O objetivo geral desta tese foi investigar como a distribuição espacial dos indivíduos influencia a organização dos sistemas de acasalamento e a intensidade da seleção sexual. A tese contém dois capítulos em que analisamos dados empíricos e dois capítulo em que abordamos questões mais teóricas mais gerais. No primeiro capítulo, avaliamos como a distribuição espacial de haréns defendidos por machos territoriais influencia a rede de competição espermática que existe entre machos do opilião Serracutisoma proximum. No segundo capítulo, propusemos um modelo probabilístico de escolha de parceiros que leva em consideração o fato de que as fêmeas estão restritas a amostrar apenas alguns machos da população, e que essa restrição é imposta principalmente pela distribuição espacial dos indivíduos. Nosso modelo foi mais acurado do que modelos alternativos que ignoram o espaço. No terceiro capítulo, investigamos os movimentos de busca de parceiros do besouro Leptinotarsa undecimlineata. Encontramos que tanto machos quanto fêmeas se movimentam estrategicamente, saindo de onde estão quando não obtém cópulas buscando áreas próximas e com muitos parceiros em potencial. Finalmente, no quarto capítulo, voltamos a explorar o efeito de restrições espaciais sobre a escolha de parceiros. Usamos simulações baseadas em indivíduos para investigar como a restrição espacial influencia a seleção sexual e a evolução de ornamentos sexualmente selecionados. Encontramos que quanto maior o número de parceiros que as fêmeas podem amostrar durante a escolha, mais intensa é a seleção sexual, o que permite a evolução de ornamentos mais exagerados nos machos. Além disso, analisamos um conjunto de dados publicados sobre a intensidade de seleção sexual e observamos que estes se ajustam às previsões do modelo teórico. Concluímos que o espaço é muito mais importante para a organização de sistemas de acasalamento e para a intensidade da seleção sexual do que se acreditava previamente. Esperamos que as idéias propostas aqui encontrem terreno fértil na mente do leitor e que gerem novos e estimulantes desdobramentos no campo teórico e empírico / The main goal of this thesis was to investigate how the spatial distribution of individuals influences the organization of the mating systems and the intensity of sexual selection. The thesis contains two empirical chapters and two chapters with a theoretical scope. In the first chapter, we investigate how the spatial distribution of harems defended by territorial males influences the sperm competition network among males of the harvestman Serracutisoma proximum. In the second chapter, we proposed a probabilistic model of mate choice that includes the spatial constraint in the analyses of mate choice. This model takes into account the fact that females are restricted to sample only some males available in the population, and that this restriction is imposed primarily by the spatial distribution of individuals. In the third chapter, we investigate the mate searching movements of the leaf beetle Leptinotarsa undecimlineata. We found that both males and females move strategically, leaving the host plant when they do not obtain copulations and seeking neighboring areas with many potential mates. Finally, in the fourth chapter, we explore the effect of spatial restrictions on mate choice. We used individual based simulations to investigate how spatial restrictions influence sexual selection and the evolution of sexually selected ornaments. We found that the higher the number of potential partners female can sample during mate choice, the more intense is sexual selection, which leads to the evolution of more exaggerated male ornaments. In addition, we analyzed a published dataset of intensity of sexual selection and found that the data adjust to the predictions made by our simulations. We conclude that the space is much more important than previously thought to mating systems organization and the intensity of sexual selection. We hope the ideas proposed here can flourish in the minds of the readers, stimulating both empirical and theoretical follow ups

Resource allocation problems have been widely studied according to various scenarios in literature. In such problems, a set of resources must be allocated to a set of agents, according to their own preferences. Self-organization issues in telecommunication, scheduling problems or supply chain management problems can be modeled using resource allocation problems. Such problems are usually solved by means of centralized techniques, where an omniscient entity determines how to optimally allocate resources. However, these solving methods are not well-adapted for applications where privacy is required. Moreover, several assumptions made are not always plausible, which may prevent their use in practice, especially in the context of agent societies. For instance, dynamic applications require adaptive solving processes, which can handle the evolution of initial data. Such techniques never consider restricted communication possibilities whereas many applications are based on them. For instance, in peer-to-peer networks, a peer can only communicate with a small subset of the systems. In this thesis, we focus on distributed methods to solve resource allocation problems. Initial allocation evolves step by step thanks to local agent negotiations. We seek to provide agent behaviors leading negotiation processes to socially optimal allocations. In this work, resulting resource allocations can be viewed as emergent phenomena. We also identify parameters favoring the negotiation efficiency. We provide the negotiation settings to use when four different social welfare notions are considered. The original method proposed in this thesis is adaptive, anytime and can handle any restriction on agent communication possibilities.

ABSTRACT Research in GIScience has identified agent-based simulation methodologies as effective in the study of complex adaptive spatial systems (CASS). CASS are characterized by the emergent nature of their spatial expressions and by the changing relationships between their constituent variables and how those variables act on the system's spatial expression over time. Here, emergence refers to a CASS property where small-scale, individual action results in macroscopic or system-level patterns over time. This research develops and executes a spatially-explicit agent based model of Muscovy Duck home range behavior. Muscovy duck home range behavior is regarded as a complex adaptive spatial system for this research, where this process can be explained and studied with simulation techniques. The general animal movement model framework presented in this research explicitly considers spatial characteristics of the landscape in its formulation, as well as provides for spatial cognition in the behavior of its agents. Specification of the model followed a three-phase framework, including: behavioral data collection in the field, construction of a model substrate depicting land cover features found in the study area, and the informing of model agents with products derived from field observations. This framework was applied in the construction of a spatially-explicit agent-based model (SE-ABM) of Muscovy Duck home range behavior. The model was run 30 times to simulate point location distributions of an individual duck's daily activity. These simulated datasets were collected, and home ranges were constructed using Characteristic Hull Polygon (CHP) and Minimum Convex Polygon (MCP) techniques. Descriptive statistics of the CHP and MCP polygons were calculated to characterize the home ranges produced and establish internal model validity. As a theoretical framework for the construction of animal movement SE-ABM's, and as a demonstration of the potential of geosimulation methodologies in support of animal home range estimator validation, the model represents an original contribution to the literature. Implications of model utility as a validation tool for home range extents as derived from GPS or radio telemetry positioning data are discussed.

Made available in DSpace on 2014-06-11T19:35:44Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-01-10Bitstream added on 2014-06-13T18:47:11Z : No. of bitstreams: 1 giocomini_hc_dr_rcla.pdf: 2415116 bytes, checksum: 60197822e40f54efd586b3c12529038a (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Um modelo baseado no indivíduo para história de vida e interações tróficas de peixes é proposto nesta tese. Ele integra teorias sobre fisiologia, crescimento, reprodução e alimentação num mesmo arcabouço dinâmico. As comunidades são formadas por um processo seqüencial de assembleamento que seleciona espécies com melhor ajuste às condições locais. No capítulo 1, experimentos computacionais foram feitos para avaliar a resposta seletiva de 10 características bionômicas em gradientes de produtividade, taxas de ataque por predadores, distribuição do tamanho corporal no conjunto regional de espécies, e a presença/ausência de assimetrias nas habilidades dos peixes em consumir presas e em evitar predação. Este último fator inclui conflitos funcionais entre a eficiência de captura versus generalidade de dieta e intensidade de forrageamento versus defesa contra predadores. As comunidades resultantes foram fortemente afetadas pelos gradientes. Picos de riqueza ocorrem em produtividades moderadamente baixas, associadas a baixas taxas de ataque, o que pode estar relacionado ao efeito estabilizador de respostas funcionais menos saturadas e às características emergentes das espécies. Com alta disponibilidade de recursos, espécies de rápido crescimento e tamanhos variados dominaram, promovendo rápida depleção dos recursos durante a formação das comunidades e ocasionando fortes efeitos de prioridade. As assimetrias de consumo aumentaram a coexistência onde ela tende a ser mais difícil, mas a diminuíram em seus pontos de pico. Mas seu principal efeito foi o de modificar a composição ao longo dos gradientes, modulando o formato das associações emergentes entre as características biológicas das espécies bem sucedidas. No capítulo 2 foram realizados experimentos de invasão e exclusão, para avaliar como as características das espécies... / An individual-based model for fish life history and trophic interactions is here proposed. It integrates theories for individual physiology, growth, reproduction, and feeding in the same dynamical framework. Communities are formed by a sequential assembly process which selects for species best adjusted to local conditions. Simulation experiments were carried out to evaluate the distribution of diversity and selective response of 10 bionomic features along gradients of resource productivity, predators maximum attack rates, body size distribution in species pool, and the presence/absence of asymmetries in both the abilities of fish to consume prey and to avoid being consumed. This last factor includes tradeoffs concerning capture efficiency versus diet generality and foraging intensity (associated to growth rate) versus defense against predators. The resulting communities were strongly affected by the gradients. Richness peaks are localized at moderately low productivities associated to low maximum attack rates, which might be related to the stabilizing effect of less saturated functional responses and to the emergent features of selected species. At high resource availability, fast growing species with variable sizes dominated, promoting early fast resource depletion during assembly and leading to strong priority effects. The hierarchical consumption asymmetries increased coexistence where it tends to be more difficult, but diminished it at its points of peak. But its main effect was modifying species trait composition along other gradients, modulating the shape of emergent associations among biological features of successful species. Additional invasion and deletion experiments were carried out to evaluate how species and community features are related invasion success and native extinctions. Successful invaders tend to possess similar life-history features to invaded community, but low... (Complete abstract click electronic access below)

L’anchois et la sardine appartiennent à la guilde des petits poissons pélagiques, qui tiennent une place considérable à l’échelle des écosystèmes et des pêcheries. Ces deux espèces sont très largement répandues dans les mers et océans du globe et souvent occupent les mêmes écosystèmes. Leurs populations montrent d’importantes fluctuations interannuelles de biomasses, dont les tendances ne suivent pas les mêmes schémas, voire sont parfois déphasées. Une littérature croissante suggère que ces dynamiques sont dues à des sensibilités relatives aux conditions environnementales différentes induites par des traits biologiques distincts. Bien que de prime abord anchois et sardines semblent très similaires, ils montrent notamment des stratégies alimentaires et reproductives quelque peu différentes. Comprendre ces divergences biologiques et de stratégies d’histoire de vie apparait donc essentiel pour appréhender les dynamiques passées et éventuellement anticiper les évolutions futures de ces stocks. L’objectif de cette thèse est de déterminer en quoi se démarquent ces deux espèces en termes de traits biologiques et d’histoire de vie sur une base physiologique. En effet, du fait de la complexité de potentielles interactions entre les traits biologiques et de leurs évolutions ontogéniques, il convient, pour répondre à cette question, de mettre en œuvre une approche intégratrice via la modélisation bioénergétique à l’échelle du cycle de vie. Dans un premier temps l’étude a été dédiée à un indice de condition : la densité énergétique (contenu énergétique par unité de masse). La densité énergétique résulte de nombreux processus physiologiques, intégrant ainsi l’historique des dépenses énergétiques diverses face aux gains acquis via l’alimentation. L’analyse de cet indice a notamment permis d’identifier divers effets sur la condition énergétique du poisson : l’espèce, la taille, la saison et la zone géographique. En lien avec l’énergie observée, un modèle du cycle de vie a été paramétré pour les deux espèces dans le golfe de Gascogne, afin de disposer d’un outil intégrateur, exploratoire et prédictif. Il s’agit d’un modèle bioénergétique basé sur la théorie du « Dynamic Energy Budget » (DEB). Ce cadre vise à prédire le cycle de vie d’un organisme, en fonction de forçages environnementaux, en simulant la résultante des différents flux d’énergies qui s’y produisent. Cette approche a notamment permis de souligner le caractère particulièrement structurant des stratégies reproductives sur le cycle bioénergétique annuel des deux espèces. / Anchovy and sardine belong to the guild of small pelagic fish and are of peculiar importance at the scales of ecosystems and fisheries. Both species are worldwide spread and commonly occur in the same ecosystems. They display large interannual variability in biomass with markedly different trends or even asynchronous. A growing literature suggests that those dynamics are due to respective sensibility to environmental conditions driven by different biological traits. A priori both species are very similar but show slightly distinct feeding behaviours and reproductive strategies. Understanding divergences in both species biology and life history strategies is thus crucial to understand and predict past and future dynamics of these stocks. The aim of this PHD is to assess how both species diverge in terms of biological and life history traits on a physiological basis. Owing to the complexity of biological traits, potential interactions among these traits and ontogenetic evolutions, to answer this question an integrative approach based on a bioenergetics model of the whole life cycle is requested. First the study focus on a condition index: the energy density (energy content per unit of mass). Energy density integrates historic of numerous physiological processes, both gain from food and diverse metabolic expenses. This analysis shows effects on the bioenergetics cycle of the fish, namely species, size, season and geographic area. Linked with bioenergetics data, a full life cycle model has been parametrised for both species in the Bay of Biscay, in order to get an integrative, predictive and exploratory tool. This model is based on the “Dynamic Energy Budget” theory. This theory aims at predicting the life cycle of an organism, using environmental forcing, by simulating energy fluxes inside the organism. This modelling approach underlines the particularly significant feature of reproductive strategies on the bioenergetics annual cycle of both species.

Cette thèse s'inscrit dans le cadre de la modélisation de systèmes biologiques complexes. En premier lieu (travail en collaboration avec l'équipe de biologistes de Louis Casteilla), nous introduisons un modèle individus-centré pour étudier l'émergence de structures cellulaires de forme lobulaire dans un réseau organisé de fibres. Une étude paramétrique sur les résultats numériques ainsi que des méthodes de traitement d'images sur les données biologiques nous permettent de montrer que l'émergence de structures biologiquement cohérentes peut être reproduite par un modèle basé essentiellement sur des règles mécaniques entre les cellules et le réseau de fibres. L'originalité de ce modèle réside dans la modélisation de structures géométriques complexes (réseaux de fibres) par un ensemble d'unités élémentaires connectées interagissant à l'aide de fonctionnelles simples. Cette nouveauté a donné lieu à d'autres types de travaux en cours présentés comme perspectives directes de ce travail. Les deuxième et troisième parties portent sur la dérivation d'un modèle cinétique puis macroscopique pour étudier la matrice extra-cellulaire dans sa globalité. L'originalité de notre résultat réside dans l'obtention d'un système d'équations fermé décrivant l'évolution de la distribution des fibres individuelles et des liens de fibres. La limite hydrodynamique de l'équation cinétique est obtenue à l'aide de techniques non conventionnelles dû au un manque d'équation de conservation pour le système étudié. Dans le cas d'une densité homogène de fibres, nous prouvons l'existence de solutions au modèle macroscopique, et les simulations numériques montrent une bonne correspondance entre le modèle macroscopique et son homologue microscopique. Finalement (travail en collaboration avec S. Motsch), nous nous intéressons à l'influence d’interactions de type répulsion cellules-cellules dans un modèle de croissance tumorale. Nous montrons que le modèle macroscopique dérivé des équations microscopiques fait apparaître une instabilité et proposons une version modifiée de l'équation macroscopique que nous sommes capables de relier à la dynamique cellulaire. Les simulations numériques montrent la bonne correspondance entre les deux modèles. / In a first part (work in collaboration with the team of biologists of L. Casteilla) we propose an Individual based model for studying the emergence of lobule-like structures of cells in an organized fiber network. A parametric analysis on the numerical results as well as image processing methods on the biological images enable us to show that biologically-relevant structures can be reproduced by a model mostly based on cell-fiber mechanical interactions. The originality of this model mainly relies in the modelling of complex geometrical structures such as fiber networks as sets of connected elementary units interacting through simple functionals. This novelty has been used to build other types of models presented as direct perspective of this work. The second and third parts lie in the derivation of kinetic and macroscopic models for an interconnected fiber network, closely linked to the microscopic one. The originality of this work lies in the obtained closed system of two evolution equations: one for the distribution of individual fibers and one for the fiber links. In the case of homogeneous fiber density, we show existence of stationary solutions to the macroscopic equation, and numerical simulations show the good correspondence between the microscopic and macroscopic models. Finally (work in collaboration with S. Motsch), we are interested in the role of cell-cell interactions in the invasion properties (speed, geometry...) of a growing mass of cells. We show that the macroscopic model derived from the microscopic one features instabilities, and we propose a modified macroscopic model that we are able to link to the particle dynamics. The numerical simulations show the relevance of the macroscopic model to describe the microscopic dynamics at large scale.

Les patrons récursifs de déplacement, où l’individu revient à des sites déjà visités, sont très répandus. L’utilisation de la mémoire, supposée être avantageuse lorsque l’environnement est prévisible, pourrait être sous-jacente à l’émergence de ces patrons. Cependant, notre compréhension de l’interface mémoire-déplacement a jusqu'à présent été limitée par un manque de méthodes adaptées et d’investigation théorique des avantages de l’utilisation de la mémoire et des patrons qui en émergent. Au cours de cette thèse j’ai cherché à combler en partie ces manques. Je propose ici trois nouveaux cadres d'analyse des patrons récursifs de déplacement. Le premier délimite les zones les plus fréquemment revisitées par un individu, le deuxième détecte la périodicité dans les revisites de sites connus, et le troisième définit formellement et quantifie la routine de déplacement en termes de répétitivité de la séquence de déplacement, et propose un algorithme pour détecter les sous-séquences répétées. A l'aide d'un modèle individu-centré, nous montrons que l'utilisation de la mémoire dans un environnement prévisible est très avantageuse énergétiquement comparée à une stratégie de recherche sans mémoire, y compris en situation de compétition, et qu'elle mène à l'émergence de domaines vitaux stables et à la ségrégation spatiale entre individus. L'utilisation de la mémoire invalide plusieurs hypothèses très courantes faites par les études populationnelles, en menant à une forte déplétion de l’environnement, à une augmentation de la taille de la population à l’équilibre, et à une relation non linéaire entre la taille de population totale et l’intensité de compétition localement ressentie par les individus. Ainsi, ma thèse contribue à une meilleure compréhension des conséquences de la mémoire sur la valeur sélective des individus, sur les patrons de déplacement, et sur la démographie des populations. Elle propose des méthodes innovantes pour quantifier et caractériser les patrons récursifs de déplacement pouvant émerger de son utilisation. Ces méthodes devraient ouvrir de nouvelles opportunités de comparaisons entre individus de différentes populations ou espèces qui permettront le test d'hypothèses sur les pressions de sélection favorisant l'utilisation de la mémoire. / Recursive movement patterns, by which an individual returns to already visited sites, are very common. Memory use, hypothesized to be advantageous when the environment is predictable, could underlie the emergence of these patterns. However, our understanding of the memory-movement interface has been limited by two knowledge gaps. We still lack appropriate methodologies and theoretical knowledge of the advantages of memory use and of the patterns that emerge from it. During this PhD project, I aimed at filling in some of these gaps. I present here three new frameworks for the analysis of recursive movement patterns. The first one delimits the areas most frequently revisited by an individual, the second one detects periodic revisit patterns, and the third one formally defines and quantifies routine movement behaviour in terms of movement sequence repetitiveness, and presents an algorithm that detects the sub-sequences that are repeated. Using an individual-based model, we show that memory use, when the environment is predictable, is very energetically advantageous compared to foraging strategies that do not use memory, including in a situation of competition, and that it leads to the emergence of stable Home Ranges and spatial segregation between individuals. Memory use invalidates several hypotheses very commonly made in population studies, by leading to a stronger environmental depletion, to a higher equilibrium population size, and to a nonlinear relationship between the total population size and the individually-experienced intensity of competition. Therefore, my PhD thesis contributes to a better understanding of the consequences of memory use for the fitness of individuals, for movement patterns, and for population dynamics. It offers innovative methodologies that quantify and characterize recursive movement patterns that can emerge from its use. These methods should open new opportunities for the comparison of the movements of individuals from different populations and species, and thus the testing of hypotheses about the pressures that select for memory use.

O objetivo geral desta tese foi investigar como a distribuição espacial dos indivíduos influencia a organização dos sistemas de acasalamento e a intensidade da seleção sexual. A tese contém dois capítulos em que analisamos dados empíricos e dois capítulo em que abordamos questões mais teóricas mais gerais. No primeiro capítulo, avaliamos como a distribuição espacial de haréns defendidos por machos territoriais influencia a rede de competição espermática que existe entre machos do opilião Serracutisoma proximum. No segundo capítulo, propusemos um modelo probabilístico de escolha de parceiros que leva em consideração o fato de que as fêmeas estão restritas a amostrar apenas alguns machos da população, e que essa restrição é imposta principalmente pela distribuição espacial dos indivíduos. Nosso modelo foi mais acurado do que modelos alternativos que ignoram o espaço. No terceiro capítulo, investigamos os movimentos de busca de parceiros do besouro Leptinotarsa undecimlineata. Encontramos que tanto machos quanto fêmeas se movimentam estrategicamente, saindo de onde estão quando não obtém cópulas buscando áreas próximas e com muitos parceiros em potencial. Finalmente, no quarto capítulo, voltamos a explorar o efeito de restrições espaciais sobre a escolha de parceiros. Usamos simulações baseadas em indivíduos para investigar como a restrição espacial influencia a seleção sexual e a evolução de ornamentos sexualmente selecionados. Encontramos que quanto maior o número de parceiros que as fêmeas podem amostrar durante a escolha, mais intensa é a seleção sexual, o que permite a evolução de ornamentos mais exagerados nos machos. Além disso, analisamos um conjunto de dados publicados sobre a intensidade de seleção sexual e observamos que estes se ajustam às previsões do modelo teórico. Concluímos que o espaço é muito mais importante para a organização de sistemas de acasalamento e para a intensidade da seleção sexual do que se acreditava previamente. Esperamos que as idéias propostas aqui encontrem terreno fértil na mente do leitor e que gerem novos e estimulantes desdobramentos no campo teórico e empírico / The main goal of this thesis was to investigate how the spatial distribution of individuals influences the organization of the mating systems and the intensity of sexual selection. The thesis contains two empirical chapters and two chapters with a theoretical scope. In the first chapter, we investigate how the spatial distribution of harems defended by territorial males influences the sperm competition network among males of the harvestman Serracutisoma proximum. In the second chapter, we proposed a probabilistic model of mate choice that includes the spatial constraint in the analyses of mate choice. This model takes into account the fact that females are restricted to sample only some males available in the population, and that this restriction is imposed primarily by the spatial distribution of individuals. In the third chapter, we investigate the mate searching movements of the leaf beetle Leptinotarsa undecimlineata. We found that both males and females move strategically, leaving the host plant when they do not obtain copulations and seeking neighboring areas with many potential mates. Finally, in the fourth chapter, we explore the effect of spatial restrictions on mate choice. We used individual based simulations to investigate how spatial restrictions influence sexual selection and the evolution of sexually selected ornaments. We found that the higher the number of potential partners female can sample during mate choice, the more intense is sexual selection, which leads to the evolution of more exaggerated male ornaments. In addition, we analyzed a published dataset of intensity of sexual selection and found that the data adjust to the predictions made by our simulations. We conclude that the space is much more important than previously thought to mating systems organization and the intensity of sexual selection. We hope the ideas proposed here can flourish in the minds of the readers, stimulating both empirical and theoretical follow ups

Les systèmes bactériens sont complexes et adaptatifs. Soumis à des perturbations, telles qu’un traitement antibiotique, ils survivent, se régénèrent et évoluent. Ceci est d’autant plus vrai pour les biofilms, capables de surmonter des traitements létaux à des bactéries planctoniques. La capacité des systèmes à retrouver leur équilibre initial, certaines fonctions ou compositions après un choc est appelée résilience. La résilience est souvent considérée comme complémentaire à la résistance en écologie. Pourtant, la résilience aux antibiotiques reçoit peu de considération en comparaison de la résistance aux antibiotiques en bactériologie. L’une des raisons de ce désintérêt est que ce concept est souvent mal défini et ambigu. Dans cette thèse, nous proposons tout d’abord une base conceptuelle de la résilience aux antibiotiques. A partir de l’analyse de différentes définitions existantes de la résilience, nous fournissons une démarche pour formaliser le concept de résilience dans le contexte d’une population bactérienne soumise à des traitements antibiotiques. De cette première analyse, le mécanisme biologique de persistance bactérienne est ressorti comme important dans la résilience aux antibiotiques. Ce phénomène repose sur la formation de cellules tolérantes aux antibiotiques, les persisters, dont la formation est influencée par les conditions environnementales. Afin de relier la formation des persisters aux conditions environnementales, nous avons développé des modèles mathématiques de transition phénotypique entre cellules sensibles et persisters que nous avons calibrés et testés à l’aide de données expérimentales. Enfin, nous avons étudié l’effet de la persistance bactérienne sur la résilience aux antibiotiques des biofilms. Pour cela, nous avons développé un modèle individu-centré de biofilm intégrant des transitions entre cellules sensibles et persisters. Différentes stratégies de transition ont été reliées à la capacité des biofilms à croître, survivre et se régénérer après un choc antibiotique. La mise en place d’expériences capables de fournir des données à comparer aux simulations est proposée dans la discussion de cette thèse. Cette thèse contribue à la clarification du concept de résilience aux antibiotiques et à la compréhension du phénomène de persistance bactérienne dans les biofilms. Elle ouvre des perspectives sur l’utilisation du concept de résilience en bactériologie clinique et souligne l’importance de l’hétérogénéité des populations bactériennes dans leur capacité à confronter les perturbations et évoluer. / Bacterial systems are complex and adaptive. When faced with disturbances, such as antibiotic treatments, they survive, recover and evolve. This is particularly true for biofilms, which survive treatments that planktonic cells cannot overcome. The capacity of systems to recover their initial state, some of their functions or composition after a disturbance is called resilience. The resilience concept is often considered complementary to resistance in ecology. However, antibiotic resilience has received little attention compared to antibiotic resistance. One reason of this lack of interest comes from the fact that the resilience concept is often poorly defined and ambiguous. In this thesis, we firstly developed a conceptual framework of antibiotic resilience and applied this framework to the case of a bacterial population faced with antibiotics. This analysis highlighted the importance of the biological mechanism of bacterial persistence. This phenomenon is based on the formation of sub-populations of antibiotic tolerant cells, the persisters, which is influenced by environmental conditions. To relate persister formation to environmental conditions, we developed mathematical models of phenotypic switches between susceptible and persister cells and calibrated and tested them with experimental data. Lastly, we studied the influence of bacterial persistence on biofilm antibiotic resilience. For this purpose, we developed an individual-based model of biofilm with phenotypic switches between susceptible and persister cells. Different strategies of phenotypic switches were related to the dynamics of growth, survival and recovery of bacterial biofilms faced with antibiotic shocks. The setting up of experimentations to obtain data to compare to simulations is presented in the discussion of this thesis. Globally, this thesis contributes to the clarification of the concept of antibiotic resilience and to the understanding of bacterial persistence in biofilms. It gives new perspectives on the use of the resilience concept in clinical bacteriology and emphasizes the importance of the heterogeneity of bacterial populations in their capacity to face disturbances and evolve.

Dans cette thèse nous nous sommes intéressés à la formation des bancs de poissons et à l'étude des interactions proies-prédateurs en présence de comportements collectifs par une approche de modélisation. Ce phénomène, bien qu'il soit le résultat d'interactions qui ont lieu à l'échelle individuelle, il engendre des conséquences à plus grande échelle, spatiale ou temporelle. L'objectif principal de cette thèse a été celui de comprendre l'influence du processus d'agrégation sur la réponse fonctionnelle. Nous avons élaboré un modèle centré sur l'individu (IBM) qui décrit les interactions intra-spécifiques ainsi que celle entre proies et prédateurs. Les agents peuvent ou pas avoir du comportement collectif.Dans un premier modèle les prédateurs sont attirés par les proies qu'ils voient. Ensuite, nous avons ajouté une composante à la vitesse du prédateur dépendante du bruit émis par les proies. Pour les deux cas, nous avons comparé les réponses fonctionnelles dans quatre configurations différentes. Nos résultats suggèrent que la prédation est plus efficace lorsque les proies s'agrègent. De plus, deux différents types de réponse fonctionnelle émergent : celle de Holling type II si les proies ne forment pas des bancs, celle de Holling type III autrement.Ensuite, nous nous sommes focalisés sur les conséquences à l'échelle de la population d'un phénomène (l'agrégation) se déroulant à l'échelle individuelle. Nous avons cherché un indice capable de détecter les bancs dans l'espace. Ensuite, en suivant une démarche mathématique, nous avons écrit une équation aux dérivées partielles représentant l'évolution spatio-temporelle de la densité des proies. / This thesis deals with the modelling of schooling phenomena and its consequences on predator-prey dynamics. Many marine species exhibit collective behaviour. While this phenomenon depends on individual interactions, it can have important effects at larger spatial and temporal scales.The main goal of this work is to understand the influence of aggregation on functional response, which represents predator feeding behaviour. We elaborated an individual-based model (IBM) describing schooling behaviour as well as predator-prey interactions. Predators can either be attracted towards visible prey, or hear, and so move towards, the noise produced by prey at a larger distance and then attack once they are close enough to see them. We analysed four different configurations, in which prey and/or predators can school or just move randomly. Our results shown an increased predation efficiency when prey school, and also different functional response shapes: Holling type II emerges if prey do not aggregate, while Holling type III emerges when prey school. Then, we focused on schooling consequences at higher scale. In particular, we analysed how to fit classical models to our emergent functional responses. Moreover, we found out a possible way to detect aggregates. Finally, we wrote a model representing the spatio-temporal evolution of prey density.