Physical Sciences and Mathematics Commons^™

Tools For Biomolecular Modeling And Simulation, Xin Yang

Mathematics Theses and Dissertations

Electrostatic interactions play a pivotal role in understanding biomolecular systems, influencing their structural stability and functional dynamics. The Poisson-Boltzmann (PB) equation, a prevalent implicit solvent model that treats the solvent as a continuum while describes the mobile ions using the Boltzmann distribution, has become a standard tool for detailed investigations into biomolecular electrostatics. There are two primary methodologies: grid-based finite difference or finite element methods and body-fitted boundary element methods. This dissertation focuses on developing fast and accurate PB solvers, leveraging both methodologies, to meet diverse scientific needs and overcome various obstacles in the field.

Predicting Biomolecular Properties And Interactions Using Numerical, Statistical And Machine Learning Methods, Elyssa Sliheet

Mathematics Theses and Dissertations

We investigate machine learning and electrostatic methods to predict biophysical properties of proteins, such as solvation energy and protein ligand binding affinity, for the purpose of drug discovery/development. We focus on the Poisson-Boltzmann model and various high performance computing considerations such as parallelization schemes.

Generation, Dynamics, And Interaction Of Quartic Solitary Waves In Nonlinear Laser Systems, Sabrina Hetzel

Mathematics Theses and Dissertations

Solitons are self-reinforcing localized wave packets that have remarkable stability features that arise from the balanced competition of nonlinear and dispersive effects in the medium. Traditionally, the dominant order of dispersion has been the lowest (second), however in recent years, experimental and theoretical research has shown that high, even order dispersion may lead to novel applications. Here, the focus is on investigating the interplay of dominant quartic (fourth-order) dispersion and the self-phase modulation due to the nonlinear Kerr effect in laser systems. One big factor to consider for experimentalists working in laser systems is the effect of noise on the …

Neural Network Learning For Pdes With Oscillatory Solutions And Causal Operators, Lizuo Liu

Mathematics Theses and Dissertations

In this thesis, we focus on developing neural networks algorithms for scientific computing. First, we proposed a phase shift deep neural network (PhaseDNN), which provides a uniform wideband convergence in approximating high frequency functions and solutions of wave equations. Several linearized learning schemes have been proposed for neural networks solving nonlinear Navier-Stokes equations. We also proposed a causality deep neural network (Causality-DeepONet) to learn the causal response of a physical system. An extension of the Causality-DeepONet to time-dependent PDE systems is also proposed. The PhaseDNN makes use of the fact that common DNNs often achieve convergence in the low frequency …

Adaptive Multirate Infinitesimal Time Integration, Alex Fish

Mathematics Theses and Dissertations

As multiphysics simulations grow in complexity and application scientists desire more accurate results, computational costs increase greatly. Time integrators typically cater to the most restrictive physical processes of a given simulation\add{,} which can be unnecessarily computationally expensive for the less restrictive physical processes. Multirate time integrators are a way to combat this increase in computational costs by efficiently solving systems of ordinary differential equations that contain physical processes which evolve at different rates by assigning different time step sizes to the different processes. Adaptivity is a technique for further increasing efficiency in time integration by automatically growing and shrinking the …

A Node Elimination Algorithm For Cubatures Of High-Dimensional Polytopes, Arkadijs Slobodkins

Mathematics Theses and Dissertations

Node elimination is a numerical approach for obtaining cubature rules for the approximation of multivariate integrals over domains in Rⁿ. Beginning with a known cubature, nodes are selected for elimination, and a new, more efficient rule is constructed by iteratively solving the moment equations. In this work, a new node elimination criterion is introduced that is based on linearization of the moment equations. In addition, a penalized iterative solver is introduced that ensures positivity of weights and interiority of nodes. We aim to construct a universal algorithm for convex polytopes that produces efficient cubature rules without any user …

Practical Implementation Of The Immersed Interface Method With Triangular Meshes For 3d Rigid Solids In A Fluid Flow, Norah Hakami

Mathematics Theses and Dissertations

When employing the immersed interface method (IIM) to simulate a fluid flow around a moving rigid object, the immersed object can be replaced by a virtual fluid enclosed by singular forces on the interface between the real and virtual fluids. These forces represent the impact of the rigid motion on the fluid flow and cause jump discontinuities across the interface in the whole flow field. Then, the IIM resolves the fluid flow on a fixed computational domain by directly incorporating the jump conditions across the interface into numerical schemes. Previous development of the method is limited to simple smooth boundaries. …

Viscous Thin-Film Models Of Nanoscale Self-Organization Under Ion Bombardment, Tyler Evans

Mathematics Theses and Dissertations

For decades, it has been observed that broad-beam irradiation of semiconductor surfaces can lead to spontaneous self-organization into highly regular patterns, sometimes at length scales of only a few nanometers. Initial theory was largely based on erosion and redistribution of material occurring on fast time scales, which are able to produce good agreement with certain aspects of surface evolution. However, further experimental and theoretical work eventually led to the realization that numerous effects are active in the irradiated target, including stresses associated with ion-implantation and the accumulation of damage leading to the development of a disordered, amorphous layer atop the …

A Fast Method For Computing Volume Potentials In The Galerkin Boundary Element Method In 3d Geometries, Sasan Mohyaddin

Mathematics Theses and Dissertations

We discuss how the Fast Multipole Method (FMM) applied to a boundary concentrated mesh can be used to evaluate volume potentials that arise in the boundary element method. If $h$ is the meshwidth near the boundary, then the algorithm can compute the potential in nearly $\Ord(h^{-2})$ operations while maintaining an $\Ord(h^p)$ convergence of the error. The effectiveness of the algorithms are demonstrated by solving boundary integral equations of the Poisson equation.

Finite Element Approximation Of Solutions Of The Equations Of Electroporoelasticity, Yu Hu

Mathematics Theses and Dissertations

In this thesis we consider the solution of the equations of electroporoelasticity, which are a combination of Maxwell's equations and the poroelasticity equations. Included is a description of suitable initial and boundary conditions, weak formulation of the equations, and the error estimate for a general numerical method.

Fast Multipole Methods For Wave And Charge Source Interactions In Layered Media And Deep Neural Network Algorithms For High-Dimensional Pdes, Wenzhong Zhang

Mathematics Theses and Dissertations

In this dissertation, we develop fast algorithms for large scale numerical computations, including the fast multipole method (FMM) in layered media, and the forward-backward stochastic differential equation (FBSDE) based deep neural network (DNN) algorithms for high-dimensional parabolic partial differential equations (PDEs), addressing the issues of real-world challenging computational problems in various computation scenarios.

We develop the FMM in layered media, by first studying analytical and numerical properties of the Green's functions in layered media for the 2-D and 3-D Helmholtz equation, the linearized Poisson--Boltzmann equation, the Laplace's equation, and the tensor Green's functions for the time-harmonic Maxwell's equations and the …

High-Order Flexible Multirate Integrators For Multiphysics Applications, Rujeko Chinomona

Mathematics Theses and Dissertations

Traditionally, time integration methods within multiphysics simulations have been chosen to cater to the most restrictive dynamics, sometimes at a great computational cost. Multirate integrators accurately and efficiently solve systems of ordinary differential equations that exhibit different time scales using two or more time steps. In this thesis, we explore three classes of time integrators that can be classified as one-step multi-stage multirate methods for which the slow dynamics are evolved using a traditional one step scheme and the fast dynamics are solved through a sequence of modified initial value problems. Practically, the fast dynamics are subcycled using a small …

Uncertainty Quantification Of Nonreflecting Boundary Schemes, Brian Citty

Mathematics Theses and Dissertations

Numerical methods have been developed to solve partial differential equations involving the far-field radiation of waves. In addition, there has been recent interest in uncertainty quantification- a burgeoning field involving solving PDEs where random variables are used to model uncertainty in the data. In this thesis we will apply uncertainty quantification methodology to the 1D and 2D wave equation with nonreflecting boundary. We first derive a boundary condition for the 1D wave equation assuming several models of the random wave speed. Later we use our result to compare to an asymptotic SDE approach, and finally we repeat our analysis for …

Modeling Fluid Phenomena In The Context Of The Constrained Vapor Bubble System, James Barrett

Mathematics Theses and Dissertations

This thesis focuses on the fluid phenomena observed within what is known as the constrained vapor bubble system. The constrained vapor bubble system is a closed system consisting of a quartz cuvette partially filled with liquid and used as a coolant device. Heat is applied to the heater end which causes the liquid to evaporate and condense on the cooled end of the cuvette. Liquid travels back to the heated end via capillary flow in the corners. A pure vapor bubble is formed in the center of the cuvette giving rise to the name of the experiment. The constrained vapor …

Multigrid For The Nonlinear Power Flow Equations, Enrique Pereira Batista

Mathematics Theses and Dissertations

The continuously changing structure of power systems and the inclusion of renewable
energy sources are leading to changes in the dynamics of modern power grid,
which have brought renewed attention to the solution of the AC power flow equations.
In particular, development of fast and robust solvers for the power flow problem
continues to be actively investigated. A novel multigrid technique for coarse-graining
dynamic power grid models has been developed recently. This technique uses an
algebraic multigrid (AMG) coarsening strategy applied to the weighted
graph Laplacian that arises from the power network's topology for the construction
of coarse-grain approximations to …

Advection-Reaction-Diffusion Model Of Drug Concentration In A Lymph Node, Ting Yan

Mathematics Theses and Dissertations

It is recognized that there exist reservoirs of HIV located outside the bloodstream, and that these reservoirs hinder the efficacy of antiretroviral medication regimens in combating the virus. The prevailing theories regarding these reservoirs point to the lymphatic system. In this work, we discuss a novel computational model of viral dynamics in the lymph node, to allow numerical studies of viral “reservoirs” causing reinfection. Our model consists of a system of advection-reaction-diffusion partial differential equations (PDEs), where the diffusion coefficients vary between species (virus, drugs, lymphocytes) and include discontinuous jumps to capture differing properties of internal lymph node structures. We …

Cell Assembly Detection In Low Firing-Rate Spike Train Data, Phan Minh Duc Truong

Mathematics Theses and Dissertations

Cell assemblies, defined as groups of neurons forming temporal spike coordination, are thought to be fundamental units supporting major cognitive functions. However, detecting cell assemblies is challenging since they can occur at a range of time scales and with a range of precisions, from synchronous spikes to co-variations in firing rate. In this dissertation, we use a recently published cell assembly detection (CAD) algorithm that is capable of detecting assemblies at a range of time scales and precisions. We first showed that the CAD method can be applied to sparser spike train data than what have previously been reported. This …

The Boundary Element Method For Parabolic Equation And Its Implementation In Bem++, Sihao Wang

Mathematics Theses and Dissertations

The goal of this work is to develop a fast method for solving Galerkin discretizations of boundary integral formulations of the heat equation. The main contribution of this work is to devise a new fast algorithm for evaluating the dense matrices of the discretized integral equations.

Similar to the parabolic FMM, this method is based on a subdivision of the matrices into an appropriate hierarchical block structure. However, instead of an expansion of the kernel in both space and time we interpolate kernel in the temporal variables and use of the adaptive cross approximation (ACA) in the spatial variables.

The …

A New Class Of Discontinuous Galerkin Methods For Wave Equations In Second-Order Form, Lu Zhang

Mathematics Theses and Dissertations

Discontinuous Galerkin methods are widely used in many practical fields. In this thesis, we focus on a new class of discontinuous Galerkin methods for second-order wave equations. This thesis is constructed by three main parts. In the first part, we study the convergence properties of the energy-based discontinuous Galerkin proposed in [3] for wave equations. We improve the existing suboptimal error estimates to an optimal convergence rate in the energy norm. In the second part, we generalize the energy-based discontinuous Galerkin method proposed in [3] to the advective wave equation and semilinear wave equation in second-order form. Energy-conserving or energy-dissipating …

Model Selection And Experimental Design Of Biological Networks With Algebraic Geometry, Anyu Zhang

Mathematics Theses and Dissertations

Model selection based on experimental data is an essential challenge in biological data science. In decades, the volume of biological data from varied sources, including laboratory experiments, field observations, and patient health records has seen an unprecedented increase. Mainly when collecting data is expensive or time-consuming, as it is often in the case with clinical trials and biomolecular experiments, the problem of selecting information-rich data becomes crucial for creating relevant models.

Motivated by certain geometric relationships between data, we partitioned input data sets, especially data sets that correspond to a unique basis, into equivalence classes with the same basis to …

Parallel Multipole Expansion Algorithms And Their Biology Applications, Jiahui Chen

Mathematics Theses and Dissertations

N-body pairwise interactions are ubiquitous in scientific areas such as astrophysics, fluids mechanics, electrical engineering, molecular biology, etc. Computing these interactions using direct sum of an O(N) cost is expensive, whereas multipole expansion methods, such as the fast multipole method (FMM) or treecode, can reduce the cost to O(N) or O(N log N). This thesis focuses on developing numerical algorithms of Cartesian FMM and treecode, as well as using these algorithms to directly or implicitly solve biological problems involving pairwise interactions. This thesis consists of the following topics. 1) A cyclic parallel scheme is developed to handle the load balancing …

Swelling As A Stabilizing Mechanism During Ion Bombardment Of Thin Films: An Analytical And Numerical Study, Jennifer M. Swenson

Mathematics Theses and Dissertations

Irradiation of semiconductor surfaces often leads to the spontaneous formation of rippled structures at certain irradiation angles. However, at high enough energies, these structures are observed to vanish for all angles, despite the absence of any identified, universally-stabilizing physical mechanisms in operation. Here, we examine the effect on pattern formation of radiation-induced swelling, which has been excluded from prior treatments of stress in irradiated films. After developing a suitable continuum model, we perform a linear stability analysis to determine its effect on stability. Under appropriate simplifying assumptions, we find swelling indeed to be stabilizing at wavenumbers typical of experimental observations. …

High-Order Relaxed Multirate Infinitesimal Step Methods For Multiphysics Applications, Jean Sexton

Mathematics Theses and Dissertations

In this work, we consider numerical methods for integrating multirate ordinary differential equations. We are interested in the development of new multirate methods with good stability properties and improved efficiency over existing methods. We discuss the development of multirate methods, particularly focusing on those that are based on Runge-Kutta theory. We introduce the theory of Generalized Additive Runge-Kutta methods proposed by Sandu and Günther. We also introduce the theory of Recursive Flux Splitting Multirate Methods with Sub-cycling described by Schlegel, as well as the Multirate Infinitesimal Step methods this work is based on. We propose a generic structure called Flexible …