), Gunzburger, Max D., Shanbhag, Sachin, Florida State University, College of Arts and Sciences, Department of Scientific Computing
Show less  Abstract/Description

Groundwater is a vital natural resource, and our ability to protect and manage this resource efficiently and effectively relies heavily on our ability to perform reliable and accurate computer modeling and simulation of subsurface systems. This frequently raises research questions involving parameter estimation and uncertainty quantification, which are often prohibitively expensive to answer using standard highdimensional computational models. We have previously demonstrated the ability to...
Show moreGroundwater is a vital natural resource, and our ability to protect and manage this resource efficiently and effectively relies heavily on our ability to perform reliable and accurate computer modeling and simulation of subsurface systems. This frequently raises research questions involving parameter estimation and uncertainty quantification, which are often prohibitively expensive to answer using standard highdimensional computational models. We have previously demonstrated the ability to replace the highdimensional models used to solve linear, uncoupled, diffusiondominated multispecies reactive transport systems with lowdimension approximations using reduced order modeling (ROM) based on proper orthogonal decomposition (POD). In this work, we seek to apply ROM to more general reactive transport systems, where the reaction terms may be nonlinear, mathematical models may be coupled, and the transport may be advectiondominated. We discuss the use of operator splitting, which is prevalent in the reactive transport field, to simplify the computation of complex systems of reactions in the transport model. We also discuss the use of some stabilization methods which have been developed in the computational science community to treat advectiondominated transport problems. We present a method by which we are able to incorporate stabilization and operator splitting together in the finite element setting. We go on to develop methods for implementing both operator splitting and stabilization in the ROM setting, as well as for incorporating both of them together within the ROM framework. We present numerical results which establish the ability of this new approach to produce accurate approximations with a significant reduction in computational cost, and we demonstrate the application of this method to a more realistic reactive transport problem involving bioremediation.
Show less  Date Issued
 2015
 Identifier
 FSU_migr_etd9649
 Format
 Thesis
 Title
 Earthquake Rebuild: A Game for the Stealth Learning of Middle School Math.
 Creator

Smith, Danial, Erlebacher, Gordon, Burkhardt, John, Ke, Fengfeng, Shanbhag, Sachin, Florida State University, College of Arts and Science, Department of Scientific Computing
 Abstract/Description

The United States has fallen below many countries in international assessments of middle school aged students in the fields math and science. Computer games have only grown in popularity. In the last few decades, the time spent playing computer and video games have increased as well. Educational games try to recapture some of this time that may otherwise be wasted, but many have failed to preserve the main reason people are drawn to them, the sense of fun. Earthquake Rebuild is a game being...
Show moreThe United States has fallen below many countries in international assessments of middle school aged students in the fields math and science. Computer games have only grown in popularity. In the last few decades, the time spent playing computer and video games have increased as well. Educational games try to recapture some of this time that may otherwise be wasted, but many have failed to preserve the main reason people are drawn to them, the sense of fun. Earthquake Rebuild is a game being developed to assist teachers in the presentation of the common core standards in mathematics in a fun and engaging way. The game is being developed for students in grades six through eight. The setting and story line are motivated by the Fukusima earthquake. The player will be rebuilding a village after its destruction by an earthquake. Earthquake Rebuild follows a progression from using temporary structures, such as the container mall found in New Zealand, to more permanent structures as the difficulty increases. Earthquake Rebuild is being developed by a small group of students, educators, and experts. The project is using Unity 4 as the game engine. A proof of concept demo is completed, with classes to score and track players, as well as classes that will ease the development of the next version.
Show less  Date Issued
 2014
 Identifier
 FSU_migr_etd9247
 Format
 Thesis
 Title
 Stochastic Modeling of Epidemic Diseases Considering Dynamic Contact Networks and Genealogy Information.
 Creator

Ashki, Haleh, Beerli, Peter, Coutts, Christopher, Shanbhag, Sachin, Slice, Dennis E., Lemmon, Alan R., Florida State University, College of Arts and Sciences, Department of...
Show moreAshki, Haleh, Beerli, Peter, Coutts, Christopher, Shanbhag, Sachin, Slice, Dennis E., Lemmon, Alan R., Florida State University, College of Arts and Sciences, Department of Scientific Computing
Show less  Abstract/Description

Human life and diseases are inseparable. For millions of years, humans and their ancestors suffered from diseases, caused by infectious pathogens (e.g., bacteria, viruses, parasites) and caused by our own bodies as they age and degenerate. Within the last century, with the advent of public health measures, improved nutrition and medicine, such as antibiotics, some of the infectious diseases have been controlled. However, infectious diseases still lead to most of the nonage related deaths in...
Show moreHuman life and diseases are inseparable. For millions of years, humans and their ancestors suffered from diseases, caused by infectious pathogens (e.g., bacteria, viruses, parasites) and caused by our own bodies as they age and degenerate. Within the last century, with the advent of public health measures, improved nutrition and medicine, such as antibiotics, some of the infectious diseases have been controlled. However, infectious diseases still lead to most of the nonage related deaths in the world, especially in nations with insufficient health support. My research has taken the complex and dynamic contact networks as well as heterogeneity in disease transmission and recovery into account. Real social networks among individuals were used to generate an adjacency matrix in my formulas. Both, transition and recovery rates have been used as unique variables for each individual. I have used the forward Kolmogorov equation to solve the system. To control and prevent the infectious diseases such as influenza, sexually transmitted diseases, we have to model the dynamics of a particular disease, estimate the parameters, and forecast the behavior of the disease over time. The estimated parameters help us to design and implement interventions, such as vaccination, closure of public places, to limit the spread of diseases. R0, the reproduction number is an important parameter in epidemiology. R0 is the average number of secondary infections produced by a primary infection. If R0 is larger than one an epidemic will most likely happen, an R0 smaller than one suggests that the disease outbreak is local and will die out. In this study I have shown that R0 estimators that only use the the number of contacts and some network features such as covariance of coefficient are not enough to estimate the epidemic threshold. I have formulated R0 to consider both node degree distribution as well as the spectral gap in the eigenvalue of a weighted adjacency matrix of contact network. Only recently, researchers have developed theoretical approaches that can take into account dynamic networks and, independently, that can use genomic data of the pathogen, sampled from infected persons, to reconstruct the path of an epidemic. By considering the location and time of the sampled pathogen sequence data we can combine the sampled infection network and the mutational history of the pathogen to reconstruct a more accurate contact network. We can reconstruct this dynamic contact network using genetic data and epidemic parameters via a Hidden Markov Model. Sampled genome sequenced data of the pathogen are the observation and a set of dynamic networks are the hidden states in our HMM framework. The system switches between the set of dynamic contact networks to fit the best pattern to observation data. The outcome of such an analysis is the accurate dynamic network among samples of the pathogen. These set of dynamic networks capture the dynamics of the social contact network of the infected people. My model will most likely enable earlier detection of infectious disease spread in dynamic social networks than currently available methods.
Show less  Date Issued
 2015
 Identifier
 FSU_migr_etd9542
 Format
 Thesis
 Title
 Simulating the Impacts and Sensitivity of the Southeastern United States Climatology to Irrigation.
 Creator

Selman, Christopher Manuel, Misra, Vasubandhu, Shanbhag, Sachin, Bourassa, Mark Allan, Liu, Guosheng, Wu, Zhaohua, Florida State University, College of Arts and Sciences,...
Show moreSelman, Christopher Manuel, Misra, Vasubandhu, Shanbhag, Sachin, Bourassa, Mark Allan, Liu, Guosheng, Wu, Zhaohua, Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
Show less  Abstract/Description

The diurnal variations from a highresolution regional climate model (Regional Spectral Model; RSM) are analyzed from 6 independent decade long integrations using lateral boundary forcing data separately from the National Centers for Environmental Prediction Reanalysis 2 (NCEPR2), and European Center for MediumRange Weather Forecasts (ECMWF) 40year Reanalysis (ERA40) and the 20th Century Reanalysis (20CR). With each of these lateral boundary forcing data, the RSM is integrated separately...
Show moreThe diurnal variations from a highresolution regional climate model (Regional Spectral Model; RSM) are analyzed from 6 independent decade long integrations using lateral boundary forcing data separately from the National Centers for Environmental Prediction Reanalysis 2 (NCEPR2), and European Center for MediumRange Weather Forecasts (ECMWF) 40year Reanalysis (ERA40) and the 20th Century Reanalysis (20CR). With each of these lateral boundary forcing data, the RSM is integrated separately using two convection schemes: the Relaxed ArakawaSchubert (RAS) and KainFritsch (KF) schemes. The results show that RSM integrations forced with 20CR have the least fidelity in depicting the seasonal cycle and diurnal variability of precipitation and surface temperature over the Southeastern United States (SEUS). The remaining four model simulations show comparable skills. The differences in the diurnal amplitude of rainfall during the summer months of the 20CR forced integration from the corresponding NCEPR2 forced integration, for example, is found to be largely from the transient component of the moisture flux convergence. The root mean square error (RMSE) of the seasonal cycle of precipitation and surface temperature of the other four simulations (not forced by 20CR) were comparable to each other and highest in the summer months. But the RMSE of the diurnal amplitude of precipitation and the timing of its diurnal zenith were largest during winter months and least during summer and fall months in the four model simulations (not forced by 20CR). The diurnal amplitude of surface temperature in comparison showed far less fidelity in all models. The phase of the diurnal maximum of surface temperature however showed significantly better validation with corresponding observations in all of the 6 model simulations The impacts of irrigation on SEUS diurnal climate are then investigated. An extreme case is assumed, wherein irrigation is set to 100% of field capacity over the growing season of May through October (IRR100). Irrigation is applied to the root zone layers of 1040cm and 40100cm soil layers only. It is found that in this regime there is a pronounced decrease in monthly averaged temperatures in irrigated regions across all months. In nonirrigated areas a slight warming is simulated. Diurnal maximum temperatures in irrigated areas warm, while diurnal minimum temperatures cool. The daytime warming is attributed to an increase in shortwave flux at the surface owing to diminished low cloud cover. Nighttime cooling results as a consequence of higher net downward ground heat flux. Both diurnal and monthly average precipitations are reduced over irrigated areas at a magnitude and spatial pattern similar to one another. Due to the excess moisture availability, evaporation is seen to increase, but this is balanced by a corresponding reduction in sensible heat flux. Concomitant with additional moisture availability is an increase in both transient and stationary moisture flux convergences. However, despite the increase, there is a largescale stabilization of the atmosphere stemming from a cold surface and a warmed vertical column. Three additional regional climate model runs centered on the SEUS assume a crop growing season of May through October and are irrigated at 25%, 50%, 75% (IRR25, IRR50, IRR75, respectively) of the root zone field capacity to assess the sensitivity of the SEUS climate to irrigation. A fifth run, assuming no irrigation (CTL), is used as the basis for comparison. Across all IRR runs, it is found that there is a general reduction in monthly mean precipitation over the irrigated cells relative to CTL, with much of the change occurring in the subdiurnal scales. This manifests as an increase dry days and reduction in > 1 mm/day rainfall events. IRR25 is seen to have the lowest change in both, while IRR100 is seen to have the greatest change. Areaaveraged precipitation over the irrigated cells reveals a strong reduction in precipitation in IRR100 (on the order of 0.4 mm/hr) with a much weaker reduction in IRR25. Vertically integrated moisture convergence is seen to have the most pronounced sensitivity pattern across all runs. Monthly averaged temperatures are reduced over irrigated areas, with the intensity of the reduction increasing as irrigation vigor increases. This is attributed to a systematic change in ground heat flux that transports heat into the subsurface soil layers in the irrigated cells. The precipitation ahead of the transient cold fronts is reduced by irrigation as it passes over the irrigated cells. The intensity of the net precipitation reduction becomes more intense as irrigation vigor increases. Lastly, heat waves in the SEUS are reduced in intensity just over the irrigated cells, though likely increasing in frequency due to lowered temperature thresholds for heat wave definition.
Show less  Date Issued
 2015
 Identifier
 FSU_migr_etd9679
 Format
 Thesis
 Title
 Experimental and Computational Studies on DNA Electrophoresis in Lyotropic Polymer Liquid Crystals.
 Creator

Wei, Ling, Van Winkle, David H., Shanbhag, Sachin, Xiong, Peng, Rikvold, Per Arne, Wahl, Horst D., Florida State University, College of Arts and Sciences, Department of Physics
 Abstract/Description

Electrophoresis as an analytical technique has made considerable contributions to the separations and analysis of macromolecules in biologyrelated research. Pluronic gels, which are composed of orderly packed spherical micelles assembled by triblock copolymers, have been developed as novel sieving media to separate oligonucleotides, duplex DNA molecules and proteins, providing ease of manipulations due to their thermoreversibility and higher resolution in comparison with other polymer gels...
Show moreElectrophoresis as an analytical technique has made considerable contributions to the separations and analysis of macromolecules in biologyrelated research. Pluronic gels, which are composed of orderly packed spherical micelles assembled by triblock copolymers, have been developed as novel sieving media to separate oligonucleotides, duplex DNA molecules and proteins, providing ease of manipulations due to their thermoreversibility and higher resolution in comparison with other polymer gels. Electrophoretic mobility of short doublestranded DNA molecules in pluronic F127 is reported to have a nonmonotonic dependence on DNA length, which is not observed in other polymerbased sieving media or explained by any welldeveloped theories. In this dissertation, the unusual DNAlength dependence of electrophoretic mobility is experimentally investigated in several different pluronic gels, and the DNA dynamics in pluronic liquid crystals is systematically studied by coarsegrained Brownian dynamics simulations. The crystal structures and micelle dimensions of pluronics P105, P123 and F127 are characterized by atomic force microscopy, smallangle xray scattering, smallangle neutron scattering and dynamic light scattering. Twodimensional gel electrophoresis is performed and the electrophoretic mobility of DNA molecules in the size range of 20500 bp is measured in pluronics P105, P123 and F127. The unusual DNA lengthdependent mobility is consistently obtained in three pluronic gels, where the mobility of very short DNA molecules increases with increasing DNA length, and the mobility of long DNA molecules monotonically decreases with DNA length. Superposed on the rising and falling trends are the subtle oscillations of mobility with DNA length in the intermediate regime. Brownian dynamics simulations are implemented to numerically calculate the DNA mobility in pluronic lattices, by including the shortranged intramolecular hydrodynamic interactions, and modeling the interactions between DNA molecules and pluronic micelles via a repulsive force and entanglement effect. The rise, fall and oscillations of mobility with DNA length, as obtained in experimental measurements, are reproduced by the Brownian dynamics simulations, and essential physics that dominates the unusual features of mobility is extracted from the simulations. In addition, electric fielddependent mobility of DNA molecules in pluronic lattices is studied by Brownian dynamics simulations, and the conceptual connection between highfield simulations along specific field directions and lowfield experiments in bulk gels is established, and the Brownian dynamic simulations are proven to be an appropriate approach to interpret the DNA electrophoretic dynamics in pluronic matrices. Moreover, electrophoretic mobility of duplex DNA flanked by singlestranded overhangs is measured in pluronic gels, and it is shown that the mobility of DNA with overhangs is higher than the corresponding bluntended DNA molecules. Brownian dynamics simulations are carried out, and the enhancement of mobility for DNA with overhangs is captured by the simulations. By integrating numerical simulations with experimental measurements, the fundamental physical quantities and interactions that manipulate the DNA electrophoretic migration in pluronic liquid crystals are revealed. Understanding the unusual DNA lengthdependent mobility in pluronic gels potentially provides profound insights in designing and optimizing highperformance sieving matrices for sizebased separation purposes.
Show less  Date Issued
 2016
 Identifier
 FSU_FA2016_Wei_fsu_0071E_13585
 Format
 Thesis
 Title
 Computational Studies of Equilibrium and NonEquilibrium Phase Diagrams and Critical Properties of Two Physical and Chemical Model Systems with Both ShortRange and LongRange Interactions or Reactivities.
 Creator

Chan, ChorHoi, Rikvold, Per Arne, Shanbhag, Sachin, Brown, Gregory, Capstick, Simon, Xiong, Peng, Florida State University, College of Arts and Sciences, Department of Physics
 Abstract/Description

In this dissertation, we introduce longrange interactions into one equilibrium model (Ising model) and one nonequilibrium system (ZiffGulariBarshad model), and study their phase diagrams and critical properties. A new approach to do WangLandau simulation: macroscopically constrained WangLandau, is proposed in connection with the former system. Our macroscopically constrained WangLandau method breaks a multidimensional random walk process in phase space into many separate, one...
Show moreIn this dissertation, we introduce longrange interactions into one equilibrium model (Ising model) and one nonequilibrium system (ZiffGulariBarshad model), and study their phase diagrams and critical properties. A new approach to do WangLandau simulation: macroscopically constrained WangLandau, is proposed in connection with the former system. Our macroscopically constrained WangLandau method breaks a multidimensional random walk process in phase space into many separate, onedimensional random walk processes in the energy space. Each of these random walks is constrained to a different value of the macroscopic order parameters. By knowing the distribution of these constrained variables, we can deduce the multivariable density of states. When the multivariable density of states for one set of external parameters is obtained, the density of states at any point in the phase diagram can be obtained by simple transformations. After that, all thermodynamic quantities can be obtained. We apply this method to an antiferromagnetic Ising model with a ferromagnetic longrange interaction. The addition of the longrange interaction induces metastable regions in the phase diagram, and a meanfield class critical point emerges for sufficiently strong longrange interaction. We demonstrate how to use the multivariable density of states obtained to sketch out the complicated phase diagrams for different values of the longrange interaction. We also give freeenergy plots, and plots of the distributions of the order parameters of the system for different special points in these phase diagrams. The ZiffGulariBarshad (ZGB) model, a simplified description of the oxidation of carbon monoxide (CO) on a catalyst surface, is widely used to study properties of nonequilibrium phase transitions. Instead of restricting the CO and atomic oxygen (O) to react to form carbon dioxide (CO₂) only when they are adsorbed in close proximity, we consider a modified model that includes an adjustable probability for adsorbed CO and O atoms located far apart on the lattice to react. We employ largescale Monte Carlo simulations to study the critical properties of this system. We find that the nonequilibrium critical point changes from the twodimensional Ising universality class to the meanfield universality class upon introducing even a weak longrange reactivity mechanism.
Show less  Date Issued
 2016
 Identifier
 FSU_FA2016_Chan_fsu_0071E_13552
 Format
 Thesis
 Title
 Detonability of Turbulent White Dwarf Plasma: Hydrodynamical Models at Low Densities.
 Creator

Fenn, Daniel Fenn, Plewa, Tomasz, Sussman, Mark, Erlebacher, Gordon, Piekarewicz, Jorge, Shanbhag, Sachin, Florida State University, College of Arts and Sciences, Department of...
Show moreFenn, Daniel Fenn, Plewa, Tomasz, Sussman, Mark, Erlebacher, Gordon, Piekarewicz, Jorge, Shanbhag, Sachin, Florida State University, College of Arts and Sciences, Department of Scientific Computing
Show less  Abstract/Description

The origins of Type Ia supernovae (SNe Ia) remain an unsolved problem of contemporary astrophysics. Decades of research indicate that these supernovae arise from thermonuclear runaway in the degenerate material of white dwarf stars; however, the mechanism of these explosions is unknown. Also, it is unclear what are the progenitors of these objects. These missing elements are vital components of the initial conditions of supernova explosions, and are essential to understanding these events. A...
Show moreThe origins of Type Ia supernovae (SNe Ia) remain an unsolved problem of contemporary astrophysics. Decades of research indicate that these supernovae arise from thermonuclear runaway in the degenerate material of white dwarf stars; however, the mechanism of these explosions is unknown. Also, it is unclear what are the progenitors of these objects. These missing elements are vital components of the initial conditions of supernova explosions, and are essential to understanding these events. A requirement of any successful SN Ia model is that a sufficient portion of the white dwarf plasma must be brought under conditions conducive to explosive burning. Our aim is to identify the conditions required to trigger detonations in turbulent, carbonrich degenerate plasma at low densities. We study this problem by modeling the hydrodynamic evolution of a turbulent region filled with a carbon/oxygen mixture at a density, temperature, and Mach number characteristic of conditions found in the 0.8+1.2 solar mass (CO0812) model discussed by Fenn et al. (2016). We probe the ignition conditions for different degrees of compressibility in turbulent driving. We assess the probability of successful detonations based on characteristics of the identified ignition kernels, using Eulerian and Lagrangian statistics of turbulent flow. We found that material with very short ignition times is abundant in the case that turbulence is driven compressively. This material forms contiguous structures that persist over many ignition time scales, and that we identify as prospective detonation kernels. Detailed analysis of the kernels revealed that their central regions are densely filled with material characterized by short ignition times and contain the minimum mass required for selfsustained detonations to form. It is conceivable that ignition kernels will be formed for lower compressibility in the turbulent driving. However, we found no detonation kernels in models driven 87.5 percent compressively. We indirectly confirmed the existence of the lower limit of the degree of compressibility of the turbulent drive for the formation of detonation kernels by analyzing simulation results of the He0609 model of Fenn et al. (2016), which produces a detonation in a heliumrich boundary layer. We found that the amount of energy in the compressible component of the kinetic energy in this model corresponds to about 96 percent compressibility in the turbulent drive. The fact that no detonation was found in the original CO0812 model for nominally the same problem conditions suggests that models with carbonrich boundary layers may require higher resolution in order to adequately represent the mass distributions in terms of ignition times.
Show less  Date Issued
 2016
 Identifier
 FSU_FA2016_Fenn_fsu_0071E_13617
 Format
 Thesis
 Title
 Reduced Order Modeling for a Nonlocal Approach to Anomalous Diffusion Problems.
 Creator

Witman, David, Gunzburger, Max D., Peterson, Janet C., Stagg, Scott, Shanbhag, Sachin, Burkardt, John V., Florida State University, College of Arts and Sciences, Department of...
Show moreWitman, David, Gunzburger, Max D., Peterson, Janet C., Stagg, Scott, Shanbhag, Sachin, Burkardt, John V., Florida State University, College of Arts and Sciences, Department of Scientific Computing
Show less  Abstract/Description

With the recent advances in using nonlocal approaches to approximate traditional partial differential equations(PDEs), a number of new research avenues have been opened that warrant further study. One such path, that has yet to be explored, is using reduced order techniques to solve nonlocal problems. Due to the interactions between the discretized nodes or particles inherent to a nonlocal model, the system sparsity is often significantly less than its PDE counterpart. Coupling a reduced...
Show moreWith the recent advances in using nonlocal approaches to approximate traditional partial differential equations(PDEs), a number of new research avenues have been opened that warrant further study. One such path, that has yet to be explored, is using reduced order techniques to solve nonlocal problems. Due to the interactions between the discretized nodes or particles inherent to a nonlocal model, the system sparsity is often significantly less than its PDE counterpart. Coupling a reduced order approach to a nonlocal problem would ideally reduce the computational cost without sacrificing accuracy. This would allow for the use of a nonlocal approach in large parameter studies or uncertainty quantification. Additionally, because nonlocal problems inherently have no spatial derivatives, solutions with jump discontinuities are permitted. This work seeks to apply reduced order nonlocal concepts to a variety of problem situations including anomalous diffusion, advection, the advectiondiffusion equation and solutions with spatial discontinuities. The goal is to show that one can use an accurate reduced order approximation to formulate a solution at a fraction of the cost of traditional techniques.
Show less  Date Issued
 2016
 Identifier
 FSU_2016SP_Witman_fsu_0071E_13130
 Format
 Thesis
 Title
 Development of Crystalline Structure in Blends of iPP and Isotactic Propylene1Alkene Random Copolymers.
 Creator

Janani, Hamed, Alamo, Rufina G., Shanbhag, Sachin, Telotte, John C., Hallinan, Daniel T., Florida State University, FAMUFSU College of Engineering, Department of Chemical and...
Show moreJanani, Hamed, Alamo, Rufina G., Shanbhag, Sachin, Telotte, John C., Hallinan, Daniel T., Florida State University, FAMUFSU College of Engineering, Department of Chemical and Biomedical Engineering
Show less  Abstract/Description

The study of melt miscibility and structureproperty relations of different types of polyolefins provide an important pathway to material design for different applications. In this work we study melt and crystalline properties of blends of iPP and isotactic propylene1hexene (PH) random copolymers with 11 and 21 mol% 1hexene, (PH11, PH21). Three types of blends are studied, namely PH11/PH21, iPP/PH11 and iPP/PH21. The study of melt miscibility using thermodynamic estimations coupled with...
Show moreThe study of melt miscibility and structureproperty relations of different types of polyolefins provide an important pathway to material design for different applications. In this work we study melt and crystalline properties of blends of iPP and isotactic propylene1hexene (PH) random copolymers with 11 and 21 mol% 1hexene, (PH11, PH21). Three types of blends are studied, namely PH11/PH21, iPP/PH11 and iPP/PH21. The study of melt miscibility using thermodynamic estimations coupled with experimental data from DSC, DMA, and AFM techniques indicate that blends of iPP/PH11 and PH11/PH21 are miscible in the melt while blends iPP/PH21 are immiscible. Depending on crystallization conditions, iPP and PH11 may crystallize in monoclinic (α) or mesophase, and PH21 crystallizes in the trigonal phase exclusively. The effect of isotactic sequence length distribution (ISLD) on polymorphism and crystallization kinetics was quantitatively studied in miscible PH11/PH21 blends. An enhanced rate of formation of trigonal phase with increasing PH11 was attributed to the increasing composition of 1hexene in the melt during evolution of the monoclinic phase in the first stage of isothermal crystallization of the blends. The rate of crystallization of iPP in miscible blends of iPP/PH11 decreases with increasing content of PH11, but it is independent of blend composition for immiscible iPP/PH21 blends, as expected. The addition of only 25 wt.% of an elastomer such as PH11 or PH21 to iPP decreases slightly the level of crystallinity, from ~70% in neat iPP to ~60% in the blend; however, blending leads to a dramatic effect on the tensile properties of iPP, i.e. makes the brittle iPP to be ductile at room temperature. The crystallization of iPP from homogeneous melts leads to an interconnected crystal network and elongations of ~ 600% in blends with 25% PH11, while lack of connectivity in melt immiscible iPP/PH21 blends lowers strain to ~ 450%. Insitu WAXStensile experiments indicate that the significant ductility and strain hardening behavior observed in iPP/PH copolymers are accompanied by a significant polymorphic transformation of monoclinic to mesophase under deformation of miscible iPP/PH11 blends, and by additional trigonal orientation in blends of iPP/PH21.
Show less  Date Issued
 2016
 Identifier
 FSU_2016SP_Janani_fsu_0071E_13125
 Format
 Thesis
 Title
 Entanglement Entropy and Entanglement Hamiltonian as Characterizations of Phases and Phase Transitions.
 Creator

Pouranvari, Mohammad, Yang, Kun, Shanbhag, Sachin, Bonesteel, N. E., Balicas, Luis, Chiorescu, Irinel, Florida State University, College of Arts and Sciences, Department of Physics
 Abstract/Description

In this thesis, we study the entanglement properties of quantum systems to characterize quantum phases and phase transitions. We focus on the free fermion lattice systems and we use numerical calculation to verify our ideas. Behavior of the entanglement entropy is used to distinguish different phases, in addition the area law of the entanglement entropy is studied. We propose that beside the entanglement entropy, there is physical information in the entanglement Hamiltonian of the reduced...
Show moreIn this thesis, we study the entanglement properties of quantum systems to characterize quantum phases and phase transitions. We focus on the free fermion lattice systems and we use numerical calculation to verify our ideas. Behavior of the entanglement entropy is used to distinguish different phases, in addition the area law of the entanglement entropy is studied. We propose that beside the entanglement entropy, there is physical information in the entanglement Hamiltonian of the reduced density matrix of a chosen subsystem. We verify our ideas by studying different free fermion models. The verification is made by comparing the results we obtain from studying the behavior of the entanglement Hamiltonian with the known previous results. As starting point, to show that entanglement Hamiltonian eigenmodes have physical information, we employ the XX spin chain model. Real space renormalization group method predicts that the ground state is the product state of singlet states and thus those singlet that cross the boundary make the entanglement. We use the entanglement Hamiltonian to show that its single particle eigenmode shows the location of the entangled singlet spins. This is done in the case of ground state at T = 0. We also studied the entanglement properties of the highly excited eigenstate of the system. We use modified version of real space renormalization group for excited state and we show that in T ≠ 0 case where singlet and triplet state with total S[subscript Z] = 0 make entanglement, entanglement Hamiltonian eigenmode shows the location of the entangled spins. We distinguish one eigenmode of the entanglement Hamiltonian as the maximally entangled mode. This mode corresponds to the smallest entanglement energy and thus contributes the most to the entanglement entropy. In addition, we use two onedimensional free fermion models, namely the random dimer model and power law random banded model to show that for a localizeddelocalized phase transition, behavior of the maximally entangled mode is similar to the behavior of the eigenmode of the original Hamiltonian at the Fermi level. We quantify this by comparing their overlaps and the inverse participation ratio of eigenmodes. The behavior of the entanglement entropy as a wellknown quantity is studied in disordered free fermion models. In random dimer model and power law random banded model where the correlated disorder yields to the localizeddelocalized phase transition, we show that entanglement entropy saturates in localized phase and diverges in delocalized phase. In addition it violates the area law in delocalized phase. Entanglement entropy of Anderson model in one, two, and three dimensions is also studied and we observed that area law is correct even for the delocalized phase of the Anderson model in three dimensions, provided that system size is larger than the mean free path. The study of a single impurity, one nonzero onsite energy, in the Anderson model is also examined. We concluded that this single impurity changes only the subleading term of the entanglement entropy which is proportional to the inverse of the subsystem size. This subleading term has nonoscillation and oscillating part.
Show less  Date Issued
 2016
 Identifier
 FSU_2016SP_Pouranvari_fsu_0071E_13052
 Format
 Thesis
 Title
 Using Deal.II to Solve Problems in Computational Fluid Dynamics.
 Creator

Bystricky, Lukas, Peterson, Janet C., Shanbhag, Sachin, Burkardt, John V., Florida State University, College of Arts and Sciences, Department of Scientific Computing
 Abstract/Description

Finite element methods are a common tool to solve problems in computational fluid dynamics (CFD). This thesis explores the finite element package deal.ii and specific applications to incompressible CFD. Some notation and results from finite element theory are summarised, and a brief overview of some of the features of deal.ii is given. Following this, several CFD applications are presented, including the Stokes equations, the NavierStokes equations and the equations for Darcy flow in porous...
Show moreFinite element methods are a common tool to solve problems in computational fluid dynamics (CFD). This thesis explores the finite element package deal.ii and specific applications to incompressible CFD. Some notation and results from finite element theory are summarised, and a brief overview of some of the features of deal.ii is given. Following this, several CFD applications are presented, including the Stokes equations, the NavierStokes equations and the equations for Darcy flow in porous media. Comparison with benchmark problems are provided for the Stokes and NavierStokes equations and a case study looking at foam deformation is provided for Darcy flow. Code is provided where applicable.
Show less  Date Issued
 2016
 Identifier
 FSU_2016SP_Bystricky_fsu_0071N_13237
 Format
 Thesis