Indiana University-Purdue University Indianapolis (IUPUI) / Topology Optimization is an optimization technique used to synthesize models without any preconceived shape. These structures are synthesized keeping in mind the minimum compliance problems. With the rapid improvement in advanced manufacturing technology and increased need for lightweight high strength designs topology optimization is being used more than ever. There exist a number of commercially available software's that can be used for optimizing a product. These software have a robust Finite Element Solver and can produce good results. However, these software offers little to no choice to the user when it comes to selecting the type of optimization method used. It is possible to use a programming language like MATLAB to develop algorithms that use a specific type of optimization method but the user himself will be responsible for writing the FEA algorithms too. This leads to a situation where the flexibility over the optimization method is achieved but the robust FEA of the commercial FEA tool is lost. There have been works done in the past that links ABAQUS with MATLAB but they are primarily used as a tool for finite element post-processing. Through this thesis, the aim is to develop an interface that can be used for solving optimization problems using different methods like hard-kill as well as the material penalization (SIMP) method. By doing so it's possible to harness the potential of a commercial FEA software and gives the user the requires flexibility to write or modify the codes to have an optimization method of his or her choice. Also, by implementing this interface, it can also be potentially used to unlock the capabilities of other Dassault Systèmes software's as the firm is implementing a tighter integration between all its products using the 3DExperience platform. This thesis as described uses this interface to implement BESO and HCA based topology optimization. Since hybrid cellular atomata is the only other method other than equivalent static load method that can be used for crashworthiness optimization this work suits well for the role when extended into a non-linear region.

The aim of this master's theses it to focuse on the usage of genetic algorithms in combination with a technique of biologically inspired development in cellular automata. The principles of the proposed method is described. The main part of this work deals with the design of combinational logic circuits. The genetic algorithm is utilized to design a nonuniform one-dimensional cellular automaton (in particular, the local transition functions) which serves as a circuit generator. Experiments have been conducted to design of basic types of combinational circuits and polymorphic circuits. Finally, the results are presented and compared with the results obtained in the previous work in which a uniform cellular automaton was applied.

Η διατριβή αφορά την ανάπτυξη και υλοποίηση ενός τετραδιάστατου, διακριτού μοντέλου προσομοίωσης της συμπεριφοράς καρκινικών κυτταρικών συστημάτων σε ελεύθερη ανάπτυξη και της απόκρισής τους σε χημειοθεραπευτική ή και ακτινοθεραπευτική αγωγή. Υλοποιήθηκαν δύο εκδοχές του μοντέλου: η χωρική και η μη χωρική προσέγγιση. Η χωρική προσέγγιση αναφέρεται στην τετραδιάστατη προσομοίωση συμπαγών όγκων. Η μη χωρική προσέγγιση βρίσκει εφαρμογή στην περίπτωση μη συμπαγών όγκων, καθώς και συμπαγών όγκων, όταν δεν δίνεται έμφαση στη χωρική εξέλιξή τους. Η ερευνητική εργασία έχει επικεντρωθεί σε τρεις τύπους καρκινικών όγκων: καρκίνος του μαστού, καρκίνος του πνεύμονα και πολύμορφο γλοιοβλάστωμα και σε θεραπευτικά σχήματα χορήγησης των σκευασμάτων: επιρουβικίνη (epirubicin), τεμοζολομίδη (temozolomide), σισπλατίνη (cisplatin), γεμσιταμπίνη (gemcitabine), βινορελμπίνη (vinorelbine) και δοσεταξέλη (docetaxel). Σκοπός της εργασίας είναι η ανάπτυξη ενός εργαλείου για την αξιόπιστη υποστήριξη ιατρών στη λήψη αποφάσεων σχετικά με την επιλογή θεραπευτικών σχημάτων και την εξατομικευμένη βελτιστοποίηση της θεραπευτικής αγωγής. Η αφετηρία είναι η μοντελοποίηση του κυτταρικού κύκλου και των πιθανών μεταβάσεων μεταξύ των καταστάσεων που μπορεί να βρεθεί ένα κύτταρο. Το μοντέλο βασίζεται στην υπόθεση ότι ο καρκινικός όγκος διατηρείται από μια συγκεκριμένη κατηγορία κυττάρων, τα καρκινικά βλαστικά κύτταρα (cancer stem cells), και έχει επεκταθεί ώστε να περιλαμβάνει σε μεγαλύτερη λεπτομέρεια διάφορους βιολογικούς μηχανισμούς σε μοριακό (πχ. εκφράσεις γονιδίων) και κυτταρικό επίπεδο. Ο μηχανισμός δράσης, η φαρμακοκινητική και η φαρμακοδυναμική των θεωρούμενων σκευασμάτων έχουν μελετηθεί βιβλιογραφικά και έχουν ενσωματωθεί στο μοντέλο. Επίσης, το μοντέλο έχει αναπτυχθεί ώστε να λαμβάνει υπόψη του την κλινική εικόνα του ασθενούς με χρήση εξατομικευμένων κλινικών δεδομένων, όπως απεικονιστικά δεδομένα (π.χ. CT, MRI, PET), ιστοπαθολογικά δεδομένα (π.χ. τύπος όγκου, βαθμός διαφοροποίησης) και μοριακά δεδομένα (π.χ. έκφραση γονιδίων). Στα πλαίσια της διατριβής πραγματοποιούνται έλεγχοι αξιοπιστίας και εκτενείς παραμετρικές μελέτες για την αποσαφήνιση της ευαισθησίας του μοντέλου στη διακύμανση των παραμέτρων του τόσο κατά την προσομοίωση της ελεύθερης ανάπτυξης όσο και κατά την εφαρμογή της χημειοθεραπευτικής αγωγής. Η ποσοτική αξιολόγηση, προσαρμογή και βελτιστοποίηση του μοντέλου πραγματοποιείται στα πλαίσια των ευρωπαϊκών ερευνητικών προγραμμάτων ACGT (Advancing Clinicogenomic Trials on Cancer, FP6-2005-IST-026996), ContraCancrum (Clinically Oriented Cancer Multilevel Modelling, FP7-ICT-2007-2-223979) και P-medicine (From data sharing and integration via VPH models to Personalized medicine, FP7-ICT-2009-6-270089) μέσω της αξιοποίησης πραγματικών κλινικών δεδομένων. Στην παρούσα διατριβή παρουσιάζονται τα αποτελέσματα της προσαρμογής του μοντέλου σε κλινικά δεδομένα του καρκίνου του μαστού, του καρκίνου του πνεύμονα και του πολύμορφου γλοιοβλαστώματος. Επιπλέον, διάφορες εκδόσεις του μοντέλου έχουν αξιοποιηθεί για ‘την επάνδρωση’ μιας ευρωπαϊκής βάσης μοντέλων για τον καρκίνο, που υλοποιείται στα πλαίσια του ευρωπαϊκού ερευνητικού προγράμματος TUMOR (Transatlantic Tumour Model Repositories, FP7-ICT-2009-5-247754). Το μοντέλο υλοποιείται σε γλώσσα προγραμματισμού C++. / In the present thesis, a clinically oriented, multiscale, discrete simulation model of cancer free growth and response to chemotherapy and/or radiotherapy is presented and investigated. Two versions of the model have been implemented: the spatial and the non spatial approach. The spatial model concerns the spatiotemporal evolution of solid tumours, whereas the non spatial model can be applied in the case of non solid cancers, as well as solid tumours, when no emphasis is put on the spatial features of a tumour evolution. The research work has been focused on the paradigms of early breast cancer treated with the single agent epirubicin, primary lung cancer treated with various combinations of cisplatin, gemcitabine, vinorelbin and docetaxel and glioblastoma multiforme treated with combined modality treatment using radiation and chemotherapy with temozolomide. The goal is to end up with a reliable simulation system able to assist clinicians in selecting the most appropriate therapeutic pattern, extracted from several candidate therapeutic schemes in the context of patient individualized treatment optimization. The model incorporates the biological mechanisms of cell cycling, quiescence, recruitment (reentry into the cell cycle), differentiation and death. It is based on the well documented assumption that tumour sustenance is due to the existence of cancer stem cells, i.e. cells which have the ability to preserve their own population, as well as give birth to cells that follow the path towards terminal differentiation. Furthermore, the mechanism of action, pharmacokinetics and pharmacodynamics of all considered agents have been bibliographically studied and incorporated into the model. Finally, the model has been developed to support and incorporate individualized clinical data such as imaging data (e.g. CT, MRI, PET slices, possibly fused), including the definition of the tumour contour and internal tumour regions (proliferating, necrotic), histopathologic (e.g., type of tumour) and genetic data (e.g., gene expression). An exhaustive and in-depth examination of the model behaviour with respect to the variation of its input parameters has been performed, in order to determine the impact of its parameters, guarantee a biologically relevant virtual tumour behaviour and enlighten aspects of the interplay and possible interdependencies of the biological mechanisms modeled. Finally, the model has been quantitativily validated and adaptated in the framework of the ACGT (Advancing Clinicogenomic Trials on Cancer, FP6-2005-IST-026996), ContraCancrum (Clinically Oriented Cancer Multilevel Modelling, FP7-ICT-2007-2-223979) and P-medicine (From data sharing and integration via VPH models to Personalized medicine, FP7-ICT-2009-6-270089) European Commission-funded projects by exploiting real clinical data. In the present thesis, the clinical adaptation of the model focuses on breast cancer, lung cancer and glioblastoma multiforme clinical cases. Moreover, various versions of the model have been uploaded to the EU cancer model repository developed by the TUMOR (Transatlantic Tumour Model Repositories, FP7-ICT-2009-5-247754) European Commission-funded project. The model has been developed in the C++ programming language.

Master of Landscape Architecture / Department of Landscape Architecture and Regional and Community Planning / Eric A. Bernard / The Kansas High Plains region is a key global agricultural production center (U.S. G.S, 2009). The High Plains physiography is ideal agricultural production landscape except for the semi-arid climate. Consequently, farmers mine vast groundwater resources from the High Plains Ogallala Aquifer formations to augment precipitation for crop production. Growing global population, current policy and subsidy programs, declining aquifer levels coupled with regional climatic changes call into question both short-term and long-term resilience of this agrarian landscape and food and water security. This project proposes a means to simulate future irrigated agriculture land use and crop cover patterns in the Kansas High Plains Aquifer region based on coupled modeling results from ongoing research at Kansas State University. A Cellular Automata (CA) modeling framework is used to simulate potential land use distribution, based on coupled modeling results from groundwater, economic, and crop models. The CA approach considers existing infrastructure resources, industrial and commercial systems, existing land use patterns, and suitability modeling results for agricultural production. The results of the distribution of irrigated land produced from the CA model provide necessary variable inputs for the next temporal coupled modeling iteration. For example, the groundwater model estimates water availability in saturated thickness and depth to water. The economic model projects which crops will be grown based on water availability and commodity prices at a county scale. The crop model estimates potential yield of a crop under specific soil, climate and growing conditions which further informs the economic model providing an estimate of profit, which informs regional economic and population models. Integrating the CA model into the coupled modeling system provides a key linkage to simulate spatial patterns of irrigated land use and crop type land cover based on coupled model results. Implementing the CA model in GIS offers visualization of coupled model components and results as well as the CA model land use and land cover. The project outcome hopes to afford decision-makers, including farmers, the ability to use the actual landscape data and the developed coupled modeling framework to strategically inform decisions with long-term resiliency.

La première partie de cette thèse porte sur les automates cellulaires probabilistes (ACP) sur la ligne et à deux voisins. Pour un ACP donné, nous cherchons l'ensemble de ces lois invariantes. Pour des raisons expliquées en détail dans la thèse, ceci est à l'heure actuelle inenvisageable de toutes les obtenir et nous nous concentrons, dans cette thèse, surles lois invariantes markoviennes. Nous établissons, tout d'abord, un théorème de nature algébrique qui donne des conditions nécessaires et suffisantes pour qu'un ACP admette une ou plusieurs lois invariantes markoviennes dans le cas où l'alphabet E est fini. Par la suite, nous généralisons ce résultat au cas d'un alphabet E polonais après avoir clarifié les difficultés topologiques rencontrées. Enfin, nous calculons la fonction de corrélation du modèleà 8 sommets pour certaines valeurs des paramètres du modèle en utilisant une partie desrésultats précédents. / The first part of this thesis is about probabilistic cellular automata (PCA) on the line and with two neighbors. For a given PCA, we look for the set of its invariant distributions. Due to reasons explained in detail in this thesis, it is nowadays unthinkable to get all of them and we concentrate our reections on the invariant Markovian distributions. We establish, first, an algebraic theorem that gives a necessary and sufficient condition for a PCA to have one or more invariant Markovian distributions when the alphabet E is finite. Then, we generalize this result to the case of a polish alphabet E once we have clarified the encountered topological difficulties. Finally, we calculate the 8-vertex model's correlation function for some parameters values using previous results.The second part of this thesis is about infinite iterations of stochastic processes. We establish the convergence of the finite dimensional distributions of the α-stable processes iterated n times, when n goes to infinite, according to parameter of stability and to drift r. Then, we describe the limit distributions. In the iterated Brownian motion case, we show that the limit distributions are linked with iterated functions system.

Disturbance in a forest’s canopy, whether caused by treefall, limbfall, landslide, or fire determines not only the distribution of well-lit patches at any given time, but also the ways in which the forest changes over time. In this dissertation, I use a 25 year record of treefall gap formation find a novel and highly patterned process of forest disturbance and regeneration, providing a local mechanism by examining the factors that influence the likelihood of treefall. I then develop a stochastic cellular automaton for disturbance and regeneration based on the analysis of this long term data set and illustrate the potential of this model for the prediction and detection of patterned forest dynamics in general. Finally, I investigate the spatial structure of a population of one of the most common gap colonist species in this forest, Didymopanax pittieri, and illustrate the effect of local aggregation of treefalls and on the population dynamics of D. pittieri in the process.

In this Doktorarbeit the Lattice Boltzmann scheme, a heuristic method for the simulation of flows in complicated boundaries, is investigated. Its theory is renewed by emphasizing the entropy maximization principle, and new means for the modelling of geometries (including moving boundaries) and the visual representation of evoluting flows are presented. An object oriented implemen- tation is given with communication between objects realized by an interpreter object and communication from outside realized via interprocess communica- tion. Within the new theoretical apprach the applicability of existing Lattice Boltzmann schemes to model thermal flows for arbitrary temperatures is reex- amined. / In dieser Doktorarbeit wird das Gitter-Boltzmann-Schema, eine heuristische Methode fuer die Simulation von Stroemungen innerhalb komplexer Raender, untersucht. Die zugrundeliegende Theorie wird unter neuen Gesichtspunkten, insbesondere dem Prinzip der Entropiemaximierung, betrachtet. Des weiteren werden neuartige Methoden fuer die Modellierung der Geometrie (einschl. beweglicher Raender) und der visuellen Darstellung aufgezeigt. Eine objektorientierte Implementierung wird vorgestellt, wobei die Kommunikation zwischen den Objekten über Interpreter-Objekte und die Kommunikation mit der Aussenwelt ueber Interprozess-Kommunikation gehandhabt wird. Mit dem neuen theoretischen Ansatz wird die Gueltigkeit bestehender Gitter-Boltzmann-Schemata fuer die Anwendung auf Stroemungen mit nicht konstanter Temperatur untersucht.

Made available in DSpace on 2016-03-15T19:37:45Z (GMT). No. of bitstreams: 1 Wander Lairson Costa.pdf: 1957133 bytes, checksum: 6819580d97bb5eaca5ea04352fcda0b8 (MD5) Previous issue date: 2013-03-15 / Universidade Presbiteriana Mackenzie / Cellular automata are totally discrete systems that act locally in a simple and deterministic way, but whose resulting global behavior can be extremely complex. The set of possible global configurations in one finite time step for a CA can be described by a regular language, which in turn can be represented by a finite automaton, more precisely the so-called process graph, in which all states are initial and final. Here, we study the temporal evolution complexity of the elementary cellular automata (i.e., one-dimensional, binary, with radius 1), and related previous works are revisited and discussed, indicating problems and their consequences. We also start up a novel approach for the problem, substituting the process graph based representation that describes the configuration at each time step by adjacency matrices derived from them. In fact, we extend the classical adjacency matrix notation, as they cannot fully represent process graphs. With this new notation, we show that it is possible to obtain the algorithm to generate a process graph for an arbitrary finite time step for each of the rules at study. In conclusion, although advancing the limit graph problem, it still remains open, and we provide suggestions for further research. / Autômatos celulares são sistemas totalmente discretos que agem localmente de forma simples e determinística, mas cujo comportamento global resultante pode ser extremamente complexo. O conjunto de possíveis configurações globais em um passo de tempo t finito para um autômato celular pode ser descrito por uma linguagem regular, a qual por sua vez pode ser representada por meio de um autômato finito, mais precisamente, pelo chamado grafo de processo, em que todos os estados são iniciais e finais. Estuda-se aqui a complexidade da evolução temporal dos autômatos celulares elementares (i.e., unidimensionais, binários, de raio 1), e trabalhos anteriores são revisitados e discutidos, no quais apontam-se problemas e suas consequências. Também inicia-se uma nova abordagem para o problema, substituindo a representação dos grafos de processo que descrevem a configuração a cada passo de tempo por matrizes de adjacência deles derivadas. De fato, estende-se a notação clássica de matriz de adjacência, já que ela se mostra insuficiente para descrever completamente os grafos de processo em questão. Com essa nova notação, mostra-se que é possível obter o algoritmo que gere o grafo de processo de tempo t para cada uma das regras estudadas. Conclui-se que, embora houve avanços para o problema do grafo limite, este ainda permanece aberto, e sugestões para continuação da pesquisa são dadas.

Made available in DSpace on 2016-03-15T19:38:03Z (GMT). No. of bitstreams: 1 RONALDO DE CASTRO CORREA.pdf: 1467426 bytes, checksum: a5e2b011297c7075c278d2dfd4502c98 (MD5) Previous issue date: 2015-11-23 / Cellular automata are discrete dynamic systems that by local action rules, even very simple, can present arbitrarily complex global processing. The reversibility is a property that a few rules have and guarantees the existence of an inverse rule capable of reversing the temporal evolution of the original rule. For a rule be reversible all possible configurations of lattices must have only one predecessor, i.e., only one pre-image. In this context, it had been proposed in the literature the concept of rules may be characterized by its relative partial reversibility, that is, rules can be more or less reversible than others. This notion is represented by the rule pre-image pattern, which is composed of the quantities ordered pre-images of all the possible configurations of lattices up to a maximum size. To sort the rules of the reversible for less reversible, or group them if they had the same reversibility was made lexicographical ordering patterns of pre-images. This paper reviewed the original definition, based on elementary cellular automata, although the results are applicable to any other one-dimensional family rules. Thus, proposed it was a measure of the reversibility level of a rule, also based on its default pre-image, but now from the probability of correctly reverse each possible configurations of lattices up to a given maximum size. This measure allows us to analyze the degree of reversibility of a rule in absolute terms and not relative to other rules. Thus, it becomes possible to individually analyze the reversibility levels of rules, making it possible to infer the degree of rules reversible for lattices arbitrarily larger than calculated, in particular, identifying rules that tend to be reversible when the size of the lattices tends to infinity. It was also possible to define an operation that, from their own state transitions rule, allows to obtain partially rules that have the same level of reversibility without the need of standard calculating preview image, which is extremely expensive computationally. / Autômatos celulares são sistemas dinâmicos discretos que, por meio de regras de ação local, até mesmo muito simples, podem apresentar processamento global arbitrariamente complexo. A reversibilidade é uma propriedade que poucas regras possuem e que garante a existência de uma regra inversa capaz de reverter a evolução temporal da regra original. Para uma regra ser reversível, todas as configurações possíveis de reticulado devem possuir somente uma única configuração antecessora, ou seja, uma única pré-imagem. Nesse contexto, havia sido proposto na literatura o conceito de regras poderem ser caracterizadas por sua reversibilidade parcial relativa, ou seja, regras poderem ser mais ou menos reversíveis que outras. Essa noção é representada por meio do padrão de pré-imagem da regra, que é composto pelas quantidades ordenadas de pré-imagens de todas as configurações possíveis de reticulado, até um tamanho máximo. Para classificar as regras das mais reversíveis para as menos reversíveis, ou agrupá-las caso possuíssem a mesma reversibilidade, era feita a ordenação lexicográfica dos padrões de pré-imagens. Este trabalho reavaliou a definição original, com base nos autômatos celulares elementares, apesar de os resultados serem aplicáveis a qualquer outra família unidimensional de regras. Assim, foi proposta uma grandeza que representa o nível de reversibilidade de uma regra, também baseada em seu padrão de pré-imagem, mas agora a partir da probabilidade de reverter corretamente cada configuração possível de reticulado, até um tamanho máximo dado. Tal medida permite analisar o nível de reversibilidade de uma regra em termos absolutos, e não mais relativamente a outras regras. Dessa forma, torna-se possível analisar individualmente os níveis de reversibilidade das regras, o que possibilitou inferir o nível de reversibilidade de regras para reticulados arbitrariamente maiores que os calculados, em particular, identificando regras que tendem a ser reversíveis conforme o tamanho do reticulado tende a infinito. Também foi possível definir uma operação que, a partir das próprias transições de estado de uma regra, permite obter parcialmente as regras que possuem o mesmo nível de reversibilidade, sem a necessidade do cálculo do padrão de pré-imagem, que é extremamente custoso computacionalmente.

L’évolution d’une phase microbienne au sein d’un milieu poreux est un processus complexe de par la prise en compte des effets de croissance (ou de mortalité) et d’étalement de la phase cellulaire. D’autres processus tels que l’arrachement d’une partie du biofilm ou l’attachement-détachement de cellules mobiles depuis la phase fluide peuvent aussi contribuer à la variation du volume de biofilm présent. Une meilleure compréhension des interactions mis en jeu entre les processus de croissance de biofilm, du transport de soluté et de l’écoulement et une modélisation rigoureuse de ce processus de croissance à l’échelle microscopique est un enjeu essentiel à une prédiction plus fine du devenir des polluants dans les sols. L’évolution temporelle d’un milieu poreux sous l’effet de l’activité biologique constitue toutefois à l’heure actuelle un défi scientifique majeur d’un point de vue de la modélisation numérique. Les variations locales de la géométrie du domaine (bio-obstruction des pores) induisent en effet une chenalisation de l’écoulement et du transport qui va évoluer au cours du temps. Si différentes méthodes numériques – lagrangiennes ou eulériennes – ont été développées (méthode de capture du front, méthode d’interface diffuse de type « Level Set » ou « Volume Of Fluid »), elles restent souvent peu adaptées à des modélisations 3D à l’échelle du pore (temps de calcul, remaillage parfois nécessaire, problème de gain ou de perte de masse). Nous combinons ici une méthode IBM (Immersed Boundary Method) à une méthode LBM (Lattice Boltzman Method) pour le calcul de l’écoulement en 3D tandis qu’une approche de type VOF (Volume of Fluid) ou par reconstruction d’interface couplée à une discrétisation en Volume Finis est utilisée pour le transport des espèces chimiques. L’intérêt ici de la méthode IB-LBM est de pouvoir bénéficier de la précision de la formulation Lattice- Boltzmann tout en travaillant sur un maillage fixe, un terme correcteur venant modifier la vitesse au voisinage des interfaces mobiles. Le modèle d’écoulement-transport en milieu poreux évolutif développé est ensuite couplé à un modèle d’automate cellulaire prenant en compte les processus d’attachement-détachement. Le modèle est comparé à des benchmarks numériques et utilisé pour étudier les différents régimes de croissance du biofilm en fonction des conditions hydrodynamiques. Dans le dernier chapitre, ce modèle est étendu à la prise en compte d’une phase non-miscible afin d’étudier l’impact des processus de biodégradation sur la dissolution d’une phase polluante piégé. On se limite aux conditions où le NAPL est à saturation résiduelle. L’influence de la production de biosurfactant sur la solubilité du polluant ainsi que la toxicité de celui-ci sur la cinétique de croissance des bactéries est prise en compte. Plusieurs résultats numériques sont présentés afin d’illustrer l’influence des différents paramètres hydrodynamiques sur la dissolution du NAPL. / Mathematical modeling of transport in porous media of organic chemical species in the presence of a bacterial population growing in the form of biofilms is an important area of research for environmental and industrial applications such as the treatment and the remediation of groundwater contaminated by organic pollutants. Biofilms, which are composed of bacteria and extracellular organic substances, grow on the pore-walls of the porous medium. Biodegradable organic solutes are converted into biomass or other organic compounds by the bacterial metabolism. This evolution of the microbial biomass phase within the porous medium is a complex process due mainly to growth (or decay) and spatial spreading of the cellular phase. Processes such as biofilm sloughing and attachment (or detachment) of cells from the fluid phase may also contribute to the biofilm volume variation. In this context, the aim of the thesis is to focus on the mechanisms that control the development of biofilms in porous media and its impact on the hydrodynamic properties of the porous matrix. The objective of this work is to model this pore-scale phenomenon of biofilm growth by integrating the various mechanisms which favor the bacterial development (bacterial proliferation, assimilation of nutrients to synthesize new cellular materials, attachment of cells) or, conversely, which are responsible for slowing down (e.g., detachment of cells, toxicity). An IB-LB model is developed for flow calculation and non-boundary conforming finite volume methods (volume of fluid and reconstruction methods) are used for reactive solute transport. A sophisticated cellular automaton model is developed to describe the spatial distribution of bacteria. Several numerical simulations have been performed on complex porous media and a quantitative diagram representing the transitions between the different biofilm growth patterns was proposed. Finally, the bioenhanced dissolution of NAPL in the presence of biofilms was simulated at the pore scale. The impact of biosurfactants and NAPL toxicity on bacterial growth has been investigated.