Bibliography

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  Stochastic modeling of the chemostat, in: Ecological Modelling, 2011, vol. 222, n^o 15, p. 2676-2689.
• 2F. Campillo, M. Klepstyna, A. Piatnitski.
  
  Homogenization of random parabolic operator with large potential, in: Stochastic Processes and Their Applications, 2001, vol. 93, p. 57–85.
• 3M. Dumont, J. Harmand, A. Rapaport, J.-J. Godon.
  
  Toward functional molecular fingerprints, in: Environmental Microbiology, 2009, vol. 11, n^o 7, p. 1717–1727.
• 4P. Gajardo, H. Ramirez, A. Rapaport.
  
  Minimal time sequential batch reactors with bounded and impulse controls for one or more species, in: SIAM Journal of Control and Optimization, 2008, vol. 47, n^o 6, p. 2827–2856.
• 5B. Haegeman, R. S. Etienne.
  
  Entropy maximization and the spatial distribution of species, in: The American Naturalist, 2009, vol. 175, p. E74–E90.
• 6B. Haegeman, D. Vanpeteghem, J.-J. Godon, J. Hamelin.
  
  DNA reassociation kinetics and diversity indices: Richness is not rich enough, in: Oikos, 2008, vol. 175, p. 177–181.
• 7C. Lobry, J. Harmand.
  
  A new hypothesis to explain the coexistence of n species in the presence of a single resource, in: Comptes Rendus de l'Académie des Sciences, Série Biologies, 2006, vol. 329, p. 40-46.
• 8N. Mabrouk, G. Deffuant, T. Toelker-Nielsen, C. Lobry.
  
  Bacteria can form interconnected microcolonies when a self-excreted product reduces their surface motility: evidence from individual-based model simulations, in: Theory in Biosciences, 2010, vol. 129, n^o 1, p. 1–13.
  
  http://www.springerlink.com/content/r276t7018n41pq23/
• 9A. Rapaport, D. Dochain, J. Harmand.
  
  Long run coexistence in the chemostat with multiple species, in: Journal of Theoretical Biology, 2009, vol. 257, n^o 2, p. 252–259.
• 10T. Sari.
  
  A Lyapunov function for the chemostat with variable yields, in: C. R. Acad. Sci. Paris, Ser. I, 2010, vol. 348, p. 747-751.

Articles in International Peer-Reviewed Journals

• 11T. Bayen, P. Gajardo, F. Mairet.
  
  Optimal Synthesis for the Minimum Time Control Problems of Fed-Batch Bioprocesses for Growth Functions with Two Maxima, in: Journal of Optimization Theory and Applications, 2012, p. 1-33.
  
  http://dx.doi.org/10.1007/s10957-012-0225-0
• 12B. Benyahia, T. Sari, B. Cherki, J. Harmand.
  
  Bifurcation and stability analysis of a two step model for monitoring anaerobic digestion processes, in: Journal of Process Control, 2012, vol. 22, n^o 6, p. 1008-1019.
• 13F. Campillo, N. Champagnat.
  
  Simulation and analysis of an individual-based model for graph-structured plant dynamics, in: Ecological Modelling, 2012, vol. 234, p. 93-105. [ DOI : 10.1016/j.ecolmodel.2012.03.017 ]
  
  http://hal.inria.fr/hal-00723209
• 14F. Campillo, M. Joannides, I. Larramendy-Valverde.
  
  Approximation of the Fokker-Planck equation of the stochastic chemostat, in: Mathematics and Computers in Simulation, 2012, to appear.
• 15F. Campillo, C. Lobry.
  
  Effect of population size in a predator-prey model, in: Ecological Modelling, August 2012, vol. 246, p. 1-10. [ DOI : 10.1016/j.ecolmodel.2012.07.015 ]
  
  http://hal.inria.fr/hal-00723793
• 16A. Charfi, N. Benamar, J. Harmand.
  
  Analysis of fouling mechanisms in anaerobic membrane bioreactors, in: Water Research, 2012, vol. 46, p. 2637-2650.
• 17C. Deygout, A. Lesne, F. Campillo, A. Rapaport.
  
  Homogenised model linking microscopic and macroscopic dynamics of a biofilm: Application to growth in a plug flow reactor, in: Ecological Modelling, 2013, vol. 250, n^o 0, p. 15-24. [ DOI : 10.1016/j.ecolmodel.2012.10.020 ]
  
  http://www.sciencedirect.com/science/article/pii/S0304380012005224
• 18M. L. Diagne, P. I. N'diaye, M. T. Niane, T. Sari.
  
  Comportement asymptotique d'un modèle à commutation de la prolifération du Typha, in: ARIMA Revue africaine de la recherche en informatique et mathématiques appliquées, 2012, vol. 15, p. 101-122.
  
  http://intranet.inria.fr/international/arima/015/015006.html
• 19R. S. Etienne, B. Haegeman.
  
  A conceptual and statistical framework for adaptive radiations with a key role for diversity-dependence, in: The American Naturalist, 2012, vol. 180, p. E75-E89.
• 20R. S. Etienne, B. Haegeman, T. Stadler, T. Aze, P. N. Pearson, A. Purvis, A. B. Phillimore.
  
  Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record, in: Proceedings of the Royal Society B: Biological Sciences, 2012, vol. 279, p. 1300-1309.
• 21R. Fekih-Salem, J. Harmand, C. Lobry, A. Rapaport, T. Sari.
  
  Extensions of the chemostat model with flocculation, in: Journal of Mathematical Analysis and Applications, 2013, vol. 397, p. 292–306.
• 22J. M. V. Groenendael, C. Mony, M. Garbey, F. Campillo, A. E. Hamidi.
  
  Introduction to the special issue of Ecological Modelling: "Modelling clonal plant growth: From ecological concepts to mathematics", in: Ecological Modelling, 2012, vol. 234, p. 1-2, Introduction à un n° spécial d'un journal. [ DOI : 10.1016/j.ecolmodel.2012.03.013 ]
  
  http://hal.inria.fr/hal-00717348
• 23B. Haegeman, J. S. Weitz.
  
  A neutral theory of genome evolution and the frequency distribution of genes, in: BMC Genomics, 2012, vol. 13, 196 p.
• 24J. Rouyer, T. Sari.
  
  As many antipodes as vertices on convex polyhedra, in: Advances in Geometry, 2012, vol. 12, n^o 1, p. 43-61. [ DOI : 10.1515/advgeom.2011.030 ]
  
  http://www.degruyter.com/view/j/advg.2012.12.issue-1/advgeom.2011.030/advgeom.2011.030.xml?format=INT
• 25T. Sari, M. E. Hajji, J. Harmand.
  
  The mathematical analysis of a syntrophic relationship between two microbial species in a chemostat, in: Mathematical Biosciences and Engineering, 2012, vol. 3, n^o 9, p. 627-645.
• 26T. Sari.
  
  Competitive Exclusion for Chemostat Equations with Variable Yields, in: Acta Applicandae Mathematicae, 2012.
  
  http://link.springer.com/article/10.1007/s10440-012-9761-8
• 27J. Sieber, A. Rapaport, S. Rodrigues, M. Desroches.
  
  A new method for the reconstruction of unknown non-monotonic growth functions in the chemostat, in: Bioprocess and Biosystems Engineering, 2012, to appear.
  
  http://hal.inria.fr/hal-00604633

International Conferences with Proceedings

• 28B. Benyahia, F. Campillo, B. Cherki, J. Harmand.
  
  Particle filtering for the chemostat, in: 20th Mediterranean Conference on Control and Automation (MED 2012), Barcelona, Barcelona, Spain, July 3-6 2012, p. 364-371.
• 29B. Benyahia, B. Cherki, T. Sari, J. Harmand.
  
  Quelques résultats sur l'observation du modèle AM2b, in: Eleventh African Conference on Research in Computer Science and Applied Mathematics (CARI 2012), Algiers (Algeria), 2012.
• 30W. Bouhafs, N. Abdellatif, F. Jean, J. Harmand.
  
  Commande optimale en temps et en énergie d'un procédé biologique d'épuration d'eau, in: Eleventh African Conference on Research in Computer Science and Applied Mathematics (CARI 2012), Algiers (Algeria), 2012.
• 31B. Brighi, A. Fruchard, T. Sari.
  
  The Blasius equation, in: Philosophie, méthodologie et applications de l'analyse non standard, Paris, A. Fruchard, V. Gautheron, T. Sari (editors), Publications de l'Université de Paris 13, 2012, p. 105-123.
  
  http://www.math.univ-paris13.fr/laga/F/pdf/2012-01-12-Actes-Isambert/
• 32F. Campillo, D. Hervé, A. Raherinirina, R. Rakotozafy.
  
  Markov analysis of land use dynamics: A Case Study in Madagascar, in: Eleventh African Conference on Research in Computer Science and Applied Mathematics (CARI 2012), Algiers (Algeria), 2012.
• 33C. Casenave, D. Dochain, G. Alvarez, H. Benkhelifa, D. Flick, D. Leducq.
  
  Steady-state and stability analysis of a population balance based nonlinear ice cream crystallization model, in: ACC, Montreal, June 27-29 2012.
• 34M. L. Diagne, T. Sari.
  
  Moyennisation du modèle dynamique de la prolifération du Typha, in: 11ème Colloque Africain sur la Recherche en Informatique en Mathématiques Appliquées, 2012.
  
  http://www.cari-info.org/prog_cari12.php
• 35D. Dochain, P. De Leenheer, A. Rapaport.
  
  About Transgressive Over-Yielding in the Chemostat, in: MATHMOD 2012 - 7th Vienna International Conference on Mathematical Modelling, Vienna, Austria, February 2012.
  
  http://hal.inria.fr/hal-00726364
• 36R. Fekih-Salem, N. Abdellatif, T. Sari, J. Harmand.
  
  Analyse mathématique d'un modèle de digestion anaérobie à trois étapes, in: Eleventh African Conference on Research in Computer Science and Applied Mathematics (CARI 2012), Algiers (Algeria), 2012.
• 37R. Fekih-Salem, N. Abdellatif, T. Sari, J. Harmand.
  
  On a Three Step Model of Anaerobic Digestion Including the Hydrolysis of Particulate Matter, in: MATHMOD, Vienna, Austria, February 2012.
• 38B. Fontez, D. I. Batonon, F. Campillo, P. Lescoat.
  
  Analyse bayésienne de courbes de croissance de poulets par un modèle hiérarchique défini à partir d'une équation différentielle stochastique à processus d'erreur autocorrélée, in: 44ième Journées de Statistique, Bruxelles, 21 au 25 mai 2012.
• 39A. Ghouali, T. Sari, C. Lobry, A. Moussaoui, J. Harmand.
  
  Analyse et contrôle optimal d'un bioréacteur de dépollution des eaux usées, in: 11ème Colloque Africain sur la Recherche en Informatique en Mathématiques Appliquées, 2012.
  
  http://www.cari-info.org/prog_cari12.php
• 40S. Hassam, B. Cherki, E. Ficara, J. Harmand.
  
  Model reduction and control of the ADM1 : a robust control approach, in: 20th Mediterranean Conference on Control and Automation (MED 2012), Barcelona, Spain, July 3-6 2012.
• 41C. Lobry, T. Sari.
  
  La modélisation de la persistance en écologie, in: Philosophie, méthodologie et applications de l'analyse non standard, Paris, A. Fruchard, V. Gautheron, T. Sari (editors), Publications de l'Université de Paris 13, 2012, p. 163-184.
  
  http://www.math.univ-paris13.fr/laga/F/pdf/2012-01-12-Actes-Isambert/
• 42J. Sieber, A. Rapaport, M. Desroches, S. Rodrigues.
  
  A new method for the reconstruction of unknown non-monotonic growth functions in the chemostat, in: MED 2012 - 20th IEEEMediterranean Conference on Control and Automation, Barcelona, Spain, July 2012.
  
  http://hal.inria.fr/hal-00723246

Conferences without Proceedings

• 43A. Bize, F. Campillo, C. Deygout, M. Joannides.
  
  Un modèle individu-centré de dégradation bactérienne d'une bille de cellulose, in: Les Biofilms au service des Biotechnologies — Journées thématiques du Réseau National Biofilm, Narbonne, 24–26 Janvier 2012.
• 44A. Bize, F. Campillo, C. Deygout, C. Lobry, M. Joannides.
  
  An individual-based modeling approach for cellulose degradation by microbial biofilms, in: Biofilm 5 International Conference, december 10-12, 2012.
• 45F. Campillo.
  
  Stochastic modeling: a simulation (and analytical) approach, in: 2nd French-Chilean Workshop on Bioprocess Modeling Pucón, January 16-17 2012.
• 46C. Fritsch.
  
  Moment closure methods for individual-based model, in: Zif Research Group Stochastic Dynamics: Mathematical Theory And Applications – Workshop on Qualitative Behaviour Of Stochastic Systems And Applications, Bielefeld University, 2012.
• 47J. Harmand.
  
  Modeling and control of the anaerobic digestion process : a review and some new results, in: 2nd French-Chilean Workshop on Bioprocess Modeling Pucón, Pucón, Chile, January 2012.
• 48C. Lobry.
  
  Effect of population size in a Prey-Predator model, in: LAWOC 2012 Latin American Workshop on Optimization and Control, Valparaiso, Chile, January 2012.
• 49C. Lobry.
  
  L'ordinateur et la dynamique des populations, conférence Inaugurale, in: Colloque de méthodes numériques et modélisation, MÉMO'2012 à l'occasion du 60ème anniversaire de Mohamed Jaoua, Tunis, Tunisia, 13 au 15 décembre 2012.
• 50C. Lobry.
  
  La compétition dans le chémostat, in: Des nombres et des Mondes, 2012.
  
  http://hal.inria.fr/hal-00711218
• 51C. Lobry.
  
  Les équations différentielles sont-elles un outil pertinent pour modéliser la dynamique des populations ?, in: Colloque en l'honneur de Gauthier Sallet, Saint-Louis, Sénégal, 3 au 7 décembre 2012.
• 52A. Rapaport, D. Dochain.
  
  Minimal time control of fed-batch processes for growth functions having several maxima, in: LAWOC 2012 Latin American Workshop on Optimization and Control, Valparaiso, Chile, January 2012.
• 53T. Sari.
  
  Elastic strips, in: Colloque de géométries, Mulhouse, 27-29 septembre 2012.
  
  http://unica2.unica.it/~piu/Conf.html
• 54T. Sari.
  
  Extensions of the chemostat model with flocculation, in: III Latin American Workshop on Optimization and Control LAWOC, Valparaiso (Chile), 2012.
  
  http://www.am2v.cl/lawoc2012/

Internal Reports

• 55S. Barbier.
  
  Modélisation de stratégies de dépollution d'une ressource hydrique en milieu naturel, Université de Reims Champagne-Ardenne, September 2012, MSc Engineeing Mathematics report, U. Reims.
• 56A. Rapaport, J.-R. de Dreuzy, J. Harmand, A. Rojas-Palma.
  
  Comparison of MINC and MRMT configurations: the n-dimensional case, Catholic University of Valparaíso, Chile, November 2012.
• 57V. Riqueleme.
  
  Bioremediation of natural water resources via optimal control techniques, DIM, Univ. Chile, Santiago, 2012.
• 58E. Tapia.
  
  A methodology for coupling DGGE and mathematical modelling. Application in bio-hydrogen productions, Escuela de Ingenieria Bioquimica Pontificia Universidad Católica de Valparaíso Valparaíso, Chile, November 2012, submitted.

Patents and standards

• 59A. Rapaport, J. Harmand, I. Haidar.
  
  Stabilisation de procédés biotechnologiques présentant une instabilité due à une inhibition par le substrat, par des configurations de type "poche", February 2012, n^o BNT210061FR00, Brevet d'invention.

Other Publications

• 60T. Bayen, F. Mairet.
  
  Minimal time control of fed-batch bioreactor with product inhibition, September 2012, Submitted.
  
  http://hal.archives-ouvertes.fr/hal-00734225
• 61T. Bayen, F. Mairet, P. Martinon, M. Sebbah.
  
  Optimizing the anaerobic digestion of microalgae in a coupled process, 2012, submitted.
• 62T. Bayen, F. Mairet, M. Mazade.
  
  Optimal feeding strategy for the minimal time problem of a fed-batch bioreactor with mortality rate, November 2012, submitted.
  
  http://hal.archives-ouvertes.fr/hal-00759058
• 63C. Casenave, G. Montseny.
  
  System identification by operatorial cancellation of nonlinear terms - application to a class of Volterra models, 2012, submitted.
• 64C. Casenave, G. Montseny, C. Prieur.
  
  Controllability of SISO Volterra Models via Diffusive Representation, 2012, submitted.
• 65B. Jaillard, A. Rapaport, J. Harmand, A. Brauman, N. Nunan.
  
  Biodiversity and ecosystem functioning: the hidden weight of neutral elements in community assembly, 2012, submitted.
• 66E. Montseny, C. Casenave.
  
  Analysis, simulation and impedance operator of a non local model of porous medium for acoustic control, 2012, submitted.
• 67A. Rapaport, I. Haidar, J. Harmand.
  
  The buffered chemostat with non-monotonic growth response functions, 2012, to appear.
  
  http://hal.inria.fr/hal-00766243

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• 73F. Campillo, V. Rossi.
  
  Convolution Particle Filter for Parameter Estimation in General State-Space Models, in: IEEE Transactions on Aerospace and Electronic Systems, 2009, vol. 45, n^o 3, p. 1063-1071.
• 74P. Del Moral.
  
  Feynman-Kac formulae – Genealogical and interacting particle approximations, Springer Verlag, New York, 2004.
• 75A. Doucet, N. de Freitas, N. J. Gordon.
  
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  Individual-based Modeling and Ecology, Princeton University Press, 2005.
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  Dynamiques microbiennes et modélisation des cycles biogéochimiques terrestres, Université Montpellier II, 2011.
• 81J. Hess, O. Bernard.
  
  Design and Study of a risk management criterion for an unstable anaerobic wastewater treatment, in: Journal of Process Control, 2007, vol. 18, p. 71-79.
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  The Unified Neutral Theory of Biodiversity and Biogeography, Princeton University Press, 2001.
• 83C. M. Jessup, R. Kassen, S. E. Forde, B. Kerr, A. Buckling, P. B. Rainey, B. J. Bohannan.
  
  Big questions, small world: microbial model systems in ecology, in: Trends in Ecology and Evolution, 2004, vol. 19, n^o 4, p. 189–197.
• 84A. Lesne.
  
  Multi-scale approaches, in: Encyclopedia of Mathematical Physics, J. Françoise, G. Naber, T. Tsun (editors), Elsevier, 2006, vol. 3, p. 465–482.
• 85R. H. MacArthur, E. O. Wilson.
  
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