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Single ventricle heart defects, where systemic and pulmonary venous returns mix in the single functional ventricle, represent the most complex form of congenital heart defect, affecting 2 babies per 1000 live births. Surgical repairs, termed "Fontan Repairs," reroute the systemic venous return directly to the pulmonary arteries, thus preventing venous return mixing and restoring normal oxygenation saturation levels. Unfortunately, these repairs are only palliative and Fontan patients are subjected to a multitude of chronic complications. It has long been suspected that hemodynamics play a role in determining patient outcome. However, the number of anatomical and functional variables that come into play and the inability to conduct large scale clinical evaluations, due to too small a patient population, has hindered decisive progress and there is still not a good understanding of the optimal care strategies on a patient-by-patient basis. Over the past decades, image-guided computational fluid dynamics (CFD) has arisen as an attractive option to accurately model such complex biomedical phenomena, providing a high degree of freedom regarding the geometry and flow conditions to be simulated, and carrying the potential to be automated for large sample size studies. Despite these theoretical advantages, few CFD studies have been able to account for the complexity of patient-specific anatomies and in vivo pulsatile flows. In this thesis, we develop an unstructured Cartesian immersed-boundary flow solver allowing for high resolution, time-accurate simulations in arbitrarily complex geometries, at low computational costs. Combining the proposed and validated CFD solver with an interactive virtual-surgery environment, we present an image-based surgical planning framework that: a) allows for in depth analysis of the pre-operative in vivo hemodynamics; b) enables surgeons to determine the optimum surgical scenario prior to the operation. This framework is first applied to retrospectively investigate the in vivo pulsatile hemodynamics of different Fontan repair techniques, and quantitatively compare their efficiency. We then report the prospective surgical planning investigations conducted for six failing Fontan patients with an interrupted inferior vena cava and azygous continuation. In addition to a direct benefit to the patients under consideration, the knowledge derived from these surgical planning studies will also have a larger impact for the clinical management of Fontan patients as they shed light onto the impact of caval offset, vessel flaring and other design parameters upon the Fontan hemodynamics depending on the underlying patient anatomy. These results provide useful surgical guidelines for each anatomical template, which could benefit the global surgical community, including centers that do not have access to patient-specific surgical planning interfaces.

La méthode de projection et l'approche variationnelle de Sasaki sont deux techniques permettant d'obtenir un champ vectoriel à divergence nulle à partir d'un champ initial quelconque. Pour une vitesse d'un vent en haute altitude, un champ de vitesse sur une grille décalée est généré au-dessus d'une topographie donnée par une fonction analytique. L'approche cartésienne nommée Embedded Boundary Method est utilisée pour résoudre une équation de Poisson découlant de la projection sur un domaine irrégulier avec des conditions aux limites mixtes. La solution obtenue permet de corriger le champ initial afin d'obtenir un champ respectant la loi de conservation de la masse et prenant également en compte les effets dûs à la géométrie du terrain. Le champ de vitesse ainsi généré permettra de propager un feu de forêt sur la topographie à l'aide de la méthode iso-niveaux. L'algorithme est décrit pour le cas en deux et trois dimensions et des tests de convergence sont effectués. / The Projection method and Sasaki's variational technique are two methods allowing one to extract a divergence-free vector field from any vector field. From a high altitude wind speed, a velocity field is generated on a staggered grid over a topography given by an analytical function. The Cartesian grid Embedded Boundary method is used for solving a Poisson equation, obtained from the projection, on an irregular domain with mixed boundary conditions. The solution of this equation gives the correction for the initial velocity field to make it such that it satisfies the conservation of mass and takes into account the effects of the terrain. The incompressible velocity field will be used to spread a wildfire over the topography with the Level Set Method. The algorithm is described for the two and three dimensional cases and convergence tests are done.

Fluid-structure interaction (FSI), occurrent in many areas of engineering and in the natural world, has been the subject of much research using a wide range of modelling strategies. However, problems with high levels of structural deformation are difficult to resolve and this is particularly the case for biomedical flows. A Lagrangian flow model coupled with a robust model for nonlinear structural mechanics seems a natural candidate since large distortion of the computational geometry is expected. Smoothed particle Hydrodynamics (SPH) has been widely applied for nonlinear interface modelling and this approach is investigated here. Biomedical applications often involve thin flexible structures and a consistent approach for modelling the interaction of fluids with such structures is also required. The Lagrangian weakly compressible SPH method is investigated in its recent delta-SPH form utilising inter-particle density fluxes to improve stability. Particle shifting is also used to maintain particle distributions sufficiently close to uniform to enable stable computation. The use of artificial viscosity is avoided since it introduces unphysical dissipation. First, solid boundary conditions are studied using a channel flow test. Results show that when the particle distribution is allowed to evolve naturally instabilities are observed and deviations are noted from the expected order of accuracy. A parallel development in the SPH group at Manchester has considered SPH in Eulerian form (for different applications). The Eulerian form is applied to the channel flow test resulting in improved accuracy and stability due to the maintenance of a uniform particle distribution. A higher-order accurate boundary model is developed and applied for the Eulerian SPH tests and third-order convergence is achieved. The well documented case of flow past a thin plate is then considered. The immersed boundary method (IBM) is now a natural candidate for the solid boundary. Again, it quickly becomes apparent that the Lagrangian SPH form has limitations in terms of numerical noise arising from anisotropic particle distributions. This corrupts the predicted flow structures for moderate Reynolds numbers (O(102)). Eulerian weakly compressible SPH is applied to the problem with the IBM and is found to give accurate and convergent results without any numerical stability problems (given the time step limitation defined by the Courant condition). Modelling highly flexible structures using the discrete element model is investigated where granular structures are represented as bonded particles. A novel vector-based form (the V-Model) is identified as an attractive approach and developed further for application to solid structures. This is shown to give accurate results for quasi-static and dynamic structural deformation tests. The V-model is applied to the decay of structural vibration in a still fluid modelled using Eulerian SPH with no artificial stabilising techniques. Again, results are in good agreement with predictions of other numerical models. A more demanding case representative of pulsatile flow through a deep leg vein valve is also modelled using the same form of Eulerian SPH. The results are free of numerical noise and complex FSI features are captured such as vortex shedding and non-linear structural deflection. Reasonable agreement is achieved with direct in-vivo observations despite the simplified two-dimensional numerical geometry. A robust, accurate and convergent method has thus been developed, at present for laminar two-dimensional low Reynolds number flows but this may be generalised. In summary a novel robust and convergent FSI model has been established based on Eulerian SPH coupled to the V-Model for large structural deformation. While these developments are in two dimensions the method is readily extendible to three-dimensional, laminar and turbulent flows for a wide range of applications in engineering and the natural world.

L'objectif de cette thèse est d'améliorer la compréhension des phénomènes jouant un rôle dans la mesure effectuée dans un analyseur sanguin, en particulier le comptage et la mesure de volumétrie d'une population de globules rouges reposant sur l'effet Coulter. Des simulations numériques sont effectuées dans le but de prédire la dynamique des globules rouges dans les zones de mesure et pour reproduire la mesure électrique associée, servant au comptage et à la volumétrie des cellules. Ces simulations sont effectuées à l'intérieur de configurations industrielles d'analyseur sanguin, en utilisant un outil numérique développé à l'IMAG, le solveur YALES2BIO. En utilisant la méthode des frontières immergées avec suivi de front, un modèle de particule déformable est introduit, celui-ci prend en compte le contraste de viscosité ainsi que les effets mécaniques de la courbure et de l'élasticité sur la membrane. Le solveur est validé grâce à de nombreux cas tests parcourant différents régimes et effets physiques. L'écoulement fluide dans cette géométrie d'analyseur sanguin est caractérisée par un fort gradient de vitesse axial dans la direction de l'écoulement, impliquant la présence d'un écoulement extensionnel au niveau du micro-orifice, là où a lieu la mesure. La dynamique des globules rouges est étudiée par des simulations numériques pour différentes conditions initiales, telles que sa position ou son orientation. Il est observé que les globules rouges vont se réorienter selon l'axe principal de l'analyseur sanguin dans tous les cas. Pour comprendre le phénomène, des modèles analytiques sont adaptés au cas des écoulements extensionnels et reproduisent correctement les tendances de réorientation.Cette thèse présente également la reproduction de la mesure électrique utilisée pour le comptage et la mesure de la distribution des volumes de globules rouges. De nombreuses simulations de la dynamique des globules rouges sont effectuées et utilisées pour générer l'impulsion électrique correspondant au passage du globule rouge dans le micro-orifice. Les amplitudes d'impulsions électriques résultantes permettent la caractérisation de la réponse électrique en fonction des paramètres initiaux de la simulation par une approche statistique. Un algorithme de Monte-Carlo est utilisé pour la quantification des erreurs de mesure liées à l'orientation et la position des globules rouges dans le micro-orifice. Ceci permet la génération d'une distribution de volume mesurée pour une population de globules rouges bien définie et la caractérisation des erreurs de mesure associées. / The aim of this thesis is to improve the understanding of the phenomena involved in the measurement performed in a blood analyzer, namely the counting and sizing of red blood cells based on the Coulter effect. Numerical simulations are performed to predict the dynamics of red blood cells in the measurement regions, and to reproduce the associated electrical measurement used to count and size the cells. These numerical simulations are performed in industrial configurations using a numerical tool developed at IMAG, the YALES2BIO solver. Using the Front-Tracking Immersed Boundary Method, a deformable particle model for the red blood cell is introduced which takes the viscosity contrast as well as the mechanical effects of the curvature and elasticity on the membrane into account. The solver is validated against several test cases spreading over a large range of regimes and physical effects.The velocity field in the blood analyzer geometry is found to consist of an intense axial velocity gradient in the direction of the flow, resulting in a extensional flow at the micro-orifice, where the measurement is performed. The dynamics of the red blood cells is studied with numerical simulations with different initial conditions, such as its position or orientation. They are found to reorient along the main axis of the blood analyzer in all cases. In order to understand the phenomenon, analytical models are adapted to the case of extensional flows and are found to reproduce the observed trends.This thesis also presents the reproduction of the electrical measurement used to count red blood cells and measure their volume distribution. Numerous dynamics simulations are performed and used to generate the electrical pulse corresponding to the passage of a red blood cell inside the micro-orifice. The resulting electrical pulse amplitudes are used to characterize the electrical response depending on the initial parameters of the simulation by means of a statistical approach. A Monte-Carlo algorithm helps quantifying the errors on the measurement of cell depending on its orientation and position inside the micro-orifice. This allows the generation of a measured volume distribution of a well defined red blood cell population and the characterization of the associated measurement errors.

Cette thèse traite plusieurs aspects scientifiques inhérents à la simulation numérique de problèmes d'interaction fluide-structure impliquant de fines membranes déformables. Deux cas spécifiques relatifs à la biomécanique cardiovasculaire sont considérés : l'interaction de l'écoulement sanguin avec la valve aortique (qui se produit à l'échelle macroscopique), et l'interaction de la membrane des globules rouges avec ses fluides interne et externe (qui se produit à l'échelle microscopique). Dans les deux cas, le couplage fluide-structure est géré par l'intermédiaire d'un formalisme de frontières immergées, en représentant la membrane par un maillage Lagrangien se mouvant au travers d'un maillage fluide Eulérien. Lorsque l'on traite la dynamique des globules rouges, la membrane est considérée comme étant une structure sans masse et infiniment fine. La première question à laquelle on s'intéresse dans cette thèse est la manière de modéliser la microstructure complexe de la membrane des globules rouges. Un moyen possible pour caractériser un modèle de membrane adapté est de simuler l'expérience des pinces optiques, qui consiste en une configuration expérimentale bien contrôlée qui permet d'étudier la mécanique individuelle d'un globule rouge isolé dans une large gamme de déformations. Plusieurs modèles pertinents sont identifiés, mais les caractéristiques de déformation mesurées durant l'expérience des pinces optiques se révèlent n'être pas assez sélectives pour être utilisées dans un contexte de validation. Des mesures de déformation additionnelles sont proposées, qui pourraient permettre une meilleure caractérisation de la mécanique de la membrane des globules rouges. En ce qui concerne les configurations macroscopiques, une méthode numérique innovante est proposée afin de gérer des simulations numériques de membranes 3D continues, en conservant le formalisme de frontières immergées. Dans cette méthode, appelée méthode des frontières immergées épaisses, la membrane a une épaisseur finie. La précision et la robustesse de la méthode sont démontrées par l'intermédiaire d'une variété de cas tests bien choisis. La méthode proposée est ensuite appliquée à un problème d'interaction fluide-structure réaliste, à savoir l'interaction d'un écoulement (sanguin) pulsé avec une valve aortique biomimétique. Une étude combinée expérimentale et numérique est menée, montrant que la méthode est capable de capturer la dynamique globale de la valve, ainsi que les principales caractéristiques de l'écoulement en aval de la valve. Tous les développements ont été effectués dans le solveur YALES2BIO (http://www.math.univ-montp2.fr/~yales2bio/) développé à l'IMAG, qui est donc disponible pour toutes autres améliorations, validations et études applicatives. / This thesis deals with several scientific aspects inherent to the numerical simulation of fluid-structure interaction problems involving thin deformable membranes. Two specific cases relevant to cardiovascular biomechanics are considered: the interaction of the blood flow with the aortic valve (which occurs at the macroscopic scale), and the interaction of the red blood cells membrane with its inner and outer fluids (which occurs at the microscopic scale). In both cases, the fluid-structure interaction coupling is handled using an immersed boundary formalism, representing the membrane by a Lagrangian mesh moving through an Eulerian fluid mesh.When dealing with red blood cells dynamics, the membrane is considered to be an infinitely thin and massless structure. The first question which is addressed in the present thesis work is how to model the complex microstructure of the red blood cells membrane. A possible way to characterize a suitable membrane model is to simulate the optical tweezers experiment, which is a well-controlled experimental configuration enabling to study the individual mechanics of an isolated red blood cell in a large range of deformation. Some relevant membrane models are identified, but the deformation characteristics measured during the optical tweezers experiment reveal to be not selective enough to be used in a validation context. Additional deformation measurements are proposed, which could allow a better characterization of the red blood cell membrane mechanics.Regarding the macroscopic configurations, an innovative numerical method is proposed to handle numerical simulations of 3D continuum membranes, still within the immersed boundary formalism. In this method, called immersed thick boundary method, the membrane has a finite thickness. The accuracy and robustness of the method are demonstrated through a variety of well-chosen test cases. Then, the proposed method is applied to a realistic fluid-structure interaction problem, namely the interaction of a pulsatile (blood) flow with a biomimetic aortic valve. A combined experimental and numerical study is led, showing that the method is able to capture the global dynamics of the valve, as well as the main features of the flow downstream of the valve.All the developments were performed within the YALES2BIO solver (http://www.math.univ-montp2.fr/~yales2bio/) developed at IMAG, which is thus available for further improvements, validations and applicative studies.

L’objectif de cette thèse est de répondre au besoin d’accélérer la restitution des résultats de calcul d’un code CFD pour la simulation d’écoulements hydrodynamiques quasi-incompressibles. Ce code présente l’originalité de résoudre explicitement les équations de Navier-Stokes sous l’hypothèse de faible compressibilité avec des schémas numériques d’ordre élevé. Les développements effectués visent à réduire les temps de calcul à précision équivalente.Une première partie est consacrée à l’implémentation d’une formulation purement incompressible avec une résolution implicite de la pression par un schéma de projection. La formulation incompressible autorise des pas de temps plus grand en s’affranchissant de la vitesse du son, mais au prix d’une algorithmique plus complexe et de la nécessité de résoudre un système linéaire. La comparaison des deux formulations,faiblement-compressible et incompressible, tend à montrer la pertinence du schéma de projection pour les écoulements laminaires instationnaires.Un deuxième axe de développement a consisté en la proposition d’une amélioration de la méthode de frontière immergée initialement présente dans le code.Si les résultats obtenus ne sont pas encore pleinement satisfaisants, ils montrent que la montée en ordre d’une méthode de frontière immergée peut être moins contraignante en formulation incompressible.Enfin la dernière partie traite de l’immersion rapide et robuste de géométries complexes telles qu’elles peuvent être rencontrées dans l’industrie. La localisation géométrique par arbre octal permet d’évaluer rapidement une fonction de distance signée indispensable pour la méthode de frontière immergée. / An original strategy to address hydrodynamic flow was recently proposed through a high-order weakly-compressible Cartesian grid approach. The method is based on a fully-explicit temporal scheme for solving the Navier-Stokes equations. The present thesis aims to reduce the computational time required to obtain the results without deteriorating the accuracy.A first part is dedicated to the implementation of a truly incompressible formulation with an implicit solution for the pressure field through a projection scheme. The incompressible solver allows larger time step size for time integration since the speed of sound tends to infinity. In return the algorithms are no longer straight forward and a linear system has to be solved through the Pressure Poisson Equation. Comparisons carried out between both formulations show that the projection scheme can be better adapted to efficiently simulate unsteady viscous flows. Then an improvement of the immersed boundary method has been proposed. Results are not fully satisfactory for now. However, it seems easier to develop a numerical scheme for the incompressible approach rather than the weakly-compressible one.Finally, the last part addresses the setup up of complex triangulations in immersed boundary simulations. A fast and robust procedure is developed for distance computation with an octree data structure.

Cette thèse s’inscrit dans le contexte de la simulation et du contrôle des vibrations de structures montées sur ressort qui peuvent apparaître sous l’effet de l’interaction avec l’écoulement de sillage instationnaire. Le contrôle de ce phénomène, appelé vibrations induites par vortex (VIV), est un enjeu critique dans l’optimisation de nombreux systèmes. Une méthode de frontières immergées (IBM) a été intégrée dans l’algorithme PISO du code OpenFOAM, dédié à la simulation d’écoulements fluides incompressibles. La méthode IBM permet une représentation précise de corps fixes ou en mouvement, tout en conservant des maillages structurés conduisant à des algorithmes plus précis et efficaces en termes de performances numériques. Pour calculer la divergence de l’équation de quantité de mouvement dans une boucle PISO et l’interpolation des flux, un calcul hybride orignal a été proposé avec une résolution analytique utilisant l’équation de la fonction noyau des quantités impliquant le terme force de l’IBM (quantités singulières). La méthode a été étendu au formalisme d’écoulements en régimes turbulents. Une loi de paroi a été intégrée permettant de modéliser la couche limite à grand nombre de Reynolds. Le travail de validation a été réalisé au regard des données expérimentales et numériques disponibles dans la littérature pour l’étude d’écoulements autour de cylindres et de sphères, sur une large gamme de nombres de Reynolds. Avec l’objectif de développer des lois de contrôle optimal pour le VIV, basées sur les mécanismes d’instabilité linéaire du système couplé dans le cadre de la théorie du contrôle, un solveur adjoint a été développé et validé. / This thesis is related to the simulation and the control of the vortex induced vibrations phenomenon (VIV), which can result from the fluid structure interactions between an unsteady wake and the body, when the shedding frequency in the wake is close to the natural frequency of the body. The control of VIV is a critical issue when optimizing many systems. An Immersed Boundaries Method (IBM) was implemented into the PISO algorithm as a new library of OpenFOAM, in order to perform reliable simulations of incompressible flows around bluff bodies.To compute the divergence of the momentum equation and the interpolation of the fluxes, an hybrid calculation with an analytical resolution of the quantities involving the force term (singular quantities) has been proposed. The mesh convergence of several errors was shown by means of a manufactured solution, allowing to analyze both the errors irelated to the discretization and to the IBM. The new algorithm was subsequently extended to the RANS and DDES formalism proposed in OpenFOAM for the simulation of turbulent flows. A wall law was integrated into theIBM method to model the boundary layers that develop around the bodies at large Reynolds numbers. Various 2D and 3D well-documented test cases of academic flows around fixed or moving solid bodies (cylinderand sphere) have been simulated and carefully validated against existing data from the literature in a large range of Reynolds numbers. With the objective of developing optimal control laws for VIV, based on the linear instability mechanisms of the coupled system within the framework of the control theory, a new adjoint solver was also developed and validated in OpenFOAM.

We study the turbulent flow of a fluid over a canopy, that we model as a deformable porous medium. This porous medium is more precisely a carpet of fibres that bend under the hydrodynamic load, hence initiating a fluid-structure coupling at the scale of a fibre's height (honami). The objective of the thesis is to develop a macroscopic model of this fluid-structure interaction in order to perform numerical simulations of this process. The volume averaging method is implemented to describe the large scales of the flow and their interaction with the deformable porous medium. An hybrid approach is followed due to the non-local nature of the solid phase; While the large scales of the flow are described within an Eulerian frame by applying the method of volume averaging, a Lagrangian approach is proposed to describe the ensemble of fibres. The interface between the free-flow and the porous medium is handle with a One-Domain- Approach, which we justify with the theoretical development of a mass- and momentum- balance at the fluid/porous interface. This hybrid model is then implemented in a parallel code written in C$++$, based on a fluid- solver available from the \openfoam CFD toolbox. Some preliminary results show the ability of this approach to simulate a honami within a reasonable computational cost. Prior to implementing a macroscopic model, insight into the small-scale is required. Two specific aspects of the small-scale are therefore studied in details; The first development deals with the inertial deviation from Darcy's law. A geometrical parameter is proposed to describe the effect of inertia on Darcy's law, depending on the shape of the microstructure of the porous medium. This topological parameter is shown to efficiently characterize inertia effects on a diversity of tested microstructures. An asymptotic filtration law is then derived from the closure problem arising from the volume averaging method, proposing a new framework to understand the relationship between the effect of inertia on the macroscopic fluid-solid force and the topology of the microstructure of the porous medium. A second research axis is then investigated. As we deal with a deformable porous medium, we study the effect of the pore-scale fluid-structure interaction on the filtration law as the flow within the pores is unsteady, inducing time-dependent fluidstresses on the solid- phase. For that purpose, we implement pore-scale numerical simulations of unsteady flows within deformable pores, focusing for this preliminary study on a model porous medium. Owing to the large displacements of the solid phase, an immersed boundary approach is implemented. Two different numerical methods are compared to apply the no-slip condition at the fluid-solid interface: a diffuse interface approach and a sharp interface approach. The objective is to find the proper method to afford acceptable computational time and a good reliability of the results. The comparison allows a cross-validation of the numerical results, as the two methods compare well for our cases. This numerical campaign shows that the pore-scale deformation has a significant impact on the pressure drop at the macroscopic scale. Some fundamental issues are then discussed, such as the size of a representative computational domain or the form of macroscopic equations to describe the momentum transport within a soft deformable porous medium.

La modélisation des phénomènes physiologiques induits par un écoulement, tels que l'écoulement sanguin au travers d'une sténose ou l'écoulement d'air lors de la production de parole, repose souvent sur des théories quasi-unidimensionnelles ou bi-dimensionnelles. Cependant, il est établi que le développement des couches limites dépend de la section transversale. Le but de cette thèse est de modéliser, simuler et caractériser l'importance potentielle de la section transversale sur les écoulements laminaires, contrôlés en pression, en l'absence ou en présence d'une constriction. Des coordonnées de translation sont utilisées pour obtenir des solutions pour des écoulement visqueux au travers d'une section de forme arbitraire. Cette paramétrisation est appliquée à la résolution des équations physiques pour des formes à deux et à trois dimensions. Un modèle d'écoulement simplifié quasi-tridimensionnel, qui prend en compte les pertes dissipatives par convection, la viscosité et la forme de la section est présenté et appliqué à la description de l'écoulement le long d'une sténose. Des données expérimentales et issues de simulations numériques sont collectées afin de caractériser l'influence de la forme de la section transversale dans le cas d'une constriction. simulation numérique sont comparées. / Physical models of physiological flow-induced phenomena, such as blood flow through a stenosis or air flow during human speech production, often rely on a quasi-one-dimensional or two-dimensional flow model, so that details of the cross section shape are neglected. Nevertheless, boundary layer development is known to depend on the cross section shape. The aim of this thesis is to model, simulate and characterize the potential impact of the cross section shape for pressure-driven laminar channel flow without and with constriction. Stretched coordinates are introduced to obtain viscous flow solutions for channels with an arbitrary cross section. The proposed cross section shape parametrization is applied to solve physical equations for two-dimensional and three-dimensional shapes. A simplified quasi-three-dimensional flow model, which accounts for kinetic losses, viscosity and the cross section shape, is presented and applied to describe the flow through a stenosis. Finally, flow data are gathered experimentally and numerically in order to characterize the influence of the cross section shape in the case of a constricted channel. Modeled, experimental and numerical data are compared.