Cette thèse présente des travaux sur l’étude et la calibration de modèles d’équations aux dérivées partielles pour la croissance tumorale. La première partie porte sur l’analyse d’un modèle de croissance tumorale pour le cas de métastases au foie de tumeurs gastro-intestinales (GIST). Le modèle est un système d’équations aux dérivées partielles couplées et prend en compte plusieurs traitements dont un traitement anti-angiogénique. Le modèle permet de reproduire des données cliniques. La première partie de ce travail concerne la preuve d’existence/unicité de la solution du modèle. La seconde partie du travail porte sur l’étude du comportement asymptotique de la solution du modèle lorsqu’un paramètre du modèle, décrivant la capacité de la tumeur à évacuer la nécrose, converge vers 0. La seconde partie de la thèse concerne le développement d’un modèle de croissance pour des sphéroïdes tumoraux ainsi que sur la calibration de ce modèle à partir de données expérimentales in vitro. L’objectif est de développer un modèle permettant de reproduire quantitativement la distribution des cellules proliférantes à l’intérieur d’un sphéroïde en fonction de la concentration en nutriments. Le travail de modélisation et de calibration du modèle a été effectué à partir de données expérimentales permettant d’obtenir la répartition spatiale de cellules proliférantes dans un sphéroïde tumoral. / In this thesis, we present several works on the study and the calibration of partial differential equations models for tumor growth. The first part is devoted to the mathematical study of a model for tumor drug resistance in the case of gastro-intestinal tumor (GIST) metastases to the liver. The model we study consists in a coupled partial differential equations system and takes several treatments into account, such as a anti-angiogenic treatment. This model is able to reproduce clinical data. In a first part, we present the proof of the existence/uniqueness of the solution to this model. Then, in a second part, we study the asymptotic behavior of the solution when a parameter of this model, describing the capacity of the tumor to evacuate the necrosis, goes to 0. In the second part of this thesis, we present the development of model for tumor spheroids growth. We also present the model calibration thanks to in vitro experimental data. The main objective of this work is to reproduce quantitatively the proliferative cell distribution in a spheroid, as a function of the concentration of nutrients. The modeling and calibration of this model have been done thanks to experimental data consisting of proliferative cells distribution in a spheroid.

The nonlinear Schrödinger equation appears in different fields of physics, for example in the theory of Bose-Einstein condensates or in wave propagation models. From a mathematical point of view, the study of this equation is interesting and delicate, notably because it can have a very rich set of solutions with various behaviours.<p><p>In this thesis, we have been interested in standing waves, which satisfy an elliptic partial differential equation. When this equation is seen as a singularly perturbed problem, its solutions concentrate, in the sense that they converge uniformly to zero outside some concentration set, while they remain positive on this set.<p><p>We have obtained three kind of new results. Firstly, under symmetry assumptions, we have found solutions concentrating on a sphere. Secondly, we have obtained the same type of solutions for the Schrödinger-Poisson system. The method consists in applying the mountain pass theorem to a penalized problem. Thirdly, we have proved the existence of solutions of the nonlinear Schrödinger equation concentrating at a local maximum of the potential. These solutions are found by a more general minimax principle. Our results are characterized by very weak assumptions on the potential./<p><p>L'équation de Schrödinger non-linéaire apparaît dans différents domaines de la physique, par exemple dans la théorie des condensats de Bose-Einstein ou dans des modèles de propagation d'ondes. D'un point de vue mathématique, l'étude de cette équation est intéressante et délicate, notamment parce qu'elle peut posséder un ensemble très riche de solutions avec des comportements variés. <p><p>Dans cette thèse ,nous nous sommes intéressés aux ondes stationnaires, qui satisfont une équation aux dérivées partielles elliptique. Lorsque cette équation est vue comme un problème de perturbations singulières, ses solutions se concentrent, dans le sens où elles tendent uniformément vers zéro en dehors d'un certain ensemble de concentration, tout en restant positives sur cet ensemble. <p><p>Nous avons obtenu trois types de résultats nouveaux. Premièrement, sous des hypothèses de symétrie, nous avons trouvé des solutions qui se concentrent sur une sphère. Deuxièmement, nous avons obtenu le même type de solutions pour le système de Schrödinger-Poisson. La méthode consiste à appliquer le théorème du col à un problème pénalisé. Troisièmement, nous avons démontré l'existence de solutions de l'équation de Schrödinger non-linéaire qui se concentrent en un maximum local du potentiel. Ces solutions sont obtenues par un principe de minimax plus général. Nos résultats se caractérisent par des hypothèses très faibles sur le potentiel. / Doctorat en sciences, Spécialisation mathématiques / info:eu-repo/semantics/nonPublished

Wound healing is a complex process, in which a sequence of interrelated events at both the cell and tissue levels interact and contribute to the reduction in wound size. For diabetic patients, many of these processes are compromised, so that wound healing slows down and in some cases halts. In this thesis we develop a series of increasingly detailed mathematical models to describe and investigate healing of full thickness skin wounds. We begin by developing a time-dependent ordinary differential equation model. This phenomenological model focusses on the main processes contributing to closure of a full thickness wound: proliferation in the epidermis and growth and contraction in the dermis. Model simulations suggest that the relative contributions of growth and contraction to healing of the dermis are altered in diabetic wounds. We investigate further the balance between growth and contraction by developing a more detailed, spatially-resolved model using continuum mechanics. Due to the initial large retraction of the wound edge upon injury, we adopt a non-linear elastic framework. Morphoelasticity theory is applied, with the total deformation of the material decomposed into an addition of mass and an elastic response. We use the model to investigate how interactions between growth and stress influence dermal wound healing. The model reveals that contraction alone generates unrealistically high tension in the dermal tissue and, hence, volumetric growth must contribute to healing. We show that, in the simplified case of homogeneous growth, the tissue must grow anisotropically in order to reduce the size of the wound and we postulate mechanosensitive growth laws consistent with this result. After closure the surrounding tissue remodels, returning to its residually stressed state. We identify the steady state growth profile associated with this remodelled state. The model is used to predict the outcome of rewounding experiments as a method of quantifying the amount of stress in the tissue and the application of pressure treatments to control tissue synthesis. The thesis concludes with an extension to the spatially-resolved mechanical model to account for the effects of the biochemical environment. Partial differential equations describing the dynamics of fibroblasts and a regulating growth factor are coupled to equations for the tissue mechanics, described in the morphoelastic framework. By accounting for biomechanical and biochemical stimuli the model allows us to formulate mechanistic laws for growth and contraction. We explore how disruption of mechanical and chemical feedback can lead to abnormal wound healing and use the model to identify specific treatments for normalising healing in these cases.

Cette thèse est dédiée à l'analyse mathématique de quelques problèmes variationnels motivés par le modèle de Ginzburg-Landau en théorie de la supraconductivité. Dans la première partie on étudie l'existence de solutions pour les équations de Ginzburg-Landau sans champ magnétique et avec données au bord de type semi-rigides. Ces données consistent à prescrire le module de la fonction sur le bord du domaine ainsi que son degré topologique. C'est un cas particulier de problèmes à bord libre, ou la donnée complète de la fonction sur le bord est une inconnue du problème. L'existence de solutions à ce problème n'est pas assurée. En effet la méthode directe du calcul des variations ne peut pas s'appliquer car le degré sur le bord n'est pas continu pour la convergence faible dans l'espace de Sobolev adapté. On dit que c'est un problème sans compacité. En étudiant le phénomène de "bubbling" qui apparaît dans l'étude de tels problèmes on donne des résultats d'existence et de non existence de solutions. Dans le Chapitre 1 on étudie des conditions qui permettent d'affirmer que la différence entre deux niveaux d'énergie est strictement optimale. Pour cela on adapte une technique due à Brezis-Coron. Ceci nous permet de redémontrer un résultat (précédemment obtenu par Berlaynd Rybalko et Dos Santos) d'existence de solutions stables pour les équations de Ginzburg-Landau dans des domaines multiplement connexes. Dans le Chapitre 2 on considère les applications harmoniques a valeurs dans $R^2$ avec des conditions au bord de type degrés prescrits sur un anneau. On fait un lien entre ce problème et la théorie des surfaces minimales dans $R^3$ grâce à la différentielle quadratique de Hopf. Ceci nous conduit à l'étude des surfaces minimales bordées par deux cercles dans des plans parallèles. On prouve l'existence de telles surfaces qui ne sont pas des catenoides grâce a un résultat de bifurcation. On utilise alors les résultats obtenus pour déduire des théorèmes d'existence et de non existence de minimiseurs de l'énergie de Ginzburg-Landau à degrés prescrits dans un anneau. Dans ce troisième Chapitre on obtient des résultats pour une valeur du paramètre " grand. Le Chapitre 4 a pour objet l'étude des problèmes a degrés prescrits en dimension n3. On y montre la non existence des minimiseurs de la n-énergie de Ginzburg-Landau a degrés prescrits dans un domaine simplement connexe. On étudie ensuite des points critiques de type min-max pour une énergie perturbée. La deuxième partie est consacrée a l'analyse asymptotique des solutions des équations deGinzburg-Landau lorsque " tend vers zero. Sandier et Serfaty ont étudié le comportement asymptotique des mesures de vorticité associées aux équations. Ils ont notamment trouvé des conditions critiques sur les mesures limites dans le cas des équations avec et sans champ magnétique. Nous nous intéressons alors à ces conditions critiques dans le cas sans champ magnétique. Le problème de la régularité locale des mesures limites se ramène ainsi a l'étude de la régularité des fonctions stationnaires harmoniques dont le Laplacien est une mesure. Nous montrons que localement de telles mesures sont supportées par une union de lignes appartenant à l'ensemble des zéros d'une fonction harmonique / This thesis is devoted to the mathematical analysis of some variational problems. These problem sare motivated by the Ginzburg-Landau model related to the super conductivity. In the first part we study existence of solutions of the Ginzburg-Landau equations without magnetic eld but with semi-sti boundary conditions. These conditions are obtained by prescribing the modulus of the function on the boundary of the domain along with its topological degree. This is a particular case of free boundary problems, where the function on the boundary is an unknown of the problem. Existence of solutions of that problem does not necessary hold. Indeed we can not apply the direct method of the calculus of variations since the degree on the boundaryis not continuous with respect to the weak convergence in an appropriated Sobolev space. This is problem with loss of compactness. By studying the bublling" phenomenon which come upin such problems we obtain some existence and non existence results .In Chapter 1 we study conditions under which the dierence between two energy levels is strictly optimal. In order to do that we adapt a technique due to Brezis-Coron. This allow us to recover known existence results (previously obtained by Berlyand and Rybalko and DosSantos) for stable solutions of the Ginzburg-Landau equations in multiply connected domains. In Chapter 2 we are interested in harmonic maps with values in $R^2$ with prescribed degree boundary condition in an annulus. We make a link between this problem and the minimal surface theory in $R^3$ thanks to the so-called Hopf quadratic differential. This leads us to study immersed minimal surfaces bounded by two circles in parallel planes. We prove the existence of such surfaces die rent from catenoids by using a bifurcation argument. We then apply the results obtained to deduce existence and non existence results for minimizers of the Ginzburg-Landau energy with prescribed degrees. This is done in Chapter 3 where the results are obtained for large ".Chapter 4 is devoted to prescribed degree problems in dimension n3 . We prove the non existence of minimizers of the Ginzburg-Landau energy in simply connected domains. We then study min-max critical points of a perturbed energy. The second part is devoted to the asymptotic analysis of solutions of the Ginzburg-Landau equations when "goes to zero. Sandier and Serfaty studied the asymptotic behavior of the vorticity measures associated to these equations. They derived critical conditions on the limiting measures both with and without magnetic Field. We are interested by these conditions when there is no magnetic Field. The problem of the local regularity of the limiting measures is then equivalent to the study of regularity of stationary harmonic functions whose Laplacianis a measure. We show that locally such measures are concentrated on a union of lines which belong to the zero set of an harmonic function

This dissertation focused on developing a numerical model of spatial and temporal changes in bed morphology of ridge and slough features in wetlands with respect to hydrology and sediment transport when a sudden change in hydrologic condition occurs. The specific objectives of this research were: (1) developing a two-dimensional hydrology model to simulate the spatial distribution of flow depth and velocity over time when a pulsed flow condition is applied, (2) developing a process-based numerical model of sediment transport coupled with flow depth and velocity in wetland ecosystems, and (3) use the developed model to explore how sediment transport may affect the changes in bed elevation of ridge and slough landscape patterns observed in wetlands when a conditional pulsed flow was applied. The results revealed the areas within deep sloughs where flow velocities and directions change continuously. This caused enhanced mixing areas within the deep slough. These mixing areas may have had the potential to affect processes such as sediment redistribution and nutrient transport. The simulation results of solute/sediment transport model also supported the existence of areas within the domain where the mixing processes happened. These areas may have caused that nutrients and suspended particles stay longer time rather than entraining toward downstream and exiting the system. The results of bed simulation have shown very small magnitude of change in bed elevation inside deep slough and no changes on the ridge portion of the study area, when a conditional pulsed flow is applied. These findings may suggest that implementing pulsed flow condition did not increase suspended sediment concentration, which results in insignificant changes in bed morphology of a ridge and slough landscape. Therefore sediment transport may not play an important role in wetland bed morphology and ridge and slough stability. Results from the model development and numerical simulations from this research will provide an improved understanding of how wetland features such as ridge may have formed and degraded by changes in water management that resulted from increasing human activity in wetlands such as The Florida Everglades, over the past decades.

In the last half a century, Computational Fluid Dynamics (CFD) has been established as an important complementary part and some times a significant alternative to Experimental and Theoretical Fluid Dynamics. Development of efficient computational algorithms for digital simulation of fluid flows has been an ongoing research effort in CFD. An accurate numerical simulation of compressible Euler equations, which are the gov-erning equations of high speed flows, is important in many engineering applications like designing of aerospace vehicles and their components. Due to nonlinear nature of governing equations, such flows admit solutions involving discontinuities like shock waves and contact discontinuities. Hence, it is nontrivial to capture all these essential features of the flows numerically. There are various numerical methods available in the literature, the popular ones among them being the Finite Volume Method (FVM), Finite Difference Method (FDM), Finite Element Method (FEM) and Spectral method. Kinetic theory based algorithms for solving Euler equations are quite popular in finite volume framework due to their ability to connect Boltzmann equation with Euler equations. In kinetic framework, instead of dealing directly with nonlinear partial differential equations one needs to deal with a simple linear partial differential equation. Recently, FEM has emerged as a significant alternative to FVM because it can handle complex geometries with ease and unlike in FVM, achieving higher order accuracy is easier. High speed flows governed by compressible Euler equations are hyperbolic partial differential equations which are characterized by preferred directions for information propagation. Such flows can not be solved using traditional FEM methods and hence, stabilized methods are typically introduced. Various stabilized finite element methods are available in the literature like Streamlined-Upwind Petrov Galerkin (SUPG) method, Galerkin-Least Squares (GLS) method, Taylor-Galerkin method, Characteristic Galerkin method and Discontinuous Galerkin Method. In this thesis a novel stabilized finite element method called as Kinetic Streamlined-Upwind Petrov Galerkin (KSUPG) method is formulated. Both explicit and implicit versions of KSUPG scheme are presented. Spectral stability analysis is done for explicit KSUPG scheme to obtain the stable time step. The advantage of proposed scheme is, unlike in SUPG scheme, diffusion vectors are obtained directly from weak KSUPG formulation. The expression for intrinsic time scale is directly obtained in KSUPG framework. The accuracy and robustness of the proposed scheme is demonstrated by solving various test cases for hyperbolic partial differential equations like Euler equations and inviscid Burgers equation. In the KSUPG scheme, diffusion terms involve computationally expensive error and exponential functions. To decrease the computational cost, two variants of KSUPG scheme, namely, Peculiar Velocity based KSUPG (PV-KSUPG) scheme and Circular distribution based KSUPG (C-KSUPG) scheme are formulated. The PV-KSUPG scheme is based on peculiar velocity based splitting which, upon taking moments, recovers a convection-pressure splitting type algorithm at the macroscopic level. Both explicit and implicit versions of PV-KSUPG scheme are presented. Unlike KSUPG and PV-KUPG schemes where Maxwellian distribution function is used, the C-KUSPG scheme uses a simpler circular distribution function instead of a Maxwellian distribution function. Apart from being computationally less expensive it is less diffusive than KSUPG scheme.

Micromagnetics is a continuum mechanics theory of magnetic materials widely used in industry and academia. In this thesis we describe a complete numerical method, with a number of novel components, for the computational solution of dynamic micromagnetic problems by solving the Landau-Lifshitz-Gilbert (LLG) equation. In particular we focus on the use of the implicit midpoint rule (IMR), a time integration scheme which conserves several important properties of the LLG equation. We use the finite element method for spatial discretisation, and use nodal quadrature schemes to retain the conservation properties of IMR despite the weak-form approach. We introduce a novel, generally-applicable adaptive time step selection algorithm for the IMR. The resulting scheme selects error-appropriate time steps for a variety of problems, including the semi-discretised LLG equation. We also show that it retains the conservation properties of the fixed step IMR for the LLG equation. We demonstrate how hybrid FEM/BEM magnetostatic calculations can be coupled to the LLG equation in a monolithic manner. This allows the coupled solver to maintain all properties of the standard time integration scheme, in particular stability properties and the energy conservation property of IMR. We also develop a preconditioned Krylov solver for the coupled system which can efficiently solve the monolithic system provided that an effective preconditioner for the LLG sub-problem is available. Finally we investigate the effect of the spatial discretisation on the comparative effectiveness of implicit and explicit time integration schemes (i.e. the stiffness). We find that explicit methods are more efficient for simple problems, but for the fine spatial discretisations required in a number of more complex cases implicit schemes become orders of magnitude more efficient.

Orientador: Lucas Catão de Freitas Ferreira / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Matemática Estatística e Computação Científica / Made available in DSpace on 2018-08-26T19:31:34Z (GMT). No. of bitstreams: 1 Moitinho_ValterVictorCerqueira_M.pdf: 1171427 bytes, checksum: 9207703fa3477244cb0e004220ae2827 (MD5) Previous issue date: 2015 / Resumo: Nesta dissertação, estudamos o problema de existência de soluções globais suaves para a equação quase-geostrófica em R2 (2DQG) com condições periódicas e no caso de valor crítico para a viscosidade fracionária. Esta equação aparece em estudos de alguns fluidos geofísicos que apresentam altas velocidades de rotação. De um ponto de vista dimensional, a equação é considerada um análogo em 2D das equações de Navier-Stokes em 3D. Primeiramente, estudamos a teoria de soluções fracas com dados iniciais em L2 via o método de Galerkin. Depois mostramos um princípio do máximo em espaços Lp e investigamos a regularidade de soluções para tempos pequenos e dados iniciais nos espaços de Sobolev Hs com s > 1. Finalmente, mostramos que a solução suave localmente no tempo de fato existe globalmente e é suave para todo tempo. Esta dissertação é baseada na Tese de Doutorado de Resnick [36] e no recente trabalho de Kiselev, Narazov e Volberg [33] / Abstract: In this dissertation, we study existence of smooth global solutions for the quasi-geostrophic equation in R2 (2DQG) with periodic conditions and critical value for the fractional viscosity. This equation appears in studies of some geophysical fluids that present high rotational speed. Dimensionally speaking, the equation is the analogue in 2D of the Navier-Stokes equations in 3D. First, we study the theory of weak solutions with initial data in L2 via the Galerkin method. After we show a maximum principle in Lp spaces and investigate regularity of solutions for small times and initial data in Sobolev spaces Hs with s > 1. Finally, we show that local-in-time smooth solutions are indeed global ones. This dissertation is based on the PhD thesis of Resnick [36] and recent work of Kiselev, Narazov e Volberg [33] / Mestrado / Matematica / Mestre em Matemática

Orientador: Lucas Catão de Freitas Ferreira / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Matemática Estatística e Computação Científica / Made available in DSpace on 2018-08-27T04:26:31Z (GMT). No. of bitstreams: 1 CastanedaCenturion_NestorFelipe_D.pdf: 1063498 bytes, checksum: bbaaad01ffead1389f469e88505aada5 (MD5) Previous issue date: 2015 / Resumo: Por apresentar basicamente fórmulas, o Resumo, na íntegra, poderá ser visualizado no texto completo da tese digital / Abstract: The complete Abstract is available with the full electronic document / Doutorado / Matematica / Doutor em Matemática

Orientador: Eduardo Cardoso de Abreu / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Matemática Estatística e Computação Científica / Made available in DSpace on 2018-08-27T06:42:03Z (GMT). No. of bitstreams: 1 Vieira_Jardel_M.pdf: 2696940 bytes, checksum: 9517d68c44824f91bd411caf141d2ef1 (MD5) Previous issue date: 2015 / Resumo: O foco desta dissertação de mestrado consiste em um estudo computacional de equações pseudo-parabólicas em mecânica dos fluidos e fenômenos de transporte de fluidos em meios porosos. Serão considerados problemas de valor de contorno e inicial associados a duas classes de modelos de equações de evolução pseudo-parabólicas: um modelo de advecção-difusão com termo pseudo-parabólico que exibe um certo caráter dispersivo e um outro modelo pseudo-parabólico "puro", i.e., sem a presença do termo de advecção. O primeiro modelo se relaciona com a modelagem física do fluxo de duas fases incompressíveis em dinâmica de fluidos em meios porosos, onde são considerados modelos de pressão capilar dinâmica, ou seja, em que os efeitos dinâmicos são também incluídos na diferença de pressão entre as fases fluidas. Uma discussão sobre a relevância física em aplicações e da importância matemática do sistema governante de equações para pressão capilar dinâmica em fenômenos de transporte de fluidos em meios porosos é também feita de modo a indicar algum suporte à escolha dos métodos estudados para aproximação numérica dos modelos consideradores. Além disso, um conjunto de experimentos numéricos é apresentado e discutido para avaliar a qualidade das soluções obtidas do estudo proposto, bem como para justificar variações dos métodos numéricos estudados. Especificamente, para o modelo pseudo-parabólico puro, os resultados são comparados com soluções analíticas para o caso linear. Para o modelo pseudo-parabólico com o termo de advecção, é avaliado se os resultados dos métodos numéricos empregados concordam qualitativamente com resultados da literatura / Abstract: The focus of this work consists of a computational study of pseudo-parabolic equations in fluid mechanics and transport phenomena in porous media. For concreteness, we consider initial-boundary value problems related to two classes of systems of evolution pseudo-parabolic equations: a advection-diffusion model, which in turn the pseudo-parabolic term exhibits a certain dispersive character, and a second of "purely" pseudo-parabolic nature, i.e., without the presence of advection term. The first model relates to the modeling of incompressible two-phase flow in porous media, which in turn takes into account the nonlinear dynamic capillary pressure effects, where the dynamic effects are also included into the pressure difference between the fluid phases. Further, a discussion of the physical and mathematical relevance of the governing system of equations for dynamic capillary pressure in porous media fluid transport phenomena is also made in order to drive the choice of the numerical approximations for the differential models under investigation. Moreover, a set of numerical experiments are presented and discussed to address the quality of the obtained solutions proposed study, as well as to justify variations of the numerical methods studied. Specifically, to the purely pseudo-parabolic model, the results are compared along with analytical solutions with respect to a linear case. On the other hand, to the nonlinear pseudo-parabolic model with advection term, it is performed numerical experiments in order to account the correct qualitative behavior of the computed solutions against the available results discussed in the recent literature / Mestrado / Matematica Aplicada / Mestre em Matemática Aplicada