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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.

Coupled nonlinear Schrodinger equations (CNLS) govern many physical phenomena, such as nonlinear optics and Bose-Einstein condensates. For their wide applications, many studies have been carried out by physicists, mathematicians and engineers from different respects. In this dissertation, we focused on standing wave solutions, which are of particular interests for their relatively simple form and the important roles they play in studying other wave solutions. We studied the multiplicity of this type of solutions of CNLS via variational methods and bifurcation methods. Variational methods are useful tools for studying differential equations and systems of differential equations that possess the so-called variational structure. For such an equation or system, a weak solution can be found through finding the critical point of a corresponding energy functional. If this equation or system is also invariant under a certain symmetric group, multiple solutions are often expected. In this work, an integer-valued function that measures symmetries of CNLS was used to determine critical values. Besides variational methods, bifurcation methods may also be used to find solutions of a differential equation or system, if some trivial solution branch exists and the system is degenerate somewhere on this branch. If local bifurcations exist, then new solutions can be found in a neighborhood of each bifurcation point. If global bifurcation branches exist, then there is a continuous solution branch emanating from each bifurcation point. We consider two types of CNLS. First, for a fully symmetric system, we introduce a new index and use it to construct a sequence of critical energy levels. Using variational methods and the symmetric structure, we prove that there is at least one solution on each one of these critical energy levels. Second, we study the bifurcation phenomena of a two-equation asymmetric system. All these bifurcations take place with respect to a positive solution branch that is already known. The locations of the bifurcation points are determined through an equation of a coupling parameter. A few nonexistence results of positive solutions are also given

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

Le contexte de cette thèse est la théorie de l'élasticité non linéaire, appelée également "élasticité finie". On y présente des résultats concernant la propagation d'ondes d'amplitude finie dans des matériaux élastiques non linéaires soumis à une grande déformation statique homogène. Bien que les matériaux considérés soient isotropes, lors de la propagation d'ondes un comportement anisotrope dû à la déformation statique se manifeste. Après un rappel des équations de base de l'élasticité non linéaire (Chapitre 1), on considère tout d'abord la classe générale des matériaux incompressibles. Pour ces matériaux, on montre que la propagation d'ondes transversales polarisées linéairement est possible pour des choix appropriés des directions de polarisation et de propagation. De plus, on propose des généralisations des modèles classiques de "Mooney-Rivlin" et "néo-Hookéen" qui conduisent à de nouvelles solutions. Bien que le contexte soit tri-dimensionnel, il s'avère que toutes ces ondes sont régies par des équations d'ondes scalaires non linéaires uni-dimensionelles. Dans le cas de solutions du type ondes simples, on met en évidence une propriété remarquable du flux et de la densité d'énergie. Dans les Chapitres 3 et 4, on se limite à un modèle particulier de matériaux compressibles appelé "modèle restreint de Blatz-Ko", qui est une version compressible du modèle néo-Hookéen. En milieu infini (Chapitre 3), on montre que des ondes transversales polarisées linéairement, faisant intervenir deux variables spatiales, peuvent se propager. Bien que la théorie soit non linéaire, le champ de déplacement de ces ondes est régi par une version anisotrope de l'équation d'onde bi-dimensionnelle classique. En particulier, on présente des solutions à symétrie "cylindrique elliptique" analogues aux ondes cylindriques. Comme cas particulier, on obtient aussi des ondes planes inhomogènes atténuées à la fois dans l'espace et dans le temps. De plus, on montre que diverses superpositions appropriées de solutions sont possibles. Dans chaque cas, on étudie les propriétés du flux et de la densité d'énergie. En particulier, dans le cas de superpositions il s'avère que des termes d'interactions interviennent dans les expressions de la densité et du flux d'énergie. Finalement (Chapitre 4), on présente une solution exacte qui constitue une généralisation non linéaire de l'onde de Love classique. On considère ici un espace semi-infini, appelé "substrat" recouvert par une couche. Le substrat et la couche sont constitués de deux matériaux restreints de Blatz-Ko pré-déformés. L'onde non linéaire de Love est constituée d'un mouvement non atténué dans la couche et d'une onde plane inhomogène dans le substrat, choisies de manière à satisfaire aux conditions aux limites. La relation de dispersion qui en résulte est analysée en détail. On présente de plus des propriétés générales du flux et de la densité d'énergie dans le substrat et dans la couche. The context of this thesis is the non linear elasticity theory, also called "finite elasticity". Results are obtained for finite-amplitude waves in non linear elastic materials which are first subjected to a large homogeneous static deformation. Although the materials are assumed to be isotropic, anisotropic behaviour for wave propagation is induced by the static deformation. After recalling the basic equations of the non linear elasticity theory (Chapter 1), we first consider general incompressible materials. For such materials, linearly polarized transverse plane waves solutions are obtained for adequate choices of the polarization and propagation directions (Chapter 2). Also, extensions of the classical Mooney-Rivlin and neo-Hookean models are introduced, for which more solutions are obtained. Although we use the full three dimensional elasticity theory, it turns out that all these waves are governed by scalar one-dimensional non linear wave equations. In the case of simple wave solutions of these equations, a remarkable property of the energy flux and energy density is exhibited. In Chapter 3 and 4, a special model of compressible material is considered: the special Blatz-Ko model, which is a compressible counterpart of the incompressible neo-Hookean model. In unbounded media (Chapter 3), linearly polarized two-dimensional transverse waves are obtained. Although the theory is non linear, the displacement field of these waves is governed by a linear equation which may be seen as an anisotropic version of the classical two-dimensional wave equation. In particular, solutions analogous to cylindrical waves, but with an "elliptic cylindrical symmetry" are presented. Special solutions representing "damped inhomogeneous plane waves" are also derived: such waves are attenuated both in space and time. Moreover, various appropriate superpositions of solutions are shown to be possible. In each case, the properties of the energy density and the energy flux are investigated. In particular, in the case of superpositions, it is seen that interaction terms enter the expressions for the energy density and the energy flux. Finally (Chapter 4), an exact finite-amplitude Love wave solution is presented. Here, an half-space, called "substrate", is assumed to be covered by a layer, both made of different prestrained special Blatz-Ko materials. The Love surface wave solution consists of an unattenuated wave motion in the layer and an inhomogeneous plane wave in the substrate, which are combined to satisfy the exact boundary conditions. A dispersion relation is obtained and analysed. General properties of the energy flux and the energy density in the substrate and the layer are exhibited.

Cette thèse est consacrée à la modélisation mathématique de l'hématopoïèse et des maladies sanguines. Plusieurs modèles traitant d'aspects différents et complémentaires de l'hématopoïèse y sont étudiés.Tout d'abord, un modèle multi-échelle de l'érythropoïèse est analysé, dans lequel sont décrits à la fois le réseau intracellulaire, qui détermine le comportement individuel des cellules, et la dynamique des populations de cellules. En utilisant des données expérimentales sur les souris, nous évaluons les rôles des divers mécanismes de retro-contrôle en réponse aux situations de stress.Ensuite, nous tenons compte de la distribution spatiale des cellules dans la moelle osseuse, question qui n'avait pas été étudiée auparavant. Nous décrivons l'hématopoïèse normale à l'aide d'un système d'équations de réaction-diffusion-convection et nous démontrons l'existence d'une distribution stationnaire des cellules. Puis, nous introduisons dans le modèle les cellules malignes. Pour certaines valeurs des paramètres, la solution "disease-free" devient instable et une autre solution, qui correspond à la leucémie, apparaît. Cela mène à la formation d'une tumeur qui se propage dans la moelle osseuse comme une onde progressive. La vitesse de cette propagation est étudiée analytiquement et numériquement. Les cellules de la moelle osseuse échangent des signaux qui régulent le comportement cellulaire. Nous étudions ensuite une équation integro-différentielle qui décrit la communication cellulaire et nous prouvons l'existence d'une solution du type onde progressive en utilisant la théorie du degré topologique et la méthode de Leray et Schauder. L'approche multi-agent est utilisée afin d'étudier la distribution des différents types de cellules dans la moelle osseuse.Finalement, nous étudions un modèle de type "Physiologically Based Pharmacokinetics-Pharmacodynamics" du traitement de la leucémie par l'AraC. L'AraC agit comme chimiothérapie et induit l'apoptose de toutes les cellules proliférantes, saines et malignes. La pharmacocinétique donne accès à la concentration intracellulaire d'AraC. Cette dernière, à son tour, détermine la dynamique des populations cellulaires et, par conséquent, l'efficacité de différents protocoles de traitement. / This PhD thesis is devoted to mathematical modelling of haematopoiesis and blood diseases. We investigate several models, which deal with different and complementary aspects of haematopoiesis.The first part of the thesis concerns a multi-scale model of erythropoiesis where intracellular regulatory networks, which determine cell choice between self-renewal, differentiation and apoptosis, are coupled with dynamics of cell populations. Using experimental data on anemia in mice, we evaluate the roles of different feedback mechanisms in response to stress situations. At the next stage of modelling, spatial cell distribution in the bone marrow is taken into account, the question which has not been studied before. We describe normal haematopoiesis with a system of reaction-diffusion-convection equations and prove existence of a stationary cell distribution. We then introduce malignant cells into the model. For some parameter values the disease free solution becomes unstable and another one, which corresponds to leukaemia, appears. This leads to the formation of tumour which spreads in the bone marrow as a travelling wave. The speed of its propagation is studied analytically and numerically. Bone marrow cells exchange different signals that regulate cell behaviour. We study, next, an integro-differential equation which describes cell communication and prove the existence of travelling wave solutions using topological degree and the Leray-Schauder method. Individual based approach is used to study distribution of different cell types in the bone marrow. Finally, we investigate a Physiologically Based Pharmacokinetics-Pharmacodynamics model of leukaemia treatment with AraC drug. AraC acts as chemotherapy, inducing apoptosis of all proliferating cells, normal and malignant. Pharmacokinetics provides the evolution of intracellular AraC. This, in turn, determines cell population dynamics and, consequently, efficacy of treatment with different protocols.