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.

<p> Polyurea microcapsules are micron-scale, hollow polymer spheres commonly used in agriculture to encapsulate pesticides for controlled diffusive release onto target crops. Diffusion of these active materials through a protective polymer wall offers a safer and more effective method of delivery compared to the direct spraying of crops with toxicants. The approach we are taking to control the release rate is to coat pre-formed porous polyurea capsules with a separate release-controlling outer layer. This allows us to separately optimize the load-bearing capsule wall and the release control layer, an approach commonly used in other membrane diffusion systems.</p> <p> Montmorillonite clay incorporation into polymer matrices can reduce membrane permeability by forcing diffusants to take a tortuous path around the stacked silicate sheets. Effective formation of clay-polyurea composites requires the delamination of clay particles into thin sheets with high aspect ratios, and their incorporation into polyurea microcapsules either during interfacial polymerization, or post-polymerization. The net negative surface charge of the silicate sheets should facilitate their initial binding to the cationic polyurea surfaces, as well as subsequent binding of polycations to the clay-coated polyurea capsules to create layer-by-layer (LbL) capsule assemblies with decreasing release rates of internal materials.</p> <p> The main focus of this project is to gain a fundamental understanding of montmorillonite clay and polyurea microcapsules, and the development of a model polyurea composite capsule for release rate analysis. Emphasis will be placed on the reduced permeability of microcapsules coated with clay by LbL assembly post-polymerization, followed by an exploration of further layering with polycations.</p> / Thesis / Master of Science (MSc)

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.

L'objet de cette thèse est d’étudier l'existence de solution pour une classe de systèmes d'évolution fortement couplés, ainsi que la limite singulière d'une équation aux dérivées partielles d'advection-réaction-diffusion.Au chapitre 1, nous d écrivons brièvement la dérivation d'un modèle d'intrusion saline pour des aquifères confinés et non confinés. Dans ce but nous nous appuyons sur la loi de Darcy et la loi de conservation de masse en négligeant l'effet de la dimension verticale.Au chapitre 2, nous considérons un système qui généralise le modèle d'intrusion saline dans des aquifères non confinés. C'est un système non linéaire parabolique dégénéré fortement couplé. Après avoir discrétisé en temps, gelé et tronqué des coefficients et finalement régularisé les équations, nous appliquons le théorème de Lax-Milgram pour prouver l'existence et l'unicité de la solution d'un problème linéaire associé. Nous appliquons ensuite un théorème du point fixe pour démontrer l'existence d'une solution du problème non linéaire approché. Nous obtenons de plus une estimation d'entropie, qui permet en particulier de démontrer la positivité de la solution. Finalement, nous passons à la limite dans le système et dans l'entropie pour prouver l'existence de solution pour le problème initial.Au chapitre 3, nous montrons l'existence de solution pour un système qui contient en particulier le modèle d'intrusion saline dans des aquifères confinés. Ce système est semblable au système du chapitre 2, mais la pression intervient comme inconnue supplémentaire. Il se rajoute la contrainte que la somme des hauteurs inconnues est une fonction donnée et la pression est en fait un multiplicateur de Lagrange associé à cette contrainte. Nous obtenons de nouveau une inégalité d'entropie et nous effectuons également une estimation sur le gradient de la pression.Au chapitre 4, nous nous intéressons à la description d'interfaces abruptes qui se déplacent selon un mouvement donné, par exemple le mouvement par courbure moyenne. Des singularités peuvent apparaître en temps fini ce qui explique la nécessité de définir une nouvelle notion de surface. Dans ce chapitre, on introduit la notion de "varifolds", ou surfaces généralisées, qui étendent la notion de "manifolds". A ces varifolds on associe une courbure moyenne généralisée ainsi qu'une vitesse normale généralisée.Au chapitre 5, nous considérons une équation d'advection-réaction-diffusion qui intervient dans un système de chimiotaxie-croissance proposé par Mimura et Tsujikawa. L'inconnue est la densité de population qui est soumise aux effets de diffusion et de croissance et qui a tendance à migrer vers des forts gradients de la substance chimiotactique. Quand un petit paramètre tend vers zéro, la solution converge vers une fonction étagée ; l'interface diffuse associée converge vers une interface abrupte qui se déplace selon un mouvement par courbure moyenne perturbé. Nous représentons ces interfaces par des varifolds définis à partir de la fonctionnelle de Lyapunov du problème d'Allen-Cahn. Nous établissons une formule de monotonie et nous montrons une propriété d'équipartition de l'énergie. Nous prouvons de plus que le varifold est rectifiable et que la fonction de multiplicité associée est presque partout entière. / The aim of this thesis is to study the existence of a solution for a class of evolution systems which are strongly coupled, as well as the singular limit of an advection-reaction-diffusion equation.In chapter 1, we describe briefly the derivation of a seawater intrusion model in confined and unconfined aquifers. For this purpose we combine Darcy's law with a mass conservation law and we neglect the effect of the vertical dimension.In chapter 2, we consider a system that generalizes the seawater intrusion model in unconfined aquifers. It is a strongly coupled nonlinear degenerate parabolic system. After discretizing in time, freezing and truncating the coefficients and finally regularizing the equations we apply Lax-Milgram theorem to prove the existence of a unique solution for the elliptic linear associated system. Then we apply a fixed point theorem to prove the existence of a solution for the nonlinear approximated problem. We obtain in addition an entropy estimate, which allows us in particular to prove the positivity of the solution. Finally, we pass to the limit in the system and the entropy in order to prove the existence of a solution for the initial problem.In chapter 3, we prove the existence of a solution for a system that contains in particular the seawater intrusion model in confined aquifers. This system is very similar to that introduced in chapter 2, only the pressure is a new unknown and we have the constraint that the sum of the unknown heights is a given function. The pressure is the Lagrange multiplier associated to the constraint. We obtain again an entropy estimate and we establish an estimate on the gradient of the pressure.In chapter 4, we are interested in the study of sharp interfaces that moves by a certain flow, by mean curvature flow for example. Singularities may occur in finite time which explains the necessity of having a differnet notion of surfaces. In this chapter, we introduce the notion of "varifolds" or generalized surfaces that extend the notion of manifolds. To these varifolds we associate a generalized mean curvature and a generalized normal velocity.In chapter 5, we consider an advection-reaction-diffusion equation arising from a chemotaxis-growth system proposed by Mimura and Tsujikawa. The unknown is the population density which is subjected to the effects of diffusion, of growth and to the tendency of migrating toward higher gradients of the chemotactic substance. When a small parameter tends to zero, the solution converges to a step function; the associated diffuse interface converges to a sharp interface which moves by perturbed mean curvature. We represent these interfaces by varifolds defined by the Lyapunov functional of the Allen-Cahn problem. We establish a monotonicity formula and we prove a property of equipartition of energy. We prove also the rectability of the varifold and that the multiplicity function is almost everywhere integer.