Physical Sciences and Mathematics Commons^™

Estimating Propensity Parameters Using Google Pagerank And Genetic Algorithms, David Murrugarra, Jacob Miller, Alex N. Mueller

Mathematics Faculty Publications

Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same time, and the asynchronous update where a random node is updated at each time step. The former produces a deterministic dynamics while the latter a stochastic dynamics. A more general stochastic setting considers propensity parameters for updating each node. Stochastic Discrete Dynamical Systems (SDDS) are a modeling framework that considers two propensity parameters for updating each node …

Identification Of Control Targets In Boolean Molecular Network Models Via Computational Algebra, David Murrugarra, Alan Veliz-Cuba, Boris Aguilar, Reinhard Laubenbacher

Mathematics Faculty Publications

Background: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type …

A Note On The Γ-Coefficients Of The Tree Eulerian Polynomial, Rafael S. González D'León

Mathematics Faculty Publications

We consider the generating polynomial of the number of rooted trees on the set {1,2,...,n} counted by the number of descending edges (a parent with a greater label than a child). This polynomial is an extension of the descent generating polynomial of the set of permutations of a totally ordered n-set, known as the Eulerian polynomial. We show how this extension shares some of the properties of the classical one. A classical product formula shows that this polynomial factors completely over the integers. From this product formula it can be concluded that this polynomial has positive coefficients …

A Model For Spheroid Versus Monolayer Response Of Sk-N-Sh Neuroblastoma Cells To Treatment With 15-Deoxy-Pgj2, Dorothy I. Wallace, Ann Dunham, Paula X. Chen, Michelle Chen, Milan Huynh, Evan Rheingold, Olivia F. Prosper

Mathematics Faculty Publications

Researchers have observed that response of tumor cells to treatment varies depending on whether the cells are grown in monolayer, as in vitro spheroids or in vivo. This study uses data from the literature on monolayer treatment of SK-N-SH neuroblastoma cells with 15-deoxy-PGJ₂ and couples it with data on growth rates for untreated SK-N-SH neuroblastoma cells grown as multicellular spheroids. A linear model is constructed for untreated and treated monolayer data sets, which is tuned to growth, death, and cell cycle data for the monolayer case for both control and treatment with 15-deoxy-PGJ₂. The monolayer …

The Spruce Budworm And Forest: A Qualitative Comparison Of Ode And Boolean Models, Raina Robeva, David Murrugarra

Mathematics Faculty Publications

Boolean and polynomial models of biological systems have emerged recently as viable companions to differential equations models. It is not immediately clear however whether such models are capable of capturing the multi-stable behaviour of certain biological systems: this behaviour is often sensitive to changes in the values of the model parameters, while Boolean and polynomial models are qualitative in nature. In the past few years, Boolean models of gene regulatory systems have been shown to capture multi-stability at the molecular level, confirming that such models can be used to obtain information about the system’s qualitative dynamics when precise information regarding …

Flag F-Vectors Of Polytopes With Few Vertices, Sarah A. Nelson

Theses and Dissertations--Mathematics

We may describe a polytope P as the convex hull of n points in space. Here we consider the numbers of chains of faces of P. The toric g-vector and CD-index of P are useful invariants for encoding this information. For a simplicial polytope P, Lee defined the winding number w_k in a Gale diagram corresponding to P. He showed that w_k in the Gale diagram equals g_k of the corresponding polytope. In this dissertation, we fully establish how to compute the g-vector for any polytope with few vertices from its …

In Search Of A Class Of Representatives For Su-Cobordism Using The Witten Genus, John E. Mosley

Theses and Dissertations--Mathematics

In algebraic topology, we work to classify objects. My research aims to build a better understanding of one important notion of classification of differentiable manifolds called cobordism. Cobordism is an equivalence relation, and the equivalence classes in cobordism form a graded ring, with operations disjoint union and Cartesian product. My dissertation studies this graded ring in two ways:

1. by attempting to find preferred class representatives for each class in the ring.

2. by computing the image of the ring under an interesting ring homomorphism called the Witten Genus.

Inverse Scattering For The Zero-Energy Novikov-Veselov Equation, Michael Music

Theses and Dissertations--Mathematics

For certain initial data, we solve the Novikov-Veselov equation by the inverse scat- tering method. This is a (2+1)-dimensional completely integrable system that gen- eralizes the (1+1)-dimensional Korteweg-de-Vries equation. The method used is the inverse scattering method. To study the direct and inverse scattering maps, we prove existence and uniqueness properties of exponentially growing solutions of the two- dimensional Schrodinger equation. For conductivity-type potentials, this was done by Nachman in his work on the inverse conductivity problem. Our work expands the set of potentials for which the analysis holds, completes the study of the inverse scattering map, and show that …

On Skew-Constacyclic Codes, Neville Lyons Fogarty

Theses and Dissertations--Mathematics

Cyclic codes are a well-known class of linear block codes with efficient decoding algorithms. In recent years they have been generalized to skew-constacyclic codes; such a generalization has previously been shown to be useful. We begin with a study of skew-polynomial rings so that we may examine these codes algebraically as quotient modules of non-commutative skew-polynomial rings. We introduce a skew-generalized circulant matrix to aid in examining skew-constacyclic codes, and we use it to recover a well-known result on the duals of skew-constacyclic codes from Boucher/Ulmer in 2011. We also motivate and develop a notion of idempotent elements in these …

Kronecker's Theory Of Binary Bilinear Forms With Applications To Representations Of Integers As Sums Of Three Squares, Jonathan A. Constable

Theses and Dissertations--Mathematics

In 1883 Leopold Kronecker published a paper containing “a few explanatory remarks” to an earlier paper of his from 1866. His work loosely connected the theory of integral binary bilinear forms to the theory of integral binary quadratic forms. In this dissertation we discover the statements within Kronecker's paper and offer detailed arithmetic proofs. We begin by developing the theory of binary bilinear forms and their automorphs, providing a classification of integral binary bilinear forms up to equivalence, proper equivalence and complete equivalence.

In the second chapter we introduce the class number, proper class number and complete class number as …

Homogenization Of Stokes Systems With Periodic Coefficients, Shu Gu

Theses and Dissertations--Mathematics

In this dissertation we study the quantitative theory in homogenization of Stokes systems. We study uniform regularity estimates for a family of Stokes systems with rapidly oscillating periodic coefficients. We establish interior Lipschitz estimates for the velocity and L^∞ estimates for the pressure as well as Liouville property for solutions in ℝ^d. We are able to obtain the boundary W^{1,p} estimates in a bounded C¹ domain for any 1 < p < ∞. We also study the convergence rates in L² and H¹ of Dirichlet and Neumann problems for Stokes systems with rapidly oscillating periodic coefficients, without any regularity assumptions on the coefficients.

New Perspectives Of Quantum Analogues, Yue Cai

Theses and Dissertations--Mathematics

In this dissertation we discuss three problems. We first show the classical q-Stirling numbers of the second kind can be expressed more compactly as a pair of statistics on a subset of restricted growth words. We extend this enumerative result via a decomposition of a new poset which we call the Stirling poset of the second kind. The Stirling poset of the second kind supports an algebraic complex and a basis for integer homology is determined. A parallel enumerative, poset theoretic and homological study for the q-Stirling numbers of the first kind is done. We also give a bijective …

Solutions To The LP Mixed Boundary Value Problem In C1,1 Domains, Laura D. Croyle

Theses and Dissertations--Mathematics

We look at the mixed boundary value problem for elliptic operators in a bounded C^1,1(ℝⁿ) domain. The boundary is decomposed into disjoint parts, D and N, with Dirichlet and Neumann data, respectively. Expanding on work done by Ott and Brown, we find a larger range of values of p, 1 < p < n/(n-1), for which the L^p mixed problem has a unique solution with the non-tangential maximal function of the gradient in L^p(∂Ω).

The Bourgain Spaces And Recovery Of Magnetic And Electric Potentials Of Schrödinger Operators, Yaowei Zhang

Theses and Dissertations--Mathematics

We consider the inverse problem for the magnetic Schrödinger operator with the assumption that the magnetic potential is in C^λ and the electric potential is of the form p₁ + div p₂ with p₁, p₂ ∈ C^λ. We use semiclassical pseudodifferential operators on semiclassical Sobolev spaces and Bourgain type spaces. The Bourgain type spaces are defined using the symbol of the operator h²Δ + hμ ⋅ D. Our main result gives a procedure for recovering the curl of the magnetic field and the electric potential from the Dirichlet to Neumann …