No description available.

This thesis is concerned with a variety of topics grouped together under the general theme of periodically driven atomic systems. Periodic driving is ubiquitous in most techniques used in atomic physics, be it laser cooling, ion trapping or AC magnetic fields. An in-depth understanding of the behaviour of such systems can be provided through Floquet theory which will develop as a central theme in the following chapters. The thesis is divided in two parts: neutral atoms, and ions and biomolecules. In the first part I discuss a new ⁴¹K-⁸⁷Rb mixture experiment, built during the first year of my DPhil. This species combination has some very broad and low-loss interspecies Feshbach resonances that are instrumental for carrying out the experiments discussed in the first chapter. Unfortunately, the mixture experiment had to be put aside and our attention was shifted to Time-Averaged Adiabatic Potentials (TAAPs) and how these can be extended using multiple Radio-Frequency (RF) fields. This technique opens up the way for precise interferometric measurements. Lastly, the peculiar behaviour of Modulation Transfer Spectroscopy (MTS) of ³⁹K is investigated and a linearising transformation for four-wave mixing processes is presented. In the second part we turn our attention to charged ions and biomolecules and the techniques of ion trapping. We propose a novel technique for co-trapping charged particles with vastly different mass-to-charge ratios and thoroughly explore its consequences. The behaviour of the trap and the stability of equations with periodic coefficients in general is studied using Floquet theory. The normal modes and symmetries of the system also need to be considered in relation to the effectiveness of the sympathetic cooling of the ions. Small systems were simulated using a Molecular Dynamics (MD) approach in order to capture the effect of micromotion and other heating processes.

Mathematical modeling of population dynamics can provide novel insight to the growth and dispersal patterns for a variety of species populations, and has become vital to the preservation of biodiversity on a global-scale. These growth and dispersal stages can be modeled using integrodifference equations that are discrete in time and continuous in space. Previous studies have identified metrics that can determine whether a given species will persist or go extinct under certain model parameters. However, a need for computational tools to compute these metrics has limited the scope and analysis within many of these studies. We aim to create computational tools that facilitate numerical explorations for a number of associated integrodifference equations, allowing modelers to explore results using a selection of models under a robust parameter set.

An energy balance model of human metabolism developed by Hall et al. is extended to compare body composition outcomes among standard and proposed obesity interventions. Standard interventions include a drastic diet or a drastic diet with endurance training. Outcomes for these interventions are typically poor in clinical studies. Proposed interventions include a gradual diet and the addition of resistance training to preserve lean mass and metabolic rate. We see that resistance training, regardless of dietary strategy, achieves these goals. Finally, we observe that the optimal obesity intervention for continued maintenance of a healthy body composition following a diet includes a combination of endurance and resistance training.

Orientador: Marta Cilene Gadotti / Banca: Carina Alves / Banca: Wladimir Seixas / Resumo: As equações diferenciais ordinárias constituem ferramenta importante na modelagem de alguns problemas, sejam físicos, ecológicos, econômicos, etc. Neste trabalho são apresentados os resultados clássicos de equações diferenciais ordinárias, são realizadas algumas aplicações e finalmente é apresentada na proposta didática para o ensino médio em como a derivada de uma função pode ser calculada de uma forma intuitiva / Abstract: The ordinary di erential equations are an important tool in the modeling of some problems, whether of physical, ecological or ecnonomical nature. In this work the classical results of ordinary di erential equations are presented. Some of them are made and at the end there is a didactic proposal to nd a derivate function in a intuitive way for high school students / Mestre

Swarms are groups of agents, which we model as point particles, whose collective behavior emerges from individual interactions. We study a first-order swarming model in a periodic coordinate system with pairwise social forces, investigating its stable configurations for differing numbers of agents relative to the periodic width. Two states emerge from numerical simulations in one dimension: even spacing throughout the period, or clumping within a certain portion of the period. A mathematical analysis of the energy of the system allows us to determine stability of these configurations. We also perform numerical simulations for evolution to equilibrium over time, and find results in agreement with our mathematical analysis. For certain values of the periodic width relative to the number of agents, our numerical simulations show that either clumping or even spacing can be stable equilibria, and which equilibrium is reached depends on on starting conditions, indicating hysteresis.

In this thesis we develop new mathematical models, using dynamical systems, to represent localized gene delivery of bone morphogenetic protein 2 into bone marrow-derived mesenchymal stem cells and rat calvarial defects. We examine two approaches, using pDNA or cmRNA treatments, respectively, towards the production of calcium deposition and bone regeneration in in vitro and in vivo experiments. We first review the relevant scientific literature and survey existing mathematical representations for similar treatment approaches. We then motivate and develop our new models and determine model parameters from literature, heuristic approaches, and estimation using sparse data. We next conduct a qualitative analysis using dynamical systems theory. Due to the nature of the parameter estimation, it was important that we obtain local and global sensitivity analyses of model outputs to changes in model inputs. Finally we compared results from different treatment protocols. Our model suggests that cmRNA treatments may perform better than pDNA treatments towards bone fracture healing. This work is intended to be a foundation for predictive models of non-viral local gene delivery systems.

The goal of this thesis is to study the dynamics behind the evolution of virulence. We examine first the underlying mechanics of linear systems of ordinary differential equations by investigating the classification of fixed points in these systems, then applying these techniques to nonlinear systems. We then seek to establish the validity of a system that models the population dynamics of uninfected and infected hosts---first with one parasite strain, then n strains. We define the basic reproductive ratio of a parasite, and study its relationship to the evolution of virulence. Lastly, we investigate the mathematics behind superinfection.

Inflammation in the lungs can occur for many reasons, from bacterial infections to stretch by mechanical ventilation. In this work we compare and contrast various mathematical models for lung injuries in the categories of acute infection, latent versus active infection, and particulate inhalation. We focus on systems of ordinary differential equations (ODEs), agent-based models (ABMs), and Boolean networks. Each type of model provides different insight into the immune response to damage in the lungs. This knowledge includes a better understanding of the complex dynamics of immune cells, proteins, and cytokines, recommendations for treatment with antibiotics, and a foundation for more well-informed experiments and clinical trials. In each chapter, we provide an in-depth analysis of one model and summaries of several others. In this way we gain a better understanding of the important aspects of modeling the immune response to lung injury and identify possible points for future research.

Delay differential equations have a wide range of applications in engineering. This work is devoted to the analysis of delay Duffing equation, which plays a crucial role in modeling performance on demand Micro Electro Mechanical Systems (MEMS). We start with the stability analysis of a linear delay model. We also show that in certain cases the delay model can be efficiently approximated with a much simpler model without delay. We proceed with the analysis of a non-linear Duffing equation. This model is a significantly more complex mathematical model. For instance, the existence of a periodic solution for this equation is a highly nontrivial question, which was established by Struwe. The main result of this work is to establish the existence of a periodic solution to delay Duffing equation. The paper claimed to establish the existence of such solutions, however their argument is wrong. In this work we establish the existence of a periodic solution under the assumption that the delay is sufficiently small.