This thesis represents a small contribution to our understanding of metastable patterns in various stochastic models from physics and biology. By a \emph{metastable pattern}, we mean a pattern that appears to persist in a regular fashion on some timescale, but disappears or undergoes an irregular change on a longer timescale. Metastable patterns frequently result from stochastic perturbations of patterns that are stable without perturbation. In this thesis, we study stochastic perturbations of stable spatiotemporal patterns in several classes of PDE and integral equations. In particular, we address two major questions: \begin{enumerate}[Q1.] \item When perturbed by noise, for how long does a pattern that is stable without noise persist? \item How does the stochastic perturbation affect the average behaviour of a pattern on the timescale where it appears to persist? \end{enumerate} To address these questions, we pursue two lines of inquiry: the first based on the theory of \emph{quasi-ergodic measures}, and the second based on \emph{phase decomposition techniques}. In our first line of inquiry we present novel, rigorous connections between metastability of general infinite dimensional stochastic evolution systems and the spectral properties of their sub-Markov generators using the theory of quasi-ergodic measures. To do so, we develop a novel $L^p$-approach to the study of quasi-ergodic measures. We are then able to draw conclusions about the metastability of travelling waves and other patterns in a class of stochastic reaction-diffusion equations. For instance, we obtain a rigorous definition of the \emph{quasi-asymptotic speed}~of a travelling wave in a stochastic PDE. We moreover find that stochastic perturbations of amplitude $\sigma>0$ cause the quasi-asymptotic speed of certain travelling waves to deviate from the deterministic wave speed by a constant that is approximately proportional to $\sigma^2$. In our second line of inquiry, the dynamics of our (infinite dimensional) stochastic evolution system are projected onto a finite dimensional manifold that captures some property of a metastable pattern. While most previous studies using phase reduction techniques have used the \emph{variational phase}, we take an approach based on the \emph{isochronal phase}, inspired by classical work on finite dimensional oscillatory systems. When the pattern in question is a travelling wave, the isochronal phase captures the position of the wave at a given point in time. By exploiting the regularity properties of the isochronal phase, we are able to prove several novel results about the metastable behaviour of the reduced dynamics in the small noise regime in a very large class of stochastic evolution systems. These results allow us to moreover compute the noise-induced changes in the speed of stochastically perturbed travelling waves and other patterns. The results we obtain using this approach are numerically precise, and may be applied to a very general class of stochastic evolution systems.

In order to better describe dense gases, a smooth attractive tail arising from a Coulomb-type potential is added to the hard core repulsion of the Enskog equation, along with a velocity diffusion. By choosing the diffusing term of Fokker-Planck type with or without dynamical friction forces. The Cauchy problem for the Diffusive-Vlasov-Poisson-Enskog equation (DVE) and the Cauchy problem for the Fokker-Planck-Vlasov-Poisson-Enskog equation (FPVE) are addressed. / Ph. D.

Cette thèse comporte deux volets indépendants mais tous deux motivés par la modélisation mathématique et la simulation numérique de procédés photovoltaïques. La Partie I traite de systèmes d’équations aux dérivées partielles de diffusion croisée, modélisant l’évolution de concentrations ou de fractions volumiques de plusieurs espèces chimiques ou biologiques. Nous présentons dans le chapitre 1 une introduction succincte aux résultats mathématiques connus sur ces systèmes lorsqu’ils sont définis sur des domaines fixes. Nous présentons dans le chapitre 2 un système unidimensionnel que nous avons introduit pour modéliser l’évolution des fractions volumiques des différentes espèces chimiques intervenant dans le procédé de déposition physique en phase vapeur (PVD) utilisé pour la fabrication de cellules solaires à couches minces. Dans ce procédé, un échantillon est introduit dans un four à très haute température où sont injectées les différentes espèces chimiques sous forme gazeuse, si bien que des atomes se déposent petit à petit sur l’échantillon, formant une couche mince qui grandit au fur et à mesure du procédé. Dans ce modèle sont pris en compte à la fois l’évolution de la surface du film solide au cours du procédé et l’évolution des fractions volumiques locales au sein de ce film, ce qui aboutit à un système de diffusion croisée défini sur un domaine dépendant du temps. En utilisant une méthode récente basée sur l’entropie, nous montrons l’existence de solutions faibles à ce système et nous étudions leur comportement asymptotique dans le cas où les flux extérieurs imposés à la surface du film sont supposés constants. De plus, nous prouvons l’existence d’une solution à un problème d’optimisation sur les flux extérieurs. Nous présentons dans le chapitre 3comment ce modèle a été adapté et calibré sur des données expérimentales. La Partie II est consacrée à des questions reliées au calcul de la structure électronique de matériaux cristallins. Nous rappelons dans le chapitre 4 certains résultats classiques relatifs à la décomposition spectrale d’opérateurs de Schrödinger périodiques. Dans le chapitre 5, nous tentons de répondre à la question suivante : est-il possible de déterminer un potentiel périodique tel que les premières bandes d’énergie de l’opérateur de Schrödinger associé soient aussi proches que possible de certaines fonctions cibles ?Nous montrons théoriquement que la réponse à cette question est positive lorsque l’on considère la première bande de l’opérateur et des potentiels unidimensionnels appartenant à un espace de mesures périodiques bornées inférieurement en un certain sens. Nous proposons également une méthode adaptative pour accélérer la procédure numérique de résolution du problème d’optimisation. Enfin, le chapitre 6 traite d’un algorithme glouton pour la compression de fonctions de Wannier en exploitant leurs symétries. Cette compression permet, entre autres, d’obtenir des expressions analytiques pour certains coefficients de tight-binding intervenant dans la modélisation de matériaux 2D / This thesis includes two independent parts, both motivated by mathematical modeling and numerical simulation of photovoltaic devices. Part I deals with cross-diffusion systems of partial differential equations, modeling the evolution of concentrations or volume fractions of several chemical or biological species. We present in Chapter 1 a succinct introduction to the existing mathematical results about these systems when they are defined on fixed domains. We present in Chapter 2 a one-dimensional system that we introduced to model the evolution of the volume fractions of the different chemical species involved in the physical vapor deposition process (PVD) used in the production of thin film solar cells. In this process, a sample is introduced into a very high temperature oven where the different chemical species are injected in gaseous form, so that atoms are gradually deposited on the sample, forming a growing thin film. In this model, both the evolution of the film surface during the process and the evolution of the local volume fractions within this film are taken into account, resulting in a cross-diffusion system defined on a time dependent domain. Using a recent method based on entropy estimates, we show the existence of weak solutions to this system and study their asymptotic behavior when the external fluxes are assumed to be constant. Moreover, we prove the existence of a solution to an optimization problem set on the external fluxes. We present in Chapter3 how was this model adapted and calibrated on experimental data. Part II is devoted to some issues related to the calculation of the electronic structure of crystalline materials. We recall in Chapter 4 some classical results about the spectral decomposition of periodic Schrödinger operators. In text of Chapter 5, we try to answer the following question: is it possible to determine a periodic potential such that the first energy bands of the associated periodic Schrödinger operator are as close as possible to certain target functions? We theoretically show that the answer to this question is positive when we consider the first energy band of the operator and one-dimensional potentials belonging to a space of periodic measures that are lower bounded in certain ness. We also propose an adaptive method to accelerate the numerical optimization procedure. Finally, Chapter 6 deals with a greedy algorithm for the compression of Wannier functions into Gaussian-polynomial functions exploiting their symmetries. This compression allows, among other things, to obtain closed expressions for certain tight-binding coefficients involved in the modeling of 2D materials

Neste trabalho estudamos problemas de reação-difusão semilineares do tipo \'u IND..t(x, t) = \'DELTA\'u(x, t)+ f (u(x, t)), x \'PERTENCE A\' \'OMEGA\' \'PARTIAL\' U/\'PARTIAL\'V (x, t) = 0, x \'PERTENCE A\' \'PARTIAL\'\' OMEGA\'. Desenvolvemos uma teoria abstrata para a obtenção da continuidade da dinâmica assintótica de (P) sob perturbações singulares do domínio espacial W e aplicamos a uma série de exemplos dos assim chamados domínios finos / In this work we study semilinear reaction-diffusion problems of the type \'u IND.t(x, t) = \'DELTA\'u(x, t)+ f (u(x, t)), x \' PERTENCE A\' \'OMEGA\' \'PARTIAL\'u/\'ARTIAL\' v (x, t) = 0, x \"PERTENCE A\' \'PARTIAL\' \' OMEGA\' We develop a abstract theory to obtain the continuity of the asymptotic dynamics of (P) under singular perturbations of the spatial domain W and we apply that to many examples in thin domains

Neste trabalho estudamos a dinâmica assintótica de uma classe de equações diferenciais de reação-difusão definidas em abertos de \'R POT. 3\' arbitrários, limitados ou não, com condições de fronteira de Dirichlet. Utilizando a técnica de estimativas de truncamento, como nos artigos de Prizzi e Rybakowski, mostramos a existência de atratores globais / In this work we study the asymptotic behavior of a class of semilinear reaction-diffusion equations defined on an arbitrary open set of R3, bounded or not, with Dirichlet boundary conditions. Using the tail-estimates technic based on papers of Prizzi and Rybakowski, we prove existence of global attractors

Thesis (MSc (Logistics))--University of Stellenbosch, 2008. / The primary question considered in this study is whether a small population of a biological species introduced into a resource-heterogeneous environment, where it competes for these resources with an already established native species, will be able to invade successfully. A two-component autonomous system of reaction-diffusion equations with spatially inhomogeneous Lotka-Volterra competitive reaction terms and diffusion coefficients is derived as the governing equations of the competitive scenario. The model parameters for which the introduced species is able to invade describe the realized niche of that species. A linear stability analysis is performed for the model in the case where the resource heterogeneity is represented by, and the diffusion coefficients are, two-toned functions. In the case where the native species is not directly affected by the resource heterogeneity, necessary and sufficient conditions for successful invasion are derived. In the case where the native species is directly affected by the resource heterogeneity only sufficient conditions for successful invasion are derived. The reaction-diffusion equations employed in the model are deterministic. However, in reality biological species are subject to stochastic population perturbations. It is argued that the ability of the invading species to recover from a population perturbation is correlated with the persistence of the species in the niche that it occupies. Hence, invasion time is used as a relative measure to quantify the rate at which a species’ population distribution recovers from perturbation. Moreover, finite difference and spectral difference methods are employed to solve the model scenarios numerically and to corroborate the results of the linear stability analysis. Finally, a case study is performed. The model is instantiated with parameters that represent two different cultivars of barley in a hypothetical environment characterized by spatially varying water availability and the sufficient conditions for successful invasion are verified for this hypothetical scenario.

Neste trabalho estudamos a dinâmica assintótica de uma classe de equações diferenciais de reação-difusão definidas em abertos de \'R POT. 3\' arbitrários, limitados ou não, com condições de fronteira de Dirichlet. Utilizando a técnica de estimativas de truncamento, como nos artigos de Prizzi e Rybakowski, mostramos a existência de atratores globais / In this work we study the asymptotic behavior of a class of semilinear reaction-diffusion equations defined on an arbitrary open set of R3, bounded or not, with Dirichlet boundary conditions. Using the tail-estimates technic based on papers of Prizzi and Rybakowski, we prove existence of global attractors

Neste trabalho estudamos problemas de reação-difusão semilineares do tipo \'u IND..t(x, t) = \'DELTA\'u(x, t)+ f (u(x, t)), x \'PERTENCE A\' \'OMEGA\' \'PARTIAL\' U/\'PARTIAL\'V (x, t) = 0, x \'PERTENCE A\' \'PARTIAL\'\' OMEGA\'. Desenvolvemos uma teoria abstrata para a obtenção da continuidade da dinâmica assintótica de (P) sob perturbações singulares do domínio espacial W e aplicamos a uma série de exemplos dos assim chamados domínios finos / In this work we study semilinear reaction-diffusion problems of the type \'u IND.t(x, t) = \'DELTA\'u(x, t)+ f (u(x, t)), x \' PERTENCE A\' \'OMEGA\' \'PARTIAL\'u/\'ARTIAL\' v (x, t) = 0, x \"PERTENCE A\' \'PARTIAL\' \' OMEGA\' We develop a abstract theory to obtain the continuity of the asymptotic dynamics of (P) under singular perturbations of the spatial domain W and we apply that to many examples in thin domains

Dans cette thèse nous nous intéressons aux équations de réaction-diffusion et à leurs applications en sciences biologiques et médicales. Plus particulièrement on étudie l'existence ou la non-existence de phénomènes de propagation en milieux hétérogènes à travers l'existence d'ondes progressives ou plus généralement l'existence de fronts de transition généralisés. On obtient des résultats d'existence de phénomènes de propagation dans trois environnements différents. Dans un premier temps on étudie une équation de réaction-diffusion de type bistable dans un domaine extérieur. Cette équation modélise l'évolution de la densité d'une population soumise à un effet Allee fort dont le déplacement suit un processus de diffusion dans un environnement contenant un obstacle. On montre que lorsque l'obstacle satisfait certaines conditions de régularité et se rapproche d'un domaine étoilé ou directionnellement convexe alors la population envahit tout l'espace. On se questionne aussi sur les conditions optimales de régularité qui garantissent une invasion complète de la population. Dans un deuxième travail, nous considérons une équation de réaction-diffusion avec vitesse forcée, modélisant l'évolution de la densité d'une population quelconque qui se diffuse dans l'espace, soumise à un changement climatique défavorable. On montre que selon la vitesse du changement climatique la population s'adapte ou s'éteint. On montre aussi que la densité de population converge en temps long vers une onde progressive et donc se propage (si elle survit) selon un profile constant et à vitesse constante. Dans un second temps on étudie une équation de réaction-diffusion de type bistable dans des domaines cylindriques variés. Ces équations modélisent l'évolution d'une onde de dépolarisation dans le cerveau humain. On montre que l'onde est bloquée lorsque le domaine passe d'un cylindre très étroit à un cylindre de diamètre d'ordre 1 et on donne des conditions géométriques plus générales qui garantissent une propagation complète de l'onde dans le domaine. On étudie aussi ce problème d'un point de vue numérique et on montre que pour les cylindres courbés la courbure peut provoquer un blocage de l'onde pour certaines conditions aux bords. / In this thesis we are interested in reaction diffusion equations and their applications in biology and medical sciences. In particular we study the existence or non-existence of propagation phenomena in non homogeneous media through the existence of traveling waves or more generally the existence of transition fronts.First we study a bistable reaction diffusion equation in exterior domain modelling the evolution of the density of a population facing an obstacle. We prove that when the obstacle satisfies some regularity properties and is close to a star shaped or directionally convex domain then the population invades the entire domain. We also investigate the optimal regularity conditions that allow a complete invasion of the population. In a second work, we look at a reaction diffusion equation with forced speed, modelling the evolution of the density of a population facing an unfavourable climate change. We prove that depending on the speed of the climate change the population keeps track with the climate change or goes extinct. We also prove that the population, when it survives, propagates with a constant profile at a constant speed at large time. Lastly we consider a bistable reaction diffusion equation in various cylindrical domains, modelling the evolution of a depolarisation wave in the brain. We prove that this wave is blocked when the domain goes from a thin channel to a cylinder, whose diameter is of order 1 and we give general conditions on the geometry of the domain that allow propagation. We also study this problem numerically and prove that for curved cylinders the curvature can block the wave for particular boundary conditions.

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