Sudden cardiac death following cardiac arrest is a major killer in the industrialised world. The leading cause of sudden cardiac death are disturbances in the normal electrical activation of cardiac tissue, known as cardiac arrhythmia, which severely compromise the ability of the heart to fulfill the body's demand of oxygen. Ventricular fibrillation (VF) is the most deadly form of cardiac arrhythmia. Furthermore, electrical defibrillation through the application of strong electric shocks to the heart is the only effective therapy against VF. Over the past decades, a large body of research has dealt with the study of the mechanisms underpinning the success or failure of defibrillation shocks. The main mechanism of shock failure involves shocks terminating VF but leaving the appropriate electrical substrate for new VF episodes to rapidly follow (i.e. shock-induced arrhythmogenesis). A large number of models have been developed for the in silico study of shock-induced arrhythmogenesis, ranging from single cell models to three-dimensional ventricular models of small mammalian species. However, no extrapolation of the results obtained in the aforementioned studies has been done in human models of ventricular electrophysiology. The main reason is the large computational requirements associated with the solution of the bidomain equations of cardiac electrophysiology over large anatomically-accurate geometrical models including representation of fibre orientation and transmembrane kinetics. In this Thesis we develop simulation technology for the study of cardiac defibrillation in the human heart in the framework of the open source simulation environment Chaste. The advances include the development of novel computational and numerical techniques for the solution of the bidomain equations in large-scale high performance computing resources. More specifically, we have considered the implementation of effective domain decomposition, the development of new numerical techniques for the reduction of communication in Chaste's finite element method (FEM) solver, and the development of mesh-independent preconditioners for the solution of the linear system arising from the FEM discretisation of the bidomain equations. The developments presented in this Thesis have brought Chaste to the level of performance and functionality required to perform bidomain simulations with large three-dimensional cardiac geometries made of tens of millions of nodes and including accurate representation of fibre orientation and membrane kinetics. This advances have enabled the in silico study of shock-induced arrhythmogenesis for the first time in the human heart, therefore bridging an important gap in the field of cardiac defibrillation research.

The work presented in this thesis aims to provide various tools to be used during design process to make maximum use of the increasing availability of accurate engine blade measurement data for high fidelity fluid mechanic simulations at a reasonable computational expense. A new method for uncertainty propagation for geometric error has been proposed for fluid mechanics codes using adjoint error correction. Inexpensive Monte Carlo (IMC) method targets small uncertainties and provides complete probability distribution for the objective function at a significantly reduced computational cost. A brief literature survey of the existing methods is followed by the formulation of IMC. An example algebraic model is used to demonstrate the IMC method. The IMC method is extended to fluid mechanic applications using Principal Component Analysis (PCA) for reduced order modelling. Implementation details for the IMC method are discussed using an example airfoil code. Finally, the IMC method has been implemented and validated for an industrial fluid mechanic code HYDRA. A consistent methodology has been developed for the automatic generation of the linear and adjoint codes by selective use of automatic differentiation (AD) technique. The method has the advantage of keeping the linear and the adjoint codes in-sync with the changes in the underlying nonlinear fluid mechanic solver. The use of various consistency checks have been demonstrated to ease the development and maintenance process of the linear and the adjoint codes. The use of AD has been extended for the calculation of the complete Hessian using forward-on-forward approach. The complete mathematical formulation for Hessian calculation using the linear and the adjoint solutions has been outlined for fluid mechanic solvers. An efficient implementation for the Hessian calculation is demonstrated using the airfoil code. A new application of the Independent Component Analysis (ICA) is proposed for manufacturing uncertainty source identification. The mathematical formulation is outlined followed by an example application of ICA for artificially generated uncertainty for the NACA0012 airfoil.

In this thesis, two algorithms are introduced for use in ultrasound elastography. Ultrasound elastography is a technique developed in the last 20 years by which anomalous regions in soft tissue are located and diagnosed without the need for biopsy. Due to this, the relativity cheap cost of ultrasound imaging and the high level of accuracy in the methods, ultrasound elastography methods have shown great potential for the diagnosis of cancer in soft tissues. The algorithms introduced in this thesis represent an advance in this field. The first algorithm is a two-step iteration procedure consisting of two minimization problems - displacement estimation and elastic parameter calculation that allow for diagnosis of any anomalous regions within soft tissue. The algorithm represents an improvement on existing methods in several ways. A weighting factor is introduced for each different point in the tissue dependent on the confidence in the accuracy of the data at that point, an exponential substitution is made for the elasticity modulus, an adjoint method is used for efficient calculation of the gradient vector and a total variation regularization technique is used. Most importantly, an adaptive mesh refinement strategy is introduced that allows highly efficient calculation of the elasticity distribution of the tissue though using a number of degrees of freedom several orders lower than methods that use a uniform mesh refinement strategy. Results are presented that show the algorithm is robust even in the presence of significant noise and that it can locate a tumour of 4mm in diameter within a 5cm square region of tissue. Also, the algorithm is extended into 3 dimensions and results are presented that show that it can calculate a 3 dimensional elasticity distribution efficiently. This extension into 3-d is a significant advance in the field. The second algorithm is a one-step algorithm that seeks to combine the two problems of elasticity distribution and displacement calculation into one. As in the two-step algorithm, a weighting factor, exponential substitution for the elasticity parameter, adjoint method for calculation of the gradient vector, total variation regularization and adaptive mesh refinement strategy are incorporated. Results are presented that show that this original approach can locate tumours of varying sizes and shapes in the presence of varying levels of added artificial noise and that it can determine the presence of a tumour in images taken from breast tissue in vivo.

Motivated by experiments on titanium alloys of Petrinic et al. (2006), which show the formation of cracks through the growth and coalescence of voids in ductile fracture, we consider the problem of formulating a variational model in nonlinear elasticity compatible both with cavitation and the appearance of discontinuities across two-dimensional surfaces. As in the model for cavitation of Müller and Spector (1995) we address this problem, which is connected to the sequential weak continuity of the determinant of the deformation gradient in spaces of functions having low regularity, by means of adding an appropriate surface energy term to the elastic energy. Based upon considerations of invertibility, we derive an expression for the surface energy that admits a physical and a geometrical interpretation, and that allows for the formulation of a model with better analytical properties. We obtain, in particular, important regularity results for the inverses of deformations, as well as the weak continuity of the determinants and the existence of minimizers. We show, further, that the creation of surface can be modeled by carefully analyzing the jump set of the inverses, and we point out some connections between the analysis of cavitation and fracture, the theory of SBV functions, and the theory of Cartesian currents of Giaquinta, Modica, and Soucek. In addition to the above, we extend previous work of Sivaloganathan, Spector and Tilakraj (2006) on the approximation of minimizers for the problem of cavitation with a constraint in the number of flaw points, and present some numerical results for this problem.

L'objectif de ce travail de thèse est de développer un modèle mathématique pour l'étude et la compréhension de la dynamique des populations d'un insecte ravageur, l'Eudémis de la vigne (Lobesia botrana Den. & Schiff.), dans son écosystème. Le modèle proposé est un système d'équations aux dérivées partielles de type hyperbolique qui décrit les variations numériques au cours du temps de la population en fonction des stades de développement, du sexe des individus et des conditions environnementales. La ressource alimentaire, la température, l'humidité et la prédation sont les principaux facteurs environnementaux du modèle expliquant les fluctuations du nombre d'individus au cours du temps. Les différences de développement qui existent dans une cohorte d'Eudémis sont aussi modélisées pour affiner les prédictions du modèle. A partir de données expérimentales obtenues par les entomologistes de l'INRA, situé à Bordeaux, les paramètres du modèle sont estimés. Ce modèle ainsi ajusté nous permet alors d’étudier quelques aspects biologiques et écologiques de l’insecte comme par exemple l'impact de scénarios climatiques sur la ponte des femelles ou sur la dynamique d’attaque de la vigne par les jeunes larves. Les analyses mathématique et numérique du modèle mathématique et des problèmes d'estimation des paramètres sont développées dans cette thèse. / The objective of the thesis is to develop a mathematical model for studying the population dynamics of the European grapevine moth (Lobesia botrana Den. & Schiff.) in its ecosystem. The model proposed is a system of hyperbolic equations that describe the numerical variations in time of the population with respect to developmental stage, the gender and the environmental conditions. The food, the temperature, the humidity and the predation are the main environmental factors of the model that explain the fluctuations of the population in time. The differences in growth inside a cohort are modeled in order to precise the model simulations. We use experimental data obtained by entomologists of the National Research Institut of Agronomy to estimate the parameters of the model. This ajusted model allows us to study some biological and ecological aspects of this pest like for example the impact of climate change on the female laying or on the young larvae dynamic, main actors in the depredation of the Vine. The mathematical analysis and the numerical analysis of the mathematical model and of the parameters estimation problems are presented in this thesis.

Ce travail présente quelques contributions mathématiques et numériques à la modélisation des fluides à l'échelle nanométrique. On considère deux niveaux de modélisation. Au premier niveau,une description atomique est adoptée. On s'intéresse aux méthodes permettant de calculer la viscosité de cisaillement d'un fluide à partir de cette description microscopique. On étudie en particulier les propriétés mathématiques de la dynamique de Langevin hors d'équilibre permet-tant de calculer la viscosité. Le deuxième niveau de description se situe à l'échelle du continu et l'on considère une classe de modèles pour les électrolytes à l'équilibre incorporant d'une part la présence d'un confinement avec des parois chargées et d'autre part des effets de non-idéalité dus aux corrélations électrostatiques entre les ions et au phénomène d'exclusion stérique. Dans un premier temps, on étudie mathématiquement le problème de minimisation de l'énergie libre dans le cas où celle ci reste convexe (non-idéalité modérée). Puis, on considère le cas non convexe (forte non-idéalité) conduisant à une séparation de phase / This work presents some contributions to the mathematical and numerical modelling of fluids at nanometric scales. We are interested in two levels of modelling. The first level consists in an atomic description. We consider the problem of computing the shear viscosity of a fluid from a microscopic description. More precisely, we study the mathematical properties of the nonequilibrium Langevin dynamics allowing to compute the shear viscosity. The second level of description is a continuous description, and we consider a class of continuous models for equilibrium electrolytes, which incorporate on the one hand a confinement by charged solid objects and on the other hand non-ideality effects stemming from electrostatic correlations and steric exclusion phenomena due to the excluded volume effects. First, we perform the mathematical analysis of the case where the free energy is a convex function (mild non-ideality). Second, we consider numerically the case where the free energy is a non convex function (strong non-ideality) leading in particular to phase separation

La modélisation du trafic routier dans un réseau dense et de grande étendue nécessite un grand nombre de données, si bien qu'une modélisation par arcs est impossible en pratique. Pour simplifier le problème, une idée est d'agréger les tronçons du réseau en un continuum sur lequel le trafic routier s'écoule comme un fluide surfacique. Cette modélisation est qualifiée de bidimensionnelle. Même si la structure géométrique détaillée du réseau est perdue, une telle modélisation évite la description très fine du trafic sur un réseau dans lequel les points de mesure ne sont pas en nombre suffisant pour permettre une évaluation exhaustive de l'état du trafic. Une série de travaux commencée dans les années 1980 a permis de dégager quelques concepts importants. Cependant, ces travaux n'ont pas résolu les problèmes de modélisation fondamentaux : comment déduire et modéliser des comportements globaux à partir de comportements locaux (flux sur un axe, interactions aux intersections) ? Deux modèles bidimensionnels de trafic sont développés. Le premier modèle est statique. Le trafic s'écoule dans des directions de propagation privilégiées (orthogonales). Le modèle prend en compte l'équilibre entre l'offre de déplacement du réseau et une demande élastique de déplacement des usagers. Les principales sorties sont constituées en chaque point et pour chaque destination par les débits directionnels et les coûts de déplacement. Le deuxième modèle est dynamique. L'écoulement du trafic est décrit au niveau de cellules élémentaires du réseau dans lesquelles on définit les notions d'offre et de demande. À partir d'une loi comportementale obtenue sur un réseau discret, on écrit l'équation dynamique de conservation du trafic routier en tout point d'un réseau anisotrope / Traffic road modelling in the dense network of a wide area needs a large amount of data. It renders a keen modelling unmanageable in practice. To simplify the problem, an idea is to aggregate the network links as continuous medium where traffic road flows as a fluid on a surface. This modelling is called two-dimensional. Even if the detailed geometric structure of the network is lost, such a modelling avoids the traffic keen description on a network where measure points are not numerous enough to allow an exhaustive evaluation of traffic state. A series of articles started in the 80's have highlighted relevant concepts. Nevertheless, these previous works have not solved fundamental modelling issues: how to deduce and model global behaviours basing on local behaviours (flow on an axe, interactions at intersections). Two models are developed. The first model is static. Traffic road flows on privileged directions (orthogonal). The model takes into account the balance between the network trip supply and the users' elastic trip demand. The principal outputs are, for each point of the network and each destination, the directional flows and the trip costs. The second model is dynamical. The description of traffic flows stands at the level of elementary traffic cells, where concepts of supply and demand are defined. With a behaviour law deduced from a discrete network, we establish the conservation dynamic equation of road traffic at each point of an anisotropic network

Le chapitre 1 introduit les modèles et donne les principaux résultats obtenus. Dans le chapitre 2, on présente des simulations numériques d'un modèle macroscopique en deux dimensions. La méthode de discrétisation par éléments finis utilisée est décrite. Pour le cas test de l'écoulement autour d'un cylindre, les phénomènes en jeu dans les fluides vieillissants sont observés. Le chapitre 3 concerne l'étude mathématique de la version unidimensionnelle du système d'équations aux dérivées partielles utilisé pour les simulations. On montre que le problème est bien posé et on examine le comportement en temps long de la solution. Dans le dernier chapitre, des équations macroscopiques sont dérivées à partir d'une équation mésoscopique. L'analyse mathématique de cette équation mésoscopique est également menée / This thesis is devoted to the modelling, the mathematical analysis and the simulation of non-Newtonian fluids. Some fluids in an intermediate liquid-solid phase are particularly considered: aging fluids. Modelling scales are macroscopic and mesoscopic. In Chapter 1, we introduce the models and give the main results obtained. In Chapter 2, we present numerical simulations of a macroscopic two-dimensional model. The finite element method used for discretization is described. For the flow past a cylinder test-case, phenomena at play in aging fluids are observed. The Chapter 3 contains a mathematical analysis of the one-dimensional version of the system of partial differential equations used for the simulations. We show well-posedness and investigate the longtime behaviour of the solution. In the last chapter, macroscopic equations are derived from a mesoscopic equation. The mathematical analysis of this mesoscopic equation is also carried out

Ce travail a pour but de proposer des outils visant `a comparer des résultats exp´erimentaux avec des modèles pour la dispersion de traceur en milieu poreux, dans le cadre de la dispersion anormale.Le “Mobile Immobile Model” (MIM) a été à l’origine d’importants progrès dans la description du transport en milieu poreux, surtout dans les milieux naturels. Ce modèle généralise l’quation d’advection-dispersion (ADE) e nsupposant que les particules de fluide, comme de solut´e, peuvent ˆetre immo-bilis´ees (en relation avec la matrice solide) puis relˆachées, le piégeage et le relargage suivant de plus une cin´etique d’ordre un. Récemment, une version stochastique de ce modèle a ´eté proposée. Malgré de nombreux succès pendant plus de trois décades, le MIM reste incapable de repr´esenter l’´evolutionde la concentration d’un traceur dans certains milieux poreux insaturés. Eneffet, on observe souvent que la concentration peut d´ecroˆıtre comme unepuissance du temps, en particulier aux grands temps. Ceci est incompatible avec la version originale du MIM. En supposant une cinétique de piégeage-relargage diff´erente, certains auteurs ont propos´e une version fractionnaire,le “fractal MIM” (fMIM). C’est une classe d’´equations aux d´eriv´ees par-tielles (e.d.p.) qui ont la particularit´e de contenir un op´erateur int´egral li´e`a la variable temps. Les solutions de cette classe d’e.d.p. se comportentasymptotiquement comme des puissances du temps, comme d’ailleurs cellesde l’´equation de Fokker-Planck fractionnaire (FFPE). Notre travail fait partie d’un projet incluant des exp´eriences de tra¸cageet de vélocimétrie par R´esistance Magn´etique Nucl´eaire (RMN) en milieuporeux insatur´e. Comme le MIM, le fMIM fait partie des mod`eles ser-vant `a interpréter de telles exp´eriences. Sa version “e.d.p.” est adapt´eeaux grandeurs mesur´ees lors d’exp´eriences de tra¸cage, mais est peu utile pour la vélocimétrie RMN. En effet, cette technique mesure la statistiquedes d´eplacements des mol´ecules excit´ees, entre deux instants fixés. Plus précisément, elle mesure la fonction caractéristique (transform´ee de Fourier) de ces d´eplacements. Notre travail propose un outil d’analyse pour ces expériences: il s’agit d’une expression exacte de la fonction caract´eristiquedes d´eplacements de la version stochastique du mod`ele fMIM, sans oublier les MIM et FFPE. Ces processus sont obtenus `a partir du mouvement Brown-ien (plus un terme convectif) par des changement de temps aléatoires. Ondit aussi que ces processus sont des mouvement Browniens, subordonnéspar des changements de temps qui sont eux-mˆeme les inverses de processusde L´evy non d´ecroissants (les subordinateurs). Les subordinateurs associés aux modèles fMIM et FFPE sont des processus stables, les subordinateursassoci´es au MIM sont des processus de Poisson composites. Des résultatsexp´erimenatux tr`es r´ecents on sugg´er´e d’´elargir ceci `a des vols de L´evy (plusg´en´eraux que le mouvement Brownien) subordonnés aussi.Le lien entre les e.d.p. fractionnaires et les mod`eles stochastiques pourla sous-diffusion a fait l’objet de nombreux travaux. Nous contribuons `ad´etailler ce lien en faisant apparaˆıtre les flux de solut´e, en insistant sur une situation peu ´etudiée: nous examinons le cas o`u la cinétique de piégeage-relargage n’est pas la mˆeme dans tout le milieu. En supposant deux cinétiques diff´erentes dans deux sous-domaines, nous obtenons une version du fMIMavec un opérateur intégro-diff´erentiel li´e au temps, mais dépendant de la position.Ces r´esultats sont obtenus au moyen de raisonnements, et sont illustrés par des simulations utilisant la discrétisation d’intégrales fractionnaires etd’e.d.p. ainsi que la méthode de Monte Carlo. Ces simulations sont en quelque sorte des preuves numériques. Les outils sur lesquels elles s’appuient sont présentés aussi. / We propose tools for to compare experimental data and models for anomalousdispersion in porous media.The “Mobile Immobile Model” (MIM) significantly improved the descrip-tion of mass transport in natural porous media. This model generalizes theadvection-dispersion equation (ADE) by assuming that fluid and solute parti-cles can be found in mobile on immobile states, exchanging matter accordingto first order kinetics. Moreover, it has a stochastic version. Nevertheless,the original MIM does not represent the power-law decrease of some break-through curves observed in some media, better described by a fractionalversion, the “fractal MIM” (fMIM) which assumes a different kinetics. Theacronym “fMIM” denotes partial differential equations (p.d.e.) involving afractional integral with respect to time, having solutions falling-off as powerof times, asymptotically. It keeps in similarity with the fractional Fokker-Planck equation (FFPE). As this equation, the fMIM describes the evolutionof the probability density function of stochastic processes, namely Brownianmotion sujected to a time change that is the hitting time of a stable sub-ordinator, strictly stable or not, according FFPE or fMIM is considered.Using probabilistic arguments and numerical simulation, we extend this re-sult to the case when the transport parameters and the time scales of thetime change vary in space. P.d.es are well suited for comparing with tracer tests data. Yet, they arenot very useful to discuss signals recorded by pulsed field gradient (PFG)nuclear magnetic resonance (NMR), a technique which measures the char-acteristic function (Fourier transform) of molecular displacements betweentwo fixed instants. For to process such data, we derive an expression of thecharacteristic function of the displacements of Brownian motions subordi-nated by the hitting times of stable subordinators, i.e. of processes whosedensity satisfies FFPE of fMIM. We also consider time changes that are hit-ting times of composite Poisson processes (CPP), which correspond to theoriginal version of the MIM.

In this thesis, we study the existence, uniqueness, and regularity of systems of degenerate linear stochastic integro-differential equations (SIDEs) of parabolic type with adapted coefficients in the whole space. We also investigate explicit and implicit finite difference schemes for SIDEs with non-degenerate diffusion. The class of equations we consider arise in non-linear filtering of semimartingales with jumps. In Chapter 2, we derive moment estimates and a strong limit theorem for space inverses of stochastic flows generated by Lévy driven stochastic differential equations (SDEs) with adapted coefficients in weighted Hölder norms using the Sobolev embedding theorem and the change of variable formula. As an application of some basic properties of flows of Weiner driven SDEs, we prove the existence and uniqueness of classical solutions of linear parabolic second order stochastic partial differential equations (SPDEs) by partitioning the time interval and passing to the limit. The methods we use allow us to improve on previously known results in the continuous case and to derive new ones in the jump case. Chapter 3 is dedicated to the proof of existence and uniqueness of classical solutions of degenerate SIDEs using the method of stochastic characteristics. More precisely, we use Feynman-Kac transformations, conditioning, and the interlacing of space inverses of stochastic flows generated by SDEs with jumps to construct solutions. In Chapter 4, we prove the existence and uniqueness of solutions of degenerate linear stochastic evolution equations driven by jump processes in a Hilbert scale using the variational framework of stochastic evolution equations and the method of vanishing viscosity. As an application, we establish the existence and uniqueness of solutions of degenerate linear stochastic integro-differential equations in the L2-Sobolev scale. Finite difference schemes for non-degenerate SIDEs are considered in Chapter 5. Specifically, we study the rate of convergence of an explicit and an implicit-explicit finite difference scheme for linear SIDEs and show that the rate is of order one in space and order one-half in time.