Thèses sur le sujet « Adaptation (biologie) – Modèles mathématiques »
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Chabrol, Olivier. « Modèles et algorithmes pour l'évolution biologique ». Thesis, Aix-Marseille, 2017. http://www.theses.fr/2017AIXM0625.
Texte intégralIn this thesis, we studied questions about biological evolution by using mathematical models and bio-informatic algorithms. This work is at the intersection of mathematics, computer science and biology.The major question addressed in this thesis is the detection molecular basisof phenotypic convergence. Evolutionary convergence is the process by which independent species develop similar traits. This evolutionary process is strongly related to fundamental questions such as the role of adaptation .After pointing out different biological concepts linked to evolutionary convergence, we proposed a novel approach combining an original measure of the extent to which a site supports a phenotypic convergence to a binary trait. Thismeasure is based on the “convergence level” of a site which is a mathematical expectation under Markov evolutionary model. We proposed a polynomial time algorithm to compute this index. Our algorithm outperformed two previous algorithms in distinguishing simulated convergent sites from non-convergent ones. With the aim to study the evolutionary convergence of continuous traits, like weight and size, we tried to detect change in evolutionary trends of continuous characters along the tree of life. We proposed a novel method based on anasymmetric version of the linear parsimony, for determining the position of the change in trend which minimizes the total evolutionary cost of the tree. By using the approach on two biological datasets, we obtained results consistentwith those given by previous stochastic approaches
Kucharavy, Andrei. « Molecular mechanisms of aneuploidy-mediated stress-resistance ». Electronic Thesis or Diss., Paris 6, 2017. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2017PA066734.pdf.
Texte intégralAneuploidy has historically been associated with detrimental phenotypes and diseases, notably cancer and Down Syndrome. However, recent experimental evidence suggests aneuploidy provides adaptation to numerous stressors, including drug resistance, making aneuploidy study critical to biomedical research. However, the molecular mechanisms underlying this process remained elusive until now. This work focused on exploring several approaches to understanding those mechanisms. Frist, we have developed a general mathematical model of organism adaptation to adverse environments. In our model, the adaptation to environments takes place as a trade-off in the space of traits, of which aneuploidy allows a more efficient and rapid sampling. This model was validated on experimental data and used to predict optimal drug combinations targeting heterogeneous populations breast tumor cells. Second, we used the framework of network biology to model biomolecular networks and apply to them results from the graph theory and existing results on weighted graphs from other domains. We were able to predict the distribution of essential genes, lethal genetic interactions and essential evolvable genes - essential genes that can be deleted in the aneuploid background. We were as well able to build a predictive model for inferring most likely pathways underlying the phenotype of large-scale genetic perturbations. Finally, we attempted to explore several possible modes besides dosage effects by which aneuploidy could impact the gene expression regulation. This required a development of an image analysis toolkit that was validated and released for as open-source software
Taing, Cécile. « Dynamique de concentration dans des équations aux dérivées partielles non locales issues de la biologie ». Thesis, Sorbonne université, 2018. http://www.theses.fr/2018SORUS077.
Texte intégralThis thesis focuses on the dynamics of Dirac mass concentrations in non-local partial differential and integro-differential equations motivated by evolutionary biology. We consider population models structured in phenotypical traits and, taking into account adaptation and mutation phenomena, we aim to describe the selection of the fittest traits in a given environment. The mathematical modeling of these biological problems leads to nonlinear and nonlocal equations, with a small parameter that induces two time-scales. The asymptotic solutions to these equations are population distributions on the traits space and concentrate in Dirac masses located on the dominant traits. In the first part, we study the Dirac mass dynamics in a chemostat model, using a Hamilton-Jacobi formulation. The chemostat model is a system of equations describing the dynamics of consumers and nutrients in a bioreactor. In a second part, we investigate a competition model structured in age and phenotypical traits. By means of an appropriate factorization, we obtain the asymptotic limit of the solution as a decomposition into two profiles, one in age, the other in traits. When mutations are introduced, a Hamilton-Jacobi equation arises and we prove a uniqueness result of the solution to this equation in the framework of viscosity solutions. The last part is devoted to sexual population models. These models under investigation include asymmetric trait heredity or asymmetric trait-dependent fecundity between the parents: each individual inherits mostly its traits from the female
Hass, Vincent. « Modèles individu-centrés en dynamiques adaptatives, comportement asymptotique et équation canonique : le cas des mutations petites et fréquentes ». Electronic Thesis or Diss., Université de Lorraine, 2023. http://www.theses.fr/2023LORR0165.
Texte intégralAdaptive dynamics theory is a branch of evolutionary biology which studies the links between ecology and evolution. The biological assumptions that define its framework are those of rare and small mutations and large asexual populations. Adaptive dynamics models describe the population at the level of individuals, which are characterised by their phenotypes, and aim to study the influence of heredity, mutation and selection mechanisms on the long term evolution of the population. The success of this theory comes in particular from its ability to provide a description of the long term evolution of the dominant phenotype in the population as a solution to the “Canonical Equation of Adaptive Dynamics” driven by a fitness gradient, where fitness describes the possibility of mutant invasions, and is constructed from ecological parameters. Two main mathematical approaches to the canonical equation have been developed so far: an approach based on PDEs and a stochastic approach. Despite its success, the stochastic approach is criticised by biologists as it is based on a non-realistic assumption of too rare mutations. The goal of this thesis is to correct this biological controversy by proposing more realistic probabilistic models. More precisely, the aim is to investigate mathematically, under a double asymptotic of large population and small mutations, the consequences of a new biological assumption of frequent mutations on the canonical equation. The goal is to determine, from a stochastic individual-based model, the long term behaviour of the mean phenotypic trait of the population. The question we ask is reformulated into a slow-fast asymptotic analysis acting on two eco-evolutionary time scales. A slow scale corresponding to the dynamics of the mean trait, and a fast scale corresponding to the evolutionary dynamics of the centred and dilated distribution of traits. This slow-fast asymptotic analysis is based on averaging techniques. This method requires the identification and characterisation of the asymptotic behaviour of the fast component and that the latter has ergodicity properties. More precisely, the long time behaviour of the fast component is non-classical and corresponds to that of an original measure-valued diffusion which is interpreted as a centered Fleming-Viot process that is characterised as the unique solution of a certain martingale problem. Part of these results is based on a duality relation on this non-classical process and requires moment conditions on the initial data. Using coupling techniques and the correspondence between Moran's particle processes and Kingman's genealogies, we establish that the centered Fleming-Viot process satisfies an ergodicity property with exponential convergence result in total variation. The implementation of averaging methods, inspired by Kurtz, is based on compactness-uniqueness arguments. The idea is to prove the compactness of the laws of the couple made up of the slow component and the occupation measure of the fast component and then to establish a martingale problem for all accumulation points of the family of laws of this couple. The last step is to identify these accumulation points. This method requires in particular the introduction of stopping times to control the moments of the fast component and to prove that they tend to infinity using large deviation arguments, to reduce the problem initially posed on the real line to the torus case in order to prove compactness, to identify the limit of the fast component by adapting an argument based on Dawson duality, to identify the limit of the slow component and then to move from the torus to the real line
Fumey, Julien. « Tempo et mode de l'évolution des populations cavernicoles de l'espèce Astyanax mexicanus ». Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLS528/document.
Texte intégralThe fish Astyanax mexicanus is a particularly suitable model for evolutionary biology studies. Indeed, in this species there are several subterranean populations which live in the total and permanent darkness of cave. These cavefish are well adapted to the life in this inhospitable environment and they show several differences with their surface conspecific such as depigmentation, eye loss and behavioral changes. A major unresolved issue is about the relative role of surface fish standing genetic variation and de novo mutations appeared in cavefish populations after their settlement in caves in their phenotypic evolution. In order to examine this issue, accurate estimations of population ages are very important because many new mutations cannot appear and fix in a recent population. In this thesis we aimed to estimate the age of the Pachón cave population which is considered as one of the oldest and most isolated populations. We developed a new method which is based on measures of the distribution of single nucleotide polymorphism within each population and between populations. Our results, as well as reanalyses of published data about mitochondrial haplotypes and microsatellite loci polymorphism suggest that cavefish populations are much more recent than previously thought (several thousand years and not several hundred thousand years). The consequences of a fast tempo of evolution on the mode of evolution of cavefish are also discussed
Collot, Dorian. « Modélisation des dynamiques adaptatives de la levure de boulanger S. cerevisae dans un environnement saisonnier ». Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS179/document.
Texte intégralAdaptation of species to their environment involves combinations of traits, and in particular life history traits, that influence an organism's selective value. To understand the complexity of adaptation, it is appropriate to decipher the contributions of traits to fitness in the presence of different biotic and abiotic environments. In this thesis, I have investigated fitness components when the environment is seasonal, revealing how such components drive the evolutionary dynamics of quantitative traits.My work is based on the mathematical modeling of experimental evolutions in successive batch cultures of Saccharomyces cerevisiae (baker's yeast). The life cycle of this yeast species is of the respiration-fermentation type: (i) in the presence of glucose, it grows by fermentation, transforming glucose into ethanol; (ii) once glucose has been consumed, it grows by respiration, consuming this time ethanol. This sequence corresponds to the two « seasons » in a batch culture and leads to a cycle of successive batches if cells are periodically transferred into fresh medium. By using differential equations for the time courses, my thesis work shows how growth dynamics and environmental features (abiotic or biotic) generate selection pressures on the different traits during these successive seasons, thereby determining evolutionary trajectories.To describe batch dynamics, I first developed and calibrated a set of differential equations describing the growth dynamics of a population of yeast cells throughout a batch, allowing for one or multiple strains to be present (Chapter 1). Based on this model where cells divide without changing genotype, I then showed that a strain's fitness can be understood in terms of just a few components that are easily specified mathematically. I was then able to determine which traits were under selection and how the corresponding selection pressures were affected by the abundances of each strain in the yeast population (Chapter 2). Selected traits were found to be of two types: life history traits associated with growth and mortality rates, and “transition” traits that correspond to the way a strain reacts to environmental change. I also showed that the contributions of the different fitness components are tied to both selected and non-selected traits via the lengths of seasons. Thus, during population dynamics arising across successive batches, these components change, modifying the selection pressure on each trait. One therefore has a feedback loop, revealing why fitness is frequency-dependent in this system.Next, using the fitness decomposition, I studied adaptive dynamics in successive batch cultures. In such a framework where genotypic changes were allowed, and assuming that there was a trade-off between two traits, I showed that adaptive evolutionary dynamics could lead to the emergence of new relations between selected and non-selected traits (Chapter 3).Furthermore, in order to compare my theoretical predictions to experimental results, I used mathematical and statistical models to analyze two datasets (Chapter 4). The first dataset provides trait measurements in “evolved” strains, i.e., strains obtained after evolution across successive batches, as well as of those same traits in the “ancestral” strains at the origin of the experimental evolution. Parameters inference for the different strains showed that selection had operated mainly on ethanol-related traits (production and consumption). A second dataset was obtained from batch experiments putting strains in competition with one another; the analysis showed that my theoretical modeling well predicted the roles of the different traits for determining the relative fitness of the strains
Pellegrin, Xavier. « Oscillations dans des modèles mathématiques issus de la biologie ». Paris 7, 2014. http://www.theses.fr/2014PA077263.
Texte intégralLn this report, we focus on mathematical analysis of two models coming from biology. The first model, a Kuramoto model, describes the time-evolution of a large number of mean-field coupled phase oscillators. The second one is an original oscillation model, based on a singuiar perturbation of a delayed differential equation. It had been introduced in relation with oscillatory patterns observed in neural networks, and it is subject fo mathematical analysis since the 1980's
Bois, Richard. « Adaptation de maillages anisotropes par un estimateur d'erreur hiérarchique ». Thesis, Université Laval, 2012. http://www.theses.ulaval.ca/2012/29273/29273.pdf.
Texte intégralIn this thesis, we present a new hierarchical error estimator that can be used in a mesh adaptation algorithm to obtain a more accurate approximation to the solution of a partial differential equation. This error estimator has many advantages that other existing error estimators do not have or lack of. For instance, it is, by construction, independant of the differential operator used to model a certain physical phenomena. It is also naturally generalisable to the case of approximations of arbitrary order, and this, without any specific treatment to the underlying theory. Finally, it is efficient, optimal in a sense that will be defined and permits the elements to stretch in a priviledged direction (anisotropy) in order to obtain high accuracy against regularly refined meshes. Many examples are given in the one, two and three dimensional cases. Analytical examples (the solution is known) is given to measure the effiency and precision of the new error estimator. Other examples of mesh adaptation for equations modeling different physical phenomena like the flow of a fluid around a cylinder, unsteady diffusion and contact between deformable elastic bodies are presented. These examples show that the new error estimator can be used for a wide variety of problems.
Yoccoz, Gilles Nigel. « Le rôle du modèle euclidien d'analyse des données en biologie évolutive ». Lyon 1, 1988. http://www.theses.fr/1988LYO10111.
Texte intégralWane, Bocar Amadou. « Adaptation de maillages et méthodes itératives avec applications aux écoulements à surfaces libres turbulents ». Thesis, Université Laval, 2012. http://www.theses.ulaval.ca/2012/29353/29353.pdf.
Texte intégralCardin-Bernier, Guillaume. « Simplification de modèles mathématiques représentant des cultures cellulaires ». Thèse, Université de Sherbrooke, 2015. http://hdl.handle.net/11143/8159.
Texte intégralCalcagno, Vincent. « Coexistence des espèces, assemblage des communautés et spéciation : rôle de la sélection naturelle : quelques modèles et expériences ». Montpellier 2, 2007. http://www.theses.fr/2007MON20171.
Texte intégralKouressy, Mamoutou. « Adaptation agro-écologique et potentialité des sorghos photopériodiques à paille courte au Mali ». Montpellier, ENSA, 2007. http://www.theses.fr/2007ENSA0024.
Texte intégralAndrade, Restrepo Martín. « Mathematical modeling and evolutionary processes ». Thesis, Sorbonne Paris Cité, 2019. http://www.theses.fr/2019USPCC021.
Texte intégralThe research presented in this thesis concerns different topics in the field of Biomathematics. I address diverse questions arising in biology (and related to complex systems) with mathematical and numerical methods. These questions are: (i) Are passive-processes enough to justify the asymmetric distribution of damaged proteins during and after yeast cytokinesis? (ii) What processes are behind the complex patterns of expansion of Amyloid beta in the brains of patients with Alzheimer’s disease? (iii) What is behind the clustering and cline-like dichotomy in models of evolution along environmental gradients? (iv) How does this dichotomy affect the spatial dynamics of invasions and range expansions? (v) How does multi-stability manifest in these models? These questions are approached (at different scales, some fully and some partially) with different theoretical methods. Results are expected to shed light on the biological processes analyzed and to motivate further experimental and empirical work which can help solve lingering uncertainties
Baup, Stéphane. « Elimination de pesticides sur lit de charbon actif en grain en présence de matière organique naturelle : élaboration d'un protocole couplant expériences et calculs numériques afin de simuler les équilibres et les cinétiques compétitifs d'adsorption ». Poitiers, 2000. https://tel.archives-ouvertes.fr/tel-00983252.
Texte intégralSoukane, Sofiane. « Modélisation des réacteurs de cvd par adaptation du code de calcul estet ». Toulouse, INPT, 1998. http://www.theses.fr/1998INPT004G.
Texte intégralCosta, Manon. « Modélisation probabiliste et éco-évolutionnaire des communautés proies-prédateurs ». Palaiseau, Ecole polytechnique, 2015. http://www.theses.fr/2015EPXX0038.
Texte intégralLesquoy-de, Turckheim Élisabeth. « Statistique et biologie : quelques exemples de modélisation ». Paris 11, 1985. http://www.theses.fr/1985PA112382.
Texte intégralThis thesis is a collection of five papers. Three of them are collective papers including biologists and show an example of the uses of statistics in biology. One is a methodological hint about regression models and the last presents the probabilistic bases for modelling survival analysis with point processes
Mirrahimi, Sepideh. « Phénomènes de concentration dans certaines EDPs issues de la biologie ». Paris 6, 2011. http://www.theses.fr/2011PA066165.
Texte intégralGuégan, Damien. « Modélisation numérique d'écoulements bifluides 3 D instationnaires avec adaptation de maillage ». Nice, 2007. http://www.theses.fr/2007NICE4097.
Texte intégralThe purpose of this thesis is to develop a numerical method dedicated to the prediction of multifluid flows. We work with unsteady Navier-Stokes equations. The fluids are considered incompressible and immiscible. We use a projection method to discretize these equations, whereas interface tracking is enforced by the Level Set method. We propose a sharp interface method, the Ghost Fluid Method, to take into account a thin interface discontinuity, on unstructured meshes. We present a comparison with dispersed interface method. An important part of our work is devoted to the development of a coupling between Navier-Stokes solver and mesh adaptation technique. After the description of these technique, we propose solutions to efficiently adapt meshes to bifluid flows. Our approach is validated on academic tests cases and tested on several simulations 2D and 3D more complicated. Comparisons with experiments are presented
Mesplé, Fabrice. « Modélisation des processus biologiques et physico-chimiques dans un écosystème aquatique eutrophe : le lagunage à haut rendement ». Montpellier 1, 1993. http://www.theses.fr/1993MON13514.
Texte intégralDiaz-Zuccarini, Vanessa Alexandra. « Étude des conditions d'efficacité du ventricule gauche par optimisation téléonomique d'un modèle de son fonctionnement ». Lille 1, 2003. https://pepite-depot.univ-lille.fr/LIBRE/Th_Num/2003/50376-2003-287-288.pdf.
Texte intégralDevys, Anne. « Modélisation, analyse mathématique et simulation numérique de problèmes issus de la biologie ». Thesis, Lille 1, 2010. http://www.theses.fr/2010LIL10087/document.
Texte intégralWe investigate four models coming from biological contexts. The first one concerns a model describing the growth of a population of tumors. This model leads to a McKendrick–Von Foerster equation : a conservation law with a non–local boundary condition. We prove the existence and unicity of a solution, then we study, using the general relative entropy, its asymptotic behavior. We provide numerical simulations using WENO scheme. The second part concerns the modelisation of the respiration. First we study the air flux in the bronchial tree using a mulstiscale model. The system present non–usual dissipative boundary conditions. The numerical scheme we use is based on a decomposition idea that reduce the system to the resolution of Stokes problems with standard Dirichlet–Neumann conditions. Then, we propose a model concerning the gas exchanges bringing to light the heterogeneity of the absorption of oxygen along the bronchial tree. The third part concerns the MAPK cascade in Xenopus oocytes. The modelisation leads to an equation of KPP type. A mathematical study shows the existence of travelling waves. Then we provide a detailed numerical study of the system. Finally, the last part, concerns the system of Patlak–Keller–Segel 1D after blow–up. The mathematical study provide a description of the system after blow–up, based on the notion of default meausure. Then we propose a numerical scheme, adopting the optimal transport viewpoint and allowing to simulate the system after blow–up
Poreau, Brice. « Biologie et complexité : histoire et modèles du commensalisme ». Phd thesis, Université Claude Bernard - Lyon I, 2014. http://tel.archives-ouvertes.fr/tel-01063917.
Texte intégralTournoud, Maud. « Adaptation du modèle de temps de promotion à l'étude du délai de détection du VIH chez l'enfant et de la survenue d'autres maladies infectieuses ». Lyon 1, 2006. http://www.theses.fr/2006LYO10166.
Texte intégralTo study the delay between transmission and detection of an infectious disease, particularly in situation of multiple exposures, we have developed a survival model, adapted to interval censored data. Initially developed in cancerology, this model enables to take into account a proportion of patients who will not undergo the studied event, ie. Patients who were not contaminated. In a first example that deals with mother-to-child transmission of HIV-1 in South Africa, we have studied the influence of infant feeding practices (formula, exclusive breastfeeding or mixed feeding) on the probability of HIV-1 transmission at birth and during breastfeeding. It was shown that the probability of transmission at birth was not significantly modified by early breastfeeding practice. While breastfeeding continued to be exclusive there was a negligible risk of transmission in comparison with that observed with mixed feeding. In a second example on nosocomial urinary tract infections in intensive care units, it was shown that the proportion of infections attributable to the catheter placement was ten fold smaller than the proportion of infections attributable to its long-term use
André, Jean-Baptiste. « Niveaux de sélection chez les microparasites : virulence, coopération, mutation ». Montpellier 2, 2003. http://www.theses.fr/2003MON20172.
Texte intégralElhallaoui, Menana. « Modélisation moléculaire d'antagonistes non compétitifs du récepteur NMDA [N-Méthyl-D-aspartate] ». Bordeaux 2, 1994. http://www.theses.fr/1994BOR2B003.
Texte intégralDuverger, Corinne. « Théorie évolutionnaire et modèles métaphoriques : étude des liens entre l'économie et la biologie ». Dijon, 1993. http://www.theses.fr/1993DIJOE011.
Texte intégralThis work is concerned by the links between economy and biology in order to understand why economists use biological theory of natural selection. In the first part, we have studied the nature and the function of metaphor and examined links between metaphor and economic models. We have not omitted the relations with the philosophical literature about the cognitive force and linguistic structure of metaphor. And so, we have explained why the gary Becker's model of altruism is perfectible. In the second part, we have studied the links between the theory of games and the evolutionary theory. And we have shown the evolutionary stable strategy can be used in economy and biology
Baratchart, Etienne. « Etude quantitative des aspects dynamiques et spatiaux du développement métastatique à l'aide de modèles mathématiques ». Thesis, Bordeaux, 2016. http://www.theses.fr/2016BORD0023/document.
Texte intégralIn this thesis, a quantitative study of the metastatic process in the mouse has been performed thanks to mathematical modeling. Precisely, longitudinal data of the total metastatic burden and MRI data on the macrometastatic size distribution are confronted to a mathematical model describing the metastatic process by the independent growths of metastatic foci starting from one or few cells. This \standard" theory, able to describe the dynamics of the total metastatic burden, is on the other hand unable to describe the observed metastatic size distributions. Indeed, this model predicts many small metastases, whereas the observed metastases are much larger and fewer. In order to explain these differences, we proposed two hypotheses that were not taken into account in the initial theory. In the first one, metastases that are growing in close vicinity could merge, resulting in one larger metastasis. In the second one, metastatic foci could attract arriving circulating tumor cells, resulting also in fewer foci but much larger ones. These hypotheses have been tested experimentally by our biologists collaborators, and in silico thanks to a spatial model of tumor growth. The results of this study show that the previously suggested phenomena could have a substantial impact on the number and the sizes of the metastatic foci during metastatic development. Another part of this thesis is devoted to the numerical and mathematical analysis of the previous spatial model. This model takes into account the effect of the pressure on the proliferation of tumor cells. Numerical convergence of the numerical method that has been used and data assimilation on imaging data of pulmonary metastases are presented. Finally, a last part deals with the interactions between metastasis and its supportive stroma. Recent studies shed light on the implication of hematopoietic progenitors in the formation of a permissive soil in the future metastatic site, a phenomenon so-called premetastatic niche. In this thesis, a mathematical model describing the premetastatic and metastatic dynamics is proposed to study quantitative aspects of this phenomenon
Yeramian, Edouard. « Étude expérimentale et théorique de récepteurs de neuromédiateurs et développement de méthodologies pour l'analyse des signaux ». Châtenay-Malabry, Ecole centrale de Paris, 1986. http://www.theses.fr/1986ECAP0032.
Texte intégralNguyen, Huu Tri. « Echelles de temps et dynamique spatiotemporelle de populations ». Aix-Marseille 2, 2007. http://theses.univ-amu.fr.lama.univ-amu.fr/2007AIX22099.pdf.
Texte intégralAggregation of variables methods allow reducing complexity of models in population dynamics by building simplified models governing fewer variables. We first use those methods to study spatial host-parasitoids models on patches. Those models are composed of a local interaction submodel and a dispersal submodel. Dispersal consists in k events of elementary dispersal on the nearest neighbours. We study the influence of parameter k on global dynamics and persistence of the system. We then develop a model of a virus in a marine environment to study the “plankton paradox”: plankton dynamics violate the principle of competitive exclusion. The study of our system shows that the presence of a virus enables the coexistence of two different species of bacteria
Bonneau, Stephane. « Chemins minimaux en analyse d’images : nouvelles contributions et applications à l’imagerie biologique ». Paris 9, 2006. https://portail.bu.dauphine.fr/fileviewer/index.php?doc=2006PA090062.
Texte intégralIntroduced first in image analysis to globally minimize the geodesic active contour functionnal, minimal paths techniques are robust tools for extracting open and closed contours from images. Minimal paths are computed by solving the Eikonal equation on a discrete grid with an efficient algorithm called Fast Marching. In this thesis, we present novel approaches based on minimal paths. The interest of these techniques is illustrated by the analysis of biological images. This thesis consists of three parts. In the first part, we review the relevant litterature in boundary-based deformable models and minimal paths techniques. In the second part, we propose a new approach for automatically detecting and tracking, in sequences of 2D fluorescence images, punctual objects which are intermittently visible. Trajectories of moving objects, considered as minimal paths in a spatiotemporal space, are retrieved using a perceptual grouping approach based on front propagation in the 2D+T volume. The third part adresses the problem of surface extraction in 3D images. First, we introduce a front propagation approach to distribute a set of points on a closed surface. Then, we propose a method to extract a surface patch from a single point by constructing a dense network of minimal paths. We finally present an extension of this method to extract a closed surface, in a fast and robust manner, from a few points lying on the surface
Calvez, Vincent. « Modèles et analyses mathématiques pour les mouvements collectifs de cellules ». Phd thesis, Université Pierre et Marie Curie - Paris VI, 2007. http://tel.archives-ouvertes.fr/tel-00255811.
Texte intégralDans une première partie nous étudions plusieurs variantes du modèle PKS classique, incluant notamment une diffusion non-linéaire des cellules, ou bien une loi de diffusion chimique à noyau de Green logarithmique. Puis nous montrons l'existence globale pour une masse sous-critique du modèle PKS classique dans tout l'espace $\mathbb{R}^2$.
On complexifie ensuite le modèle de base en ajoutant un intermédiaire chimique réactionnel, ce qui modifie l'homogénéité du système. Enfin les conditions d'existence globale pour le modèle cinétique ODA avec effets délocalisants sont affaiblies par rapport aux travaux précédents.
Dans une deuxième partie nous appliquons le modèle phénoménologique de PKS, et son principe de masse critique, à un processus d'auto-organisation remarquable dans le cerveau: la sclérose concentrique de Baló. Un couplage adéquat entre un front de propagation et une instabilité de PKS décrit raisonnablement les motifs en anneaux de la maladie.
La troisième partie adopte le point de vue du transport optimal de masse pour analyser le modèle de PKS unidimensionnel modifié auparavant (afin de partager les caractéristiques de PKS 2D). Bien que la fonctionnelle d'énergie ne soit pas convexe par déplacement, nous démontrons la convergence vers un unique état d'équilibre, lorsqu'il existe. Ces nouvelles idées sont mises en oeuvre numériquement~: un flot gradient discret pour la distance de Wasserstein est analysé, puis simulé en dimension un d'espace.
Plusieurs annexes viennent compléter ce travail, dont une annexe qui regroupe tous les aspects numériques de la thèse.
Mbinky, Estelle Carine. « Adaptation de maillages pour des schémas numériques d'ordre très élevé ». Paris 6, 2013. http://www.theses.fr/2013PA066696.
Texte intégralMesh adaptation is an iterative process which consists in changing locally the size and orientation of the mesh according the behavior of the studied physical solution. It generates the best mesh for a given problem and a fix number of degrees of freedom. Mesh adaptation methods have proven to be extremely effective in reducing significantly the mesh size for a given precision and reaching quickly an second-order asymptotic convergence for problems containing singularities when they are coupled to high order numerical methods. In metric-based mesh adaptation, two approaches have been proposed: Multi-scale methods based on a control of the interpolation error in Lp-norm and Goal oriented methods that control the approximation error of a functional through the use of the adjoint state. However, with the emergence of very high order numerical methods such as the discontinuous Galerkin method, it becomes necessary to take into account the order of the numerical scheme in mesh adaptation process. Mesh adaptation is even more crucial for such schemes as they converge to first-order in flow singularities. Therefore, the mesh refinement at the singularities of the solution must be as important as the order of the method is high. This thesis deals with the extension of the theoretical and numerical results getting in the case of mesh adaptation for piecewise linear solutions to high order piecewise polynomial solutions. These solutions are represented using kth-order Lagrangian finite elements (k ≥ 2). This thesis will focus on modeling the local interpolation error of order k ≥ 3 on a continuous mesh. However, for metric-based mesh adaptation methods, the error model must be a quadratic form, which shows an intrinsic metric space. Therefore, to be able to produce such an area, it is necessary to decompose the homogeneous polynomial and to approximate it by a quadratic form taken at power k. This modeling allows us to define a metric field necessary to communicate with the mesh generator. The decomposition method will be an extension of the diagonalization method to high order homogeneous polynomials. Indeed, in 2D and 3D, symmetric tensor decomposition methods such as Sylvester decomposition and its extension to high dimensions will allow us to decompose locally the error function, then, to deduce the quadratic error model. Then, this local error model is used to control the overall error in Lp-norm and the optimal mesh is obtained by minimizing this error. In this thesis, we seek to demonstrate the kth-order convergence of high order mesh adaptation method for analytic functions and numerical simulations using kth-order solvers (k ≥ 3)
Liu, Ming Gang. « Étude de la texture des membranes et de leur interaction avec des suspensions au cours d'une filtration dynamique ». Compiègne, 1992. http://www.theses.fr/1992COMPD496.
Texte intégralJoron, Mathieu. « Coloration avertissante et mimétisme müllérien : le problème de la diversification ». Montpellier 2, 2000. http://www.theses.fr/2000MON20197.
Texte intégralGrange, Sophie. « Le grand dilemme des équidés sauvages : coexister avec les bovidés et éviter les grands prédateurs ». Poitiers, 2006. http://www.theses.fr/2006POIT2319.
Texte intégralThe Plains zebra is currently the most widespread wild equid; however there is still little information on the regulation/limitation of their populations. Comparative studies on the relative abundance and the population dynamics of Plains zebras and grazing bovids support the hypothesis that predation has a greater impact on the number of zebras in African ecosystems, and probably also play an important role in the limitation of some zebra populations. Given these findings, it will be necessary to link population models of zebra and their main predators. However a major problem is the lack of accurate data on zebra survival rates. The study on the population dynamics of Plains zebra in Hwange National Park (Zimbabwe) is the first one to use a capture-mark-recapture method based on photo-identification. After only one year and a half, this method already proves to be promising to study zebra population dynamics. This thesis also shows that the feralization of domestic horses leads to an unnatural population dynamics, which means that Camargue horses cannot be used as surrogates of wild equids to restore natural ecosystems. In terms of species conservation it is therefore now important to acquire a good knowledge on the regulating/limiting factors acting on current wild equid populations in order to facilitate translocations and reintroductions in their natural ecosystems
Géan, Julie. « Réalisation de systèmes membranaires modèles et étude de leur organisation par microscopie à l'angle de Brewster, spéctroscopie PM-IRRAS et dichroi͏̈sme circulaire vibrationnel ». Bordeaux 1, 2003. http://www.theses.fr/2003BOR12896.
Texte intégralMartens, Johannes. « L' évolution des organisations biologiques : vers une théorie unifiée de la coopération et du conflit ». Paris 1, 2012. http://www.theses.fr/2012PA010737.
Texte intégralBeau, Noëlle. « Application du maximum de vraisemblance à la comparaison de deux méthodes de dosage biologique : cas des variances inconnues ». Paris 11, 1990. http://www.theses.fr/1990PA11P171.
Texte intégralGindre, Cyrille. « Modélisation des relations entraînements – performances – adaptations physiologiques chez des athlètes spécialistes de demi-fond court et de fond ». Reims, 2009. http://www.theses.fr/2009REIMS011.
Texte intégralBanister's model has been used to correlate training with performance. The basic assumption is that a dose of training contributes to both fitness and fatigue. Performance is related to the difference between these two first-order transfer functions. In the present study we tested the validity of the Banister model. For this, we followed developments of performance and physical qualities (aerobic, anaerobic, strength, speed, muscle power) with training of two group of runners specialists of long (≥ 10 km) and short (800 m) distances. The consideration of joint performance, physical and biological parameters allowed us 1) to have an integrated view of organism adaptations with training 2) to assess the validity of antagonist functions of the Banister's model. We were thus able to show that physical qualities evolution of short distances specialists on a season is done according to principles that can bring changes to the organization from those of an ecosystem consisting of different "species". Although Banister's model could be used to estimate performances, we have shown that fitness and fatigue functions may not be so valid linked to the physiological parameters of actual performance and fatigue. We conclude that the Banister's model is more a model of data than a model of structure. These results are a preliminary step in developing a new kind of model – which we proposed the foundation-for – linking training, performance and physical adaptation
Pradel, Roger. « Estimation et comparaison de probabilités de survie par suivi individuel et utilisation en biologie des populations ». Montpellier 2, 1992. http://www.theses.fr/1992MON20152.
Texte intégralRodriguez, Jean-Michel. « Adaptation interactive de documents dans le contexte de la transaction électronique ». Montpellier 2, 1999. http://www.theses.fr/1999MON20066.
Texte intégralFirippi, Eleni. « Analyse mathématique, couplage et contrôle pour modèles d'oscillateurs biologiques synthétiques ». Thesis, Université Côte d'Azur, 2020. http://theses.univ-cotedazur.fr/2020COAZ4105.
Texte intégralBiological oscillators are present in most living organisms and play major roles in their development and regulation. Synthetic biology is a rising multidisciplinary field that aims to create new circuits from biomolecular elements, with the goal to better understand the dynamics underlying complex biological systems. Mathematical models play a crucial role in the study and improvement of synthetic gene circuit design, to ensure the desired functionality of the new genetic circuits, as well as to provide predictions on the efficient and robust performance of the implementation. To contribute to the design and analysis of synthetic oscillators, in a first step, we analytically study a two-gene synthetic oscillator, applying both bifurcation analysis and the piecewise affine (PWA) framework, and propose a variant of the model to enhance its oscillatory capacity. In a second step, inspired by circadian rhythms, we study a network of N two-gene synthetic PWA oscillators, and compare the effect of three different coupling topologies on the dynamics and synchronization properties of the network. In a third step, motivated by the interconnection of the cell cycle and circadian clock, we analyze the coupling of the two-gene oscillator with two other synthetic oscillators: the repressilator and a reduced cell cycle model. Two main bidirectional coupling schemes are considered and we perform a "controller-follower" analysis to characterize the capacity of each system to determine or control the period of the coupled system. Based on this analysis, we can identify the coupling schemes admitting a wider range of dynamical responses, as well as suggest strategies for period-control of two coupled oscillators and tunability of a system through the coupling with another system
Motsch, Sébastien. « Modélisation mathématique des déplacements d'animaux et dérivation de modèles macroscopiques ». Toulouse 3, 2009. http://thesesups.ups-tlse.fr/841/.
Texte intégralThe modeling of animals displacements can occur at two different scales. One may either describes the trajectories of each individual using the so-called individual based models (at a "microscopic" scale), or we can describe the dynamics of the all group with "macroscopic" quantities (density, flux. . . ). In this thesis, we want to connect these two descriptions, the microscopic and the macroscopic scale. Therefore, we can link individual and global dynamics. In a first part, we have introduced a new model for fish displacement called "Persistent Turning Walker" (PTW) based on experimental data. We have given two methods to derive a diffusion equation from this model, a method using tools from functional analysis and a second method using probabilistic tools. The originality of the PTW model mainly relies in the use of curvature to describe individual displacement, this novelty has been used to extend other types of models and to analyse experimental trajectories. In a second part, we have studied the so-called Vicsek model which is an individual based model widespread used in the modeling of animals displacements. We have derived for the first time a macroscopic model from this model (a non-conservative hyperbolic system with a geometric constraint). The numerical simulations of the macroscopic model obtained have shown the relevance of the macroscopic model to describe the microscopic dynamics of the Vicsek model at large scales. Key words : Mathematical biology, Individual based model, Stochastic diffential equation, Kinetic equation, Asymptotic analysis, Diffusion approximation, Hyperbolic systems
Martin, Hugo. « Étude de données et analyse de modèles intégro-différentiels en biologie cellulaire ». Electronic Thesis or Diss., Sorbonne université, 2019. http://www.theses.fr/2019SORUS668.
Texte intégralIn this dissertation, we are interested in the study of some dynamics in molecular biology, making us of mathematical analysis of established models, modelling and data analysis. The first two chapters focus on growth-fragmentation equations with linear growth rate. We are first interested in the recent so-called incremental model, describing a bacterial population. We prove the existence and uniqueness of the solution of the eigenproblem in a weighted Lebesgue space. Then we study the asymptotic behaviour of measures solutions of the growth-fragmentation equation in the equal mitosis case. A solution is then expressed as a semigroup acting on an initial condition. We extend to this framework a known phenomenon of long time oscillating dynamics, which results here in a weak convergence of the solution towards a periodic family of measures. The third chapter deals with the joint dynamics between mesenchymal, pre-adipocyte and adipocyte cells. We propose a non-linear model in which the growth rate depends on the average size of the latter and analyze it using both analytical and numerical approaches. In the last chapter, we carry out a statistical analysis of experimental data from individual yeast lines. In particular, we highlight the existence of distinct phenomena between early arrests and replicative senescence. Finally, we propose a refinement of an existing model, now able to describe the generation of onset of senescence for all the lineages
Guziolowski, Carito. « Étude des réseaux biologiques à grande échelle par modélisation statique et résolution des contraintes ». Rennes 1, 2010. http://www.theses.fr/2010REN1S006.
Texte intégralIl existe plusieurs approches qui modélisent des réseaux de régulation génétiques afin d'élucider la dynamique d'un système biologique. Cependant, ces approches concernent des modèles à petite-échelle. Dans cette thèse nous utilisons un approche formelle sur les réseaux de régulation à grande-échelle qui modélise les variations des concentrations des molécules d'une cellule entre deux états stationnaires. On teste la cohérence entre la topologie du réseau et des données d'expression génétique en utilisant une règle causale de consistance. Les résultats de cette approche sont : test de la consistance entre les données et un réseau, diagnostic des régions du réseau inconsistantes avec les données expérimentales, et inférence des variations des éléments du réseau. Notre méthode raisonne sur la topologie globale du réseau en utilisant des algorithmes efficaces basés sur des diagrammes de décision, des graphes de dépendance, ou la programmation par ensemble réponse. Nous avons proposé des programmes et des outils bioinformatiques basés sur ces algorithmes qui automatisent ces raisonnements. On a validé cette approche en utilisant des réseaux transcriptionnels des espèces E. Coli et S. Cerevisiae, et le réseau de signalisation de l'oncogène EWS-FLI1. Nos résultats principaux sont: (1) un pourcentage élevé de validation des prédictions sur la variation des molécules du réseau, (2) des corrections manuelles et automatiques efficaces du modèle et/ou données, (3) l'inférence automatique des rôles des facteurs de transcription, et (4) raisonnement automatique sur les causes qui influencent des phénotypes importants dans des réseaux de signalisation
Niknahad, Ghar Makher Hamid. « Minéralisation du soufre associée à la décomposition des matières organiques dans les sols et relations avec les dynamiques du carbone et de l'azote ». Paris, AgroParisTech, 2008. http://www.theses.fr/2008AGPT0051.
Texte intégralLê, Cao Kim-Anh. « Outils statistiques pour la sélection de variables et l'intégration de données "omiques" ». Toulouse, INSA, 2008. http://eprint.insa-toulouse.fr/archive/00000225/.
Texte intégralRecent advances in biotechnology allow the monitoring of large quantities of biological data of various types, such as genomics, proteomics, metabolomics, phenotypes. . . , that are often characterized by a small number of samples or observations. The aim of this thesis was to develop, or adapt, appropriate statistical methodologies to analyse highly dimensional data, and to present efficient tools to biologists for selecting the most biologically relevant variables. In the first part, we focus on microarray data in a classification framework, and on the selection of discriminative genes. In the second part, in the context of data integration, we focus on the selection of different types of variables with two-block omics data. Firstly, we propose a wrapper method, which agregates two classifiers (CART or SVM) to select discriminative genes for binary or multiclass biological conditions. Secondly, we develop a PLS variant called sparse PLS that adapts l1 penalization and allows for the selection of a subset of variables, which are measured from the same biological samples. Either a regression or canonical analysis frameworks are proposed to answer biological questions correctly. We assess each of the proposed approaches by comparing them to similar methods known in the literature on numerous real data sets. The statistical criteria that we use are often limited by the small number of samples. We always try, therefore, to combine statistical assessments with a thorough biological interpretation of the results. The approaches that we propose are easy to apply and give relevant results that answer the biologists needs
Malgras, Jacques. « Applications, à des données de la biologie des populations et de l'écologie, de méthodes d'analyse des séries temporelles ». Lyon 1, 1996. http://www.theses.fr/1996LYO10240.
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