Physical Sciences and Mathematics Commons^™

On Flow Polytopes, Nu-Associahedra, And The Subdivision Algebra, Matias Von Bell

Theses and Dissertations--Mathematics

This dissertation studies the geometry and combinatorics related to a flow polytope F_car(ν) constructed from a lattice path ν, whose volume is given by the ν-Catalan numbers. It begins with a study of the ν-associahedron introduced by Ceballos, Padrol, and Sarmiento in 2019, but from the perspective of Schröder combinatorics. Some classical results for Schröder paths are extended to the ν-setting, and insights into the geometry of the ν-associahedron are obtained by describing its face poset with two ν-Schröder objects. The ν-associahedron is then shown to be dual to a framed triangulation of F_car(ν), which is a …

Tropical Geometry Of T-Varieties With Applications To Algebraic Statistics, Joseph Cummings

Theses and Dissertations--Mathematics

Varieties with group action have been of interest to algebraic geometers for centuries. In particular, toric varieties have proven useful both theoretically and in practical applications. A rich theory blending algebraic geometry and polyhedral geometry has been developed for T-varieties which are natural generalizations of toric varieties. The first results discussed in this dissertation study the relationship between torus actions and the well-poised property. In particular, I show that the well-poised property is preserved under a geometric invariant theory quotient by a (quasi-)torus. Conversely, I argue that T-varieties built on a well-poised base preserve the well-poised property when the base …

An Integrated Computational Pipeline To Construct Patient-Specific Cancer Models, Daniel Plaugher

Theses and Dissertations--Mathematics

Precision oncology largely involves tumor genomics to guide therapy protocols. Yet, it is well known that many commonly mutated genes cannot be easily targeted. Even when genes can be targeted, resistance to therapy is quite common. A rising field with promising results is that of mathematical biology, where in silico models are often used for the discovery of general principles and novel hypotheses that can guide the development of new treatments. A major goal is that eventually in silico models will accurately predict clinically relevant endpoints and find optimal control interventions to stop (or reverse) disease progression. Thus, it is …

Awegnn: Auto-Parametrized Weighted Element-Specific Graph Neural Networks For Molecules., Timothy Szocinski, Duc Duy Nguyen, Guo-Wei Wei

Mathematics Faculty Publications

While automated feature extraction has had tremendous success in many deep learning algorithms for image analysis and natural language processing, it does not work well for data involving complex internal structures, such as molecules. Data representations via advanced mathematics, including algebraic topology, differential geometry, and graph theory, have demonstrated superiority in a variety of biomolecular applications, however, their performance is often dependent on manual parametrization. This work introduces the auto-parametrized weighted element-specific graph neural network, dubbed AweGNN, to overcome the obstacle of this tedious parametrization process while also being a suitable technique for automated feature extraction on these internally complex …

Algebraic Graph-Assisted Bidirectional Transformers For Molecular Property Prediction, Dong Chen, Kaifu Gao, Duc Duy Nguyen, Xin Chen, Yi Jiang, Guo-Wei Wei, Feng Pan

Mathematics Faculty Publications

The ability of molecular property prediction is of great significance to drug discovery, human health, and environmental protection. Despite considerable efforts, quantitative prediction of various molecular properties remains a challenge. Although some machine learning models, such as bidirectional encoder from transformer, can incorporate massive unlabeled molecular data into molecular representations via a self-supervised learning strategy, it neglects three-dimensional (3D) stereochemical information. Algebraic graph, specifically, element-specific multiscale weighted colored algebraic graph, embeds complementary 3D molecular information into graph invariants. We propose an algebraic graph-assisted bidirectional transformer (AGBT) framework by fusing representations generated by algebraic graph and bidirectional transformer, as well as …

Mathematical Modeling Of The Candida Albicans Yeast To Hyphal Transition Reveals Novel Control Strategies, David J. Wooten, Jorge Gómez Tejeda Zañudo, David Murrugarra, Austin M. Perry, Anna Dongari-Bagtzoglou, Reinhard Laubenbacher, Clarissa J. Nobile, Réka Albert

Mathematics Faculty Publications

Candida albicans, an opportunistic fungal pathogen, is a significant cause of human infections, particularly in immunocompromised individuals. Phenotypic plasticity between two morphological phenotypes, yeast and hyphae, is a key mechanism by which C. albicans can thrive in many microenvironments and cause disease in the host. Understanding the decision points and key driver genes controlling this important transition and how these genes respond to different environmental signals is critical to understanding how C. albicans causes infections in the host. Here we build and analyze a Boolean dynamical model of the C. albicans yeast to hyphal transition, integrating …

Proctoring And Apps In College Algebra, Cynthia M. Shelton

Theses and Dissertations--Education Sciences

The pandemic forced more instructors and students to move to online learning. For the first time, many experienced a loosening of the reigns and were forced to allow students to submit non-proctored work. Many may have questioned what students really learned in the year 2020. Many college math course competencies emphasize procedures. Now that apps can do that for students, where does that leave math instructors? Additionally, online instruction has exploded over the last decade and has challenged the teaching of college mathematics. While online instruction opens the door to access, it does beg the question of whether students complete …

Using Semialgebraic Parametric Analysis By Metaprogramming In Portfolio Optimization, Philip Blaine Meersman

Lewis Honors College Capstone Collection

One classic problem in quantitative finance is portfolio optimization, which consists of assigning weights to assets in a portfolio to maximize one’s expected return while keeping the level of risk at a desired level. This problem can be modeled as a linear program (LP), using a risk aversion parameter mu. For a given single value of mu, the LP can be solved using any standard LP solver. In this work, however, the problem is considered parametrically: the optimal solution is sought for every possible value of mu. This describes how weights to the portfolio assets would be assigned from the …

Computational Utilities For The Game Of Simplicial Nim, Nelson Penn

Theses and Dissertations--Computer Science

Simplicial nim games, a class of impartial games, have very interesting mathematical properties. Winning strategies on a simplicial nim game can be determined by the set of positions in the game whose Sprague-Grundy values are zero (also zero positions). In this work, I provide two major contributions to the study of simplicial nim games. First, I provide a modern and efficient implementation of the Sprague-Grundy function for an arbitrary simplicial complex, and discuss its performance and scope of viability. Secondly, I provide a method to find a simple mathematical expression to model that function if it exists. I show the …

Solubility Of Additive Forms Over Local Fields, Drew Duncan

Theses and Dissertations--Mathematics

Michael Knapp, in a previous work, conjectured that every additive sextic form over $\mathbb{Q}_2(\sqrt{-1})$ and $\mathbb{Q}_2(\sqrt{-5})$ in seven variables has a nontrivial zero. In this dissertation, I show that this conjecture is true, establishing that $$\Gamma^*(6, \mathbb{Q}_2(\sqrt{-1})) = \Gamma^*(6, \mathbb{Q}_2(\sqrt{-5})) = 7.$$ I then determine the minimal number of variables $\Gamma^*(d, K)$ which guarantees a nontrivial solution for every additive form of degree $d=2m$, $m$ odd, $m \ge 3$ over the six ramified quadratic extensions of $\mathbb{Q}_2$. We prove that if $$K \in \{\mathbb{Q}_2(\sqrt{2}), \mathbb{Q}_2(\sqrt{10}), \mathbb{Q}_2(\sqrt{-2}), \mathbb{Q}_2(\sqrt{-10})\},$$ then $$\Gamma^*(d,K) = \frac{3}{2}d,$$ and if $$K \in \{\mathbb{Q}_2(\sqrt{-1}), \mathbb{Q}_2(\sqrt{-5})\},$$ then $$\Gamma^*(d,K) = …

Weight Distributions, Automorphisms, And Isometries Of Cyclic Orbit Codes, Hunter Lehmann

Theses and Dissertations--Mathematics

Cyclic orbit codes are subspace codes generated by the action of the Singer subgroup Fqn* on an Fq-subspace U of Fqn. The weight distribution of a code is the vector whose ith entry is the number of codewords with distance i to a fixed reference space in the code. My dissertation investigates the structure of the weight distribution for cyclic orbit codes. We show that for full-length orbit codes with maximal possible distance the weight distribution depends only on q,n and the dimension of U. For full-length orbit codes with …

Maximums Of Total Betti Numbers In Hilbert Families, Jay White

Theses and Dissertations--Mathematics

Fix a family of ideals in a polynomial ring and consider the problem of finding a single ideal in the family that has Betti numbers that are greater than or equal to the Betti numbers of every ideal in the family. Or decide if this special ideal even exists. Bigatti, Hulett, and Pardue showed that if we take the ideals with a fixed Hilbert function, there is such an ideal: the lexsegment ideal. Caviglia and Murai proved that if we take the saturated ideals with a fixed Hilbert polynomial, there is also such an ideal. We present a generalization of …

Combinatorial Invariants Of Rational Polytopes, Andrés R. Vindas Meléndez

Theses and Dissertations--Mathematics

The first part of this dissertation deals with the equivariant Ehrhart theory of the permutahedron. As a starting point to determining the equivariant Ehrhart theory of the permutahedron, Ardila, Schindler, and I obtain a volume formula for the rational polytopes that are fixed by acting on the permutahedron by a permutation, which generalizes a result of Stanley’s for the volume for the standard permutahedron. Building from the aforementioned work, Ardila, Supina, and I determine the equivariant Ehrhart theory of the permutahedron, thereby resolving an open problem posed by Stapledon. We provide combinatorial descriptions of the Ehrhart quasipolynomial and Ehrhart series …

A Tropical Approach To The Brill-Noether Theory Over Hurwitz Spaces, Kaelin Cook-Powell

Theses and Dissertations--Mathematics

The geometry of a curve can be analyzed in many ways. One way of doing this is to study the set of all divisors on a curve of prescribed rank and degree, known as a Brill-Noether variety. A sequence of results, starting in the 1980s, answered several fundamental questions about these varieties for general curves. However, many of these questions are still unanswered if we restrict to special families of curves. This dissertation has three main goals. First, we examine Brill-Noether varieties for these special families and provide combinatorial descriptions of their irreducible components. Second, we provide a natural generalization …

The Smallest Solution Of An Isotropic Quadratic Form, Deborah H. Blevins

Theses and Dissertations--Mathematics

An isotropic quadratic form f(x₁,...,x_n) = ∑ ⁿ_i=1 ∑ ⁿ_j=1 f_ijx_ix_j defined on a Z- lattice has a smallest solution, where the size of the solution is measured using the infinity norm (∥ ∥_∞), the l₁ norm (∥ ∥₁), or the Euclidean norm (∥ ∥₂). Much work has been done to find the least upper bound and greatest lower bound on the smallest solution, beginning with Cassels in the mid-1950’s. Defining F := (f₁₁,...,f …

The Plus-Minus Davenport Constant Of Finite Abelian Groups, Darleen S. Perez-Lavin

Theses and Dissertations--Mathematics

Let G be a finite abelian group, written additively. The Davenport constant, D(G), is the smallest positive number s such that any subset of the group G, with cardinality at least s, contains a non-trivial zero-subsum. We focus on a variation of the Davenport constant where we allow addition and subtraction in the non-trivial zero-subsum. This constant is called the plus-minus Davenport constant, D_±(G). In the early 2000’s, Marchan, Ordaz, and Schmid proved that if the cardinality of G is less than or equal to 100, then the D_±(G) …

Some Proofs Regarding Minami Estimates And Local Eigenvalue Statistics For Some Random Schrödinger Operator Models, Samuel Herschenfeld

Theses and Dissertations--Mathematics

We provide three proofs on different, but related models in the field of random Schrödinger operators. All three results are motivated by the desire to extend results and techniques on eigenvalue statistics or Minami estimates (an essential ingredient Poisson eigenvalue statistics).

Chapters 2 and 4 are explorations of the only two known techniques for proving Minami estimates for continuum Minami estimates. In Chapter 2, we provide an alternative and simplified proof of Klopp that holds in d = 1. Chapter 4 is an application of the techniques of Dietlein and Elgart to prove a Minami estimate for finite rank lattice …

Effective Number Theory: Counting The Identities Of A Quantum State, Ivan Horváth, Robert Mendris

Anesthesiology Faculty Publications

Quantum physics frequently involves a need to count the states, subspaces, measurement outcomes, and other elements of quantum dynamics. However, with quantum mechanics assigning probabilities to such objects, it is often desirable to work with the notion of a “total” that takes into account their varied relevance. For example, such an effective count of position states available to a lattice electron could characterize its localization properties. Similarly, the effective total of outcomes in the measurement step of a quantum computation relates to the efficiency of the quantum algorithm. Despite a broad need for effective counting, a well-founded prescription has not …

Unveiling The Molecular Mechanism Of Sars-Cov-2 Main Protease Inhibition From 137 Crystal Structures Using Algebraic Topology And Deep Learning, Duc Duy Nguyen, Kaifu Gao, Jiahui Chen, Rui Wang, Guo-Wei Wei

Mathematics Faculty Publications

Currently, there is neither effective antiviral drugs nor vaccine for coronavirus disease 2019 (COVID-19) caused by acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Due to its high conservativeness and low similarity with human genes, SARS-CoV-2 main protease (M^pro) is one of the most favorable drug targets. However, the current understanding of the molecular mechanism of M^pro inhibition is limited by the lack of reliable binding affinity ranking and prediction of existing structures of M^pro-inhibitor complexes. This work integrates mathematics (i.e., algebraic topology) and deep learning (MathDL) to provide a reliable ranking of the binding …

Simulating Phase Transitions And Control Measures For Network Epidemics Caused By Infections With Presymptomatic, Asymptomatic, And Symptomatic Stages, Benjamin Braun, Başak Taraktaş, Brian Beckage, Jane Molofsky

Mathematics Faculty Publications

We investigate phase transitions associated with three control methods for epidemics on small world networks. Motivated by the behavior of SARS-CoV-2, we construct a theoretical SIR model of a virus that exhibits presymptomatic, asymptomatic, and symptomatic stages in two possible pathways. Using agent-based simulations on small world networks, we observe phase transitions for epidemic spread related to: 1) Global social distancing with a fixed probability of adherence. 2) Individually initiated social isolation when a threshold number of contacts are infected. 3) Viral shedding rate. The primary driver of total number of infections is the viral shedding rate, with probability of …

Effects Of Aperiodicity And Frustration On The Magnetic Properties Of Artificial Quasicrystals, Barry Farmer

Theses and Dissertations--Physics and Astronomy

Quasicrystals have been shown to exhibit physical properties that are dramatically different from their periodic counterparts. A limited number of magnetic quasicrystals have been fabricated and measured, and they do not exhibit long-range magnetic order, which is in direct conflict with simulations that indicate such a state should be accessible. This dissertation adopts a metamaterials approach in which artificial quasicrystals are fabricated and studied with the specific goal of identifying how aperiodicity affects magnetic long-range order. Electron beam lithography techniques were used to pattern magnetic thin films into two types of aperiodic tilings, the Penrose P2, and Ammann-Beenker tilings. SQUID …

Solutions To Systems Of Equations Over Finite Fields, Rachel Petrik

Theses and Dissertations--Mathematics

This dissertation investigates the existence of solutions to equations over finite fields with an emphasis on diagonal equations. In particular:

1. Given a system of equations, how many solutions are there?
2. In the case of a system of diagonal forms, when does a nontrivial solution exist?

Many results are known that address (1) and (2), such as the classical Chevalley--Warning theorems. With respect to (1), we have improved a recent result of D.R. Heath--Brown, which provides a lower bound on the total number of solutions to a system of polynomials equations. Furthermore, we have demonstrated that several of our lower bounds …

Graph-Theoretic Simplicial Complexes, Hajos-Type Constructions, And K-Matchings, Julianne Vega

Theses and Dissertations--Mathematics

A graph property is monotone if it is closed under the removal of edges and vertices. Given a graph G and a monotone graph property P, one can associate to the pair (G,P) a simplicial complex, which serves as a way to encode graph properties within faces of a topological space. We study these graph-theoretic simplicial complexes using combinatorial and topological approaches as a way to inform our understanding of the graphs and their properties.

In this dissertation, we study two families of simplicial complexes: (1) neighborhood complexes and (2) k-matching complexes. A neighborhood complex is a simplicial …

Geometry Of Linear Subspace Arrangements With Connections To Matroid Theory, William Trok

Theses and Dissertations--Mathematics

This dissertation is devoted to the study of the geometric properties of subspace configurations, with an emphasis on configurations of points. One distinguishing feature is the widespread use of techniques from Matroid Theory and Combinatorial Optimization. In part we generalize a theorem of Edmond's about partitions of matroids in independent subsets. We then apply this to establish a conjectured bound on the Castelnuovo-Mumford regularity of a set of fat points.

We then study how the dimension of an ideal of point changes when intersected with a generic fat subspace. In particular we introduce the concept of a ``very unexpected hypersurface'' …

Scrollar Invariants Of Tropical Chains Of Loops, Kalila Joelle Sawyer

Theses and Dissertations--Mathematics

We define scrollar invariants of tropical curves with a fixed divisor of rank 1. We examine the behavior of scrollar invariants under specialization, and compute these invariants for a much-studied family of tropical curves. Our examples highlight many parallels between the classical and tropical theories, but also point to some substantive distinctions.

Periodic Points On Tori: Vanishing And Realizability, Shane Clark

Theses and Dissertations--Mathematics

Let $X$ be a finite simplicial complex and $f\colon X \to X$ be a continuous map. A point $x\in X$ is a fixed point if $f(x)=x$. Classically fixed point theory develops invariants and obstructions to the removal of fixed points through continuous deformation. The Lefschetz Fixed number is an algebraic invariant that obstructs the removal of fixed points through continuous deformation. \[L(f)=\sum_{i=0}^\infty (-1)^i \tr\left(f_i:H_i(X;\bQ)\to H_i(X;\bQ)\right). \] The Lefschetz Fixed Point theorem states if $L(f)\neq 0$, then $f$ (and therefore all $g\simeq f$) has a fixed point. In general, the converse is not true. However, Lefschetz Number is a complete invariant …

The Direct Scattering Map For The Intermediate Long Wave Equation, Joel Klipfel

Theses and Dissertations--Mathematics

In the early 1980's, Kodama, Ablowitz and Satsuma, together with Santini, Ablowitz and Fokas, developed the formal inverse scattering theory of the Intermediate Long Wave (ILW) equation and explored its connections with the Benjamin-Ono (BO) and KdV equations. The ILW equation\begin{align*} u_t + \frac{1}{\delta} u_x + 2 u u_x + Tu_{xx} = 0, \end{align*} models the behavior of long internal gravitational waves in stratified fluids of depth $0< \delta < \infty$, where $T$ is a singular operator which depends on the depth $\delta$. In the limit $\delta \to 0$, the ILW reduces to the Korteweg de Vries (KdV) equation, and in the limit $\delta \to \infty$, the ILW (at least formally) reduces to the Benjamin-Ono (BO) equation.

While the KdV equation is very well understood, a rigorous analysis of inverse scattering for the ILW equation remains to be accomplished. There is currently no rigorous proof that the Inverse Scattering …

Eigenvalue Statistics And Localization For Random Band Matrices With Fixed Width And Wegner Orbital Model, Benjamin Brodie

Theses and Dissertations--Mathematics

We discuss two models from the study of disordered quantum systems. The first is the Random Band Matrix with a fixed band width and Gaussian or more general disorder. The second is the Wegner $n$-orbital model. We establish that the point process constructed from the eigenvalues of finite size matrices converge to a Poisson Point Process in the limit as the matrix size goes to infinity.

The proof is based on the method of Minami for the Anderson tight-binding model. As a first step, we expand upon the localization results by Schenker and Peled-Schenker-Shamis-Sodin to account for complex energies. We …

Simultaneous Zeros Of A System Of Two Quadratic Forms, Nandita Sahajpal

Theses and Dissertations--Mathematics

In this dissertation we investigate the existence of a nontrivial solution to a system of two quadratic forms over local fields and global fields. We specifically study a system of two quadratic forms over an arbitrary number field. The questions that are of particular interest are:

1. How many variables are necessary to guarantee a nontrivial zero to a system of two quadratic forms over a global field or a local field? In other words, what is the u-invariant of a pair of quadratic forms over any global or local field?
2. What is the relation between u-invariants of a …

Algebraic And Geometric Properties Of Hierarchical Models, Aida Maraj

Theses and Dissertations--Mathematics

In this dissertation filtrations of ideals arising from hierarchical models in statistics related by a group action are are studied. These filtrations lead to ideals in polynomial rings in infinitely many variables, which require innovative tools. Regular languages and finite automata are used to prove and explicitly compute the rationality of some multivariate power series that record important quantitative information about the ideals. Some work regarding Markov bases for non-reducible models is shown, together with advances in the polyhedral geometry of binary hierarchical models.