We consider reaction-diffusion systems of two variables with Neumann boundary conditions on a finite interval with diffusion rates of different orders. Solutions of these systems can exhibit a variety of patterns and behaviours; one common type is called a mesa pattern; these are solutions that in the spatial domain exhibit highly localized interfaces connected by almost constant regions. The main focus of this thesis is to examine three different mechanisms by which the mesa patterns become unstable. These patterns can become unstable due to the effect of the heterogeneity of the domain, through an oscillatory instability, or through a coarsening effect from the exponentially small interaction with the boundary. We compute instability thresholds such that, as the larger diffusion coefficient is increased past this threshold, the mesa pattern transitions from stable to unstable. As well, the dynamics of the interfaces making up these mesa patterns are determined. This allows us to describe the mechanism leading up to the instabilities as well as what occurs past the instability threshold. For the oscillatory solutions, we determine the amplitude of the oscillations. For the coarsening behaviour, we determine the motion of the interfaces away from the steady state. These calculations are accomplished by using the methods of formal asymptotics and are verified by comparison with numerical computations. Excellent agreement between the asymptotic and the numerical results is found.

Reaction Diffusion Master Equation (RDME) framework, characterized by the discretization of the spatial domain, is one of the most widely used methods in the stochastic simulation of reaction-diffusion systems. Discretization sizes for RDME have to be appropriately chosen such that each discrete compartment is "well-stirred" and the computational cost is not too expensive. An efficient discretization size based on the reaction-diffusion dynamics of each species is derived in this dissertation. Usually, the species with larger diffusion rate yields a larger discretization size. Partitioning with an efficient discretization size for each species, a multiple grid discretization (MGD) method is proposed. MGD avoids unnecessary molecular jumping and achieves great simulation efficiency improvement. Moreover, reaction-diffusion systems with reaction dynamics modeled by highly nonlinear functions, show large simulation error when discretization sizes are too small in RDME systems. The switch-like Hill function reduces into a simple bimolecular mass reaction when the discretization size is smaller than a critical value in RDME framework. Convergent Hill function dynamics in RDME framework that maintains the switch behavior of Hill functions with fine discretization is proposed. Furthermore, the application of stochastic modeling and simulation techniques to the spatiotemporal regulatory network in Caulobacter crescentus is included. A stochastic model based on Turing pattern is exploited to demonstrate the bipolarization of a scaffold protein, PopZ, during Caulobacter cell cycle. In addition, the stochastic simulation of the spatiotemporal histidine kinase switch model captures the increased variability of cycle time in cells depleted of the divJ genes. / Ph. D.

The biodegradation process of some types of polymers occurs due to many different factors including their morphology, structure and chemical composition. Although this is a complicated process, most of its important stages like the diffusion of monomers and the hydrolysis reactions have been modeled phenomenologically through reaction-diffusion equations, where the properties of the polymers were encompassed. Using a simplified reaction-diffusion model for the biodegradation of polymers, in this contribution we study the possible effects of the curvature of the system’s geometry in the degradation process, which is characterized by the interaction of the corresponding reaction rate and the diffusion coefficient. To illustrate the problem of diffusion on a curved surface we consider the surface of a cylinder and of the so-called Gaussian bump. We show how the degradation process is affected by the curvature of the system for the simplified model.

Sistemas de reação-difusão têm sido largamente estudados em diferentes contextos e através de diferentes métodos, motivados pela sua constante aparição em modelos de interação em contextos químicos, biológicos e ainda em fenômenos ecológicos. Neste trabalho nos propomos a estudar existência e unicidade - tanto do ponto de vista local como global - de soluções para uma classe de sistemas de reação-difusão acoplados, denidos em R^2, utilizando como ferramenta a teoria de semigrupos de operadores lineares. Apresentamos dois importantes exemplos: o modelo de Rosenzweig-MacArthur e um particular caso da classe de equações lambda-omega. Para o primeiro obtemos um resultado de existência e unicidade global utilizando um método de comparação envolvendo sub e super-soluções. Investigamos ainda a existência de soluções de ondas viajantes periódicas através do teorema de Bifurcação de Hopf. Já para o caso da equação lambda-omega obtemos a existência e unicidade de solucões, entretanto, a partir da aplicação da teoria de semigrupos de operadores lineares. / Reaction-diffusion systems have been widely studied in a broad variety of contexts in a large amount of disctinct approaches. It is due firstly by their constant appearance in interaction models in disciplines such as chemistry, biology and, more specific, ecology. The aim of this thesis is to provide an existence-uniqueness result - both from the local as well as from the global point of view - for solutions of a particular class of coupled reaction-diffusion systems defined over R^2. It is done applying the well established theory of semigroups of linear operators. Two remarkable examples of such systems are discussed: the Rosenzweig-MacArthur predator-prey model and a special case of lambda-omega class of equations. For the former one, an existence and uniqueness result is obtained through a comparison method - based on the notions of lower and upper solutions. Moreover, we investigate the existence of periodic travelling wave solutions via a Hopf bifurcation theorem. For the lambda-omega model another existence and uniqueness for solutions is obtained, on its turn, through the machinery obtained previously from the theory of semigroups for linear operators.

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Sistemas de reação-difusão têm sido largamente estudados em diferentes contextos e através de diferentes métodos, motivados pela sua constante aparição em modelos de interação em contextos químicos, biológicos e ainda em fenômenos ecológicos. Neste trabalho nos propomos a estudar existência e unicidade - tanto do ponto de vista local como global - de soluções para uma classe de sistemas de reação-difusão acoplados, denidos em R^2, utilizando como ferramenta a teoria de semigrupos de operadores lineares. Apresentamos dois importantes exemplos: o modelo de Rosenzweig-MacArthur e um particular caso da classe de equações lambda-omega. Para o primeiro obtemos um resultado de existência e unicidade global utilizando um método de comparação envolvendo sub e super-soluções. Investigamos ainda a existência de soluções de ondas viajantes periódicas através do teorema de Bifurcação de Hopf. Já para o caso da equação lambda-omega obtemos a existência e unicidade de solucões, entretanto, a partir da aplicação da teoria de semigrupos de operadores lineares. / Reaction-diffusion systems have been widely studied in a broad variety of contexts in a large amount of disctinct approaches. It is due firstly by their constant appearance in interaction models in disciplines such as chemistry, biology and, more specific, ecology. The aim of this thesis is to provide an existence-uniqueness result - both from the local as well as from the global point of view - for solutions of a particular class of coupled reaction-diffusion systems defined over R^2. It is done applying the well established theory of semigroups of linear operators. Two remarkable examples of such systems are discussed: the Rosenzweig-MacArthur predator-prey model and a special case of lambda-omega class of equations. For the former one, an existence and uniqueness result is obtained through a comparison method - based on the notions of lower and upper solutions. Moreover, we investigate the existence of periodic travelling wave solutions via a Hopf bifurcation theorem. For the lambda-omega model another existence and uniqueness for solutions is obtained, on its turn, through the machinery obtained previously from the theory of semigroups for linear operators.

No description available.

Cette thèse est dédiée à l’étude des propriétés de propagation de systèmes de réaction – diffusion issus de la dynamique des populations. Dans la première partie, on étudie la limite de forte compétition de systèmes à deux espèces. À l’aide de la ségrégation spatiale, on détermine le signe de la vitesse de l’onde progressive bistable. La généralisation aux ondes pulsatoires bistables en milieu spatialement périodique est ensuite envisagée afin d’étudier le rôle de l’hétérogénéité spatiale. Après avoir donné une condition suffisante pour l’existence de telles ondes ainsi qu’une condition suffisante pour l’existence d’états stationnaires stables susceptibles au contraire de bloquer l’invasion, on suppose qu’une famille d’ondes pulsatoires existe et on prouve un résultat semblable à celui obtenu en milieu homogène. Dans la seconde partie, des systèmes de type KPP à un nombre arbitraire d’espèces sont considérés. On étudie l’existence d’états stationnaires et d’ondes progressives, les propriétés qualitatives de ces solutions ainsi que la vitesse asymptotique de propagation de certaines solutions du problème de Cauchy. Cela résout des questions ouvertes sur les systèmes de mutation – compétition – diffusion, qui constituent le prototype de système de type KPP. Dans la troisième partie, on revient aux systèmes à deux espèces. Considérant cette fois-ci le cas monostable, on étudie les vitesses asymptotiques de propagation de certaines solutions du problème de Cauchy et, ce faisant, on montre l’existence de solutions décrivant l’invasion d’un territoire inhabité par un compétiteur faible mais rapide suivie de l’invasion de ce territoire par un compétiteur fort mais lent. / This thesis is dedicated to the study of propagation properties of various reaction–diffusion systems coming from population dynamics. In the first part, we study the strong competition limit of competition–diffusion systems with two species. Thanks to the spatial segregation, we determine the sign of the speed of the bistable traveling wave. The generalization to bistable pulsating fronts in spatially periodic media is then considered in order to study the role of spatial heterogeneity. We find a condition sufficient for the existence of such fronts as well as a condition sufficient for the existence of stable steady states which might on the contrary block the propagation. Then we show that whenever a family of strongly competing pulsating fronts exists, we can establish a result very similar to the one obtained in homogeneous media. In the second part, systems of KPP type with any number of species are considered. We study the existence of steady states and traveling waves, the qualitative properties of these solutions as well as the asymptotic speed of spreading of certain solutions of the Cauchy problem. This settles several open questions on the prototypical KPP systems that are mutation–competition–diffusion systems. In the third part, we go back to competition–diffusion systems with two species. Considering this time the monostable case, we study the asymptotic speeds of spreading of certain solutions of the Cauchy problem. By so doing, we show the existence of propagating terraces describing the invasion of an uninhabited territory by a weak but fast competitor followed by the invasion by a strong but slow competitor.

Reaction-diffusion models have been widely successful in explaining a large variety of patterning phenomena in biology ranging from embryonic development to cancer growth and angiogenesis. Firstly proposed by Alan Turing in 1952 and applied to a simple two-component system, reaction-diffusion models describe spontaneous spatial pattern formation, driven purely by interactions of the system components and their diffusion in space. Today, access to unprecedented amounts of quantitative biological data allows us to build and test biochemically accurate reaction-diffusion models of intracellular processes. However, any increase in model complexity increases the number of unknown parameters and thus the computational cost of model analysis. To efficiently characterize the behavior and robustness of models with many unknown parameters is, therefore, a key challenge in systems biology. Here, we propose a novel computational framework for efficient high-dimensional parameter space characterization of reaction-diffusion models. The method leverages the $L_p$-Adaptation algorithm, an adaptive-proposal statistical method for approximate high-dimensional design centering and robustness estimation. Our approach is based on an oracle function, which describes for each point in parameter space whether the corresponding model fulfills given specifications. We propose specific oracles to estimate four parameter-space characteristics: bistability, instability, capability of spontaneous pattern formation, and capability of pattern maintenance. We benchmark the method and demonstrate that it allows exploring the ability of a model to undergo pattern-forming instabilities and to quantify model robustness for model selection in polynomial time with dimensionality. We present an application of the framework to reconstituted membrane domains bearing the small GTPase Rab5 and propose molecular mechanisms that potentially drive pattern formation.

Ziel dieser Arbeit ist es zwei verschiedene Klassen von Systemen nichtlinearer parabolischer Gleichungen zu homogenisieren, und zwar Reaktions-Diffusions-Systeme mit verschiedenen Diffusionslängenskalen und Gleichungen vom Typ Cahn-Hilliard. Wir betrachten parabolische Gleichungen mit periodischen Koeffizienten, wobei die Periode dem Verhältnis der charakteristischen mikroskopischen zu der makroskopische Längenskala entspricht. Unser Ziel ist es, effektive Gleichungen rigoros herzuleiten, um die betrachteten Systeme besser zu verstehen und den Simulationsaufwand zu minimieren. Wir suchen also einen Konvergenzbegriff, mit dem die Lösung des Ausgangsmodells im Limes der Periode gegen Null gegen die Lösung des effektiven Modells konvergiert. Um die periodische Mikrostruktur und die verschiedenen Diffusivitäten zu erfassen, verwenden wir die Zwei-Skalen Konvergenz mittels periodischer Auffaltung. Der erste Teil der Arbeit handelt von Reaktions-Diffusions-Systemen, in denen einige Spezies mit der charakteristischen Diffusionslänge der makroskopischen Skala und andere mit der mikroskopischen diffundieren. Die verschiedenen Diffusivitäten führen zu einem Verlust der Kompaktheit, sodass wir nicht direkt den Grenzwert der nichtlinearen Terme bestimmen können. Wir beweisen mittels starker Zwei-Skalen Konvergenz, dass das effektive Modell ein zwei-skaliges Modell ist, welches von der makroskopischen und der mikroskopischen Skale abhängt. Unsere Methode erlaubt es uns, explizite Raten für die Konvergenz der Lösungen zu bestimmen. Im zweiten Teil betrachten wir Gleichungen vom Typ Cahn-Hilliard, welche ortsabhängige Mobilitätskoeffizienten und allgemeine Potentiale beinhalten. Wir beweisen evolutionäre Gamma-Konvergenz der zugehörigen Gradientensysteme basierend auf der Gamma-Konvergenz der Energien und der Dissipationspotentiale. / The aim of this thesis is to derive homogenization results for two different types of systems of nonlinear parabolic equations, namely reaction-diffusion systems involving different diffusion length scales and Cahn-Hilliard-type equations. The coefficient functions of the considered parabolic equations are periodically oscillating with a period which is proportional to the ratio between the charactersitic microscopic and macroscopic length scales. In view of greater structural insight and less computational effort, it is our aim to rigorously derive effective equations as the period tends to zero such that solutions of the original model converge to solutions of the effective model. To account for the periodic microstructure as well as for the different diffusion length scales, we employ the method of two-scale convergence via periodic unfolding. In the first part of the thesis, we consider reaction-diffusion systems, where for some species the diffusion length scale is of order of the macroscopic length scale and for other species it is of order of the microscopic one. Based on the notion of strong two-scale convergence, we prove that the effective model is a two-scale reaction-diffusion system depending on the macroscopic and the microscopic scale. Our approach supplies explicit rates for the convergence of the solution. In the second part, we consider Cahn-Hilliard-type equations with position-dependent mobilities and general potentials. It is well-known that the classical Cahn-Hilliard equation admits a gradient structure. Based on the Gamma-convergence of the energies and the dissipation potentials, we prove evolutionary Gamma-convergence, for the associated gradient system such that we obtain in the limit of vanishing periods a Cahn-Hilliard equation with homogenized coefficients.