Dynamical Systems Commons^™

Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel

Dissertations, Theses, and Capstone Projects

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access …

Categorical Chain Conditions For Étale Groupoid Algebras, Sunil Philip

Dissertations, Theses, and Capstone Projects

Let R be a unital commutative ring and G an ample groupoid. Using the topology of the groupoid G, Steinberg defined an étale groupoid algebra RG. These étale groupoid algebras generalize various algebras, including group algebras, commutative algebras over a field generated by idempotents, traditional groupoid algebras, Leavitt path algebras, higher-rank graph algebras, and inverse semigroup algebras. Steinberg later characterized the classical chain conditions for étale groupoid algebras. In this work, we characterize categorically noetherian and artinian, locally noetherian and artinian, and semisimple étale groupoid algebras, thereby generalizing existing results for Leavitt path algebras and introducing new results for inverse …

Bifurcations And Resultants For Rational Maps And Dynatomic Modular Curves In Positive Characteristic, Colette Lapointe

Dissertations, Theses, and Capstone Projects

No abstract provided.

A Causal Inference Approach For Spike Train Interactions, Zach Saccomano

Dissertations, Theses, and Capstone Projects

Since the 1960s, neuroscientists have worked on the problem of estimating synaptic properties, such as connectivity and strength, from simultaneously recorded spike trains. Recent years have seen renewed interest in the problem coinciding with rapid advances in experimental technologies, including an approximate exponential increase in the number of neurons that can be recorded in parallel and perturbation techniques such as optogenetics that can be used to calibrate and validate causal hypotheses about functional connectivity. This thesis presents a mathematical examination of synaptic inference from two perspectives: (1) using in vivo data and biophysical models, we ask in what cases the …

On The Spectrum Of Quaquaversal Operators, Josiah Sugarman

Dissertations, Theses, and Capstone Projects

In 1998 Charles Radin and John Conway introduced the Quaquaversal Tiling. A three dimensional hierarchical tiling with the property that the orientations of its tiles approach a uniform distribution faster than what is possible for hierarchical tilings in two dimensions. The distribution of orientations is controlled by the spectrum of a certain Hecke operator, which we refer to as the Quaquaversal Operator. For example, by showing that the largest eigenvalue has multiplicity equal to one, Charles Radin and John Conway showed that the orientations of this tiling approach a uniform distribution. In 2008, Bourgain and Gamburd showed that this operator …

Symmetric Rigidity For Circle Endomorphisms With Bounded Geometry And Their Dual Maps, John Adamski

Dissertations, Theses, and Capstone Projects

Let $f$ be a circle endomorphism of degree $d\geq2$ that generates a sequence of Markov partitions that either has bounded nearby geometry and bounded geometry, or else just has bounded geometry, with respect to normalized Lebesgue measure. We define the dual symbolic space $\S^*$ and the dual circle endomorphism $f^*=\tilde{h}\circ f\circ{h}^{-1}$, which is topologically conjugate to $f$. We describe some properties of the topological conjugacy $\tilde{h}$. We also describe an algorithm for generating arbitrary circle endomorphisms $f$ with bounded geometry that preserve Lebesgue measure and their corresponding dual circle endomorphisms $f^*$ as well as the conjugacy $\tilde{h}$, and implement it …

Dynamics Of The Family Lambda Tan Z^2, Santanu Nandi

Dissertations, Theses, and Capstone Projects

We prove some topological properties of the dynamical plane ($z$-plane) and a combinatorial structure of the parameter plane of a holomorphic family of meromorphic maps $\lambda \tan z^2$. In the dynamical plane, we prove that there is no Herman ring and the Julia set is a Cantor set for the map when the parameter is in the central capture component. Julia set is connected for the maps when the parameters are in other hyperbolic components. In the parameter plane, I prove that the capture components are simply connected and there are always four hyperbolic shell components attached to a virtual …

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 …

Gradient Estimation For Attractor Networks, Thomas Flynn

Dissertations, Theses, and Capstone Projects

It has been hypothesized that neural network models with cyclic connectivity may be more powerful than their feed-forward counterparts. This thesis investigates this hypothesis in several ways. We study the gradient estimation and optimization procedures for several variants of these networks. We show how the convergence of the gradient estimation procedures are related to the properties of the networks. Then we consider how to tune the relative rates of gradient estimation and parameter adaptation to ensure successful optimization in these models. We also derive new gradient estimators for stochastic models. First, we port the forward sensitivity analysis method to the …

Asymptotic Counting Formulas For Markoff-Hurwitz Tuples, Ryan Ronan

Dissertations, Theses, and Capstone Projects

The Markoff equation is a Diophantine equation in 3 variables first studied in Markoff's celebrated work on indefinite binary quadratic forms. We study the growth of solutions to an n variable generalization of the Markoff equation, which we refer to as the Markoff-Hurwitz equation. We prove explicit asymptotic formulas counting solutions to this generalized equation with and without a congruence restriction. After normalizing and linearizing the equation, we show that all but finitely many solutions appear in the orbit of a certain semigroup of maps acting on finitely many root solutions. We then pass to an accelerated subsemigroup of maps …

Morphogenesis And Growth Driven By Selection Of Dynamical Properties, Yuri Cantor

Dissertations, Theses, and Capstone Projects

Organisms are understood to be complex adaptive systems that evolved to thrive in hostile environments. Though widely studied, the phenomena of organism development and growth, and their relationship to organism dynamics is not well understood. Indeed, the large number of components, their interconnectivity, and complex system interactions all obscure our ability to see, describe, and understand the functioning of biological organisms.

Here we take a synthetic and computational approach to the problem, abstracting the organism as a cellular automaton. Such systems are discrete digital models of real-world environments, making them more accessible and easier to study then their physical world …

The Fourth Movement Of György Ligeti's Piano Concerto: Investigating The Musical-Mathematical Connection, Cynthia L. Wong

Dissertations, Theses, and Capstone Projects

This interdisciplinary study explores musical-mathematical analogies in the fourth movement of Ligeti’s Piano Concerto. Its aim is to connect musical analysis with the piece’s mathematical inspiration. For this purpose, the dissertation is divided into two sections. Part I (Chapters 1-2) provides musical and mathematical context, including an explanation of ideas related to Ligeti’s mathematical inspiration. Part II (Chapters 3-5) delves into an analysis of the rhythm, form, melody / motive, and harmony. Appendix A is a reduced score of the entire movement, labeled according to my analysis.