The main part of this work establishes existence, uniqueness and regularity properties of measure-valued solutions of a nonlinear hyperbolic conservation law with non-local velocities. Major challenges stem from in- and out-fluxes containing nonzero pure-point parts which cause discontinuities of the velocities. This part is preceded, and motivated, by an extended study which proves that an associated optimal control problem has no optimal $L^1$-solutions that are supported on short time intervals.

The hyperbolic conservation law considered here is a well-established model for a highly re-entrant semiconductor manufacturing system. Prior work established well-posedness for $L^1$-controls and states, and existence of optimal solutions for $L^2$-controls, states, and control objectives. The results on measure-valued solutions presented here reduce to the existing literature in the case of initial state and in-flux being absolutely continuous measures. The surprising well-posedness (in the face of measures containing nonzero pure-point part and discontinuous velocities) is directly related to characteristic features of the model that capture the highly re-entrant nature of the semiconductor manufacturing system.

More specifically, the optimal control problem is to minimize an $L^1$-functional that measures the mismatch between actual and desired accumulated out-flux. The focus is on the transition between equilibria with eventually zero backlog. In the case of a step up to a larger equilibrium, the in-flux not only needs to increase to match the higher desired out-flux, but also needs to increase the mass in the factory and to make up for the backlog caused by an inverse response of the system. The optimality results obtained confirm the heuristic inference that the optimal solution should be an impulsive in-flux, but this is no longer in the space of $L^1$-controls.

The need for impulsive controls motivates the change of the setting from $L^1$-controls and states to controls and states that are Borel measures. The key strategy is to temporarily abandon the Eulerian point of view and first construct Lagrangian solutions. The final section proposes a notion of weak measure-valued solutions and proves existence and uniqueness of such.

In the case of the in-flux containing nonzero pure-point part, the weak solution cannot depend continuously on the time with respect to any norm. However, using semi-norms that are related to the flat norm, a weaker form of continuity of solutions with respect to time is proven. It is conjectured that also a similar weak continuous dependence on initial data holds with respect to a variant of the flat norm.

The role of climate change, as measured in terms of changes in the climatology of geophysical variables (such as temperature and rainfall), on the global distribution and burden of vector-borne diseases (VBDs) remains a subject of considerable debate. This dissertation attempts to contribute to this debate via the use of mathematical (compartmental) modeling and statistical data analysis. In particular, the objective is to find suitable values and/or ranges of the climate variables considered (typically temperature and rainfall) for maximum vector abundance and consequently, maximum transmission intensity of the disease(s) they cause.

Motivated by the fact that understanding the dynamics of disease vector is crucial to understanding the transmission and control of the VBDs they cause, a novel weather-driven deterministic model for the population biology of the mosquito is formulated and rigorously analyzed. Numerical simulations, using relevant weather and entomological data for Anopheles mosquito (the vector for malaria), show that maximum mosquito abundance occurs when temperature and rainfall values lie in the range [20-25]C and [105-115] mm, respectively.

The Anopheles mosquito ecology model is extended to incorporate human dynamics. The resulting weather-driven malaria transmission model, which includes many of the key aspects of malaria (such as disease transmission by asymptomatically-infectious humans, and enhanced malaria immunity due to repeated exposure), was rigorously analyzed. The model which also incorporates the effect of diurnal temperature range (DTR) on malaria transmission dynamics shows that increasing DTR shifts the peak temperature value for malaria transmission from 29C (when DTR is 0C) to about 25C (when DTR is 15C).

Finally, the malaria model is adapted and used to study the transmission dynamics of chikungunya, dengue and Zika, three diseases co-circulating in the Americas caused by the same vector (Aedes aegypti). The resulting model, which is fitted using data from Mexico, is used to assess a few hypotheses (such as those associated with the possible impact the newly-released dengue vaccine will have on Zika) and the impact of variability in climate variables on the dynamics of the three diseases. Suitable temperature and rainfall ranges for the maximum transmission intensity of the three diseases are obtained.

Biogeography is the study of the spatial distribution of the earth's biota, both in the present and the past. Traditionally, biogeographical studies have relied on a combination of surveys of existing populations, fossil evidence, and the geological record of the earth. However, with the advent of relatively inexpensive methods of DNA sequencing, it is now possible to use information concerning the genetic relatedness of individuals in populations to address questions about how those populations came to be where they are today. For example, biogeographical studies of HIV-I provide strong support for the hypothesis that this virus arose in Africa through a host switch from chimpanzees to humans and only began to spread to human populations located on other continents some 60 to 70 years ago (Sharp & Hahn, 2010).

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.

This dissertation investigates the dynamics of evolutionary games based on the framework of interacting particle systems in which individuals are discrete, space is explicit, and dynamics are stochastic. Its focus is on 2-strategy games played on a d-dimensional integer lattice with a range of interaction M. An overview of related past work is given along with a summary of the dynamics in the mean-field model, which is described by the replicator equation. Then the dynamics of the interacting particle system is considered, first when individuals are updated according to the best-response update process and then the death-birth update process. Several interesting results are derived, and the differences between the interacting particle system model and the replicator dynamics are emphasized. The terms selfish and altruistic are defined according to a certain ordering of payoff parameters. In these terms, the replicator dynamics are simple: coexistence occurs if both strategies are altruistic; the selfish strategy wins if one strategy is selfish and the other is altruistic; and there is bistability if both strategies are selfish. Under the best-response update process, it is shown that there is no bistability region. Instead, in the presence of at least one selfish strategy, the most selfish strategy wins, while there is still coexistence if both strategies are altruistic. Under the death-birth update process, it is shown that regardless of the range of interactions and the dimension, regions of coexistence and bistability are both reduced. Additionally, coexistence occurs in some parameter region for large enough interaction ranges. Finally, in contrast with the replicator equation and the best-response update process, cooperators can win in the prisoner's dilemma for the death-birth process in one-dimensional nearest-neighbor interactions.

In a 2004 paper, John Nagy raised the possibility of the existence of a hypertumor \emph{i.e.}, a focus of aggressively reproducing parenchyma cells that invade part or all of a tumor. His model used a system of nonlinear ordinary differential equations to find a suitable set of conditions for which these hypertumors exist. Here that model is expanded by transforming it into a system of nonlinear partial differential equations with diffusion, advection, and a free boundary condition to represent a radially symmetric tumor growth. Two strains of parenchymal cells are incorporated; one forming almost the entirety of the tumor while the much more aggressive strain

appears in a smaller region inside of the tumor. Simulations show that if the aggressive strain focuses its efforts on proliferating and does not contribute to angiogenesis signaling when in a hypoxic state, a hypertumor will form. More importantly, this resultant aggressive tumor is paradoxically prone to extinction and hypothesize is the cause of necrosis in many vascularized tumors.

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.

Rabies disease remains enzootic among raccoons, skunks, foxes and bats in the United States. It is of primary concern for public-health agencies to control spatial spread of rabies in wildlife and its potential spillover infection of domestic animals and humans. Rabies is invariably fatal in wildlife if untreated, with a non-negligible incubation period. Understanding how this latency affects spatial spread of rabies in wildlife is the concern of chapter 2 and 3. Chapter 1 deals with the background of mathematical models for rabies and lists main objectives. In chapter 2, a reaction-diffusion susceptible-exposed-infected (SEI) model and a delayed diffusive susceptible-infected (SI) model are constructed to describe the same epidemic process -- rabies spread in foxes. For the delayed diffusive model a non-local infection term with delay is resulted from modeling the dispersal during incubation stage. Comparison is made regarding minimum traveling wave speeds of the two models, which are verified using numerical experiments. In chapter 3, starting with two Kermack and McKendrick's models where infectivity, death rate and diffusion rate of infected individuals can depend on the age of infection, the asymptotic speed of spread $c^\ast$ for the cumulated force of infection can be analyzed. For the special case of fixed incubation period, the asymptotic speed of spread is governed by the same integral equation for both models. Although explicit solutions for $c^\ast$ are difficult to obtain, assuming that diffusion coefficient of incubating animals is small, $c^\ast$ can be estimated in terms of model parameter values. Chapter 4 considers the implementation of realistic landscape in simulation of rabies spread in skunks and bats in northeast Texas. The Finite Element Method (FEM) is adopted because the irregular shapes of realistic landscape naturally lead to unstructured grids in the spatial domain. This implementation leads to a more accurate description of skunk rabies cases distributions.

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.