Ce travail de thèse est consacré à l'étude numérique de la forme instationnaire des équations de Navier--Stokes incompressibles en dimension trois d'espace. Ces équations sont étudiées dans leur formulation classique mais aussi dans leur formulation hydrostatique. Le schéma en temps est résolu à l'aide d'une méthode de projection, la méthode de projection incrémentale standard qui sert de référence à l'étude numérique des nouvelles méthodes proposées: la méthode de projection hydrostatique et la méthode de projection dynamique étendue. Ces méthodes sont combinées à la méthode de pénalisation de volume qui permet de tenir compte de la présence d'obstacles de forme quelconque dans le domaine de simulation en utilisant un maillage cartésien. Une nouvelle expression des équations de Navier--Stokes hydrostatiques issue de l'application de la méthode de pénalisation de volume est obtenue et étudiée. La discrétisation en espace s'effectue en utilisant la méthode des volumes finis sur une maillage décalé de type MAC. Un nouveau code de calcul baptisé VivAn'O a été conçu et validé durant ce travail. Il a permis l'étude numérique des différentes méthodes proposées et a également permis de réaliser des simulations dans la zone portuaire de Pointe-à-Pitre à partir de données bathymétriques réelles. / The present work is about the numerical study of the three dimensional form of the unstationnary Navier--Stokesequations. These equations are studied under their classical form but also under their hydrostatic one. Thetime--dependent problem is solved using a projection method called the standard incremental projection method which isused as the reference to the numerical study of the new projection methods we proposed : the hydrostatic projectionmethod and the extended dynamical projection method. These methods are combined with a volume penalization methodto take into account obstacles of any shape in the simulation domain using cartesian meshes. A new formulation of the hydrostatic Navier--Stokes equations is obtained from the use of the penalization method and studied. The space isdiscretized using the finite volume method on a staggered MAC mesh.A new computational fluid dynamic code nammed VivAn'O have been developped during this work. It had permitted thenumerical study of the proposed methods. It was also used to carry out simulations in the harbour area of Pointe--à--Pitre usine real bathvmetric data.

Visualization and image filtering are important parts of cryo-electron tomography analysis. ArtiaX, a plugin developed for UCSF ChimeraX, has been extended to improve the functionality of these two parts. For the visualization, a method of moving 3D surfaces to remove overlap between them has been developed and implemented. To accommodate this, a Monte Carlo approach using Poisson disc sampling for approximating volume of overlap between 3D surfaces is used, and a novel method for measuring overlap has been invented, called the Normal Projection Method, useful for measuring the depth of overlap between surfaces. For the image filtering, tomogram averaging and frequency filters have been added to the ArtiaX toolbox. / Visualisering och bildfiltrering är viktiga delar inom kryoelektrontomografianalys. ArtiaX, ett plugin utvecklat för UCSF ChimeraX, har utökats för att förbättra funktionaliteten inom dessa två områden. För visualiseringen har en metod för att flytta 3D ytor så att de inte överlappar utvecklats och implmenterats. För att skapa denna funktion används en Monte Carlo metod med Poisson disk sampling för att uppskatta volymen av 3D ytor, och normalprojektionsmetoden, en ny metod för att mäta överlappsdjup har skapts och implementerats. För att förbättra bildfiltreringen har tomogram-snittning och frekvensfilter lagts till bland verktygen i ArtiaX.

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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.

O foco principal do presente trabalho é estender uma metodologia numérica embasada no uso de uma técnica de refinamento adaptativo de malha (AMR - Adaptive Mesh Refinement) e no uso de esquemas temporais multipasso implícitos-explícitos (IMEX) a aplicações envolvendo escoamentos reativos com baixo número de Mach. Originalmente desenvolvida para escoamentos incompressíveis, a formulação euleriana daquela metodologia emprega as equações de Navier-Stokes como modelo matemático para descrever a dinâmica do escoamento e o Método da Projeção, baseado no divergente nulo da velocidade do escoamento, para tratar o acoplamento pressão-velocidade presente na formulação com variáveis primitivas. Tal formulação euleriana original é estendida para acomodar novas equações agregadas ao modelo matemático da fase contínua: conservação de massa, fração de mistura (para representar as concentrações de combustível e oxidante), e energia. Além disso, uma equação termodinâmica de estado é integrada ao modelo matemático estendido e é empregada juntamente com a equação de conservação de massa para produzir uma nova restrição (não nula desta vez) ao divergente do campo de velocidade. Assume-se que o escoamento ocorre a baixo número de Mach (hipótese principal). O Método de Diferença Finita é empregado na discretização espacial das variáveis eulerianas de estado, empregando-se uma malha AMR. As vantagens e dificuldades desta extensão são cuidadosamente investigadas e reportadas. Pela importância, do ponto de vista de aplicações práticas, alguns estudos numéricos preliminares envolvendo escoamentos incompressíveis turbulentos com sprays são realizados (as gotículas compõem a fase dispersa). Num primeiro momento, apenas sprays com gotículas inertes são considerados. Embora ainda apenas iniciais, tais estudos já se mostram importantes pois identificam com clareza, em primeira instância, algumas das dificuldades inerentes a serem enfrentadas ao se tratar dentro desta nova metodologia um conjunto relativamente grande de gotículas lagrangianas. No caso de escoamentos incompressíveis turbulentos com sprays, a integração temporal se dá com métodos IMEX para a fase contínua e com o Método de Euler Modificado para a fase dispersa. A turbulência, em todos os casos que a envolvem, é tratada pelo modelo de Simulação das Grandes Escalas (LES - Large Eddy Simulation). As simulações computacionais se dão em um domínio tridimensional, um parelelepípedo, e empregam uma extensão (resultante do presente trabalho) do código AMR3D, um programa de computador sequencial implementado em Fortran90, oriundo de uma colaboração de longa data entre o IME-USP e o MFLab/FEMEC-UFU (Laboratório de Dinâmica de Fluidos da Universidade Federal de Uberlândia). O processamento foi efetuado no LabMAP (Laboratório da Matemática Aplicada do IME-USP). / It is the main goal of the present work to extend a numerical methodology based on both the use of an adaptive mesh refinement technique (AMR) and the use of a multistep, implicit-explicit time-step strategy (IMEX) to applications involving low Mach number reactive flows. Originally developed for incompressible flows, the Eulerian formulation of that methodology employs the Navier-Stokes equations to model the flow dynamics and the Projection Method, based on the vanishing divergence of the velocity field, to tackle the pressure-velocity coupling present when using primitive variables. That Eulerian formulation is extended by adding a new set of equations to the original mathematical model, describing the various properties of the continuous phase: mass conservation, mixture fraction (to represent concentrations of fuel and oxidizer) and energy. Also, a thermodynamic equation of state is included into the extended mathematical model which is employed, along with the equation for the conservation of mass, to derive a new restriction (this time, different from zero) to the divergence of the velocity field. It is assumed that one is dealing with a low Mach number flow (the main hipothesis). The discretization in space employs the Finite Difference Method for the Eulerian variables on a AMR mesh. Advantages and difficulties of such an extension of the previous methodology are carefully investigated and reported. For its importance in the real-world applications, few preliminary numerical studies involving incompressible turbulent flows with sprays are performed (the droplets form what it is called the dispersed phase). Only sprays formed by inert droplets are considered. Even though initial yet, such studies are most important because they clearly identify, first hand, certain difficulties in handling relatively large sets of Lagrangian droplets in the context of this new AMR methodology. In the context of turbulent incompressible flows with sprays, the overall time-step scheme is given by IMEX methods for the continuous phase and by the Improved Euler Method for the dispersed phase. In all the cases in which it is considered, turbulence is modeled by the Large Eddy Simulation (LES) model. The computational simulations are held in a tridimensional domain given by a paralellepiped and all of them employ the extention (resulting of the present work) of the AMR3D code, a sequencial computer program implemented in Fortran90, whose origin is the collaborative work between IMEUSP and MFLab/FEMEC-UFU (Fluid Dynamics Laboratory, Federal University of Uberlândia). Computations were performed at LabMAP (Applied Mathematics Laboratory at IME-USP).

No desenvolvimento de códigos paralelos, a biblioteca PETSc se destaca como uma ferramenta prática e útil. Com o uso desta ferramenta, este trabalho apresenta um estudo sobre resolvedores de sistemas lineares aplicados a escoamentos incompressíveis de fluidos em microescala, além de uma análise de seu comportamento em paralelo. Após um estudo dos diversos aspectos dos métodos de fronteira imersa, é apresentado um método de fronteira imersa paralelo de primeira ordem. Na sequência, é apresentada uma proposta de melhoria na precisão do método, baseada na minimização da distância entre a condição de contorno exata e aproximada, no sentido de mínimos quadrados. O desenvolvimento de uma ferramenta paralela eficiente é demonstrado na solução numérica de problemas envolvendo escoamentos incompressíveis de fluidos viscosos com fronteiras imersas / In the development of parallel codes, PETSc library has an important position as a practical and useful tool. With this tool, this work presents a study about linear system solvers applied to incompressible flow in microscale problems, furthermore an analysis of the parallel behavior of these methods is presented. After a study of several aspects of immersed boundary methods, and taking advantage of the flexibility of PETSc, a parallel first order immersed boundary method is presented. Thereafter, an improvement in the accuracy of the method is presented, based on the minimization of the distance between exact and approximated boundary conditions, in the least square sense. The development of a parallel and efficient tool is demonstrated in the numerical solution of incompressible viscous flow problems with immersed boundary

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No desenvolvimento de códigos paralelos, a biblioteca PETSc se destaca como uma ferramenta prática e útil. Com o uso desta ferramenta, este trabalho apresenta um estudo sobre resolvedores de sistemas lineares aplicados a escoamentos incompressíveis de fluidos em microescala, além de uma análise de seu comportamento em paralelo. Após um estudo dos diversos aspectos dos métodos de fronteira imersa, é apresentado um método de fronteira imersa paralelo de primeira ordem. Na sequência, é apresentada uma proposta de melhoria na precisão do método, baseada na minimização da distância entre a condição de contorno exata e aproximada, no sentido de mínimos quadrados. O desenvolvimento de uma ferramenta paralela eficiente é demonstrado na solução numérica de problemas envolvendo escoamentos incompressíveis de fluidos viscosos com fronteiras imersas / In the development of parallel codes, PETSc library has an important position as a practical and useful tool. With this tool, this work presents a study about linear system solvers applied to incompressible flow in microscale problems, furthermore an analysis of the parallel behavior of these methods is presented. After a study of several aspects of immersed boundary methods, and taking advantage of the flexibility of PETSc, a parallel first order immersed boundary method is presented. Thereafter, an improvement in the accuracy of the method is presented, based on the minimization of the distance between exact and approximated boundary conditions, in the least square sense. The development of a parallel and efficient tool is demonstrated in the numerical solution of incompressible viscous flow problems with immersed boundary

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La méthode IIM (Immersed Interface Method) permet d'étendre certaines méthodes numériques à des problèmes présentant des discontinuités. Elle est utilisée ici pour étudier un fluide incompressible régi par les équations de Navier-Stokes, dans lequel est immergée une membrane exerçant une force singulière. Nous utilisons une méthode de projection dans une grille de différences finies de type MAC. Une dérivation très complète des conditions de saut dans le cas où la viscosité est continue est présentée en annexe. Deux exemples numériques sont présentés : l'un sans membrane, et l'un où la membrane est immobile. Le cas général d'une membrane mobile est aussi étudié en profondeur. / The Immersed Interface Method allows us to extend the scope of some numerical methods to discontinuous problems. Here we use it in the case of an incompressible fluid governed by the Navier-Stokes equations, in which a membrane is immersed, inducing a singular force. We use a projection method and staggered (MAC-type) finite difference approximations. A very complete derivation for the jump conditions is presented in the Appendix, for the case where the viscosity is continuous. Two numerical examples are shown : one without a membrane, and the other where the membrane is motionless. The general case of a moving membrane is also thoroughly studied.