Physical Sciences and Mathematics Commons^™

Statistical Methods For Meta-Analysis In Large-Scale Genomic Experiments, Wimarsha Thathsarani Jayanetti

Mathematics & Statistics Theses & Dissertations

Recent developments in high throughput genomic assays have opened up the possibility of testing hundreds and thousands of genes simultaneously. With the availability of vast amounts of public databases, researchers tend to combine genomic analysis results from multiple studies in the form of a meta-analysis. Meta-analysis methods can be broadly classified into two main categories. The first approach is to combine the statistical significance (pvalues) of the genes from each individual study, and the second approach is to combine the statistical estimates (effect sizes) from the individual studies. In this dissertation, we will discuss how adherence to the standard null …

Kinetic Simulations Of Active Nematic Polymers In Channel Flow, Lacey Savoie Schenk

Mathematics & Statistics Theses & Dissertations

Suspensions of active nematic liquid crystalline polymers exhibit complex phenomena such as spontaneous flows, pattern formations, and defects. They have many applications in industry, commercial settings, and our daily lives. We employ the Kinetic Model for our research, an extensive model that couples the Smoluchowski Equation and the incompressible Navier-Stokes Equations to solve for the active nanorod number density function–a function dependent on the polymer’s physical orientation and space at a given time. Using this function, we can derive the polymer’s polarity and nematic orientations as well as other rheological properties. In this research, we conduct numerical simulations of active, …

Inexact Fixed-Point Proximity Algorithms For Nonsmooth Convex Optimization, Jin Ren

Mathematics & Statistics Theses & Dissertations

The aim of this dissertation is to develop efficient inexact fixed-point proximity algorithms with convergence guaranteed for nonsmooth convex optimization problems encountered in data science. Nonsmooth convex optimization is one of the core methodologies in data science to acquire knowledge from real-world data and has wide applications in various fields, including signal/image processing, machine learning and distributed computing. In particular, in the context of image reconstruction, compressed sensing and sparse machine learning, either the objective functions or the constraints of the modeling optimization problems are nondifferentiable. Hence, traditional methods such as the gradient descent method and the Newton method are …

A Direct Method For Modeling And Simulations Of Elliptic And Parabolic Interface Problems, Kumudu Janani Gamage

Mathematics & Statistics Theses & Dissertations

Interface problems have many applications in physics. In this dissertation, we develop a direct method for solving three-dimensional elliptic interface problems and study their application in solving parabolic interface problems. As many of the physical applications of interface problems can be approximated with partial differential equations (PDE) with piecewise constant coefficients, our derivation of the model is focused on interface problems with piecewise constant coefficients but have a finite jump across the interface. The critical characteristic of the method is that our computational framework is based on a finite difference scheme on a uniform Cartesian grid system and does not …

On The P-Inner Functions Of ℓPA, James G. Dragas

Mathematics & Statistics Theses & Dissertations

Define ℓ^p_A as the space of all functions holomorphic over the unit disk whose Taylor coefficients are p-summable. Despite their classical origins and simple definition, these spaces are not as well understood as one might expect. This is particularly true when compared with the Hardy spaces, which provide a useful road map for the types of questions we might consider reasonable. In this work we examine the zero sets of ℓ^p_A, p ∈ (1;∞), as well as a notion of inner function that is consistent with the approach taken on numerous other function spaces. …

Electrohydrodynamic Simulations Of Capsule Deformation Using A Dual Time-Stepping Lattice Boltzmann Scheme, Charles Leland Armstrong

Mathematics & Statistics Theses & Dissertations

Capsules are fluid-filled, elastic membranes that serve as a useful model for synthetic and biological membranes. One prominent application of capsules is their use in modeling the response of red blood cells to external forces. These models can be used to study the cell’s material properties and can also assist in the development of diagnostic equipment. In this work we develop a three dimensional model for numerical simulations of red blood cells under the combined influence of hydrodynamic and electrical forces. The red blood cell is modeled as a biconcave-shaped capsule suspended in an ambient fluid domain. Cell deformation occurs …

High-Order Positivity-Preserving L2-Stable Spectral Collocation Schemes For The 3-D Compressible Navier-Stokes Equations, Johnathon Keith Upperman

Mathematics & Statistics Theses & Dissertations

High-order entropy stable schemes are a popular method used in simulations with the compressible Euler and Navier-Stokes equations. The strength of these methods is that they formally satisfy a discrete entropy inequality which can be used to guarantee L₂ stability of the numerical solution. However, a fundamental assumption that is explicitly or implicitly used in all entropy stability proofs available in the literature for the compressible Euler and Navier-Stokes equations is that the thermodynamic variables (e.g., density and temperature) are strictly positive in the entire space{time domain considered. Without this assumption, any entropy stability proof for a numerical scheme …

Finite Difference Schemes For Integral Equations With Minimal Regularity Requirements, Wesley Cameron Davis

Mathematics & Statistics Theses & Dissertations

Volterra integral equations arise in a variety of applications in modern physics and engineering, namely in interactions that contain a memory term. Classical formulations of these problems are largely inflexible when considering non-homogeneous media, which can be problematic when considering long term interactions of real-world applications. The use of fractional derivative and integral terms naturally relax these restrictions in a natural way to consider these problems in a more general setting. One major drawback to the use of fractional derivatives and integrals in modeling is the regularity requirement for functions, where we can no longer assume that functions are as …

Inference And Estimation In Change Point Models For Censored Data, Kristine Gierz

Mathematics & Statistics Theses & Dissertations

In general, the change point problem considers inference of a change in distribution for a set of time-ordered observations. This has applications in a large variety of fields and can also apply to survival data. With improvements to medical diagnoses and treatments, incidences and mortality rates have changed. However, the most commonly used analysis methods do not account for such distributional changes. In survival analysis, change point problems can concern a shift in a distribution for a set of time-ordered observations, potentially under censoring or truncation.

In this dissertation, we first propose a sequential testing approach for detecting multiple change …

Investigating The Feasibility And Stability For Modeling Acoustic Wave Scattering Using A Time-Domain Boundary Integral Equation With Impedance Boundary Condition, Michelle E. Rodio

Mathematics & Statistics Theses & Dissertations

Reducing aircraft noise is a major objective in the field of computational aeroacoustics. When designing next generation quiet and environmentally friendly aircraft, it is important to be able to accurately and efficiently predict the acoustic scattering by an aircraft body from a given noise source. Acoustic liners are an effective tool for aircraft noise reduction and are characterized by a frequency-dependent impedance. Converted into the time-domain using Fourier transforms, an impedance boundary condition can be used to simulate the acoustic wave scattering by geometric bodies treated with acoustic liners

This work considers using either an impedance or an admittance (inverse …

Electrohydrodynamic Simulations Of The Deformation Of Liquid-Filled Capsules, Pai Song

Mathematics & Statistics Theses & Dissertations

A comprehensive two- and three-dimensional framework for the electrohydrodynamic simulation of deformable capsules is provided. The role of a direct current (DC) electric field on the deformation and orientation of a liquid-filled capsule is thoroughly considered numerically. This framework is based on lattice Boltzmann method for the fluid, finite element method for the membrane structure of the capsule, fast immersed interface method for the electric field and immersed boundary method being used to consider the fluid-structure-electric interaction. Under the effect of electric field, two different types of equilibrium states, prolate or oblate are obtained. The numerical algorithm is also applied …

Extended Poisson Models For Count Data With Inflated Frequencies, Monika Arora

Mathematics & Statistics Theses & Dissertations

Count data often exhibits inflated counts for zero. There are numerous papers in the literature that show how to fit Poisson regression models that account for the zero inflation. However, in many situations the frequencies of zero and of some other value k tends to be higher than the Poisson model can fit appropriately. Recently, Sheth-Chandra (2011), Lin and Tsai (2012) introduced a mixture model to account for the inflated frequencies of zero and k. In this dissertation, we study basic properties of this mixture model and parameter estimation for grouped and ungrouped data. Using stochastic representation we show …

A Partitioned Approach For Computing Fluid-Structure Interaction, With Application To Tumor Modeling And Simulation, Asim Timalsina

Mathematics & Statistics Theses & Dissertations

Modeling and Simulation plays a critical role in understanding complex physical and biological phenomena as it provides an efficient and controlled test environment, without the risk of costly experiments and clinical trials. In this dissertation, we present an extensive study of two such systems with integrated application: Fluid structure interaction (FSI) and virotherapy on tumor. Moreover, we substantiate a few preliminary results of FSI application on tumor.

The FSI problem comprises of fluid forces exerted on the solid body and the motion of the structure affecting the fluid flow. FSI problems are of great interest to applied industries, however they …

Modeling And Simulation Of Molecular Couette Flows And Related Flows, Wei Li

Mathematics & Statistics Theses & Dissertations

In this thesis, molecular Couette flow is clearly defined and the modeling and simulation of this kind of flow is systematically investigated. First, the integral equations for the velocity of gaseous Couette flow and related flows are derived from linearized Boltzmann BGK equation with Maxwell boundary condition and solved with high precision by using Chebyshev collocation and chunk-based collocation methods. The velocity profiles of gaseous Couette flows and related flows with a wide range of Knudsen number and the Maxwell boundary condition of various accommodation ratios are obtained. Moreover, the order of convergence of the numerical methods is also discussed …

Analyzing Cholera Dynamics In Homogeneous And Heterogeneous Environments, Drew Posny

Mathematics & Statistics Theses & Dissertations

Cholera continues to be a serious public health concern in developing countries and the global increase in the number of reported outbreaks suggests that activities to control the diseases and surveillance programs to identify or predict the occurrence of the next outbreaks are not adequate. Mathematical models play a critical role in predicting and understanding disease mechanisms, and have long provided basic insights in the possible ways to control infectious diseases. This dissertation is concerned with mathematical modeling and analysis of cholera dynamics. First, we study an autonomous model in a homogeneous environment with added controls that involves both direct …

Modeling And Simulation Of Shape Changes Of Red Blood Cells In Shear Flow, John Gounley

Mathematics & Statistics Theses & Dissertations

A description of the biomechanical character of red blood cells is given, along with an introduction to current computational schemes which use deformable capsules to simulate red blood cell shape change. A comprehensive two- and three-dimensional framework for the fluid-structure interaction between a deformable capsule and an ambient flow is provided. This framework is based on the immersed boundary method, using lattice Boltzmann and finite element methods for the fluid and structure, respectively. The characteristic response and recovery times of viscoelastic circular and spherical capsules are compared, and their dependence on simulation parameters is shown. The shape recovery of biconcave …

Optimal Control Modeling And Simulation, With Application To Cholera Dynamics, Chairat Modnak

Mathematics & Statistics Theses & Dissertations

The theory of optimal control, a modern extension of the calculus of variations. has found many applications in a wide range of scientific fields, particularly in epidemiology with respect to disease prevention and intervention. In this dissertation. we conduct optimal control modeling, simulation and analysis to cholera dynamics. Cholera is a severe intestinal infectious disease that remains a serious public health threat in developing countries. Transmission of cholera involves complex interactions between the human host, the pathogen, and the environment. The worldwide cholera outbreaks and their increasing severity, frequency and duration in recent years underscore the gap between the complex …

Modelling Locally Changing Variance Structured Time Series Data By Using Breakpoints Bootstrap Filtering, Rajan Lamichhane

Mathematics & Statistics Theses & Dissertations

Stochastic processes have applications in many areas such as oceanography and engineering. Special classes of such processes deal with time series of sparse data. Studies in such cases focus in the analysis, construction and prediction in parametric models. Here, we assume several non-linear time series with additive noise components, and the model fitting is proposed in two stages. The first stage identifies the density using all the clusters information, without specifying any prior knowledge of the underlying distribution function of the time series. The effect of covariates is controlled by fitting the linear regression model with serially correlated errors. In …

Topics In Electromagnetic, Acoustic, And Potential Scattering Theory, Umaporn Nuntaplook

Mathematics & Statistics Theses & Dissertations

With recent renewed interest in the classical topics of both acoustic and electromagnetic aspects for nano-technology, transformation optics, fiber optics, metamaterials with negative refractive indices, cloaking and invisibility, the topic of time-independent scattering theory in quantum mechanics is becoming a useful field to re-examine in the above contexts. One of the key areas of electromagnetic theory scattering of plane electromagnetic waves — is based on the properties of the refractive indices in the various media. It transpires that the refractive index of a medium and the potential in quantum scattering theory are intimately related. In many cases, understanding such scattering …

Perfectly Matched Layer Absorbing Boundary Conditions For The Discrete Velocity Boltzmann-Bgk Equation, Elena Craig

Mathematics & Statistics Theses & Dissertations

Perfectly Matched Layer (PML) absorbing boundary conditions were first proposed by Berenger in 1994 for the Maxwell's equations of electromagnetics. Since Hu first applied the method to Euler's equations in 1996, progress made in the application of PML to Computational Aeroacoustics (CAA) includes linearized Euler equations with non-uniform mean flow, non-linear Euler equations, flows with an arbitrary mean flow direction, and non-linear clavier-Stokes equations. Although Boltzmann-BGK methods have appeared in the literature and have been shown capable of simulating aeroacoustics phenomena, very little has been done to develop absorbing boundary conditions for these methods. The purpose of this work was …

An Extensible Mathematical Model Of Glucose Metabolism, Caleb L. Adams

Mathematics & Statistics Theses & Dissertations

The American Diabetes Association reports that diabetes is the fifth leading cause of death by disease in the United States. An estimated 23.6 million individuals, or seven percent of the population, have diabetes. Nearly one-third are unaware that they have the disease. The total of the direct and indirect medical costs associated with diabetes in 2007 was projected to be $174 billion, or approximately one out of every ten health care dollars.

One must understand the glucose regulatory system of the healthy body to understand diabetes. Blood glucose concentration returns to a constant level after eating and is maintained during …

A Least Squares Closure Approximation For Liquid Crystalline Polymers, Traci Ann Sievenpiper

Mathematics & Statistics Theses & Dissertations

An introduction to existing closure schemes for the Doi-Hess kinetic theory of liquid crystalline polymers is provided. A new closure scheme is devised based on a least squares fit of a linear combination of the Doi, Tsuji-Rey, Hinch-Leal I, and Hinch-Leal II closure schemes. The orientation tensor and rate-of-strain tensor are fit separately using data generated from the kinetic solution of the Smoluchowski equation. The known behavior of the kinetic solution and existing closure schemes at equilibrium is compared with that of the new closure scheme. The performance of the proposed closure scheme in simple shear flow for a variety …

A Solution Of The Heat Equation With The Discontinuous Galerkin Method Using A Multilivel Calculation Method That Utilizes A Multiresolution Wavelet Basis, Robert Gregory Brown

Mathematics & Statistics Theses & Dissertations

A numerical method to solve the parabolic problem is developed that utilizes the Discontinuous Galerkin Method for space and time discretization. A multilevel method is employed in the space variable. It is shown that use of this process yields the same level of accuracy as the standard Discontinuous Galerkin Method for the heat equation, but with cheaper computational cost. The results are demonstrated using a standard one-dimensional homogeneous heat problem.

Post-Processing Techniques And Wavelet Applications For Hammerstein Integral Equations, Khomsan Neamprem

Mathematics & Statistics Theses & Dissertations

This dissertation is focused on the varieties of numerical solutions of nonlinear Hammerstein integral equations. In the first part of this dissertation, several acceleration techniques for post-processed solutions of the Hammerstein equation are discussed. The post-processing techniques are implemented based on interpolation and extrapolation. In this connection, we generalize the results in [29] and [28] to nonlinear integral equations of the Hammerstein type. Post-processed collocation solutions are shown to exhibit better accuracy. Moreover, an extrapolation technique for the Galerkin solution of Hammerstein equation is also obtained. This result appears new even in the setting of the linear Fredholm equation.

In …

Mathematical Models And Stability Analysis Of Cholera Dynamics, Shu Liao

Mathematics & Statistics Theses & Dissertations

In this dissertation, we present a careful mathematical study of several epidemic cholera models, including the model of Codeco [11] in 2001, that of Hartley, Morris and Smith [22] in 2006, and that of Mukandavire, Liao, Wang and Gaff et al. [60] in 2010. We formally derive the basic reproduction number R0 for each model by computing the spectral radius of the next generation matrix. We focus our attention on the stability analysis at the disease-free equilibrium which determines the short-term epidemic behavior, and the endemic equilibrium which determines the long-term disease dynamics. Particularly, we incorporate the Volterra-Lyapunov matrix …

An Adaptive Method For Calculating Blow-Up Solutions, Charles F. Touron

Mathematics & Statistics Theses & Dissertations

Reactive-diffusive systems modeling physical phenomena in certain situations develop a singularity at a finite value of the independent variable referred to as "blow-up." The attempt to find the blow-up time analytically is most often impossible, thus requiring a numerical determination of the value. The numerical methods often use a priori knowledge of the blow-up solution such as monotonicity or self-similarity. For equations where such a priori knowledge is unavailable, ad hoc methods were constructed. The object of this research is to develop a simple and consistent approach to find numerically the blow-up solution without having a priori knowledge or resorting …

Three Methods For Solving The Low Energy Neutron Boltzmann Equation, Tony Charles Slaba

Mathematics & Statistics Theses & Dissertations

The solution to the neutron Boltzmann equation is separated into a straightahead component dominating at high energies and an isotropic component dominating at low energies. The high-energy solution is calculated using HZETRN-05, and the low-energy isotropic component is modeled by two non-coupled integro-differential equations describing both forward and backward neutron propagation. Three different solution methods are then used to solve the equations. The collocation method employs linear I3-splines to transform each equation into a system of ODES; the resulting system is then solved exactly and evaluated using numerical integration techniques. Wilson's method uses a perturbational approach in which a fundamental …

A Forward-Backward Fluence Model For The Low-Energy Neutron Boltzmann Equation, Gary Alan Feldman

Mathematics & Statistics Theses & Dissertations

In this research work, the neutron Boltzmann equation was separated into two coupled integro-differential equations describing forward and backward neutron fluence in selected materials. Linear B-splines were used to change the integro-differential equations into a coupled system of ordinary differential equations (O.D.E.'s). Difference approximations were then used to recast the O.D.E.'s into a coupled system of linear equations that were solved for forward and backward neutron fluences. Adding forward and backward fluences gave the total fluence at selected energies and depths in the material. Neutron fluences were computed in single material shields and in a shield followed by a target …

Error-Correcting Codes Associated With Generalized Hadamard Matrices Over Groups, Iem H. Heng

Mathematics & Statistics Theses & Dissertations

Classical Hadamard matrices are orthogonal matrices whose elements are ±1. It is well-known that error correcting codes having large minimum distance between codewords can be associated with these Hadamard matrices. Indeed, the success of early Mars deep-space probes was strongly dependent upon this communication technology.

The concept of Hadamard matrices with elements drawn from an Abelian group is a natural generalization of the concept. For the case in which the dimension of the matrix is q and the group consists of the p-th roots of unity, these generalized Hadamard matrices are called “Butson Hadamard Matrices BH(p, q)”, …

Mathematical Models Of Chemotherapy, John Carl Panetta

Mathematics & Statistics Theses & Dissertations

Several mathematical models are developed to describe the effects of chemotherapy on both cancerous and normal tissue. Each model is defined by either a single homogeneous equation or a system of heterogeneous equations which describe the states of the normal and/or cancer cells. Periodic terms are added to model the effects of the chemotherapy. What we obtain are regions, in parameter space (dose and period), of acceptable drug regimens.

The models take into account various aspects of chemotherapy. These include, interactions between the cancer and normal tissue, cell specific chemotherapeutic drug, the use of non-constant parameters to aid in modeling …