APPEL À RÉSEAUX “Réseau National des Systèmes Complexes” RNSC 2012
This project aims to initiate a reflection on the numerical modeling of microbial ecosystem dynamics: how to articulate existing models, discrete or continuous, deterministic or random in a framework including multiple scales and interactions between these different scales?
The network
List of collaborators
- MODEMIC (EPC INRA-INRIA) et UMR MISTEA (Supagro, INRA), Montpellier. Alain Rapaport, Tewfik Sari, Fabien Campillo, Claude Lobry, Céline Casenave, Jérôme Harmand
- LISC, IRSTEA, Clermont Ferrand, Guillaume Deffuant, Jean-Denis Mathias et Franck Jabot
- LPTMC, UMR CNRS-Univ Paris 6, Annick Lesne
- HBAN, IRSTEA, Antony, Théodore Bouchez, Ariane Bize d’Avezac, Elie Desmond et Arnaud Bridier
- Unité MIA, INRA, Jouy-en-Josas, Béatrice Laroche
- MICALIS, INRA, Jouy en Josas, Romain Briandet
- LBE, INRA, Narbonne, Jean-Jacques Godon
Project supported by the network
The objectives of this network are:
- First, to identify the important actors at the national level interested in microbial ecosystem modeling and simulation issues;
- to federate within a network these different teams (modellers, simulators as well as ecologists and/or microbiologists);
- to propose common actions allowing to contribute to the acquisition of new knowledge relative to the theme (response to national or international calls for projects), to develop this problematic at the doctoral and post-doctoral levels (workshops, co-supervision, or even trainings if precise needs were identified) and possibly to propose new tools of common interest (e.g. proposal of a software development specification)
The originality of this network is to bring together biologists and various specialists in dynamical systems (from continuous deterministic to stochastic discrete), with the objective of identifying situations where hybrid modeling reserves “surprises” or non-intuitive behaviors (cf. for example Campillo and Lobry, 2012).
Relationship to complex systems
The vast majority of models used to describe the dynamics of microbial ecosystems consist of deterministic continuous dynamical systems (mathematized as systems of differential equations). These models generally describe the evolution in time of the “size” of the population. However, by definition, the size of a population is a discrete quantity. When the population size is very large, the approximation of infinitesimal changes in the population (plus or minus 1 individual) by a continuous model is satisfactory, whereas stochastic models are more appropriate for describing the dynamics of small populations. Molecular approaches have shown that natural ecosystems are made up of a large diversity of species, some of which are very abundant while others have very low numbers. This raises the question of the validity of the models classically used to describe these ecosystems. If we have to use a discrete model for all the species, it is obvious that the necessary computing power will be prohibitive. There is therefore a clear need to i) develop new hybrid models where discrete or continuous stochastic models, in population size or individual-centered (IBM), could play a major role and ii) develop and validate simulation tools capable of supporting the implementation of these new models.
Results
Publications
[A1] Mohamed Amara. Apport de la modélisation et de la simulation dans la compréhension du fonctionnement des écosystèmes microbiens, stage de master, Ecole polytechnique de Nantes, mars-septembre 2013
[C1] F. Campillo. Modélisation en dynamique des populations. Revue TDC (Textes et documents pour la classe) n°1062, 15 Octobre 2013.
[CF1] F. Campillo, C. Fritsch. A mass-structured individual-based model of the chemostat: convergence and simulation. Aug. 2013.
[CL1] F. Campillo and C. Lobry. Effect of population size in a predator–prey model, Ecological Modelling, 246:1-10, 2012.
[GHMD1] T. Guélon, R.C. Hunter, J.D. Mathias, and G. Deffuant. Homogenization of Pseudomonas aeruginosa PAO1 biofilms visualized by freeze-substitution electron microscopy. Biotechnology and Bioengineering, 2013, Vol. 110, Issue 5, pages 1405-1418
[GMD1] T. Guélon, J.-D. Mathias and G. Deffuant. Influence of spatial structure on effective nutrient diffusion in bacterial biofilms. Journal of Biological Physics, Vol. 38, Issue 4, 2013, pages 573-588.
[JRHBN1] Jaillard B., A. Rapaport, J. Harmand, A. Brauman, N. Nunan. Community assembly effects shape the biodiversity-ecosystem functioning relationships. Accepté dans Functional Ecology.
[JVR1] Jaillard B., C. Violle, A. Rapaport, Biodiversity and ecosystem functioning: a probabilistic approach provides a parsimonious and unified formalism. En préparation.
[L1] A. Lesne (2013) Multi-scale analysis of biological functions, Acta Biotheoretica 61, 3-19.
Communications
F. Campillo, M. Joannides, I. Larramendy. Stochastic models for the chemostat at different scales15th Applied Stochastic Models and Data Analysis International Conference (ASMDA 2013), June 25–28, Jun 2013, Barcelona, Spain.
Several members of the network are participating in the days “From singularly disturbed dynamics to population dynamics” in La Rochelle in December 2013.
Achievements
Within the framework of the MnMs network, we have continued the development of an IBM model to simulate the degradation of a cellulose bead (see here).
Other projects
The reflections conducted within the MNMs network have led to other projects such as the NuWat project, led by LIRIMA, dealing with numerical modeling for water treatment processes.
Activities 2013
Coupled days DyLeRBio & MnMs
The meeting will be held September 30, October 1-2 in Montpellier on the SupAgro Campus (see this link for the location of the campus and for a list of hotels).
Salle Ferguson – Campus SupAgro – building #21, 1st floor (RDC).
| Monday, September 30 |
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| Tuesday, October 1 |
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| Wednesday, October 2 |
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List of participants:
Térence Bayen (Université de Montpellier 2)
Romain Briandet (INRA MICALIS)
Fabien Campillo (INRIA MODEMIC)
Céline Casenave (INRA MODEMIC)
Guillaume Deffuant (IRSTEA LISC)
Mathieu Desroches (INRIA SISYPHE)
Yves Dumont (IRD AMAP)
Albert Granados (INRIA Rocquencourt)
Antoni Guillamon (UPC, Barcelona)
Jérôme Harmand (INRA LBE and MODEMIC)
Gemma Huguet (UPC, Barcelona)
Martin Krupa (INRIA SISYPHE)
Annick Lesnes (CNRS/UPMC LPTMC)
Jean-Denis Mathias (IRSTEA LISC)
Claude Lobry (UNSA MODEMIC)
Enrique Ponce (Univ. Sevilla)
Rafel Prohens (UIB, Palma de Mallorque)
Ovidiu Radulescu (DIMNP Université de Montpellier 2)
Alain Rapaport (INRA MODEMIC)
Tewfik Sari (IRSTEA ITAP)
Tere Seara (UPC, Barcelona)
Antonio Teruel (UIB, Palma de Mallorca).