Most models for the spread of an invasive species into a new environment are based on Fisher's reaction-diffusion equation. They assume that habitat quality is independent of the presence or absence of the invading population. Ecosystem engineers are species that modify their environment to make it (more) suitable for them. A potentially more appropriate modeling approach for such an invasive species is to adapt the well-known Stefan problem of melting ice. Ahead of the front, the habitat is unsuitable for the species (the ice); behind the front, the habitat is suitable (the open water). The engineering action of the population moves the boundary ahead (the melting). This approach leads to a free boundary problem. In this thesis, we mathematically analyze a novel free-boundary model for the spread of ecosystem engineers that was recently derived from an individual random walk model. The Stefan condition for the moving boundary is replaced by a biologically derived two-sided condition that models the movement behavior of individuals at the boundary as well as the process by which the population moves the boundary to expand their territory. We first consider the model with logistic growth and study its well-posedness. We assign a convex functional to this problem so that the evolution system governed by this convex potential is exactly the system of evolution equations describing the above model. We then apply variational and fixed-point methods to deal with this free boundary problem and prove the existence of local in-time solutions. We next study traveling wave solutions of the model with the strong Allee growth function. We use phase plane analysis to find traveling wave solutions of different types and their corresponding existence range of speed for the model with an imposed speed of the moving boundary. We then find the speeds in those ranges at which the corresponding traveling wave follows the speed of the free boundary.

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O sistema de FitzHugh-Nagumo possui um tipo especial de solução chamadas ondas viajantes, que são da forma &micro(x,t)=&oslash(x+ct) e w(x,t)=&#1137(x+ct) e além disso sabe-se que ela é estável. Tem-se o interesse de obter uma caracterização de seu perfil (&oslash,&#1137) e sua velocidade de propagação c. Fazendo uma mudança de variáveis, transformamos tal problema em encontrar equilíbrios de uma equação não local. Esta equação não local possui uma onda viajante de velocidade zero cujo perfil é o mesmo da equação original e, com esta equação, é possível aproximar, ao mesmo tempo, o perfil e a velocidade da onda viajante. Como a intenção é usar métodos numéricos para aproximar tais soluções, o problema não local foi analisado em um intervalo limitado verificando a existência e algumas propriedades espectrais em domínios limitados. / The FitzHugh-Nagumo systems have a special kind of solution named traveling wave, which has a form &micro(x,t)=&oslash(x+ct) and w(x,t)=&#1137(x+ct) and furthermore it is a stable solution. It is our interest to obtain a characterization of its profile (&oslash,&#1137) and speed of propagation c. Changing variables, we transform the problem of finding these solutions in the problem of finding an equilibria in a nonlocal equation. This nonlocal equation has a traveling wave with zero speed whose profile is the same of the original equation, and the nonlocal equation is used to approximate the profile and speed of the traveling wave at the same time. To use numerical methods for approximating such solutions, the nonlocal problem was analyzed in a finite interval to check that the existence and some spectral properties on bounded domains.

O sistema de FitzHugh-Nagumo possui um tipo especial de solução chamadas ondas viajantes, que são da forma &micro(x,t)=&oslash(x+ct) e w(x,t)=&#1137(x+ct) e além disso sabe-se que ela é estável. Tem-se o interesse de obter uma caracterização de seu perfil (&oslash,&#1137) e sua velocidade de propagação c. Fazendo uma mudança de variáveis, transformamos tal problema em encontrar equilíbrios de uma equação não local. Esta equação não local possui uma onda viajante de velocidade zero cujo perfil é o mesmo da equação original e, com esta equação, é possível aproximar, ao mesmo tempo, o perfil e a velocidade da onda viajante. Como a intenção é usar métodos numéricos para aproximar tais soluções, o problema não local foi analisado em um intervalo limitado verificando a existência e algumas propriedades espectrais em domínios limitados. / The FitzHugh-Nagumo systems have a special kind of solution named traveling wave, which has a form &micro(x,t)=&oslash(x+ct) and w(x,t)=&#1137(x+ct) and furthermore it is a stable solution. It is our interest to obtain a characterization of its profile (&oslash,&#1137) and speed of propagation c. Changing variables, we transform the problem of finding these solutions in the problem of finding an equilibria in a nonlocal equation. This nonlocal equation has a traveling wave with zero speed whose profile is the same of the original equation, and the nonlocal equation is used to approximate the profile and speed of the traveling wave at the same time. To use numerical methods for approximating such solutions, the nonlocal problem was analyzed in a finite interval to check that the existence and some spectral properties on bounded domains.

In this thesis we employ two recent analytical approaches to investigate the possible classes of traveling wave solutions of some members of recently derived integrable family of generalized Camassa-Holm (GCH) equations. In the first part, a novel application of phase-plane analysis is employed to analyze the singular traveling wave equations of four GCH equations, i.e. the possible non-smooth peakon, cuspon and compacton solutions. Two of the GCH equations do no support singular traveling waves. We generalize an existing theorem to establish the existence of peakon solutions of the third GCH equation. This equation is found to also support four segmented, non-smooth M-wave solutions. While the fourth supports both solitary (peakon) and periodic (cuspon) cusp waves in different parameter regimes. In the second part of the thesis, smooth traveling waves of the four GCH equations are considered. Here, we use a recent technique to derive convergent multi-infinite series solutions for the homoclinic and heteroclinic orbits of their traveling-wave equations, corresponding to pulse and front (kink or shock) solutions respectively of the original PDEs. Unlike the majority of unaccelerated convergent series, high accuracy is attained with relatively few terms. Of course, the convergence rate is not comparable to typical asymptotic series. However, asymptotic solutions for global behavior along a full homoclinic/heteroclinic orbit are currently not available.

Lipopolysaccharides (LPS) représentent le composant principal de la membrane externe des bactéries Gram-négatives. Étant libérés dans le flux sanguin, les LPS induisent une forte réponse immunitaire accompagnée d'une coagulation intensifiée du sang activée à la fois par l'endommagement de la paroi vasculaire et par l'activation de la voie de contact. Dans cette thèse, nous développons des modèles théoriques pour élucider les détails de la coagulation sanguine induite par les molécules LPS. Dans les deux premiers chapitres, nous décrivons l'état de l'art du problème et les méthodes utilisées. Le troisième chapitre est consacré à l'analyse des modèles mathématiques de la coagulation sanguine. Nous déterminons les conditions de l'existence de solutions en ondes progressives dans le modèle de la croissance du caillot, estimons la vitesse de leur propagation et démontrons l'existence de la solution en forme de pulse déterminante la valeur critique de la condition initiale qui assure le processus de coagulation. Ensuite, nous étudions le modèle de la formation de caillot dans l'écoulement sanguin et déterminons la taille critique de la zone endommagée conduisante à l'occlusion complète du vaisseau par le caillot. Enfin, nous développons et analysons le modèle de l'activation du système de contact par les agrégats des LPS. Dans le quatrième chapitre, nous modélisons la structure supramoléculaire des LPS, qui a un impact crucial sur leur activité biologique. Nous développons des modèles de la dynamique moléculaire des LPS, de leurs agrégats et des membranes des compositions variées, et analysons le comportement conformationnel des LPS en fonction de leur environnement / The outer membrane of the Gram-negative bacteria cell wall is composed of lipopolysaccharide (LPS) molecules. Being released to the blood flow during sepsis, LPS induce strong immune response accompanied by pathological blood clotting. Blood coagulation is activated both due to the vessel wall damage, and the activation of the contact pathway. The details of the mechanisms involved remain obscure despite the extensive experimental studies. In the present work we develop theoretical models of the different time and space scales to elucidate the details of the LPS-induced blood coagulation during the Gram-negative sepsis. In the first two chapters we provide the state of the art of the problem and describe the methods we use. The third chapter is devoted to the analysis of the mathematical models of blood coagulation. We determine the conditions of the existence of the traveling wave solutions in the model of the self-sustained clot growth, estimate the speed of their propagation and demonstrate existence of the pulse solution determining the critical value of the initial condition. Then, we consider the model of blood coagulation under flow conditions and determine the critical size of the damaged zone leading to the complete vessel occlusion by the clot. Finally, we develop and analyze the model of the contact system activation by the LPS aggregates. In the fourth chapter we model the LPS supramolecular structure, which has crucial impact on the LPS biological activity. We develop molecular dynamics models of the LPS molecules, their aggregates and LPS-containing membranes of different composition and analyze LPS conformational behavior in different environment