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Bibliography

Major publications by the team in recent years
  • 1F. Campillo, M. Joannides, I. Larramendy-Valverde.
    Stochastic modeling of the chemostat, in: Ecological Modelling, 2011, vol. 222, no 15, pp. 2676-2689.
  • 2F. Campillo, C. Lobry.
    Effect of population size in a predator-prey model, in: Ecological Modelling, 2012, vol. 246, pp. 1-10.
  • 3M. Dumont, J. Harmand, A. Rapaport, J.-J. Godon.
    Toward functional molecular fingerprints, in: Environmental Microbiology, 2009, vol. 11, no 7, pp. 1717–1727.
  • 4P. Gajardo, J. Harmand, H. Ramirez, A. Rapaport.
    Minimal time bioremediation of natural water resources, in: Automatica, 2011, vol. 47, no 8, pp. 1764–1769.
  • 5P. 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, no 6, pp. 2827–2856.
  • 6C. 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, pp. 40-46.
  • 7P. Loisel, J. Harmand, O. Zemb, E. Latrille, C. Lobry, J.-P. Delgenes, J.-J. Godon.
    Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity, in: Environmental Microbiology, 2006, vol. 8, no 4, pp. 720–731.
  • 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, no 1, pp. 1–13.
  • 9A. Rapaport, D. Dochain, J. Harmand.
    Long run coexistence in the chemostat with multiple species, in: Journal of Theoretical Biology, 2009, vol. 257, no 2, pp. 252–259.
  • 10T. Sari.
    A Lyapunov function for the chemostat with variable yields, in: C. R. Acad. Sci. Paris, Ser. I, 2010, vol. 348, pp. 747-751.
Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 11R. Fekih-Salem.
    Modèles Mathématiques pour la compétition et la coexistence des espèces microbiennes dans un chémostat, Université Montpellier II - Sciences et Techniques du Languedoc, September 2013.
    http://hal.inria.fr/tel-00940100
  • 12A. Raherinirina.
    Modélisation markovienne des dynamiques d'usages des sols. Cas des parcelles situées sur le bord du corridor forestier Ranomafana-Andringitra, Université de Fianarantsoa, February 2013.
    http://hal.inria.fr/tel-00936305

Articles in International Peer-Reviewed Journals

  • 13T. Bayen, F. Mairet.
    Minimal time control of fed-batch bioreactor with product inhibition, in: Bioprocess and Biosystems Engineering, October 2013, vol. 36, no 10, pp. 1485-1496. [ DOI : 10.1007/s00449-013-0911-9 ]
    http://hal.inria.fr/hal-00734225
  • 14T. Bayen, F. Mairet, M. Mazade.
    Optimal feeding strategy for the minimal time problem of a fed-batch bioreactor with mortality rate, in: Optimal Control Applications and Methods, December 2013. [ DOI : 10.1002/oca.2102 ]
    http://hal.inria.fr/hal-00936339
  • 15B. Benyahia, T. Sari, B. Cherki, J. Harmand.
    Anaerobic Membrane BioReactor modeling in the presence of Soluble Microbial Products (SMP) - the Anaerobic Model AM2b, in: Chemical Engineering Journal, 2013, vol. 228, pp. 1011-1022. [ DOI : 10.1016/j.cej.2013.05.073 ]
    http://hal.inria.fr/hal-00859541
  • 16W. Bouhafs, N. Abdellatif, F. Jean, J. Harmand.
    Commande optimale en temps minimal d'un procédé biologique d'épuration de l'eau, in: ARIMA, 2013.
    http://hal.inria.fr/hal-00859549
  • 17F. Campillo, D. Hervé, A. Raherinirina, R. Rakotozafy.
    Markov analysis of land use dynamics: A Case Study in Madagascar, in: ARIMA, 2014, To appear.
    http://hal.inria.fr/hal-00936315
  • 18F. Campillo, M. Joannides, I. Larramendy-Valverde.
    Approximation of the Fokker-Planck equation of the stochastic chemostat, in: Mathematics and Computers in Simulation, 2013.
    http://hal.inria.fr/hal-00821857
  • 19J.-R. De Dreuzy, A. Rapaport, T. Babey, J. Harmand.
    Influence of porosity structures on mixing-induced reactivity at chemical equilibrium in mobile/immobile Multi-Rate Mass Transfer (MRMT) and Multiple INteracting Continua (MINC) models, in: Water Resources Research, 2013, no 49, pp. 1-19, in press. [ DOI : 10.1002/2013WR013808 ]
    http://hal.inria.fr/hal-00914049
  • 20C. 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, February 2013, vol. 250, pp. 15-24. [ DOI : 10.1016/j.ecolmodel.2012.10.020 ]
    http://hal.inria.fr/hal-00823991
  • 21R. Fekih-Salem, N. Abdellatif, T. Sari, J. Harmand.
    Analyse mathématique d'un modèle de digestion anaérobie à trois étapes, in: ARIMA, 2013.
    http://hal.inria.fr/hal-00859551
  • 22R. Fekih-Salem, J. Harmand, C. Lobry, A. Rapaport, T. Sari.
    Extension of the chemostat model with flocculation, in: Journal of Mathematical Analysis and applications, 2013, vol. 397, no 1, pp. 292-306. [ DOI : 10.1016/j.jmaa.2012.07.055 ]
    http://hal.inria.fr/hal-00777539
  • 23B. Haegeman, J. Hamelin, J. Moriarty, P. Neal, J. Dushoff, J. S. Weitz.
    Robust estimation of microbial diversity in theory and in practice, in: the ISME Journal, 2013, pp. 1–10.
    http://hal.inria.fr/hal-00859547
  • 24B. Haegeman, T. Sari, R. S. Etienne.
    Predicting coexistence of plants subject to a tolerance-competition trade-off, in: Journal of Mathematical Biology, 2013.
    http://hal.inria.fr/hal-00859548
  • 25B. Jaillard, A. Rapaport, J. Harmand, A. Brauman, N. Nunan.
    Community assembly effects shape the biodiversity ecosystem functioning relationships, in: Functional Ecology, 2014, in press.
    http://hal.inria.fr/hal-00937779
  • 26E. Montseny, C. Casenave.
    Analysis, simulation and impedance operator of a nonlocal model of porous medium for acoustic control, in: Journal of Vibration and Control, 2013, 35 p. [ DOI : 10.1177/1077546313493815 ]
    http://hal.inria.fr/hal-00854312
  • 27N. Perveen, S. Barot, G. Alvarez, K. Klumpp, A. Rapaport, S. Fontaine.
    Priming effect and microbial diversity in ecosystem functioning and response to global change: a modeling approach using the SYMPHONY model, in: Global Change Biology, 2013. [ DOI : 10.1111/gcb.12493 ]
    http://hal.inria.fr/hal-00914045
  • 28A. Rapaport, I. Haidar, J. Harmand.
    Global dynamics of the buffered chemostat for a general class of response functions, in: Journal of Mathematical Biology, 2014, (under revision).
    http://hal.inria.fr/hal-00923826
  • 29J. Sieber, A. Rapaport, S. Rodrigues, M. Desroches.
    A method for the reconstruction of unkwnown non-monotonic growth functions in the chemostat, in: Bioprocess and Biosystems Engineering, 2013, vol. 36, no 10, pp. 1496-1507. [ DOI : 10.1007/s00449-013-0912-8 ]
    http://hal.inria.fr/hal-00860573
  • 30E. Tapia, A. Donoso-Bravo, L. Cabrol, M. M. Alves, A. Pereira, A. Rapaport, G. Ruiz-Filippi.
    A methodology for a functional interpretation of DGGE with the help of mathematical modelling. Application in bio-hydrogen production, in: Water Science and Technology, 2013, in press. [ DOI : 10.2166/wst.2013.719 ]
    http://hal.inria.fr/hal-00914058

Articles in National Peer-Reviewed Journals

  • 31F. Campillo.
    Modélisation en dynamique des populations, in: TDC (Textes et Documents pour la Classe), October 2013, no 1062, pp. 26-27.
    http://hal.inria.fr/hal-00873512
  • 32J.-R. De Dreuzy, A. Rapaport.
    Mieux gérer les ressources naturelles, in: TDC (Textes et Documents pour la Classe), October 2013, no 1062, pp. 20-23.
    http://hal.inria.fr/hal-00914257

Articles in Non Peer-Reviewed Journals

  • 33A. Rapaport.
    Biophysique : le sol est-il un bioréacteur?, in: Lettre d'Informations Inra, 2013, vol. Inra - Actualité Chercheurs, étudiant, La Modélisation Est Partout.
    http://hal.inria.fr/hal-00859546

Invited Conferences

  • 34A. Rapaport.
    A propos de l'effet d'échantillonnage dans l'étude d'écosystèmes microbiens complexes, in: Rencontres du Réseau National des Systèmes Complexes 2013, Evian, France, E. Perrier, G. Deffuant (editors), RNSC, October 2013.
    http://hal.inria.fr/hal-00923823

International Conferences with Proceedings

  • 35G. Araujo Pimentel, A. Vande Wouwer, A. Rapaport, J. Harmand.
    Modeling of submerged membrane bioreactors with a view to control, in: 11th IWA conference on instrumentation control and automation, Narbonne, France, September 2013.
    http://hal.inria.fr/hal-00925592
  • 36T. Bayen, F. Mairet, M. Mazade.
    Fed-batch bioreactor with mortality rate, in: 9th IFAC Symposium on Nonlinear Control Systems (NOLCOS), Toulouse, France, S. Tarbouriech, M. Krstic (editors), IFAC, 2013, vol. 9 Part 1, pp. 158-163. [ DOI : 10.3182/20130904-3-FR-2041.00024 ]
    http://hal.inria.fr/hal-00850367
  • 37T. Bayen, F. Silva.
    Weak and strong minima : from calculus of variation toward PDE optimization, in: First IFAC Workshop on Control of Systems Modeled by Partial Differential Equations (CPDE 2013), Paris, France, 2013.
    http://hal.inria.fr/hal-00859570
  • 38W. Bouhafs, N. Abdellatif, F. Jean, J. Harmand.
    A geometrical approach for the resolution of an optimal control problem, in: International Conference on Advances in Applied Mathematics ICAAM-2013, Hammamet, Tunisia, December 2013.
    http://hal.inria.fr/hal-00925667
  • 39W. Bouhafs, N. Abdellatif, F. Jean, J. Harmand.
    Commande optimale en temps minimal d'un procédé biologique d'épuration de l'eau, in: Proceedings of the International Joint Conference CB-WR-MED Conference/ 2nd AOP' Tunisia Conference for Sustainable Water Management, Tunis, Tunisia, April, 24–27 2013, pp. 225-226.
    http://hal.inria.fr/hal-00859572
  • 40F. Campillo, M. Joannides, I. Larramendy-Valverde.
    Stochastic models for the chemostat at different scales, in: 15th Applied Stochastic Models and Data Analysis International Conference (ASMDA 2013), Barcelona, Spain, June 25–28 2013.
    http://hal.inria.fr/hal-00843062
  • 41C. Casenave, D. Dochain, G. Alvarez, M. Arellano, H. Benkhelifa, D. Leducq.
    Control of a nonlinear ice cream crystallization process, in: 9th IFAC Symposium on Nonlinear Control Systems (NOLCOS), France, 2013.
    http://hal.inria.fr/hal-00859552
  • 42A. Charfi, J. Harmand, N. Benamar, A. Grasmick, M. Héran.
    Fouling models for Membrane BioReactors (MBR), in: Membranes for liquid separation and water treatment: Environmental Applications and Future Perspectives, Torino, Italy, October 2013.
    http://hal.inria.fr/hal-00925662
  • 43A. Charfi, M. Héran, J. Harmand, N. Benamar, A. Grasmick.
    Membrane fouling models for Membrane BioReactors (MBR), in: 7th IWA Specialised Conference and Exhibition on Membrane Technology in Water and Wastewater Treatment, Toronto, Canada, August 2013.
    http://hal.inria.fr/hal-00925615
  • 44R. Fekih-Salem, N. Abdellatif, T. Sari, J. Harmand.
    Qualitative properties of 3-step model of anaerobic digestion including hydrolysis of particulate matter, in: International Joint Conference CB-WR-MED Conference/ 2nd AOP' Tunisia Conference for Sustainable Water Management, Tunis, Tunisia, 2013, pp. 93–94.
    http://hal.inria.fr/hal-00859567
  • 45J. Harmand, F. Mazenc.
    Stabilization of the chemostat with delayed sampled measurements, in: SIAM Conference on Control and Its Applications, San Diego, United States, July 2013.
    http://hal.inria.fr/hal-00925619
  • 46F. Mazenc, J. Harmand, H. Mounier.
    Global stabilization of the chemostat with delayed and sampled measurements and control, in: NOLCOS - 9th IFAC Symposium on Nonlinear Control Systems - 2013, Toulouse, France, September 2013.
    http://hal.inria.fr/hal-00823970
  • 47P. Miranda Almeida, G. Araujo Pimentel, J.-L. Vasel, A.-L. Hantson, A. Rapaport, J. Harmand, A. Vande Wouwer.
    Analysis of two recirculating aquaculture systems (RAS): Submerged membrane bioreactor and fixed bed biofilter technologies, in: 3rd IWA Benelux Young Water Professional Regional Conference, Belval, Luxembourg, October 2013.
    http://hal.inria.fr/hal-00925681
  • 48A. Rapaport, I. Haidar, J. Harmand.
    The buffered chemostat with non-monotonic response functions, in: 9th IFAC Symposium on Nonlinear Control Systems (NOLCOS 2013), Toulouse, France, 2013.
    http://hal.inria.fr/hal-00766243
  • 49A. Rapaport.
    Chemostat stabilisation through delayed buffering, in: The SIAM Conference on Control and Applications (CT13), San Diego, United States, 2013.
    http://hal.inria.fr/hal-00859569
  • 50A. Rapaport, J. Sieber, S. Rodrigues, M. Desroches.
    Extremum seeking via continuation techniques for optimizing biogas production in the chemostat, in: 9th IFAC Symposium on Nonlinear Control Systems (NOLCOS 2013), Toulouse, France, 2013.
    http://hal.inria.fr/hal-00787510
  • 51E. Tapia, A. Donoso-Bravo, L. Cabrol, M. M. Alves, A. Pereira, A. Rapaport, G. Ruiz-Filippi.
    A methodology for coupling DGGE and mathematical modelling: Application in bio-hydrogen production, in: 13th IWA World Congress on Anaerobic Digestion, Santiago de Compostela, Spain, 2013.
    http://hal.inria.fr/hal-00859568

Conferences without Proceedings

  • 52G. Araujo Pimentel, J. Harmand, A. Vande Wouwer, A. Rapaport.
    Time Scaling Study Using Tikhonov's Theorem in a Submerged Membrane Bioreactor, in: IAP DYSCO Study Day : Dynamical systems, control and optimization, Bruxelles, Belgium, November 2013.
    http://hal.inria.fr/hal-00925692
  • 53G. Araujo Pimentel, A. Vande Wouwer, A. Rapaport, J. Harmand.
    A simplified model of a submerged membrane bioreactor, in: 32th Benelux Meeting on Systems and Control, Houffalize, Belgium, March 2013.
    http://hal.inria.fr/hal-00925700
  • 54A. Charfi, N. Benamar, J. Harmand.
    Fouling in Anaerobic Membrane BioReactors, in: International workshop on modeling membrane bioreactors for wastewater reuse: fundamental design and operation, Tunis, Tunisia, November 2013.
    http://hal.inria.fr/hal-00925659
  • 55A. Rapaport.
    A propos de commande de systèmes dynamiques vers un extremum d'une fonction de sortie mal connue et applications, in: Séminaire Avignon-Montpellier d'Optimisation, Contrôle et Dynamique (SAMOCOD), Montpellier, France, 2013.
    http://hal.inria.fr/hal-00859558
  • 56A. Rapaport.
    Some Control and Optimization Problems for the Biological Wastewater treatment, in: GDRE ConEDP Meeting 2013 : Modeling and control of systems: applications to nano-sciences, environment and energy, Grenoble, France, 2013.
    http://hal.inria.fr/hal-00859559

Scientific Books (or Scientific Book chapters)

  • 57C. Lobry.
    La compétition dans le chémostat, in: TVC 81 : Des Nombres et des Mondes, E. Benoit, J.-P. Furter (editors), édition Herman, 2013, pp. 119-187.
    http://hal.inria.fr/hal-00711218

Internal Reports

  • 58T. Bayen, F. Mairet.
    Optimization of the separation of two species in a chemostat, April 2013, under revision.
    http://hal.inria.fr/hal-00817147
  • 59T. Bayen, F. Mairet, P. Martinon, M. Sebbah.
    Optimizing the anaerobic digestion of microalgae in a coupled process, September 2013.
    http://hal.inria.fr/hal-00860570
  • 60T. Bayen, F. Mairet, M. Mazade.
    Minimal time problem for a fed-batch bioreactor with saturating singular control, November 2013.
    http://hal.inria.fr/hal-00879385
  • 61T. Bayen, F. Mairet, M. Sebbah.
    Study of a controlled Kolmogorov periodic equation connected to the optimization of periodic bioprocess, August 2013.
    http://hal.inria.fr/hal-00855054
  • 62T. Bayen, M. Sebbah, A. Rapaport.
    Minimal time control of the two tanks gradostat model under a cascade inputs constraint, September 2013.
    http://hal.inria.fr/hal-00798651
  • 63F. Campillo, C. Fritsch.
    A mass-structured individual-based model of the chemostat: convergence and simulation, November 2013.
    http://hal.inria.fr/hal-00850959
  • 64F. Campillo, M. Joannides, I. Larramendy-Valverde.
    Estimation of the parameters of a stochastic logistic growth model, July 2013.
    http://hal.inria.fr/hal-00842291
  • 65F. Campillo, C. Lobry.
    L'effet de la migration dans la relation ressource-consommateur du point de vue de "l'atto-fox problem", March 2013.
    http://hal.inria.fr/hal-00800370
  • 66C. Casenave, D. Dochain.
    European project CAFE WP7: Process monitoring and control - Deliverable 7.2: Full-scale performance of the control laws in different product manufacturing end users, 2013.
    http://hal.inria.fr/hal-00859574
  • 67C. Casenave, C. Trelea, J.-R. Mouret, J.-M. Sablayrolles, S. Passot, B. Perret, F. Fonseca, C. Vilas, H. Benkhelifa, D. Leducq, G. Alvarez, V. Eisner-Schadler, J. De Kramer, A. Togtema, Y. Grushkin, R. van der Sman, M. Vollebregt.
    European project CAFE WP3: Process experiments - Deliverable 3.3: Test of optimal control strategies, 2013.
    http://hal.inria.fr/hal-00859575
  • 68R. van der Sman, M. Vollebregt, R. David, D. Dochain, D. Flick, H. Benkhelifa, J. E. Gonzalez-Ramirez, D. Leducq, G. Alvarez, M. Arellano Salazar, C. Trelea, I. Douania, S. Passot, F. Fonseca, C. Vilas, E. López-Quiroga, A. A. Alonso, M. Binns, W. Xie, C. Theodoropoulos, C. Casenave.
    European project CAFE WP4: Model reduction, validation and simulation - Deliverable 4.2: Portable and documented simulation software for each demonstration process, 2013.
    http://hal.inria.fr/hal-00859579

Patents

  • 69A. Rapaport, A. Rousseau, J. Harmand.
    Procédé de traitement d'une ressource fluide, programme d'ordinateur et module de traitement associés, 2013.
    http://hal.inria.fr/hal-00859584

Other Publications

  • 70A. Boutoub.
    Le filtre non linéaire pour le chemostat, Master d'Automatique - Université Aboubekr Belkaid Tlemcen, January 2013.
    http://hal.inria.fr/hal-00935752
  • 71C. Droin.
    Modélisation d'un écosystème de sol, INSA Lyon, August 2013, Mémoire d'Ingénieur.
    http://hal.inria.fr/hal-00934654
  • 72J. Harmand, F. Campillo, B. Cherki.
    Recycler les eaux usées pour l'irrigation, May 2013, Brève de Mathématiques de la Planète Terre 2013.
    http://hal.inria.fr/hal-00935646
  • 73A. Rapaport, J.-P. Terreaux.
    Cigale ou fourmi ? Quand la programmation dynamique guide nos décisions, 2013, Brève de Mathématiques de la Planète Terre 2013.
    http://hal.inria.fr/hal-00859582
  • 74S. Sekkat.
    Modélisation d'un fermenteur continu multi-étagé pour l'étude de la fermentation alcoolique du vin, Polytech Nice-Sophia - Université Nice Sophia-Antipolis, September 2013, Mémoire de Master 1.
    http://hal.inria.fr/hal-00934448
References in notes
  • 75K. B. Ariyur, M. Krstic.
    Real-Time Optimization by Extremum-Seeking Control, John Wiley & Sons, 2006.
  • 76S. N. Ethier, T. G. Kurtz.
    Markov Processes – Characterization and Convergence, John Wiley & Sons, 1986.
  • 77S. J. Pirt.
    Principles of microbe and cell cultivation, John Wiley & Sons, 1975.
  • 78H. Smith, P. Waltman.
    The Theory of the Chemostat: Dynamics of Microbial Competition, Cambridge University Press, 1995.
  • 79O. Wanner, H. Eberl, E. Morgenroth, D. Noguera, C. Picioreanu, B. Rittmann, M. Van Loosdrecht.
    Mathematical Modeling of Biofilms, IWA Scientific and Technical Report No.18, IWA Publishing, 2006, IWA Task Group on Biofilm Modeling.

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