Numerical Analysis and Scientific Computing Commons^™

Krylov Subspace Spectral Methods With Non-Homogenous Boundary Conditions, Abbie Hendley

Master's Theses

For this thesis, Krylov Subspace Spectral (KSS) methods, developed by Dr. James Lambers, will be used to solve a one-dimensional, heat equation with non-homogenous boundary conditions. While current methods such as Finite Difference are able to carry out these computations efficiently, their accuracy and scalability can be improved. We will solve the heat equation in one-dimension with two cases to observe the behaviors of the errors using KSS methods. The first case will implement KSS methods with trigonometric initial conditions, then another case where the initial conditions are polynomial functions. We will also look at both the time-independent and time-dependent …

The Effects Of Finite Precision On The Simulation Of The Double Pendulum, Rebecca Wild

Senior Honors Projects, 2010-2019

We use mathematics to study physical problems because abstracting the information allows us to better analyze what could happen given any range and combination of parameters. The problem is that for complicated systems mathematical analysis becomes extremely cumbersome. The only effective and reasonable way to study the behavior of such systems is to simulate the event on a computer. However, the fact that the set of floating-point numbers is finite and the fact that they are unevenly distributed over the real number line raises a number of concerns when trying to simulate systems with chaotic behavior. In this research we …

Reducing Memory Access Latencies Using Data Compression In Sparse, Iterative Linear Solvers, Neil Lindquist

All College Thesis Program, 2016-2019

Solving large, sparse systems of linear equations plays a significant role in certain scientific computations, such as approximating the solutions of partial differential equations. However, solvers for these types of problems usually spend most of their time fetching data from main memory. In an effort to improve the performance of these solvers, this work explores using data compression to reduce the amount of data that needs to be fetched from main memory. Some compression methods were found that improve the performance of the solver and problem found in the HPCG benchmark, with an increase in floating point operations per second …

Algorithms To Approximate Solutions Of Poisson's Equation In Three Dimensions, Ray Dambrose

Rose-Hulman Undergraduate Mathematics Journal

The focus of this research was to develop numerical algorithms to approximate solutions of Poisson's equation in three dimensional rectangular prism domains. Numerical analysis of partial differential equations is vital to understanding and modeling these complex problems. Poisson's equation can be approximated with a finite difference approximation. A system of equations can be formed that gives solutions at internal points of the domain. A computer program was developed to solve this system with inputs such as boundary conditions and a nonhomogenous source function. Approximate solutions are compared with exact solutions to prove their accuracy. The program is tested with an …

Universal Quantum Computation, Junya Kasahara

Theses, Dissertations and Capstones

We study quantum computers and their impact on computability. First, we summarize the history of computer science. Only a few articles have determined the direction of computer science and industry despite the fact that many works have been dedicated to the present success. We choose articles by A. M. Turing and D. Deutsch, because A. M. Turing proposed the basic architecture of modern computers while D. Deutsch proposed an architecture for the next generation of computers called quantum computers. Second, we study the architecture of modern computers using Turing machines. The Turing machine has the basic design of modern computers …

Randomized Algorithms For Preconditioner Selection With Applications To Kernel Regression, Conner Dipaolo

HMC Senior Theses

The task of choosing a preconditioner M to use when solving a linear system Ax=b with iterative methods is often tedious and most methods remain ad-hoc. This thesis presents a randomized algorithm to make this chore less painful through use of randomized algorithms for estimating traces. In particular, we show that the preconditioner stability || I - M^-1A ||_F, known to forecast preconditioner quality, can be computed in the time it takes to run a constant number of iterations of conjugate gradients through use of sketching methods. This is in spite of folklore which …

Equilibrium Structures And Thermal Fluctuations In Interacting Monolayers, Emmanuel Rivera

Williams Honors College, Honors Research Projects

Coherency strains appear in interacting atomic monolayers due to differing bond lengths, which can arise from different materials or geometries. Examples include extended monolayers interacting with a substrate and the interacting walls of a multi-walled carbon nanotube. These strains can induce various equilibrium configurations, which we will analyze by means of a phenomenological model that incorporates forces from bond stretching and bending within each layer and the weak van der Waals interactions connecting the separate layers. We vary the strengths of each interaction to explore their effects on equilibrium structures, and the specific case of a two-walled carbon nanotube is …

Description Of Motor Control Using Inverse Models, Anton Sobinov

Graduate Theses, Dissertations, and Problem Reports (ETD)

Humans can perform complicated movements like writing or running without giving them much thought. The scientific understanding of principles guiding the generation of these movements is incomplete. How the nervous system ensures stability or compensates for injury and constraints – are among the unanswered questions today. Furthermore, only through movement can a human impose their will and interact with the world around them. Damage to a part of the motor control system can lower a person’s quality of life. Understanding how the central nervous system (CNS) forms control signals and executes them helps with the construction of devices and rehabilitation …

Calculating The Cohomology Of A Lie Algebra Using Maple And The Serre Hochschild Spectral Sequence, Jacob Kullberg

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Lie algebra cohomology is an important tool in many branches of mathematics. It is used in the Topology of homogeneous spaces, Deformation theory, and Extension theory. There exists extensive theory for calculating the cohomology of semi simple Lie algebras, but more tools are needed for calculating the cohomology of general Lie algebras. To calculate the cohomology of general Lie algebras, I used the symbolic software program called Maple. I wrote software to calculate the cohomology in several different ways. I wrote several programs to calculate the cohomology directly. This proved to be computationally expensive as the number of differential forms …

Reaction Simulations: A Rapid Development Framework, Brendan Drake Donohoe

Shared Knowledge Conference

Chemical Reaction Networks (CRNs) are a popular tool in the chemical sciences for providing a means of analyzing and modeling complex reaction systems. In recent years, CRNs have attracted attention in the field of molecular computing for their ability to simulate the components of a digital computer. The reactions within such networks may occur at several different scales relative to one another – at rates often too difficult to directly measure and analyze in a laboratory setting. To facilitate the construction and analysis of such networks, we propose a reduced order model for simulating such networks as a system of …

Introducing The Fractional Differentiation For Clinical Data-Justified Prostate Cancer Modelling Under Iad Therapy, Ozlem Ozturk Mizrak

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Mathematical Modeling And Simulation With Deep Learning Methods Of Cancer Growth For Patient-Specific Therapy, Vishal Kobla, Joshua P. Smith, Pranav Unni, Padmanabhan Seshaiyer

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Recta: Regulon Identification Based On Comparative Genomics And Transcriptomics Analysis, Xin Chen, Anjun Ma, Adam Mcdermaid, Hanyuan Zhang, Chao Liu, Huansheng Cao, Qin Ma

School of Computing: Faculty Publications

Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on Lactococcus lactis MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to …

Physical Applications Of The Geometric Minimum Action Method, George L. Poppe Jr.

Dissertations, Theses, and Capstone Projects

This thesis extends the landscape of rare events problems solved on stochastic systems by means of the \textit{geometric minimum action method} (gMAM). These include partial differential equations (PDEs) such as the real Ginzburg-Landau equation (RGLE), the linear Schroedinger equation, along with various forms of the nonlinear Schroedinger equation (NLSE) including an application towards an ultra-short pulse mode-locked laser system (MLL).

Additionally we develop analytical tools that can be used alongside numerics to validate those solutions. This includes the use of instanton methods in deriving state transitions for the linear Schroedinger equation and the cubic diffusive NLSE.

These analytical solutions are …

Predicting The Next Us President By Simulating The Electoral College, Boyan Kostadinov

Publications and Research

We develop a simulation model for predicting the outcome of the US Presidential election based on simulating the distribution of the Electoral College. The simulation model has two parts: (a) estimating the probabilities for a given candidate to win each state and DC, based on state polls, and (b) estimating the probability that a given candidate will win at least 270 electoral votes, and thus win the White House. All simulations are coded using the high-level, open-source programming language R. One of the goals of this paper is to promote computational thinking in any STEM field by illustrating how probabilistic …

Developing A Cyberterrorism Policy: Incorporating Individual Values, Osama Bassam J. Rabie

Theses and Dissertations

Preventing cyberterrorism is becoming a necessity for individuals, organizations, and governments. However, current policies focus on technical and managerial aspects without asking for experts and non-experts values and preferences for preventing cyberterrorism. This study employs value focused thinking and public value forum to bare strategic measures and alternatives for complex policy decisions for preventing cyberterrorism. The strategic measures and alternatives are per socio-technical process.

High-Order Integral Equation Methods For Quasi-Magnetostatic And Corrosion-Related Field Analysis With Maritime Applications, Robert Pfeiffer

Theses and Dissertations--Electrical and Computer Engineering

This dissertation presents techniques for high-order simulation of electromagnetic fields, particularly for problems involving ships with ferromagnetic hulls and active corrosion-protection systems.

A set of numerically constrained hexahedral basis functions for volume integral equation discretization is presented in a method-of-moments context. Test simulations demonstrate the accuracy achievable with these functions as well as the improvement brought about in system conditioning when compared to other basis sets.

A general method for converting between a locally-corrected Nyström discretization of an integral equation and a method-of-moments discretization is presented next. Several problems involving conducting and magnetic-conducting materials are solved to verify the accuracy …

Wildfire Emissions In The Context Of Global Change And The Implications For Mercury Pollution, Aditya Kumar

Dissertations, Master's Theses and Master's Reports

Wildfires are episodic disturbances that exert a significant influence on the Earth system. They emit substantial amounts of atmospheric pollutants, which can impact atmospheric chemistry/composition and the Earth’s climate at the global and regional scales. This work presents a collection of studies aimed at better estimating wildfire emissions of atmospheric pollutants, quantifying their impacts on remote ecosystems and determining the implications of 2000s-2050s global environmental change (land use/land cover, climate) for wildfire emissions following the Intergovernmental Panel on Climate Change (IPCC) A1B socioeconomic scenario.

A global fire emissions model is developed to compile global wildfire emission inventories for major atmospheric …

Sports Analytics With Computer Vision, Colby T. Jeffries

Senior Independent Study Theses

Computer vision in sports analytics is a relatively new development. With multi-million dollar systems like STATS’s SportVu, professional basketball teams are able to collect extremely fine-detailed data better than ever before. This concept can be scaled down to provide similar statistics collection to college and high school basketball teams. Here we investigate the creation of such a system using open-source technologies and less expensive hardware. In addition, using a similar technology, we examine basketball free throws to see whether a shooter’s form has a specific relationship to a shot’s outcome. A system that learns this relationship could be used to …

Underwater Acoustic Signal Analysis Toolkit, Kirk Bienvenu Jr

LSU New Orleans Theses and Dissertations

This project started early in the summer of 2016 when it became evident there was a need for an effective and efficient signal analysis toolkit for the Littoral Acoustic Demonstration Center Gulf Ecological Monitoring and Modeling (LADC-GEMM) Research Consortium. LADC-GEMM collected underwater acoustic data in the northern Gulf of Mexico during the summer of 2015 using Environmental Acoustic Recording Systems (EARS) buoys. Much of the visualization of data was handled through short scripts and executed through terminal commands, each time requiring the data to be loaded into memory and parameters to be fed through arguments. The vision was to develop …

Examining The Electrical Excitation, Calcium Signaling, And Mechanical Contraction Cycle In A Heart Cell, Kristen Deetz, Nygel Foster, Darius Leftwich, Chad Meyer, Shalin Patel, Carlos Barajas, Matthias K. Gobbert, Zana Coulibaly

Spora: A Journal of Biomathematics

As the leading cause of death in the United States, heart disease has become a principal concern in modern society. Cardiac arrhythmias can be caused by a dysregulation of calcium dynamics in cardiomyocytes. Calcium dysregulation, however, is not yet fully understood and is not easily predicted; this provides motivation for the subsequent research. Excitation-contraction coupling (ECC) is the process through which cardiomyocytes undergo contraction from an action potential. Calcium induced calcium release (CICR) is the mechanism through which electrical excitation is coupled with mechanical contraction through calcium signaling. The study of the interplay between electrical excitation, calcium signaling, and mechanical …

Distributed Evolution Of Spiking Neuron Models On Apache Mahout For Time Series Analysis, Andrew Palumbo

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Electrodynamical Modeling For Light Transport Simulation, Michael G. Saunders

Undergraduate Honors Theses

Modernity in the computer graphics community is characterized by a burgeoning interest in physically based rendering techniques. That is to say that mathematical reasoning from first principles is widely preferred to ad hoc, approximate reasoning in blind pursuit of photorealism. Thereby, the purpose of our research is to investigate the efficacy of explicit electrodynamical modeling by means of the generalized Jones vector given by Azzam [1] and the generalized Jones matrix given by Ortega-Quijano & Arce-Diego [2] in the context of stochastic light transport simulation for computer graphics. To augment the status quo path tracing framework with such a modeling …

High Performance Techniques Applied In Partial Differential Equations Library, Shilei Lin

All College Thesis Program, 2016-2019

This thesis explores various Trilinos packages to determine a method for updating the deal.ii library, which specializes in solving partial differential equations by finite element methods. It begins with introducing related concepts and general goals, followed by exploring computational and mathematical methods which are analytical solutions of one-dimensional Boussinesq equations and developing newer prototypes for solvers in deal.ii based on Trilinos packages. After demonstrating the methods, it indicates the reducing solving time in newer prototypes. Based on results from the prototype, similar methods are applied to update the deal.ii library. In the end, a testing program is exploited to demonstrate …

A Physics-Based Approach To Modeling Wildland Fire Spread Through Porous Fuel Beds, Tingting Tang

Theses and Dissertations--Mechanical and Aerospace Engineering

Wildfires are becoming increasingly erratic nowadays at least in part because of climate change. CFD (computational fluid dynamics)-based models with the potential of simulating extreme behaviors are gaining increasing attention as a means to predict such behavior in order to aid firefighting efforts. This dissertation describes a wildfire model based on the current understanding of wildfire physics. The model includes physics of turbulence, inhomogeneous porous fuel beds, heat release, ignition, and firebrands. A discrete dynamical system for flow in porous media is derived and incorporated into the subgrid-scale model for synthetic-velocity large-eddy simulation (LES), and a general porosity-permeability model is …

End-To-End Molecular Communication Channels In Cell Metabolism: An Information Theoretic Study, Zahmeeth Sayed Sakkaff, Jennie L. Catlett, Mikaela Cashman, Massimiliano Pierobon, Nicole R. Buan, Myra B. Cohen, Christine A. Kelley

Department of Biochemistry: Faculty Publications

The opportunity to control and fine-tune the behavior of biological cells is a fascinating possibility for many diverse disciplines, ranging from medicine and ecology, to chemical industry and space exploration. While synthetic biology is providing novel tools to reprogram cell behavior from their genetic code, many challenges need to be solved before it can become a true engineering discipline, such as reliability, safety assurance, reproducibility and stability. This paper aims to understand the limits in the controllability of the behavior of a natural (non-engineered) biological cell. In particular, the focus is on cell metabolism, and its natural regulation mechanisms, and …

Triple Non-Negative Matrix Factorization Technique For Sentiment Analysis And Topic Modeling, Alexander A. Waggoner

CMC Senior Theses

Topic modeling refers to the process of algorithmically sorting documents into categories based on some common relationship between the documents. This common relationship between the documents is considered the “topic” of the documents. Sentiment analysis refers to the process of algorithmically sorting a document into a positive or negative category depending whether this document expresses a positive or negative opinion on its respective topic. In this paper, I consider the open problem of document classification into a topic category, as well as a sentiment category. This has a direct application to the retail industry where companies may want to scour …

Computational Fluid Dynamics In A Terminal Alveolated Bronchiole Duct With Expanding Walls: Proof-Of-Concept In Openfoam, Jeremy Myers

Theses and Dissertations

Mathematical Biology has found recent success applying Computational Fluid Dynamics (CFD) to model airflow in the human lung. Detailed modeling of flow patterns in the alveoli, where the oxygen-carbon dioxide gas exchange occurs, has provided data that is useful in treating illnesses and designing drug-delivery systems. Unfortunately, many CFD software packages have high licensing fees that are out of reach for independent researchers. This thesis uses three open-source software packages, Gmsh, OpenFOAM, and ParaView, to design a mesh, create a simulation, and visualize the results of an idealized terminal alveolar sac model. This model successfully demonstrates that OpenFOAM can be …

Network Analytics For The Mirna Regulome And Mirna-Disease Interactions, Joseph Jayakar Nalluri

Theses and Dissertations

miRNAs are non-coding RNAs of approx. 22 nucleotides in length that inhibit gene expression at the post-transcriptional level. By virtue of this gene regulation mechanism, miRNAs play a critical role in several biological processes and patho-physiological conditions, including cancers. miRNA behavior is a result of a multi-level complex interaction network involving miRNA-mRNA, TF-miRNA-gene, and miRNA-chemical interactions; hence the precise patterns through which a miRNA regulates a certain disease(s) are still elusive. Herein, I have developed an integrative genomics methods/pipeline to (i) build a miRNA regulomics and data analytics repository, (ii) create/model these interactions into networks and use optimization techniques, motif …

An Environmental Impact Evaluation Model Generated By Compound Probability Distributions, Devin Akman, Olcay Akman

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.