Ordinary Differential Equations and Applied Dynamics Commons^™

Modeling Gene Expression With Differential Equations, Madison Kuduk

Capstone Showcase

Gene expression is the process by which the information stored in DNA is convertedinto a functional gene product, such as protein. The two main functions that makeup the process of gene expression are transcription and translation. Transcriptionand translation are controlled by the number of mRNA and protein in the cell. Geneexpression can be represented as a system of first order differential equations for the rateof change of mRNA and proteins. These equations involve transcription, translation,degradation and feedback loops. In this paper, I investigate a system of first orderdifferential equations to model gene expression proposed by Hunt, Laplace, Miller andPham in …

Exploration And Implementation Of Neural Ordinary Differential Equations, Long Huu Nguyen, Andy Malinsky

Capstone Showcase

Neural ordinary differential equations (ODEs) have recently emerged as a novel ap- proach to deep learning, leveraging the knowledge of two previously separate domains, neural networks and differential equations. In this paper, we first examine the back- ground and lay the foundation for traditional artificial neural networks. We then present neural ODEs from a rigorous mathematical perspective, and explore their advantages and trade-offs compared to traditional neural nets.

Integrating Mathematics And Biology In The Classroom: A Compendium Of Case Studies And Labs, Becky Sanft, Anne Walter

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Period Drift In A Neutrally Stable Stochastic Oscillator, Kevin Sanft

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

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 …

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.

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 …

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 …

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 …

Teaching Systems Biology Of The Circadian Clock With Journal Articles And Matlab, Stephanie R. Taylor

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Teaching Numerical Methods In The Context Of Galaxy Mergers, Maria Kourjanskaia

Physics

Methods of teaching numerical methods to solve ordinary differential equations in the context of galaxy mergers were explored. The research published in a paper by Toomre and Toomre in 1972 describing the formation of galactic tails and bridges from close tidal interactions was adapted into a project targeting undergraduate physics students. Typically undergraduate physics students only take one Computational Physics class in which various techniques and algorithms are taught. Although it is important to study computational physics techniques, it is just as important to apply this knowledge to a problem that is representative of what computational physics researchers are investigating …

Spontaneous Synchrony On Graphs And The Emergence Of Order From Disorder, Dylan Linville, Daniel Trugillo Martins Fontes

Rose-Hulman Undergraduate Research Publications

From pulsars to pedestrians and bacteria to brain cells, objects that exhibit cyclical behavior, called oscillators, are found in a variety of different settings. When oscillators adjust their behavior in response to nearby oscillators, they often achieve a state of synchrony, in which they all have the same phase and frequency. Here, we explore the Kuramoto model, a simple and general model which describes oscillators as dynamical systems on a graph and has been used to study synchronization in systems ranging from firefly swarms to the power grid. We discuss analytical and numerical methods used to investigate the governing system …

Smarticles: A Method For Identifying And Correcting Instability And Error Caused By Explicit Integration Techniques In Physically Based Simulations, Susan Aileen Marano

Master's Theses

Using an explicit integration method in physically based animations has many advantages including conceptual and computational simplicity, however, it re- quires small time steps to ensure low numerical instability. Simulations with large numbers of individually interacting components such as cloth, hair, and fluid models, are limited by the sections of particles most susceptible to error. This results in the need for smaller time steps than required for the majority of the system. These sections can be diverse and dynamic, quickly changing in size and location based on forces in the system. Identifying and handling these trou- blesome sections could allow …

Epistasis In Predator-Prey Relationships, Iuliia Inozemtseva

College of Graduate Studies: Theses & Dissertations

Epistasis is the interaction between two or more genes to control a single phenotype. We model epistasis of the prey in a two-locus two-allele problem in a basic predator- prey relationship. The resulting model allows us to examine both population sizes as well as genotypic and phenotypic frequencies. In the context of several numerical examples, we show that if epistasis results in an undesirable or desirable phenotype in the prey by making the particular genotype more or less susceptible to the predator or dangerous to the predator, elimination of undesirable phenotypes and then genotypes occurs.