Physical Sciences and Mathematics Commons^™

The Effect Of The Initial Structure On The System Relaxation Time In Langevin Dynamics, Omid Mozafar

Electronic Thesis and Dissertation Repository

In recent decades, computer experiments have allowed an accurate and fundamental understanding of molecular mechanisms at the microscopic level, such as the process of relaxation at a stable physical state. However, computer simulations may sometimes produce non-physical results or relations due to the incompleteness of mathematical models describing physical systems. In this thesis, we have investigated whether the initial structure in a computer simulation affects the system relaxation time, which is denoted by τ_sys, in the Langevin NVT ensemble. We found that for an initial structure, which is inhomogeneous in the number density of atoms, the system relaxation …

Longitudinal Partitioning Waveform Relaxation Methods For The Analysis Of Transmission Line Circuits, Tarik Menkad

Electronic Thesis and Dissertation Repository

Three research projects are presented in this manuscript. Projects one and two describe two waveform relaxation algorithms (WR) with longitudinal partitioning for the time-domain analysis of transmission line circuits. Project three presents theoretical results about the convergence of WR for chains of general circuits.

The first WR algorithm uses a assignment-partition procedure that relies on inserting external series combinations of positive and negative resistances into the circuit to control the speed of convergence of the algorithm. The convergence of the subsequent WR method is examined, and fast convergence is cast as a generic optimization problem in the frequency-domain. An automatic …

Analytical And Computational Modelling Of The Ranque-Hilsch Vortex Tube, Nolan J. Dyck

Electronic Thesis and Dissertation Repository

The Ranque-Hilsch vortex tube (RHVT) is a simple mechanical device with no moving parts capable of separating a supply of compressed fluid into hot and cold streams through a process called temperature separation. The overall aim is to develop models which can be used to assess the temperature separation mechanisms in the RHVT, leading to a better overall understanding of the underlying physics. The introductory chapter contains a thermodynamic analysis and introduction to the flow physics, alongside three miniature literature reviews and critiques identifying research gaps.

The body of the thesis contains three articles. The first article studies the flow …

Mathematical Modelling Of Prophage Dynamics, Tyler Pattenden

Electronic Thesis and Dissertation Repository

We use mathematical models to study prophages, viral genetic sequences carried by bacterial genomes. In this work, we first examine the role that plasmid prophage play in the survival of de novo beneficial mutations for the associated temperate bacteriophage. Through the use of a life-history model, we determine that mutations first occurring in a plasmid prophage are far more likely to survive drift than those first occurring in a free phage. We then analyse the equilibria and stability of a system of ordinary differential equations that describe temperate phage-host dynamics. We elucidate conditions on dimensionless parameters to determine a parameter …

Hybrid Symbolic-Numeric Computing In Linear And Polynomial Algebra, Leili Rafiee Sevyeri

Electronic Thesis and Dissertation Repository

In this thesis, we introduce hybrid symbolic-numeric methods for solving problems in linear and polynomial algebra. We mainly address the approximate GCD problem for polynomials, and problems related to parametric and polynomial matrices. For symbolic methods, our main concern is their complexity and for the numerical methods we are more concerned about their stability. The thesis consists of 5 articles which are presented in the following order:

Chapter 1, deals with the fundamental notions of conditioning and backward error. Although our results are not novel, this chapter is a novel explication of conditioning and backward error that underpins the rest …

Edge-Cloud Iot Data Analytics: Intelligence At The Edge With Deep Learning, Ananda Mohon M. Ghosh

Electronic Thesis and Dissertation Repository

Rapid growth in numbers of connected devices, including sensors, mobile, wearable, and other Internet of Things (IoT) devices, is creating an explosion of data that are moving across the network. To carry out machine learning (ML), IoT data are typically transferred to the cloud or another centralized system for storage and processing; however, this causes latencies and increases network traffic. Edge computing has the potential to remedy those issues by moving computation closer to the network edge and data sources. On the other hand, edge computing is limited in terms of computational power and thus is not well suited for …

Contraction Analysis Of Functional Competitive Lotka-Volterra Systems: Understanding Competition Between Modified Bacteria And Plasmodium Within Mosquitoes., Nickolas Goncharenko

Electronic Thesis and Dissertation Repository

We propose and analyze an extension to the classic Competitive Lotka-Volterra (CLV) model. The goal is to model competition between species, with a response from the environment. This response is a function of the population of all species and can represent numerous physical phenomena including resource limitation and immune response of a host due to infection. We name this new system a Functional Competitive Lotka-Volterra (FCLV) model. We mainly use the construction of contraction metrics, to determine global properties of the model. We use this result to analyze the competition between Plasmodium sp. and genetically engineered bacteria within the midgut …

Abelian Integral Method And Its Application, Xianbo Sun

Electronic Thesis and Dissertation Repository

Oscillation is a common natural phenomenon in real world problems. The most efficient mathematical models to describe these cyclic phenomena are based on dynamical systems. Exploring the periodic solutions is an important task in theoretical and practical studies of dynamical systems.

Abelian integral is an integral of a polynomial differential 1-form over the real ovals of a polynomial Hamiltonian, which is a basic tool in complex algebraic geometry. In dynamical system theory, it is generalized to be a continuous function as a tool to study the periodic solutions in planar dynamical systems. The zeros of Abelian integral and their distributions …

Phage-Bacteria Interaction And Prophage Sequences In Bacterial Genomes, Amjad Khan

Electronic Thesis and Dissertation Repository

In this investigation, we examined the interaction of phages and bacteria in bacterial biofilm colonies, the evolution of prophages (viral genetic material inserted into the bacterial genome) and their genetic repertoire. To study the synergistic effects of lytic phages and antibiotics on bacterial biofilm colonies, we have developed a mathematical model of ordinary differential equations (ODEs). We have also presented a mathematical model consisting of a partial differential equation (PDEs), to study evolutionary forces acting on prophages. We fitted the PDE model to three publicly available databases and were able to show that induction is the prominent fate of intact …