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- Genre: Academic theses
Description
Advances in experimental techniques have allowed for investigation of molecular dynamics at ever smaller temporal and spatial scales. There is currently a varied and growing body of literature which demonstrates the phenomenon of \emph{anomalous diffusion} in physics, engineering, and biology. In particular many diffusive type processes in the cell have been observed to follow a power law $\left \propto t^\alpha$ scaling of the mean square displacement of a particle. This contrasts with the expected linear behavior of particles undergoing normal diffusion. \emph{Anomalous sub-diffusion} ($\alpha<1$) has been attributed to factors such as cytoplasmic crowding of macromolecules, and trap-like structures in the subcellular environment non-linearly slowing the diffusion of molecules. Compared to normal diffusion, signaling molecules in these constrained spaces can be more concentrated at the source, and more diffuse at longer distances, potentially effecting the signalling dynamics. As diffusion at the cellular scale is a fundamental mechanism of cellular signaling and additionally is an implicit underlying mathematical assumption of many canonical models, a closer look at models of anomalous diffusion is warranted. Approaches in the literature include derivations of fractional differential diffusion equations (FDE) and continuous time random walks (CTRW). However these approaches are typically based on \emph{ad-hoc} assumptions on time- and space- jump distributions. We apply recent developments in asymptotic techniques on collisional kinetic equations to develop a FDE model of sub-diffusion due to trapping regions and investigate the nature of the space/time probability distributions assosiated with trapping regions. This approach both contrasts and compliments the stochastic CTRW approach by positing more physically realistic underlying assumptions on the motion of particles and their interactions with trapping regions, and additionally allowing varying assumptions to be applied individually to the traps and particle kinetics.
ContributorsHoleva, Thomas Matthew (Author) / Ringhofer, Christian (Thesis advisor) / Baer, Steve (Thesis advisor) / Crook, Sharon (Committee member) / Gardner, Carl (Committee member) / Taylor, Jesse (Committee member) / Arizona State University (Publisher)
Created2014
Description
The theme for this work is the development of fast numerical algorithms for sparse optimization as well as their applications in medical imaging and source localization using sensor array processing. Due to the recently proposed theory of Compressive Sensing (CS), the $\ell_1$ minimization problem attracts more attention for its ability to exploit sparsity. Traditional interior point methods encounter difficulties in computation for solving the CS applications. In the first part of this work, a fast algorithm based on the augmented Lagrangian method for solving the large-scale TV-$\ell_1$ regularized inverse problem is proposed. Specifically, by taking advantage of the separable structure, the original problem can be approximated via the sum of a series of simple functions with closed form solutions. A preconditioner for solving the block Toeplitz with Toeplitz block (BTTB) linear system is proposed to accelerate the computation. An in-depth discussion on the rate of convergence and the optimal parameter selection criteria is given. Numerical experiments are used to test the performance and the robustness of the proposed algorithm to a wide range of parameter values. Applications of the algorithm in magnetic resonance (MR) imaging and a comparison with other existing methods are included. The second part of this work is the application of the TV-$\ell_1$ model in source localization using sensor arrays. The array output is reformulated into a sparse waveform via an over-complete basis and study the $\ell_p$-norm properties in detecting the sparsity. An algorithm is proposed for minimizing a non-convex problem. According to the results of numerical experiments, the proposed algorithm with the aid of the $\ell_p$-norm can resolve closely distributed sources with higher accuracy than other existing methods.
ContributorsShen, Wei (Author) / Mittlemann, Hans D (Thesis advisor) / Renaut, Rosemary A. (Committee member) / Jackiewicz, Zdzislaw (Committee member) / Gelb, Anne (Committee member) / Ringhofer, Christian (Committee member) / Arizona State University (Publisher)
Created2011
Description
In vertebrate outer retina, changes in the membrane potential of horizontal cells affect the calcium influx and glutamate release of cone photoreceptors via a negative feedback. This feedback has a number of important physiological consequences. One is called background-induced flicker enhancement (BIFE) in which the onset of dim background enhances the center flicker response of horizontal cells. The underlying mechanism for the feedback is still unclear but competing hypotheses have been proposed. One is the GABA hypothesis, which states that the feedback is mediated by gamma-aminobutyric acid (GABA), an inhibitory neurotransmitter released from horizontal cells. Another is the ephaptic hypothesis, which contends that the feedback is non-GABAergic and is achieved through the modulation of electrical potential in the intersynaptic cleft between cones and horizontal cells. In this study, a continuum spine model of the cone-horizontal cell synaptic circuitry is formulated. This model, a partial differential equation system, incorporates both the GABA and ephaptic feedback mechanisms. Simulation results, in comparison with experiments, indicate that the ephaptic mechanism is necessary in order for the model to capture the major spatial and temporal dynamics of the BIFE effect. In addition, simulations indicate that the GABA mechanism may play some minor modulation role.
ContributorsChang, Shaojie (Author) / Baer, Steven M. (Thesis advisor) / Gardner, Carl L (Thesis advisor) / Crook, Sharon M (Committee member) / Kuang, Yang (Committee member) / Ringhofer, Christian (Committee member) / Arizona State University (Publisher)
Created2012
Description
Factory production is stochastic in nature with time varying input and output processes that are non-stationary stochastic processes. Hence, the principle quantities of interest are random variables. Typical modeling of such behavior involves numerical simulation and statistical analysis. A deterministic closure model leading to a second order model for the product density and product speed has previously been proposed. The resulting partial differential equations (PDE) are compared to discrete event simulations (DES) that simulate factory production as a time dependent M/M/1 queuing system. Three fundamental scenarios for the time dependent influx are studied: An instant step up/down of the mean arrival rate; an exponential step up/down of the mean arrival rate; and periodic variation of the mean arrival rate. It is shown that the second order model, in general, yields significant improvement over current first order models. Specifically, the agreement between the DES and the PDE for the step up and for periodic forcing that is not too rapid is very good. Adding diffusion to the PDE further improves the agreement. The analysis also points to fundamental open issues regarding the deterministic modeling of low signal-to-noise ratio for some stochastic processes and the possibility of resonance in deterministic models that is not present in the original stochastic process.
ContributorsWienke, Matthew (Author) / Armbruster, Dieter (Thesis advisor) / Jones, Donald (Committee member) / Platte, Rodrigo (Committee member) / Gardner, Carl (Committee member) / Ringhofer, Christian (Committee member) / Arizona State University (Publisher)
Created2015
Description
Swarms of animals, fish, birds, locusts etc. are a common occurrence but their coherence and method of organization poses a major question for mathematics and biology.The Vicsek and the Attraction-Repulsion are two models that have been proposed to explain the emergence of collective motion. A major issue for the Vicsek Model is that its particles are not attracted to each other, leaving the swarm with alignment in velocity but without spatial coherence. Restricting the particles to a bounded domain generates global spatial coherence of swarms while maintaining velocity alignment. While individual particles are specularly reflected at the boundary, the swarm as a whole is not. As a result, new dynamical swarming solutions are found.
The Attraction-Repulsion Model set with a long-range attraction and short-range repulsion interaction potential typically stabilizes to a well-studied flock steady state solution. The particles for a flock remain spatially coherent but have no spatial bound and explore all space. A bounded domain with specularly reflecting walls traps the particles within a specific region. A fundamental refraction law for a swarm impacting on a planar boundary is derived. The swarm reflection varies from specular for a swarm dominated by
kinetic energy to inelastic for a swarm dominated by potential energy. Inelastic collisions lead to alignment with the wall and to damped pulsating oscillations of the swarm. The fundamental refraction law provides a one-dimensional iterative map that allows for a prediction and analysis of the trajectory of the center of mass of a flock in a channel and a square domain.
The extension of the wall collisions to a scattering experiment is conducted by setting two identical flocks to collide. The two particle dynamics is studied analytically and shows a transition from scattering: diverging flocks to bound states in the form of oscillations or parallel motions. Numerical studies of collisions of flocks show the same transition where the bound states become either a single translating flock or a rotating (mill).
The Attraction-Repulsion Model set with a long-range attraction and short-range repulsion interaction potential typically stabilizes to a well-studied flock steady state solution. The particles for a flock remain spatially coherent but have no spatial bound and explore all space. A bounded domain with specularly reflecting walls traps the particles within a specific region. A fundamental refraction law for a swarm impacting on a planar boundary is derived. The swarm reflection varies from specular for a swarm dominated by
kinetic energy to inelastic for a swarm dominated by potential energy. Inelastic collisions lead to alignment with the wall and to damped pulsating oscillations of the swarm. The fundamental refraction law provides a one-dimensional iterative map that allows for a prediction and analysis of the trajectory of the center of mass of a flock in a channel and a square domain.
The extension of the wall collisions to a scattering experiment is conducted by setting two identical flocks to collide. The two particle dynamics is studied analytically and shows a transition from scattering: diverging flocks to bound states in the form of oscillations or parallel motions. Numerical studies of collisions of flocks show the same transition where the bound states become either a single translating flock or a rotating (mill).
ContributorsThatcher, Andrea (Author) / Armbruster, Hans (Thesis advisor) / Motsch, Sebastien (Committee member) / Ringhofer, Christian (Committee member) / Platte, Rodrigo (Committee member) / Gardner, Carl (Committee member) / Arizona State University (Publisher)
Created2015
Description
Need-based transfers (NBTs) are a form of risk-pooling in which binary welfare exchanges
occur to preserve the viable participation of individuals in an economy, e.g. reciprocal gifting
of cattle among East African herders or food sharing among vampire bats. With the
broad goal of better understanding the mathematics of such binary welfare and risk pooling,
agent-based simulations are conducted to explore socially optimal transfer policies
and sharing network structures, kinetic exchange models that utilize tools from the kinetic
theory of gas dynamics are utilized to characterize the wealth distribution of an NBT economy,
and a variant of repeated prisoner’s dilemma is analyzed to determine whether and
why individuals would participate in such a system of reciprocal altruism.
From agent-based simulation and kinetic exchange models, it is found that regressive
NBT wealth redistribution acts as a cutting stock optimization heuristic that most efficiently
matches deficits to surpluses to improve short-term survival; however, progressive
redistribution leads to a wealth distribution that is more stable in volatile environments and
therefore is optimal for long-term survival. Homogeneous sharing networks with low variance
in degree are found to be ideal for maintaining community viability as the burden and
benefit of NBTs is equally shared. Also, phrasing NBTs as a survivor’s dilemma reveals
parameter regions where the repeated game becomes equivalent to a stag hunt or harmony
game, and thus where cooperation is evolutionarily stable.
occur to preserve the viable participation of individuals in an economy, e.g. reciprocal gifting
of cattle among East African herders or food sharing among vampire bats. With the
broad goal of better understanding the mathematics of such binary welfare and risk pooling,
agent-based simulations are conducted to explore socially optimal transfer policies
and sharing network structures, kinetic exchange models that utilize tools from the kinetic
theory of gas dynamics are utilized to characterize the wealth distribution of an NBT economy,
and a variant of repeated prisoner’s dilemma is analyzed to determine whether and
why individuals would participate in such a system of reciprocal altruism.
From agent-based simulation and kinetic exchange models, it is found that regressive
NBT wealth redistribution acts as a cutting stock optimization heuristic that most efficiently
matches deficits to surpluses to improve short-term survival; however, progressive
redistribution leads to a wealth distribution that is more stable in volatile environments and
therefore is optimal for long-term survival. Homogeneous sharing networks with low variance
in degree are found to be ideal for maintaining community viability as the burden and
benefit of NBTs is equally shared. Also, phrasing NBTs as a survivor’s dilemma reveals
parameter regions where the repeated game becomes equivalent to a stag hunt or harmony
game, and thus where cooperation is evolutionarily stable.
ContributorsKayser, Kirk (Author) / Armbruster, Dieter (Thesis advisor) / Lampert, Adam (Committee member) / Ringhofer, Christian (Committee member) / Motsch, Sebastien (Committee member) / Gardner, Carl (Committee member) / Arizona State University (Publisher)
Created2018
Description
The geotechnical community typically relies on recommendations made from numerical simulations. Commercial software exhibits (local) numerical instabilities in layered soils across soil interfaces. This research work investigates unsaturated moisture flow in layered soils and identifies a possible source of numerical instabilities across soil interfaces and potential improvement in numerical schemes for solving the Richards' equation. The numerical issue at soil interfaces is addressed by a (nonlinear) interface problem. A full analysis of the simplest soil hydraulic model, the Gardner model, identifies the conditions of ill-posedness of the interface problem. Numerical experiments on various (more advanced and practical) soil hydraulic models show that the interface problem can also be ill-posed under certain circumstances. Spurious numerical ponding and/or oscillations around soil interfaces are observed consequently. This work also investigates the impact of different averaging schemes for cell-centered conductivities on the propensity of ill-posedness of the interface problem and concludes that smaller averaging conductivities are more likely to trigger numerical instabilities. In addition, an agent-based stochastic soil model, with hydraulic properties defined at the finite difference cell level, results in a large number of interface problems. This research compares sequences of stochastic realizations in heterogeneous unsaturated soils with the numerical solution using homogenized soil parameters. The mean of stochastic realizations is not identical to the solution obtained from homogenized soil parameters.
ContributorsLiu, Ruowen (Author) / Welfert, Bruno D (Thesis advisor) / Houston, Sandra L. (Committee member) / Jackiewicz, Zdzislaw (Committee member) / Ringhofer, Christian (Committee member) / Zapata, Claudia E (Committee member) / Arizona State University (Publisher)
Created2017
Description
A general continuum model for simulating the flow of ions in the salt baths that surround and fill excitable neurons is developed and presented. The ion densities and electric potential are computed using the drift-diffusion equations. In addition, a detailed model is given for handling the electrical dynamics on interior membrane boundaries, including a model for ion channels in the membranes that facilitate the transfer of ions in and out of cells. The model is applied to the triad synapse found in the outer plexiform layer of the retina in most species. Experimental evidence suggests the existence of a negative feedback pathway between horizontal cells and cone photoreceptors that modulates the flow of calcium ions into the synaptic terminals of cones. However, the underlying mechanism for this feedback is controversial and there are currently three competing hypotheses: the ephaptic hypothesis, the pH hypothesis and the GABA hypothesis. The goal of this work is to test some features of the ephaptic hypothesis using detailed simulations that employ rigorous numerical methods. The model is first applied in a simple rectangular geometry to demonstrate the effects of feedback for different extracellular gap widths. The model is then applied to a more complex and realistic geometry to demonstrate the existence of strictly electrical feedback, as predicted by the ephaptic hypothesis. Lastly, the effects of electrical feedback in regards to the behavior of the bipolar cell membrane potential is explored. Figures for the ion densities and electric potential are presented to verify key features of the model. The computed steady state IV curves for several cases are presented, which can be compared to experimental data. The results provide convincing evidence in favor of the ephaptic hypothesis since the existence of feedback that is strictly electrical in nature is shown, without any dependence on pH effects or chemical transmitters.
ContributorsJones, Jeremiah (Author) / Gardner, Carl (Committee member) / Baer, Steven (Committee member) / Crook, Sharon (Committee member) / Kostelich, Eric (Committee member) / Ringhofer, Christian (Committee member) / Arizona State University (Publisher)
Created2013
Description
Semiconductor devices often face reliability issues due to their operational con-
ditions causing performance degradation over time. One of the root causes of such
degradation is due to point defect dynamics and time dependent changes in their
chemical nature. Previously developed Unified Solver was successful in explaining
the copper (Cu) metastability issues in cadmium telluride (CdTe) solar cells. The
point defect formalism employed there could not be extended to chlorine or arsenic
due to numerical instabilities with the dopant chemical reactions. To overcome these
shortcomings, an advanced version of the Unified Solver called PVRD-FASP tool was
developed. This dissertation presents details about PVRD-FASP tool, the theoretical
framework for point defect chemical formalism, challenges faced with numerical al-
gorithms, improvements for the user interface, application and/or validation of the
tool with carefully chosen simulations, and open source availability of the tool for the
scientific community.
Treating point defects and charge carriers on an equal footing in the new formalism
allows to incorporate chemical reaction rate term as generation-recombination(G-R)
term in continuity equation. Due to the stiff differential equations involved, a reaction
solver based on forward Euler method with Newton step is proposed in this work.
The Jacobian required for Newton step is analytically calculated in an elegant way
improving speed, stability and accuracy of the tool. A novel non-linear correction
scheme is proposed and implemented to resolve charge conservation issue.
The proposed formalism is validated in 0-D with time evolution of free carriers
simulation and with doping limits of Cu in CdTe simulation. Excellent agreement of
light JV curves calculated with PVRD-FASP and Silvaco Atlas tool for a 1-D CdTe
solar cell validates reaction formalism and tool accuracy. A closer match with the Cu
SIMS profiles of Cu activated CdTe samples at four different anneal recipes to the
simulation results show practical applicability. A 1D simulation of full stack CdTe
device with Cu activation at 350C 3min anneal recipe and light JV curve simulation
demonstrates the tool capabilities in performing process and device simulations. CdTe
device simulation for understanding differences between traps and recombination
centers in grain boundaries demonstrate 2D capabilities.
ditions causing performance degradation over time. One of the root causes of such
degradation is due to point defect dynamics and time dependent changes in their
chemical nature. Previously developed Unified Solver was successful in explaining
the copper (Cu) metastability issues in cadmium telluride (CdTe) solar cells. The
point defect formalism employed there could not be extended to chlorine or arsenic
due to numerical instabilities with the dopant chemical reactions. To overcome these
shortcomings, an advanced version of the Unified Solver called PVRD-FASP tool was
developed. This dissertation presents details about PVRD-FASP tool, the theoretical
framework for point defect chemical formalism, challenges faced with numerical al-
gorithms, improvements for the user interface, application and/or validation of the
tool with carefully chosen simulations, and open source availability of the tool for the
scientific community.
Treating point defects and charge carriers on an equal footing in the new formalism
allows to incorporate chemical reaction rate term as generation-recombination(G-R)
term in continuity equation. Due to the stiff differential equations involved, a reaction
solver based on forward Euler method with Newton step is proposed in this work.
The Jacobian required for Newton step is analytically calculated in an elegant way
improving speed, stability and accuracy of the tool. A novel non-linear correction
scheme is proposed and implemented to resolve charge conservation issue.
The proposed formalism is validated in 0-D with time evolution of free carriers
simulation and with doping limits of Cu in CdTe simulation. Excellent agreement of
light JV curves calculated with PVRD-FASP and Silvaco Atlas tool for a 1-D CdTe
solar cell validates reaction formalism and tool accuracy. A closer match with the Cu
SIMS profiles of Cu activated CdTe samples at four different anneal recipes to the
simulation results show practical applicability. A 1D simulation of full stack CdTe
device with Cu activation at 350C 3min anneal recipe and light JV curve simulation
demonstrates the tool capabilities in performing process and device simulations. CdTe
device simulation for understanding differences between traps and recombination
centers in grain boundaries demonstrate 2D capabilities.
ContributorsShaik, Abdul Rawoof (Author) / Vasileska, Dragica (Thesis advisor) / Ringhofer, Christian (Committee member) / Sankin, Igor (Committee member) / Brinkman, Daniel (Committee member) / Goodnick, Stephen (Committee member) / Bertoni, Mariana (Committee member) / Arizona State University (Publisher)
Created2019
Description
Dimensionality reduction methods are examined for large-scale discrete problems, specifically for the solution of three-dimensional geophysics problems: the inversion of gravity and magnetic data. The matrices for the associated forward problems have beneficial structure for each depth layer of the volume domain, under mild assumptions, which facilitates the use of the two dimensional fast Fourier transform for evaluating forward and transpose matrix operations, providing considerable savings in both computational costs and storage requirements. Application of this approach for the magnetic problem is new in the geophysics literature. Further, the approach is extended for padded volume domains.
Stabilized inversion is obtained efficiently by applying novel randomization techniques within each update of the iteratively reweighted scheme. For a general rectangular linear system, a randomization technique combined with preconditioning is introduced and investigated. This is shown to provide well-conditioned inversion, stabilized through truncation. Applying this approach, while implementing matrix operations using the two dimensional fast Fourier transform, yields computationally effective inversion, in memory and cost. Validation is provided via synthetic data sets, and the approach is contrasted with the well-known LSRN algorithm when applied to these data sets. The results demonstrate a significant reduction in computational cost with the new algorithm. Further, this new algorithm produces results for inversion of real magnetic data consistent with those provided in literature.
Typically, the iteratively reweighted least squares algorithm depends on a standard Tikhonov formulation. Here, this is solved using both a randomized singular value de- composition and the iterative LSQR Krylov algorithm. The results demonstrate that the new algorithm is competitive with these approaches and offers the advantage that no regularization parameter needs to be found at each outer iteration.
Given its efficiency, investigating the new algorithm for the joint inversion of these data sets may be fruitful. Initial research on joint inversion using the two dimensional fast Fourier transform has recently been submitted and provides the basis for future work. Several alternative directions for dimensionality reduction are also discussed, including iteratively applying an approximate pseudo-inverse and obtaining an approximate Kronecker product decomposition via randomization for a general matrix. These are also topics for future consideration.
Stabilized inversion is obtained efficiently by applying novel randomization techniques within each update of the iteratively reweighted scheme. For a general rectangular linear system, a randomization technique combined with preconditioning is introduced and investigated. This is shown to provide well-conditioned inversion, stabilized through truncation. Applying this approach, while implementing matrix operations using the two dimensional fast Fourier transform, yields computationally effective inversion, in memory and cost. Validation is provided via synthetic data sets, and the approach is contrasted with the well-known LSRN algorithm when applied to these data sets. The results demonstrate a significant reduction in computational cost with the new algorithm. Further, this new algorithm produces results for inversion of real magnetic data consistent with those provided in literature.
Typically, the iteratively reweighted least squares algorithm depends on a standard Tikhonov formulation. Here, this is solved using both a randomized singular value de- composition and the iterative LSQR Krylov algorithm. The results demonstrate that the new algorithm is competitive with these approaches and offers the advantage that no regularization parameter needs to be found at each outer iteration.
Given its efficiency, investigating the new algorithm for the joint inversion of these data sets may be fruitful. Initial research on joint inversion using the two dimensional fast Fourier transform has recently been submitted and provides the basis for future work. Several alternative directions for dimensionality reduction are also discussed, including iteratively applying an approximate pseudo-inverse and obtaining an approximate Kronecker product decomposition via randomization for a general matrix. These are also topics for future consideration.
ContributorsHogue, Jarom David (Author) / Renaut, Rosemary A. (Thesis advisor) / Jackiewicz, Zdzislaw (Committee member) / Platte, Rodrigo B (Committee member) / Ringhofer, Christian (Committee member) / Wlefert, Bruno (Committee member) / Arizona State University (Publisher)
Created2020