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, 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 Cabrera, 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.

Publications of the year

Doctoral Dissertations and Habilitation Theses

11I. Haidar.

Dynamiques microbiennes et modélisation des cycles biogéochimiques terrestres, Université Montpellier II, 2011.

Articles in International Peer-Reviewed Journal

12F. Campillo, M. Joannides, I. Larramendy-Valverde.

Stochastic modeling of the chemostat, in: Ecological Modelling, 2011, vol. 222, n^o 15, p. 2676-2689.
13R. S. Etienne, B. Haegeman.

The neutral theory of biodiversity with random fission speciation, in: Theoretical Ecology, 2011, vol. 4, p. 87-109.
14R. Fekih-Salem, T. Sari, N. Abdellatif.

Sur un modèle de compétition et de coexistence dans le chémostat, in: ARIMA, 2011, vol. 14, p. 15-30.
15P. Gajardo, H. Ramirez Cabrera, A. Rapaport, J. Harmand.

Minimal-time bioremediation of natural water resources, in: Automatica, 2011, vol. 47, n^o 8, p. 1764-1769.
16B. Haegeman, R. S. Etienne.

Independent species in independent niches behave neutrally, in: Oikos, 2011, vol. 120, p. 961-963.
17B. Haegeman, M. Loreau.

A mathematical synthesis of niche and neutral theories in community ecology, in: Journal of Theoretical Biology, 2011, vol. 269, p. 150-165.
18I. Haidar, F. Gérard, A. Rapaport.

Comparison of numerical simulations of reactive transport and chemostat-like models, in: Computational Ecology and Software, 2011, vol. 1, n^o 4, p. 224-239.
19I. Haidar, A. Rapaport, F. Gérard.

Effects of spatial structure and diffusion on the performances of the chemostat, in: Mathematical Biosciences and Engineering, 2011, vol. 8, n^o 4, p. 953-971.
20M. Jerry, N. Raissi, A. Rapaport.

Viability analysis for an explicit inshore-offshore model, in: JP Journal of Applied Mathematics, 2011, vol. 1, n^o 1, p. 41-60.
21A. Kislyuk, B. Haegeman, N. Bergman, J. Weitz.

Genomic fluidity: an integrative view of gene diversity within microbial populations, in: BMC Genomics, 2011, vol. 12, n^o 1, 32 p. [ DOI : 10.1186/1471-2164-12-32 ]

http://www.biomedcentral.com/1471-2164/12/32
22A. Rapaport, D. Dochain.

Minimal time control of fed-batch processes with growth functions having several maxima, in: IEEE Transactions on Automatic Control, 2011, vol. 56, n^o 11, p. 2671-2676.
23J. Rouyer, T. Sari.

As many antipodes as vertices on some convex polyhedra, in: Advances in Geometry, 2011, published online.
24T. Sari, F. Mazenc.

Global dynamics of the chemostat with different removal rates and variable yields, in: Mathematical Biosciences and Engineering, 2011, vol. 8, n^o 3, p. 827-840.

International Conferences with Proceedings

25B. Benyahia, T. Sari, B. Cherki, J. Harmand.

Modélisation mathématique d'un bioréacteur membranaire anaérobie, in: Proceedings of the 5th conference on Trends in Applied Mathematics in Tunisia, Tunisia, M. Hassine, M. Moakher (editors), Centre de Publication Universitaire, 23-26 Avril 2011, p. 465-470.
26F. Campillo, N. Champagnat.

An individual-based model for clonal plant dynamics, in: MAMERN11: 4th International Conference on Approximation Methods and Numerical Modelling in Environment and Natural Resources, Saidia (Morocco, May 23-26 2011.
27F. Campillo, M. Joannides, I. Larramendy-Valverde.

Stochastic models for the chemostat, in: MAMERN11: 4th International Conference on Approximation Methods and Numerical Modelling in Environment and Natural Resources, Saidia (Morocco, May 23-26 2011.
28M. El Hajji, T. Sari, J. Harmand.

Analyse d'un relation syntrophique: cas d'un chemostat, in: Proceedings of the 5th conference on Trends in Applied Mathematics in Tunisia, Tunisia, M. Hassine, M. Moakher (editors), Centre de Publication Universitaire, 23-26 Avril 2011, p. 451-456.
29R. Fekih-Salem, N. Abdellatif, T. Sari, J. Harmand.

Sur un modèle de digestion anaréobie avec dégradation enzymatique du substrat sous forme solide, in: Proceedings of the 5th conference on Trends in Applied Mathematics in Tunisia, Tunisia, M. Hassine, M. Moakher (editors), Centre de Publication Universitaire, 23-26 Avril 2011, p. 457-463.
30R. Fekih-Salem, T. Sari, A. Rapaport.

La floculation et la coexistence dans le chemostat, in: Proceedings of the 5th conference on Trends in Applied Mathematics in Tunisia, Tunisia, M. Hassine, M. Moakher (editors), Centre de Publication Universitaire, 23-26 Avril 2011, p. 477-483.
31P. Gajardo, H. Ramirez Cabrera, V. Riqueleme, A. Rapaport.

Bioremediation of natural water resources via optimal control techniques, in: International Symposium on Mathematical and Computational Biology, Santiago (Chile), november 2011.
32T. Sari, N. Abdellatif, B. Benyahia, Lamine Mamadou. Diagne, M. El Hajji, R. Fekih-Salem.

Modélisation mathématique en biologie : compétition, coexistence et croissance, in: Proceedings of the 5th conference on Trends in Applied Mathematics in Tunisia, Tunisia, M. Hassine, M. Moakher (editors), Centre de Publication Universitaire, 23-26 Avril 2011, p. 19-25.

National Conferences with Proceeding

33I. Haidar, A. Rapaport, F. Gérard.

Effects of spatial structure and diffusion on the performances of the chemostat, in: STIC & Environnement, Saint-Etienne (France), mai 2011.
34J. B. Rivas, J. Harmand, B. Ivorra, A. R. del Omo, A. Rapaport.

Bioreactor shape optimization: modeling, simulation, and shape optimization of a simple bioreactor for water treatment, in: STIC & Environnement, Saint-Etienne (France), mai 2011.

Conferences without Proceedings

35F. Campillo, N. Champagnat.

Simulation and Analysis of a Markovian Individual-Based Model for Clonal Plant Dynamics, in: 7th International Congress on Industrial and Applied Mathematics, Vancouver, Canada, July 2011.

http://hal.inria.fr/hal-00651758/en/
36F. Campillo, N. Champagnat, C. Mony.

Monte Carlo simulation and mathematical analysis of an individual-based model for clonal plant dynamics, in: 54th Symposium of the International Association for Vegetation Science (IAVS), Lyon, France, June 2011.

http://hal.inria.fr/hal-00651732/en/
37F. Campillo, M. Joannides, I. Larramendy-Valverde.

Stochastic Models for the Chemostat, in: 7th International Congress on Industrial and Applied Mathematics, Vancouver, Canada, July 2011.

http://hal.inria.fr/hal-00651777/en/

Internal Reports

38F. Campillo, D. Hervé, A. Raherinirina, R. Rakotozafy.

A Markov model of land use dynamics, INRIA, July 2011, n^o RR-7670.

http://hal.inria.fr/inria-00605925/en

Other Publications

39F. Campillo, M. Joannides, I. Larramendy-Valverde.

Approximation of the Fokker-Planck equation of the stochastic chemostat, 2011, ArXiv Mathematics e-prints.
40F. Campillo, C. Lobry.

Effect of population size in a Prey-Predator model, 2011, ArXiv Mathematics e-prints.
41C. Deygout, A. Lesne, F. Campillo, A. Rapaport.

A multiscale approach for biofilm modelling: application for growth in a plug flow reactor, June 2011.

http://hal.archives-ouvertes.fr/hal-00604377/en/
42R. Fekih-Salem, A. Rapaport, T. Sari, C. Lobry, J. Harmand.

Extensions of the chemostat model with flocculation, September 2011.

http://hal.archives-ouvertes.fr/hal-00604633/en/
43R. Fekih-Salem, A. Rapaport, T. Sari, C. Lobry, J. Harmand.

Extensions of the chemostat model with flocculation, June 2011, ArXiv e-prints.
44P. Gajardo, J. Harmand, H. Ramirez Cabrera, A. Rapaport.

Minimal-time bioremediation of natural water resources, May 2011.

http://hal.archives-ouvertes.fr/hal-00521118/en/
45I. Haidar, F. Gérard, A. Rapaport.

Comparison of numerical simulations of reactive transport and chemostat-like models, August 2011, ArXiv e-prints.

References in notes

46O. Bernard, Z. Hadj-Sadok, D. Dochain, A. Genovesi, J.-P. Steyer.

Dynamical model development and parameter identification for an anaerobic wastewater treatment process, in: Biotechnology and Bioengineering, 2001, vol. 75, p. 424-438.
47G. Butler, S.K. Wolkowicz.

A Mathematical model of the chemostat with general class of the function describing nutrient uptake, in: SIAM Journal on Applied Mathematics, 1985, vol. 45, n^o 1, p. 138-151.
48N. Fournier, S. Méléard.

A microscopic probabilistic description of a locally regulated population and macroscopic approximations, in: Annals of Applied Probability, 2004, vol. 14, p. 1880-1919.
49J. Hess, O. Bernard.

Design and Study of a risk management criterion for an unstable anaerobic wastewater treatment, in: J. Process Control, 2007, vol. 18, p. 71-79.
50S. Hubbell.

The Unified Neutral Theory of Biodiversity and Biogeography, Princeton University Press, 2001.
51J. Moreno.

Optimal control of bioreactors for the wastewater treatment, in: Optim. Control, Appl. Methods, 1999, vol. 20, p. 145-164.
52C. Silva, E. Trélat.

Smooth regularization of bang-bang optimal control problems, in: IEEE Trans. Autom. Control, 2010, vol. 55, n^o 11, p. 2488-2500.
53P. Spinelli, G. Rakotonirainy.

Minimum time problem synthesis, in: System and Control Letters, 1988, vol. 10, n^o 4, p. 281-290.

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