Physical Sciences and Mathematics Commons^™

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

All Dissertations

In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …

New Preconditioned Conjugate Gradient Methods For Some Structured Problems In Physics, Tianqi Zhang

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This dissertation concerns the development and analysis of new preconditioned conjugate gradient (PCG) algorithms for three important classes of large-scale and complex physical problems characterized by special structures. We propose several new iterative methods for solving the eigenvalue problem or energy minimization problem, which leverage the unique structures inherent in these problems while preserving the underlying physical properties. The new algorithms enable more efficient and robust large-scale modeling and simulations in many areas, including condensed matter physics, optical properties of materials, stabilities of dynamical systems arising from control problems, and many more. Some methods are expected to be applicable to …

Controlled Manipulation And Transport By Microswimmers In Stokes Flows, Jake Buzhardt

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Remotely actuated microscale swimming robots have the potential to revolutionize many aspects of biomedicine. However, for the longterm goals of this field of research to be achievable, it is necessary to develop modelling, simulation, and control strategies which effectively and efficiently account for not only the motion of individual swimmers, but also the complex interactions of such swimmers with their environment including other nearby swimmers, boundaries, other cargo and passive particles, and the fluid medium itself. The aim of this thesis is to study these problems in simulation from the perspective of controls and dynamical systems, with a particular focus …

Null Space Removal In Finite Element Discretizations, Pengfei Jia

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Partial differential equations are frequently utilized in the mathematical formulation of physical problems. Boundary conditions need to be applied in order to obtain the unique solution to such problems. However, some types of boundary conditions do not lead to unique solutions because the continuous problem has a null space. In this thesis, we will discuss how to solve such problems effectively. We first review the foundation of all three problems and prove that Laplace problem, linear elasticity problem and Stokes problem can be well posed if we restrict the test and trial space in the continuous and discrete finite element …

Acceleration Methods For Nonlinear Solvers And Application To Fluid Flow Simulations, Duygu Vargun

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This thesis studies nonlinear iterative solvers for the simulation of Newtonian and non- Newtonian fluid models with two different approaches: Anderson acceleration (AA), an extrapolation technique that accelerates the convergence rate and improves the robustness of fixed-point iterations schemes, and continuous data assimilation (CDA) which drives the approximate solution towards coarse data measurements or observables by adding a penalty term.

We analyze the properties of nonlinear solvers to apply the AA technique. We consider the Picard iteration for the Bingham equation which models the motion of viscoplastic materials, and the classical iterated penalty Picard and Arrow-Hurwicz iterations for the incompressible …

Multi-Commodity Flow Models For Logistic Operations Within A Contested Environment, Isabel Strinsky

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Today's military logistics officers face a difficult challenge, generating route plans for mass deployments within contested environments. The current method of generating route plans is inefficient and does not assess the vulnerability within supply networks and chains. There are few models within the current literature that provide risk-averse solutions for multi-commodity flow models. In this thesis, we discuss two models that have the potential to aid military planners in creating route plans that account for risk and uncertainty. The first model we introduce is a continuous time model with chance constraints. The second model is a two-stage discrete time model …

Asymptotic Cones Of Quadratically Defined Sets And Their Applications To Qcqps, Alexander Joyce

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Quadratically constrained quadratic programs (QCQPs) are a set of optimization problems defined by a quadratic objective function and quadratic constraints. QCQPs cover a diverse set of problems, but the nonconvexity and unboundedness of quadratic constraints lead to difficulties in globally solving a QCQP. This thesis covers properties of unbounded quadratic constraints via a description of the asymptotic cone of a set defined by a single quadratic constraint. A description of the asymptotic cone is provided, including properties such as retractiveness and horizon directions.

Using the characterization of the asymptotic cone, we generalize existing results for bounded quadratically defined regions with …

Recovering Coefficients Of Second-Order Hyperbolic And Plate Equations Via Finite Measurements On The Boundary, Scott Randall Scruggs

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Abstract In this dissertation, we consider the inverse problem for a second-order hyperbolic equation of recovering n + 3 unknown coefficients defined on an open bounded domain with a smooth enough boundary. We also consider the inverse problem of recovering an unknown coefficient on the Euler- Bernoulli plate equation on a lower-order term again defined on an open bounded domain with a smooth enough boundary. For the second-order hyperbolic equation, we show that we can uniquely and (Lipschitz) stably recover all these coefficients from only using half of the corresponding boundary measurements of their solutions, and for the plate equation, …

Advancements In Fluid Simulation Through Enhanced Conservation Schemes, Sean Ingimarson

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To better understand and solve problems involving the natural phenomenon of fluid and air flows, one must understand the Navier-Stokes equations. Branching several different fields including engineering, chemistry, physics, etc., these are among the most important equations in mathematics. However, these equations do not have analytic solutions save for trivial solutions. Hence researchers have striven to make advancements in varieties of numerical models and simulations. With many variations of numerical models of the Navier-Stokes equations, many lose important physical meaningfulness. In particular, many finite element schemes do not conserve energy, momentum, or angular momentum. In this thesis, we will study …

Machine Learning-Based Data And Model Driven Bayesian Uncertanity Quantification Of Inverse Problems For Suspended Non-Structural System, Zhiyuan Qin

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Inverse problems involve extracting the internal structure of a physical system from noisy measurement data. In many fields, the Bayesian inference is used to address the ill-conditioned nature of the inverse problem by incorporating prior information through an initial distribution. In the nonparametric Bayesian framework, surrogate models such as Gaussian Processes or Deep Neural Networks are used as flexible and effective probabilistic modeling tools to overcome the high-dimensional curse and reduce computational costs. In practical systems and computer models, uncertainties can be addressed through parameter calibration, sensitivity analysis, and uncertainty quantification, leading to improved reliability and robustness of decision and …

Improving Efficiency Of Rational Krylov Subspace Methods, Shengjie Xu

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This thesis studies two classes of numerical linear algebra problems, approximating the product of a function of a matrix with a vector, and solving the linear eigenvalue problem $Av=\lambda Bv$ for a small number of eigenvalues. These problems are solved by rational Krylov subspace methods (RKSM). We present several improvements in two directions: pole selection and applying inexact methods.

In Chapter 3, a flexible extended Krylov subspace method ($\mathcal{F}$-EKSM) is considered for numerical approximation of the action of a matrix function $f(A)$ to a vector $b$, where the function $f$ is of Markov type. $\mathcal{F}$-EKSM has the same framework as …

On Variants Of Sliding And Frank-Wolfe Type Methods And Their Applications In Video Co-Localization, Seyed Hamid Nazari

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In this dissertation, our main focus is to design and analyze first-order methods for computing approximate solutions to convex, smooth optimization problems over certain feasible sets. Specifically, our goal in this dissertation is to explore some variants of sliding and Frank-Wolfe (FW) type algorithms, analyze their convergence complexity, and examine their performance in numerical experiments. We achieve three accomplishments in our research results throughout this dissertation. First, we incorporate a linesearch technique to a well-known projection-free sliding algorithm, namely the conditional gradient sliding (CGS) method. Our proposed algorithm, called the conditional gradient sliding with linesearch (CGSls), does not require the …

Optimal First Order Methods For Reducing Gradient Norm In Unconstrained Convex Smooth Optimization, Yunheng Jiang

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In this thesis, we focus on convergence performance of first-order methods to compute an $\epsilon$-approximate solution of minimizing convex smooth function $f$ at the $N$-th iteration.

In our introduction of the above research question, we first introduce the gradient descent method with constant step size $h=1/L$. The gradient descent method has a $\mathcal{O}(L^2\|x_0-x^*\|^2/\epsilon)$ convergence with respect to $\|\nabla f(x_N)\|^2$. Next we introduce Nesterov’s accelerated gradient method, which has an $\mathcal{O}(L\|x_0-x^*\|\sqrt{1/\epsilon})$ complexity in terms of $\|\nabla f(x_N)\|^2$. The convergence performance of Nesterov’s accelerated gradient method is much better than that of the gradient descent method but still not optimal. We also …

Efficiency Of Homomorphic Encryption Schemes, Kyle Yates

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In 2009, Craig Gentry introduced the first fully homomorphic encryption scheme using bootstrapping. In the 13 years since, a large amount of research has gone into improving efficiency of homomorphic encryption schemes. This includes implementing leveled homomorphic encryption schemes for practical use, which are schemes that allow for some predetermined amount of additions and multiplications that can be performed on ciphertexts. These leveled schemes have been found to be very efficient in practice. In this thesis, we will discuss the efficiency of various homomorphic encryption schemes. In particular, we will see how to improve sizes of parameter choices in homomorphic …

Managing Risk For Power System Operations And Planning: Applications Of Conditional Value-At-Risk And Uncertainty Quantification To Optimal Power Flow And Distributed Energy Resources Investment, Thanh To

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Renewable energy sources are indispensable components of sustainable electrical systems that reduce human dependence on fossil fuels. However, due to their intermittent nature, there are issues that need to be addressed to ensure the security and resiliency of these power systems. This dissertation formulates several practical problems, from an optimization perspective, stemming from the increasing penetration of intermittent renewable energy to power systems. A number of Optimal Power Flow (OPF) formulations are investigated and new formulations are proposed to control both operations and planning risks by utilizing the Conditional Value–at–Risk (CVaR) measure. Our formulations provide system operators and investors analysis …

Advancements In Gaussian Process Learning For Uncertainty Quantification, John C. Nicholson

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Gaussian processes are among the most useful tools in modeling continuous processes in machine learning and statistics. The research presented provides advancements in uncertainty quantification using Gaussian processes from two distinct perspectives. The first provides a more fundamental means of constructing Gaussian processes which take on arbitrary linear operator constraints in much more general framework than its predecessors, and the other from the perspective of calibration of state-aware parameters in computer models. If the value of a process is known at a finite collection of points, one may use Gaussian processes to construct a surface which interpolates these values to …

A Conservative Numerical Scheme For The Multilayer Shallow Water Equations, Evan Butterworth

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An energy-conserving numerical scheme is developed for the multilayer shallow water equations (SWE’s). The scheme is derived through the Hamiltonian formulation of the inviscid shallow water flows related to the vorticity-divergence variables. Through the employment of the skew-symmetric Poisson bracket, the continuous system for the multilayer SWE’s is shown to preserve an infinite number of quantities, most notably the energy and enstrophy. An energy-preserving numerical scheme is then developed through the careful discretization of the Hamiltonian and the Poisson bracket, ensuring the skew-symmetry of the latter. This serves as the groundwork for developing additional schemes that preserve other conservation properties …

An Algorithm For Biobjective Mixed Integer Quadratic Programs, Pubudu Jayasekara Merenchige

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Multiobjective quadratic programs (MOQPs) are appealing since convex quadratic programs have elegant mathematical properties and model important applications. Adding mixed-integer variables extends their applicability while the resulting programs become global optimization problems. Thus, in this work, we develop a branch and bound (BB) algorithm for solving biobjective mixed-integer quadratic programs (BOMIQPs). An algorithm of this type does not exist in the literature.

The algorithm relies on five fundamental components of the BB scheme: calculating an initial set of efficient solutions with associated Pareto points, solving node problems, fathoming, branching, and set dominance. Considering the properties of the Pareto set of …

A Parallelized And Layered Model For The Shallow-Water Equations, Alexander Stevens

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An energy- and enstrophy-conserving and optimally-dispersive numerical scheme for the shallow- water equations is accelerated through implementation in the GPU environment. Previous research showed the viability of the numerical scheme under standard shallow-water test cases, but was limited in applications by computation time constraints. We overcome these limitations by paral- lelizing the numerical computation in the GPU environment. We also extend the capabilities of the implementation to support not just a single shallow-water layer, but multiple. These improvements significantly expand the range of tests that can be used to exercise the model, and enable better understanding of the power of …

Numerical Decoding, Johnson-Lindenstrauss Transforms, And Linear Codes, Yue Mao

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Many computational problems are related to the model y = Ax + e, including compressive sensing, coding theory, dimensionality reduction, etc. The related algorithms are extremely useful in practical applications for high performance computing, for example, digital communications, biological imaging and data streaming, etc. This thesis studies two important problems. One problem is related to efficient decoding for Reed-Solomon codes over complex numbers. In this case, A and y are given, and the goal is to find an efficient stable algorithm to compute x. This is related to magnetic resonance imaging (MRI). The other problem is related to fast algorithms …

Computational Exploration Of Chaotic Dynamics With An Associated Biological System, Akshay Galande

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Study of microbial populations has always been topic of interest for researchers. This is because microorganisms have been of instrumental use in the various studies related to population dynamics, artificial bio-fuels etc. Comparatively short lifespan and availability are two big advantages they have which make them suitable for aforementioned studies. Their population dynamic helps us understand evolution. A lot can be revealed about resource consumption of a system by comparing it to the similar system where bacteria play the role of different factors in the system. Also, study of population dynamics of bacteria can reveal necessary initial conditions for the …

Homomorphic Encryption And The Approximate Gcd Problem, Nathanael Black

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With the advent of cloud computing, everyone from Fortune 500 businesses to personal consumers to the US government is storing massive amounts of sensitive data in service centers that may not be trustworthy. It is of vital importance to leverage the benefits of storing data in the cloud while simultaneously ensuring the privacy of the data. Homomorphic encryption allows one to securely delegate the processing of private data. As such, it has managed to hit the sweet spot of academic interest and industry demand. Though the concept was proposed in the 1970s, no cryptosystem realizing this goal existed until Craig …

Grobner Bases: Degree Bounds And Generic Ideals, Juliane Golubinski Capaverde

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In this thesis, we study two problems related to Gröbner basis theory: degree bounds for general ideals and Gröbner bases structure for generic ideals. We start by giving an introduction to Gröbner bases and their basic properties and presenting a recent algorithm by Gao, Volny and Wang. Next, we survey degree bounds for the ideal membership problem, the effective Nullstellensatz, and polynomials in minimal Gröbner bases. We present general upper bounds, and bounds for several classes of special ideals. We provide classical examples showing some of these bounds cannot be improved in general. We present a comprehensive study of a …

Applied Statistics In Environmental Monitoring: Case Studies And Analysis For The Michigan Bald Eagle Biosentinel Program, Katherine Leith

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The bald eagle (Haliaeetus leucocephalus) is an extensively researched tertiary predator. Its life history and the impact of various stressors on its reproductive outcomes have been documented in many studies, and over many years. Furthermore, the bald eagle population recovery in Michigan has been closely monitored since the 1960s, as it has continued to recover from a contaminant-induced bottleneck. Because of its position at the top of the aquatic food web and the large body of ethological knowledge, the bald eagle has become a sentinel species for the Michigan aquatic ecosystem. In April 1999, the Michigan Department of Environmental Qualtity, …

On Numerical Algorithms For Fluid Flow Regularization Models, Abigail Bowers

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This thesis studies regularization models as a way to approximate a flow simulation at a lower computational cost. The Leray model is more easily computed than the Navier-Stokes equations (NSE), and it is more computationally attractive than the NS-α regularization because it admits a natural linearization which decouples the mass/momentum system and the filter system, allowing for efficient and stable computations. A major disadvantage of the Leray model lies in its inaccuracy. Thus, we study herein several methods to improve the accuracy of the model, while still retaining many of its attractive properties. This thesis is arranged as follows. Chapter …

Level Stripping Of Genus 2 Siegel Modular Forms, Rodney Keaton

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In this Dissertation we consider stripping primes from the level of genus 2 cuspidal Siegel eigenforms. Specifically, given an eigenform of level Nlr which satisfies certain mild conditions, where l is a prime not dividing N, we construct an eigenform of level N which is congruent to our original form. To obtain our results, we use explicit constructions of Eisenstein series and theta functions to adapt ideas from a level stripping result on elliptic modular forms. Furthermore, we give applications of this result to Galois representations and provide evidence for an analog of Serre's conjecture in the genus 2 case.

Computational Bases For Hdiv, Alistair Bentley

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The \(H_{div}\) vector space arises in a number of mixed method formulations, particularly in fluid flow through a porous medium. First we present a Lagrangian computational basis for the Raviert-Thomas (\(RT\)) and Brezzi-Douglas-Marini (\(BDM\)) approximation subspaces of \(H_{div}\) in \(\mathbb{R}^{3}\). Second, we offer three solutions to a numerical problem that arises from the Piola mapping when \(RT\) and \(BDM\) elements are used in practice.

Convergence Of A Reinforcement Learning Algorithm In Continuous Domains, Stephen Carden

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In the field of Reinforcement Learning, Markov Decision Processes with a finite number of states and actions have been well studied, and there exist algorithms capable of producing a sequence of policies which converge to an optimal policy with probability one. Convergence guarantees for problems with continuous states also exist. Until recently, no online algorithm for continuous states and continuous actions has been proven to produce optimal policies. This Dissertation contains the results of research into reinforcement learning algorithms for problems in which both the state and action spaces are continuous. The problems to be solved are introduced formally as …

The Intelligent Driver Model: Analysis And Application To Adaptive Cruise Control, Rachel Malinauskas

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There are a large number of models that can be used to describe traffic flow. Although some were initially theoretically derived, there are many that were constructed with utility alone in mind. The Intelligent Driver Model (IDM) is a microscopic model that can be used to examine traffic behavior on an individual level with emphasis on the relation to an ahead vehicle. One application for this model is that it is easily molded to performing the operations for an Adaptive Cruise Control (ACC) system. Although it is clear that the IDM holds a number of convenient properties, like easily interpreted …

Improved Mixed-Integer Models Of A Two-Dimensional Cutting Stock Problem, William Lassiter

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This paper is concerned with a family of two-dimensional cutting stock problems that seeks to cut rectangular regions from a finite collection of sheets in such a manner that the minimum number of sheets is used. A fixed number of rectangles are to be cut, with each rectangle having a known length and width. All sheets are rectangular, and have the same dimension. We review two known mixed-integer mathematical formulations, and then provide new representations that both economize on the number of discrete variables and tighten the continuous relaxations. A key consideration that arises repeatedly in all models is the …