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Persistence theory provides a mathematically rigorous answer to the question of population survival by establishing an initial-condition- independent positive lower bound for the long-term value of the population size. This study focuses on the persistence of discrete semiflows in infinite-dimensional state spaces that model the year-to-year dynamics of structured populations.

Persistence theory provides a mathematically rigorous answer to the question of population survival by establishing an initial-condition- independent positive lower bound for the long-term value of the population size. This study focuses on the persistence of discrete semiflows in infinite-dimensional state spaces that model the year-to-year dynamics of structured populations. The map which encapsulates the population development from one year to the next is approximated at the origin (the extinction state) by a linear or homogeneous map. The (cone) spectral radius of this approximating map is the threshold between extinction and persistence. General persistence results are applied to three particular models: a size-structured plant population model, a diffusion model (with both Neumann and Dirichlet boundary conditions) for a dispersing population of males and females that only mate and reproduce once during a very short season, and a rank-structured model for a population of males and females.
ContributorsJin, Wen (Author) / Thieme, Horst (Thesis advisor) / Milner, Fabio (Committee member) / Quigg, John (Committee member) / Smith, Hal (Committee member) / Spielberg, John (Committee member) / Arizona State University (Publisher)
Created2014
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Description
In 1968, phycologist M.R. Droop published his famous discovery on the functional relationship between growth rate and internal nutrient status of algae in chemostat culture. The simple notion that growth is directly dependent on intracellular nutrient concentration is useful for understanding the dynamics in many ecological systems. The cell quota

In 1968, phycologist M.R. Droop published his famous discovery on the functional relationship between growth rate and internal nutrient status of algae in chemostat culture. The simple notion that growth is directly dependent on intracellular nutrient concentration is useful for understanding the dynamics in many ecological systems. The cell quota in particular lends itself to ecological stoichiometry, which is a powerful framework for mathematical ecology. Three models are developed based on the cell quota principal in order to demonstrate its applications beyond chemostat culture.

First, a data-driven model is derived for neutral lipid synthesis in green microalgae with respect to nitrogen limitation. This model synthesizes several established frameworks in phycology and ecological stoichiometry. The model demonstrates how the cell quota is a useful abstraction for understanding the metabolic shift to neutral lipid production that is observed in certain oleaginous species.

Next a producer-grazer model is developed based on the cell quota model and nutrient recycling. The model incorporates a novel feedback loop to account for animal toxicity due to accumulation of nitrogen waste. The model exhibits rich, complex dynamics which leave several open mathematical questions.

Lastly, disease dynamics in vivo are in many ways analogous to those of an ecosystem, giving natural extensions of the cell quota concept to disease modeling. Prostate cancer can be modeled within this framework, with androgen the limiting nutrient and the prostate and cancer cells as competing species. Here the cell quota model provides a useful abstraction for the dependence of cellular proliferation and apoptosis on androgen and the androgen receptor. Androgen ablation therapy is often used for patients in biochemical recurrence or late-stage disease progression and is in general initially effective. However, for many patients the cancer eventually develops resistance months to years after treatment begins. Understanding how and predicting when hormone therapy facilitates evolution of resistant phenotypes has immediate implications for treatment. Cell quota models for prostate cancer can be useful tools for this purpose and motivate applications to other diseases.
ContributorsPacker, Aaron (Author) / Kuang, Yang (Thesis advisor) / Nagy, John (Committee member) / Smith, Hal (Committee member) / Kostelich, Eric (Committee member) / Kang, Yun (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Bacteriophage (phage) are viruses that infect bacteria. Typical laboratory experiments show that in a chemostat containing phage and susceptible bacteria species, a mutant bacteria species will evolve. This mutant species is usually resistant to the phage infection and less competitive compared to the susceptible bacteria species. In some experiments, both

Bacteriophage (phage) are viruses that infect bacteria. Typical laboratory experiments show that in a chemostat containing phage and susceptible bacteria species, a mutant bacteria species will evolve. This mutant species is usually resistant to the phage infection and less competitive compared to the susceptible bacteria species. In some experiments, both susceptible and resistant bacteria species, as well as phage, can coexist at an equilibrium for hundreds of hours. The current research is inspired by these observations, and the goal is to establish a mathematical model and explore sufficient and necessary conditions for the coexistence. In this dissertation a model with infinite distributed delay terms based on some existing work is established. A rigorous analysis of the well-posedness of this model is provided, and it is proved that the susceptible bacteria persist. To study the persistence of phage species, a "Phage Reproduction Number" (PRN) is defined. The mathematical analysis shows phage persist if PRN > 1 and vanish if PRN < 1. A sufficient condition and a necessary condition for persistence of resistant bacteria are given. The persistence of the phage is essential for the persistence of resistant bacteria. Also, the resistant bacteria persist if its fitness is the same as the susceptible bacteria and if PRN > 1. A special case of the general model leads to a system of ordinary differential equations, for which numerical simulation results are presented.
ContributorsHan, Zhun (Author) / Smith, Hal (Thesis advisor) / Armbruster, Dieter (Committee member) / Kawski, Matthias (Committee member) / Kuang, Yang (Committee member) / Thieme, Horst (Committee member) / Arizona State University (Publisher)
Created2012
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Description
The uncrossing partially ordered set $P_n$ is defined on the set of matchings on $2n$ points on a circle represented with wires. The order relation is $\tau'\leq \tau$ in $P_n$ if and only if $\tau'$ is obtained by resolving a crossing of $\tau$. %This partial order has been studied by

The uncrossing partially ordered set $P_n$ is defined on the set of matchings on $2n$ points on a circle represented with wires. The order relation is $\tau'\leq \tau$ in $P_n$ if and only if $\tau'$ is obtained by resolving a crossing of $\tau$. %This partial order has been studied by Alman-Lian-Tran, Huang-Wen-Xie, Kenyon, and Lam. %The posets $P_n$ emerged from studies of circular planar electrical networks. Circular planar electrical networks are finite weighted undirected graphs embedded into a disk, with boundary vertices and interior vertices. By Curtis-Ingerman-Morrow and de Verdi\`ere-Gitler-Vertigan, the electrical networks can be encoded with response matrices. By Lam the space of response matrices for electrical networks has a cell structure, and this cell structure can be described by the uncrossing partial orders. %Lam proves that the posets can be identified with dual Bruhat order on affine permutations of type $(n,2n)$. Using this identification, Lam proves the poset $\hat{P}_n$, the uncrossing poset $P_n$ with a unique minimum element $\hat{0}$ adjoined, is Eulerian. This thesis consists of two sets of results: (1) flag enumeration in intervals in the uncrossing poset $P_n$ and (2) cyclic sieving phenomenon on the set $P_n$.

I identify elements in $P_n$ with affine permutations of type $(0,2n)$. %This identification enables us to explicitly describe the elements in $P_n$ with the elements in $\mathcal{MP}_n$.

Using this identification, I adapt a technique in Reading for finding recursions for the cd-indices of intervals in Bruhat order of Coxeter groups to the uncrossing poset $P_n$. As a result, I produce recursions for the cd-indices of intervals in the uncrossing poset $P_n$. I also obtain a recursion for the ab-indices of intervals in the poset $\hat{P}_n$, the poset $P_n$ with a unique minimum $\hat0$ adjoined. %We define an induced subposet $\mathcal{MP}_n$ of the affine permutations under Bruhat order.

Reiner-Stanton-White defined the cyclic sieving phenomenon (CSP) associated to a finite cyclic group action on a finite set and a polynomial. Sagan observed the CSP on the set of non-crossing matchings with the $q$-Catalan polynomial. Bowling-Liang presented similar results on the set of $k$-crossing matchings for $1\leq k \leq 3$. In this dissertation, I focus on the set of all matchings on $[2n]:=\{1,2,\dots,2n\}$. I find the number of matchings fixed by $\frac{2\pi}{d}$ rotations for $d|2n$. I then find the polynomial $X_n(q)$ such that the set of matchings together with $X_n(q)$ and the cyclic group of order $2n$ exhibits the CSP.
ContributorsKim, Younghwan (Author) / Fishel, Susanna (Thesis advisor) / Bremner, Andrew (Committee member) / Czygrinow, Andrzej (Committee member) / Kierstead, Henry (Committee member) / Paupert, Julien (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Since the seminal work of Tur ́an, the forbidden subgraph problem has been among the central questions in extremal graph theory. Let ex(n;F) be the smallest number m such that any graph on n vertices with m edges contains F as a subgraph. Then the forbidden subgraph problem asks to

Since the seminal work of Tur ́an, the forbidden subgraph problem has been among the central questions in extremal graph theory. Let ex(n;F) be the smallest number m such that any graph on n vertices with m edges contains F as a subgraph. Then the forbidden subgraph problem asks to find ex(n; F ) for various graphs F . The question can be further generalized by asking for the extreme values of other graph parameters like minimum degree, maximum degree, or connectivity. We call this type of question a Tura ́n-type problem. In this thesis, we will study Tura ́n-type problems and their variants for graphs and hypergraphs.

Chapter 2 contains a Tura ́n-type problem for cycles in dense graphs. The main result in this chapter gives a tight bound for the minimum degree of a graph which guarantees existence of disjoint cycles in the case of dense graphs. This, in particular, answers in the affirmative a question of Faudree, Gould, Jacobson and Magnant in the case of dense graphs.

In Chapter 3, similar problems for trees are investigated. Recently, Faudree, Gould, Jacobson and West studied the minimum degree conditions for the existence of certain spanning caterpillars. They proved certain bounds that guarantee existence of spanning caterpillars. The main result in Chapter 3 significantly improves their result and answers one of their questions by proving a tight minimum degree bound for the existence of such structures.

Chapter 4 includes another Tur ́an-type problem for loose paths of length three in a 3-graph. As a corollary, an upper bound for the multi-color Ramsey number for the loose path of length three in a 3-graph is achieved.
ContributorsYie, Jangwon (Author) / Czygrinow, Andrzej (Thesis advisor) / Kierstead, Henry (Committee member) / Colbourn, Charles (Committee member) / Fishel, Susanna (Committee member) / Spielberg, John (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Rabies is an infectious viral disease. It is usually fatal if a victim reaches the rabid stage, which starts after the appearance of disease symptoms. The disease virus attacks the central nervous system, and then it migrates from peripheral nerves to the spinal cord and brain. At the time when

Rabies is an infectious viral disease. It is usually fatal if a victim reaches the rabid stage, which starts after the appearance of disease symptoms. The disease virus attacks the central nervous system, and then it migrates from peripheral nerves to the spinal cord and brain. At the time when the rabies virus reaches the brain, the incubation period is over and the symptoms of clinical disease appear on the victim. From the brain, the virus travels via nerves to the salivary glands and saliva.

A mathematical model is developed for the spread of rabies in a spatially distributed fox population to model the spread of the rabies epizootic through middle Europe that occurred in the second half of the 20th century. The model considers both territorial and wandering rabid foxes and includes a latent period for the infection. Since the model assumes these two kinds of rabid foxes, it is a system of both partial differential and integral equations (with integration

over space and, occasionally, also over time). To study the spreading speeds of the rabies epidemic, the model is reduced to a scalar Volterra-Hammerstein integral equation, and space-time Laplace transform of the integral equation is used to derive implicit formulas for the spreading speed. The spreading speeds are discussed and implicit formulas are given for latent periods of fixed length, exponentially distributed length, Gamma distributed length, and log-normally distributed length. A number of analytic and numerical results are shown pertaining to the spreading speeds.

Further, a numerical algorithm is described for the simulation

of the spread of rabies in a spatially distributed fox population on a bounded domain with Dirichlet boundary conditions. I propose the following methods for the numerical approximation of solutions. The partial differential and integral equations are discretized in the space variable by central differences of second order and by

the composite trapezoidal rule. Next, the ordinary or delay differential equations that are obtained this way are discretized in time by explicit

continuous Runge-Kutta methods of fourth order for ordinary and delay differential systems. My particular interest

is in how the partition of rabid foxes into

territorial and diffusing rabid foxes influences

the spreading speed, a question that can be answered by purely analytic means only for small basic reproduction numbers. I will restrict the numerical analysis

to latent periods of fixed length and to exponentially

distributed latent periods.

The results of the numerical calculations

are compared for latent periods

of fixed and exponentially distributed length

and for various proportions of territorial

and wandering rabid foxes.

The speeds of spread observed in the

simulations are compared

to spreading speeds obtained by numerically solving the analytic formulas

and to observed speeds of epizootic frontlines

in the European rabies outbreak 1940 to 1980.
ContributorsAlanazi, Khalaf Matar (Author) / Thieme, Horst R. (Thesis advisor) / Jackiewicz, Zdzislaw (Committee member) / Baer, Steven (Committee member) / Gardner, Carl (Committee member) / Kuang, Yang (Committee member) / Smith, Hal (Committee member) / Arizona State University (Publisher)
Created2018
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Description
The Tamari lattices have been intensely studied since they first appeared in Dov Tamari’s thesis around 1952. He defined the n-th Tamari lattice T(n) on bracketings of a set of n+1 objects, with a cover relation based on the associativity rule in one direction. Despite their interesting aspects and the

The Tamari lattices have been intensely studied since they first appeared in Dov Tamari’s thesis around 1952. He defined the n-th Tamari lattice T(n) on bracketings of a set of n+1 objects, with a cover relation based on the associativity rule in one direction. Despite their interesting aspects and the attention they have received, a formula for the number of maximal chains in the Tamari lattices is still unknown. The purpose of this thesis is to convey my results on progress toward the solution of this problem and to discuss future work.

A few years ago, Bergeron and Préville-Ratelle generalized the Tamari lattices to the m-Tamari lattices. The original Tamari lattices T(n) are the case m=1. I establish a bijection between maximum length chains in the m-Tamari lattices and standard m-shifted Young tableaux. Using Thrall’s formula, I thus derive the formula for the number of maximum length chains in T(n).

For each i greater or equal to -1 and for all n greater or equal to 1, I define C(i,n) to be the set of maximal chains of length n+i in T(n). I establish several properties of maximal chains (treated as tableaux) and identify a particularly special property: each maximal chain may or may not possess a plus-full-set. I show, surprisingly, that for all n greater or equal to 2i+4, each member of C(i,n) contains a plus-full-set. Utilizing this fact and a collection of maps, I obtain a recursion for the number of elements in C(i,n) and an explicit formula based on predetermined initial values. The formula is a polynomial in n of degree 3i+3. For example, the number of maximal chains of length n in T(n) is n choose 3.

I discuss current work and future plans involving certain equivalence classes of maximal chains in the Tamari lattices. If a maximal chain may be obtained from another by swapping a pair of consecutive edges with another pair in the Hasse diagram, the two maximal chains are said to differ by a square move. Two maximal chains are said to be in the same equivalence class if one may be obtained from the other by making a set of square moves.
ContributorsNelson, Luke (Author) / Fishel, Susanna (Thesis advisor) / Czygrinow, Andrzej (Committee member) / Jones, John (Committee member) / Kierstead, Henry (Committee member) / Spielberg, John (Committee member) / Arizona State University (Publisher)
Created2016
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Description
In recent decades, marine ecologists have conducted extensive field work and experiments to understand the interactions between bacteria and bacteriophage (phage) in marine environments. This dissertation provides a detailed rigorous framework for gaining deeper insight into these interactions. Specific features of the dissertation include the design of a new deterministic

In recent decades, marine ecologists have conducted extensive field work and experiments to understand the interactions between bacteria and bacteriophage (phage) in marine environments. This dissertation provides a detailed rigorous framework for gaining deeper insight into these interactions. Specific features of the dissertation include the design of a new deterministic Lotka-Volterra model with n + 1 bacteria, n
+ 1 phage, with explicit nutrient, where the jth phage strain infects the first j bacterial strains, a perfectly nested infection network (NIN). This system is subject to trade-off conditions on the life-history traits of both bacteria and phage given in an earlier study Jover et al. (2013). Sufficient conditions are provided to show that a bacteria-phage community of arbitrary size with NIN can arise through the succession of permanent subcommunities, by the successive addition of one new population. Using uniform persistence theory, this entire community is shown to be permanent (uniformly persistent), meaning that all populations ultimately survive.

It is shown that a modified version of the original NIN Lotka-Volterra model with implicit nutrient considered by Jover et al. (2013) is permanent. A new one-to-one infection network (OIN) is also considered where each bacterium is infected by only one phage, and that phage infects only that bacterium. This model does not use the trade-offs on phage infection range, and bacterium resistance to phage. The OIN model is shown to be permanent, and using Lyapunov function theory, coupled with LaSalle’s Invariance Principle, the unique coexistence equilibrium associated with the NIN is globally asymptotically stable provided that the inter- and intra-specific bacterial competition coefficients are equal across all bacteria.

Finally, the OIN model is extended to a “Kill the Winner” (KtW) Lotka-Volterra model

of marine communities consisting of bacteria, phage, and zooplankton. The zooplankton

acts as a super bacteriophage, which infects all bacteria. This model is shown to be permanent.
ContributorsKorytowski, Daniel (Author) / Smith, Hal (Thesis advisor) / Gumel, Abba (Committee member) / Kuang, Yang (Committee member) / Gardner, Carl (Committee member) / Thieme, Horst (Committee member) / Arizona State University (Publisher)
Created2016
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Description
Every graph can be colored with one more color than its maximum degree. A well-known theorem of Brooks gives the precise conditions under which a graph can be colored with maximum degree colors. It is natural to ask for the required conditions on a graph to color with one less

Every graph can be colored with one more color than its maximum degree. A well-known theorem of Brooks gives the precise conditions under which a graph can be colored with maximum degree colors. It is natural to ask for the required conditions on a graph to color with one less color than the maximum degree; in 1977 Borodin and Kostochka conjectured a solution for graphs with maximum degree at least 9: as long as the graph doesn't contain a maximum-degree-sized clique, it can be colored with one fewer than the maximum degree colors. This study attacks the conjecture on multiple fronts. The first technique is an extension of a vertex shuffling procedure of Catlin and is used to prove the conjecture for graphs with edgeless high vertex subgraphs. This general approach also bears more theoretical fruit. The second technique is an extension of a method Kostochka used to reduce the Borodin-Kostochka conjecture to the maximum degree 9 case. Results on the existence of independent transversals are used to find an independent set intersecting every maximum clique in a graph. The third technique uses list coloring results to exclude induced subgraphs in a counterexample to the conjecture. The classification of such excludable graphs that decompose as the join of two graphs is the backbone of many of the results presented here. The fourth technique uses the structure theorem for quasi-line graphs of Chudnovsky and Seymour in concert with the third technique to prove the Borodin-Kostochka conjecture for claw-free graphs. The fifth technique adds edges to proper induced subgraphs of a minimum counterexample to gain control over the colorings produced by minimality. The sixth technique adapts a recoloring technique originally developed for strong coloring by Haxell and by Aharoni, Berger and Ziv to general coloring. Using this recoloring technique, the Borodin-Kostochka conjectured is proved for graphs where every vertex is in a large clique. The final technique is naive probabilistic coloring as employed by Reed in the proof of the Borodin-Kostochka conjecture for large maximum degree. The technique is adapted to prove the Borodin-Kostochka conjecture for list coloring for large maximum degree.
ContributorsRabern, Landon (Author) / Kierstead, Henry (Thesis advisor) / Colbourn, Charles (Committee member) / Czygrinow, Andrzej (Committee member) / Fishel, Susanna (Committee member) / Hurlbert, Glenn (Committee member) / Arizona State University (Publisher)
Created2013
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Description
The primary focus of this dissertation lies in extremal combinatorics, in particular intersection theorems in finite set theory. A seminal result in the area is the theorem of Erdos, Ko and Rado which finds the upper bound on the size of an intersecting family of subsets of an n-element set

The primary focus of this dissertation lies in extremal combinatorics, in particular intersection theorems in finite set theory. A seminal result in the area is the theorem of Erdos, Ko and Rado which finds the upper bound on the size of an intersecting family of subsets of an n-element set and characterizes the structure of families which attain this upper bound. A major portion of this dissertation focuses on a recent generalization of the Erdos--Ko--Rado theorem which considers intersecting families of independent sets in graphs. An intersection theorem is proved for a large class of graphs, namely chordal graphs which satisfy an additional condition and similar problems are considered for trees, bipartite graphs and other special classes. A similar extension is also formulated for cross-intersecting families and results are proved for chordal graphs and cycles. A well-known generalization of the EKR theorem for k-wise intersecting families due to Frankl is also considered. A stability version of Frankl's theorem is proved, which provides additional structural information about k-wise intersecting families which have size close to the maximum upper bound. A graph-theoretic generalization of Frankl's theorem is also formulated and proved for perfect matching graphs. Finally, a long-standing conjecture of Chvatal regarding structure of maximum intersecting families in hereditary systems is considered. An intersection theorem is proved for hereditary families which have rank 3 using a powerful tool of Erdos and Rado which is called the Sunflower Lemma.
ContributorsKamat, Vikram M (Author) / Hurlbert, Glenn (Thesis advisor) / Colbourn, Charles (Committee member) / Czygrinow, Andrzej (Committee member) / Fishel, Susanna (Committee member) / Kierstead, Henry (Committee member) / Arizona State University (Publisher)
Created2011