Mathematical models are important tools in systems biology, since the regulatory networks in biological cells are too complicated to understand by biological experiments alone. Analytical solutions can be derived only for the simplest models and numerical simulations are necessary in most cases to evaluate the models and their properties and to compare them with measured data. This thesis focuses on the mesoscopic simulation level, which captures both, space dependent behavior by diffusion and the inherent stochasticity of cellular systems. Space is partitioned into compartments by a mesh and the number of molecules of each species in each compartment gives the state of the system. We first examine how to compute the jump coefficients for a discrete stochastic jump process on unstructured meshes from a first exit time approach guaranteeing the correct speed of diffusion. Furthermore, we analyze different methods leading to non-negative coefficients by backward analysis and derive a new method, minimizing both the error in the diffusion coefficient and in the particle distribution. The second part of this thesis investigates macromolecular crowding effects. A high percentage of the cytosol and membranes of cells are occupied by molecules. This impedes the diffusive motion and also affects the reaction rates. Most algorithms for cell simulations are either derived for a dilute medium or become computationally very expensive when applied to a crowded environment. Therefore, we develop a multiscale approach, which takes the microscopic positions of the molecules into account, while still allowing for efficient stochastic simulations on the mesoscopic level. Finally, we compare on- and off-lattice models on the microscopic level when applied to a crowded environment.

Pagrindinis šio darbo tikslas - sudaryti efektyvius skaitinius algoritmus elipsinio tipo uždaviniams spręsti. Galiorkino metodu sprendžiami du uždaviniai: vienmatis pasienio sluoksnio uždavinys ir dvimatis elipsinis uždavinys su L formos geometrijos sritimi. Algoritmų efektyvumui gerinti naudojami adaptyvieji tinklai, sudaryti remiantis aposterioriniais įverčiais. Darbe parodyta kaip iš dualiųjų įverčių teorijos gauti Bakhvalovo tinklą. Taip pat parodytas Šiškino tinklo ryšys su Bakhvalovo tinklu. Iš aposteriorinių įverčių teorijos gautos σ parametro (jis naudojamas Bakhvalovo ir Šiškino tinkluose) reikšmės, kurios skiriasi skirtinguose normose. Teorinės σ reikšmės patvirtintos skaitiniais eksperimentais, jas galima naudoti kaip rekomendacija sudarant Šiškino arba Bakhvalovo tinklus. Remiantis aposterioriniais įverčiais sudaryta Šiškino tinklo modifikacija, kuri prisitaiko prie šaltinio ir reakcijos funkcijų ypatumų, atlikti skaitiniai eksperimentai. Aposteriorinių įverčių metodas pritaikytas dvimačiam uždaviniui, atlikti eksperimentai, ištirtas adaptyviojo tinklo efektyvumas. / The objective of this paper is to construct effective numerical algorithms for elliptic problems. We use Galerkin method to solve two problems: a one-dimensional boundary layer problem and the two-dimensional elliptic problem with a specific geometry of L form. To optimize computations we use adaptive meshes that are constructed from aposteriori error estimates. We show how to derive Bakhvalov mesh from aposteriori estimates. Also we show the relation between Shishkin and Bakhvalov meshes. From aposteriori estimates we derive the exact values of σ parameter(which is used in Shishkin and Bakhvalov meshes), which depends on a norm in which we calculate the error. Theoretical σ values were confirmed by calculations, they can be used as a recommendation, when a problem is being solved using Shishkin or Bakhvalov meshes. Also we use duality-based aposteriori error estimation to construct a modification of Shishkin mesh, which use additional information about parameters in differential equation, we experimentally compare this mesh with the original(Shishkin) one. We apply aposteriori error estimation technique to a two-dimensional problem and investigate efficiency of an adaptive mesh.

This is a book on numerical methods for singular perturbation problems - in particular stationary convection-dominated convection-diffusion problems. More precisely it is devoted to the construction and analysis of layer-adapted meshes underlying these numerical methods. An early important contribution towards the optimization of numerical methods by means of special meshes was made by N.S. Bakhvalov in 1969. His paper spawned a lively discussion in the literature with a number of further meshes being proposed and applied to various singular perturbation problems. However, in the mid 1980s this development stalled, but was enlivend again by G.I. Shishkin's proposal of piecewise- equidistant meshes in the early 1990s. Because of their very simple structure they are often much easier to analyse than other meshes, although they give numerical approximations that are inferior to solutions on competing meshes. Shishkin meshes for numerous problems and numerical methods have been studied since and they are still very much in vogue. With this contribution we try to counter this development and lay the emphasis on more general meshes that - apart from performing better than piecewise-uniform meshes - provide a much deeper insight in the course of their analysis. In this monograph a classification and a survey are given of layer-adapted meshes for convection-diffusion problems. It tries to give a comprehensive review of state-of-the art techniques used in the convergence analysis for various numerical methods: finite differences, finite elements and finite volumes. While for finite difference schemes applied to one-dimensional problems a rather complete convergence theory for arbitrary meshes is developed, the theory is more fragmentary for other methods and problems and still requires the restriction to certain classes of meshes.

Dans ce travail, nous étudions le cadre de la morphologie mathématique sur les complexes simpliciaux. Complexes simpliciaux sont une structure versatile et largement utilisée pour représenter des données multidimensionnelles, telles que des maillages, qui sont des complexes tridimensionnels, ou des graphes, qui peuvent être interprétées comme des complexes bidimensionnels. La morphologie mathématique est l'un des cadres les plus puissants pour le traitement de l'image, y compris le traitement des structures numériques, et est largement utilisé pour de nombreuses applications. Toutefois, les opérateurs de morphologie mathématique sur des espaces complexes simpliciaux n'est pas un concept entièrement développé dans la littérature. Dans ce travail, nous passons en revue certains opérateurs classiques des complexes simpliciaux sous la lumière de la morphologie mathématique, de montrer qu'ils sont des opérateurs de morphologie. Nous définissons certains treillis de base et les opérateurs agissant sur ces treillis: dilatations, érosions, ouvertures, fermetures et filtres alternés séquentiels, et aussi leur extension à simplexes pondérés. Cependant, les principales contributions de ce travail sont ce que nous appelions les opérateurs dimensionnels, petites et polyvalents opérateurs qui peuvent être utilisés pour définir de nouveaux opérateurs sur les complexes simpliciaux, qui garde les propriétés de la morphologie mathématique. Ces opérateurs peuvent également être utilisés pour exprimer pratiquement n'importe quel opérateur dans la littérature. Nous illustrons les opérateurs définis et nous comparons les filtres alternés séquentiels contre filtres définis dans la littérature, où nos filtres présentent de meilleurs résultats pour l'enlèvement du petit, intense bruit des images binaires / In this work we study the framework of mathematical morphology on simplicial complex spaces. Simplicial complexes are a versatile and widely used structure to represent multidimensional data, such as meshes, that are tridimensional complexes, or graphs, that can be interpreted as bidimensional complexes. Mathematical morphology is one of the most powerful frameworks for image processing, including the processing of digital structures, and is heavily used for many applications. However, mathematical morphology operators on simplicial complex spaces is not a concept fully developped in the literature. In this work, we review some classical operators from simplicial complexes under the light of mathematical morphology, to show that they are morphology operators. We define some basic lattices and operators acting on these lattices: dilations, erosions, openings, closings and alternating sequential filters, including their extension to weighted simplexes. However, the main contributions of this work are what we called dimensional operators, small, versatile operators that can be used to define new operators on simplicial complexes, while mantaining properties from mathematical morphology. These operators can also be used to express virtually any operator from the literature. We illustrate all the defined operators and compare the alternating sequential filters against filters defined in the literature, where our filters show better results for removal of small, intense, noise from binary images

Cette thèse s'intéresse à la conception de méthodes de discrétisation non-conforme pour un modèle de poromécanique. Le but de ce travail est de simplifier les couplages liant la géomécanique d'un milieu poreux à l'écoulement polyphasique compositionnel ayant cours en son sein tels qu'ils sont réalisés actuellement dans l'industrie pétrolière, en discrétisant sur un même maillage, typiquement non-conforme car à l'image de la lithologie, la mécanique et l'écoulement. La nouveauté consiste donc à traiter la mécanique par une méthode d'approximation non-conforme sur maillages généraux. Dans cette thèse, nous nous concentrons sur un modèle d'élasticité linéaire. Les difficultés inhérentes à son approximation non-conforme sont son manque de coercivité (se traduisant par la nécessité de satisfaire une inégalité de Korn sur un espace discret discontinu), ainsi que le phénomène de verrouillage numérique lorsque le matériau tend à devenir incompressible. Dans une première partie, nous construisons un espace d'approximation sur maillages généraux, s'apparentant à une extension de l'espace de Crouzeix-Raviart. Nous explicitons ses propriétés d'approximation et de conformité, et montrons que ce dernier est adapté à une discrétisation primale coercive et robuste au locking du modèle d'élasticité sur maillages généraux. La méthode proposée est moins coûteuse que son équivalent éléments finis (en termes de propriétés) P2. Nous nous intéressons dans une deuxième partie à l'approximation non-conforme d'un modèle couplé de poroélasticité. Nous étudions la convergence d'une famille de schémas numériques dont la discrétisation en espace utilise le formalisme des schémas Gradient, auquel appartient la méthode développée pour la mécanique. Nous prouvons la convergence de telles approximations vers la solution de régularité minimale du problème continu, indépendamment des paramètres physiques du système / This manuscript focuses on the conception of nonconforming discretization methods for a poromechanical model. The aim of this work is to ease the coupling between the geomechanics and the multiphase compositional Darcy flow in porous media by discretizing mechanics and flow on the same mesh, typically nonconforming as it represents the lithology. Hence, the novelty hinges on a nonconforming treatment of mechanics on general meshes. In this work, we focus on a linear elasticity model. The nonconforming approximation of such a model is not straightforward owing to its lack of coercivity (meaning that a discrete Korn's inequality must hold on a discontinuous discrete space) and to the numerical locking phenomenon occurring as the material becomes incompressible. In a first part, we design an approximation space on general meshes, which can be viewed as an extension of the so-called Crouzeix-Raviart space. We study its approximation and conformity properties, and prove that this latter is well-adapted to the design of a primal, coercive, and locking-free discretization of the elasticity model on general meshes. The proposed method is less costly than its finite element equivalent (in terms of properties) P2. In a second part, we tackle the nonconforming approximation of a coupled poroelasticity model. We study the convergence of a family of numerical schemes whose space discretization relies on the Gradient schemes framework, to which belongs the method developed for mechanics. We prove the convergence of such approximations toward the minimal regularity solution of the continuous problem, and independently of the choice of physical parameters

L'objectif de cette thèse était de proposer, puis de valider expérimentalement, un ensemble de méthodes algorithmiques permettant le remaillage parallèle de maillages distribués, en s'appuyant sur une méthode séquentielle de remaillage préexistante. Cet objectif a été atteint par étapes : définition de structures de données et de schémas de communication adaptés aux maillages distribués, permettant le déplacement à moindre coût des interfaces entre sous-domaines sur les processeurs d'une architecture à mémoire distribuée ; utilisation d'algorithmes de répartition dynamique de la charge adaptés aux techniques parallèles de remaillage ; conception d'algorithmes parallèles permettant de scinder le problème global de remaillage parallèle en plusieurs sous-tâches séquentielles, susceptibles de s'exécuter concurremment sur les processeurs de la machine parallèle. Ces contributions ont été mises en oeuvre au sein de la bibliothèque parallèle PaMPA, en s'appuyant sur les briques logicielles MMG3D (remaillage séquentiel de maillages tétraédriques) et PT-Scotch (repartitionnement parallèle de graphes). La bibliothèque PaMPA offre ainsi les fonctionnalités suivantes : communication transparente entre processeurs voisins des valeurs portées par les noeuds, les éléments, etc. ;remaillage, selon des critères fournis par l'utilisateur, de portions du maillage distribué, en offrant une qualité constante, que les éléments à remailler soient portés par un unique processeur ou bien répartis sur plusieurs d'entre eux ; répartition et redistribution de la charge des maillages pour préserver l'efficacité des simulations après remaillage. / The purpose of this thesis was to propose and to validate experimentally a set of algorithmic methods for the parallel remeshing of distributed meshes, based on a preexisting sequential remeshing method. This goal has been achieved through several steps : definition of data structures and of communication schemes suitable for distributed meshes, allowing for cheap migration of subdomain interfaces across the processors of a distributed-memory architecture ; use of dynamic load balancing algorithms suitable for parallel remeshing techniques ; design of parallel algorithms for splitting the global remeshing problem into several independent sequential tasks, susceptible to be executed concurrently across the processors of the parallel machine. These contributions have been implemented into the PaMPA parallel library, taking advantage of the MMG3D (sequential anisotropic tetrahedral remesher) PT-Scotch (parallel graph repartitioning) software. The PaMPA library consequently provides the following features : transparent communication across neighboring processors of data borne by nodes, elements, etc.; remeshing, according to used-defined criteria, of portions of the distributed mesh, that yields constant quality, irrespective of whether elements to be remeshed are located on a single processor or distributed across several of them ; balancing and redistribution of the workload of the mesh, to preserve the efficiency of simulations after the remeshing phase.

[pt] Subdivisão de superfícies triangulares é um problema importante nas atividades de modelagem e animação. Ao deformar uma superfície a qualidade da triangulação pode ser bastante prejudicada na medida em que triângulos, antes equiláteros, se tornam alongados. Uma solução para este problema consiste em refinar a região deformada. As técnicas de refinamento requerem uma estrutura de dados topológica que seja eficiente em termos de memória e tempo de consulta, além de serem facilmente armazenadas em memória secundária. Esta dissertação propõe um framework baseado na estrutura Corner Table com suporte para subdivisão de malhas triangulares. O framework proposto foi implementado numa biblioteca C mais mais de forma a dar suporte a um conjunto de testes que comprovam a eficiência pretendida. / [en] Subdivision of triangular surfaces is an important problem in modeling and animation activities. Deforming a surface can be greatly affected the quality of the triangulation when as equilateral triangles become elongated. One solution to this problem is to refine the deformed region. Refinement techniques require the support of topological data structure. These structures must be efficient in terms of memory and time. An additional requirement is that these structures must also be easily stored in secondary memory. This dissertation proposes a framework based on the Corner Table data structure with support for subdivision of triangular meshes. The proposed framework was implemented in a C plus plus library. With this library this work presents a set of test results that demonstrate the desired efficiency.

La morphologie mathématique est une théorie puissante pour l’analyse d’images 2 D. Elle se base sur la dilatation et l’érosion, qui correspondent à l’addition et la soustraction de Minkowski. Afin d’analyser des maillages 3D par morphologie mathématique, on doit disposer d’algorithmes performants et robustes pour le calcul exact de l’addition et de la soustraction pour ces maillages. Malheureusement, les travaux existants sont, soit approximés, soit non robustes ou limités par des contraintes. Aucun travail n’a traité la différence. Ces difficultés sont dues au fait qu’un maillage représente une surface linéaire par morceaux englobant un ensemble contenu et non dénombrable. Nous avons introduit la notion de sommets contributeurs et nous avons développé un algorithme efficace et robuste pour le calcul de la somme de polyèdres convexes. Nous l’avons par la suite adapté et proposé deux algorithmes performants pour la somme d’une paire de polyèdres non convexe/convexe, tout en gérant correctement les polyèdres complexes, les situations de non-variété ainsi que les changements topologiques. Nous avons également démontré la dualité des sommets contributeurs et nous l’avons exploité pour développer la première approche du calcul exact et efficace de la différence de polyèdres convexes. La dualité des sommets contributeurs ainsi que la robustesse et l’efficacité de nos approches motivent le développement d’une approche unifiée pour l’addition et la soustraction de polyèdres quelconques, ce qui permettra d’appliquer des traitements morphologiques à des maillages 3D. D’autres domaines tels que l’imagerie médicale, la robotique, la géométrie ou la chimie pourront en tirer profit / Mathematical morphology is a powerful theory for the analysis of 2D digital images. It is based on dilation and erosion, which correspond to Minkowski addition and subtraction. To be able to analyze 3D meshes using mathematical morphology, we must use efficient and robust algorithms for the exact computation of the addition and subtraction of meshes. Unfortunately, existing approaches are approximated, non-robust or limited by some constraints. No work has addressed the difference. These difficulties come from the the fact that a mesh represents a piecewise linear surface bounding a continuous and uncountable set. We introduced the concept of contributing vertices and developed an efficient and robust algorithm for the computation of the Minkowski sum of convex polyhedra. After that, we adapted and proposed two efficient algorithms for the computation of the Minkowski sum of a non-convex/convex pair of polyhedra, while properly handling complex polyhedra, non-manifold situations and topological changes. We also demonstrated the duality of the contributing vertices concept and exploited it to develop the first approach for the efficient and exact computation of the Minkowski difference of convex polyhedra. The duality of the contributing vertices concept as well as the robustness and efficiency of our approaches motivate the development of a unified approach for the Minkowski addition and subtraction of arbitrary polyhedral, which will permit the morphological analysis of 3D meshes. Other areas such as medical imaging, robotics, geometry or chemistry may benefit from our approaches

L’un des défis de la science planétaire est la détermination de l’âge des surfaces des différents corps célestes du système solaire, pour comprendre leurs processus de formation et d’évolution. Une approche repose sur l’analyse de la densité et de la taille des cratères d’impact. En raison de l’énorme quantité de données à traiter, des approches automatiques ont été proposées pour détecter les cratères d’impact afin de faciliter ce processus de datation. Ils utilisent généralement les valeurs de couleur des images ou les valeurs d’altitude de "modèles numériques d’élévation" (DEM). Dans cette thèse, nous proposons une nouvelle approche pour détecter les bords des cratères. L’idée principale est de combiner l’analyse de la courbure avec une classification basée sur un réseau de neurones. Cette approche comporte deux étapes principales : premièrement, chaque sommet du maillage est étiqueté avec la valeur de la courbure minimale; deuxièmement, cette carte de courbure est injectée dans un réseau de neurones pour détecter automatiquement les formes d’intérêt. Les résultats montrent que la détection des formes est plus efficace en utilisant une carte en deux dimensions s’appuyant sur le calcul d’estimateurs différentiels discrets, plutôt qu’en utilisant la valeur de l’élévation en chaque sommet. Cette approche réduit significativement le nombre de faux négatifs par rapport aux approches précédentes basées uniquement sur une information topographique. La validation de la méthode est effectuée sur des DEM de Mars, acquis par un altimètre laser à bord de la sonde spatiale "Mars Global Surveyor" de la NASA et combinés avec une base de données de cratères identifiés manuellement. / One of the challenges of planetary science is the age determination of the surfaces of the different celestial bodies in the solar system, to understand their formation and evolution processes. An approach relies on the analysis of the crater impact density and size. Due to the huge quantity of data to process, automatic approaches have been proposed for automatically detecting impact craters in order to facilitate this dating process. They generally use the color values from images or the elevation values from Digital Elevation Model (DEM). In this PhD thesis, we propose a new approach for detecting craters rims. The main idea is to combine curvature analysis with Neural Network based classification. This approach contains two main steps: first, each vertex of the mesh is labeled with the value of the minimal curvature; second, this curvature map is injected into a neural network to automatically detect the shapes of interest. The results show that detecting forms are more efficient using a two-dimensional map based on the computation of discrete differential estimators, than by the value of the elevation at each vertex. This approach significantly reduces the number of false negatives compared to previous approaches based on topographic information only. The validation of the method is performed on DEMs of Mars, acquired by a laser altimeter aboard NASA’s Mars Global Surveyor spacecraft and combined with a database of manually identified craters.

Moldagem por injeção é um dos mais importantes processos industriais para produção de produtos plásticos finos. Esse processo é dividido essencialmente em quatro estágios: plastificação, preenchimento, empacotamento e resfriamento. O escoamento de um fluido caracterizado por alta viscosidade em uma cavidade estreita é um problema tipicamente encontrado em processos de moldagem por injeção.Neste caso, o escoamento pode ser descrito por uma formulação conhecida como aproximação de Hele-Shaw. Tal formulação pode ser derivada das equações de conservação tridimensionais usando um número de suposições a respeito do polímero injetado e da geometria da cavidade do molde, juntamente com a integração e o acoplamento das equações da conservação da quantidade de movimento e da continuidade. Essa formulação, referindo às limitações da geometria do molde como sendo canais estreitos e quase sem curvatura, é comumente denominada formulação 2 1/2D. Neste trabalho, é apresentada uma técnica para a simulação da fase de preenchimento de um processo de moldagem por injeção, usando essa formulação 2 1/2D, com um método de volumes finitos e malhas não estruturadas. O modelo de Cross modificado com dependência da temperatura de Arrhenius é empregado para descrever a viscosidade do polímero fundido. O campo de distribuição de temperatura é tridimensional e é resolvido usando um esquema semi-Lagrangeano baseado em volumes finitos. As malhas não estruturadas utilizadas são geradas por triangulação de Delaunay e o método numérico implementado usa a estrutura de dados topológica SHE - Singular Handle Edge, que é capaz de lidar com condições de contorno e singularidades, aspectos comumente encontrados em simulações numéricas de escoamento de fluidos. / Injection molding is one of the most important industrial processes for the manufacturing of thin plastic products. This process can be divided into four stages: plastic melting, filling, packing and cooling phases. The flow of a fluid characterized by high viscosity in a narrow gap is a problem typically found in injection molding processes. In this case, the flow can be described by a formulation known as Hele-Shaw approach. Such formulation can be btained from the three-dimensional conservation equation using a number of assumptions regarding the injected polymer and the geometry of the mold, together with the integration and the coupling of the momentum and continuity equations. This approach, referring to limitations of the mould geometry to narrow, weakly curved channels, is usually called 2 1/2D approach. In this work a technique for the simulation of the filling stage of the injection molding process, using this 2 1/2D approach, with a finite volume method and unstructured meshes, is presented. The modified-Cross model with Arrhenius temperature dependence is employed to describe the viscosity of the melt. The temperature field is 3D and it is solved using a semi-Lagrangian scheme based on the finite volume method. The employed unstructured meshes are generated by Delaunay triangulation and the implemented numerical method uses the topological data structure SHE - Singular Handle Edge, capable to deal with boundary conditions and singularities, aspects commonly found in numerical simulation of fluid flow.