There is a debate in ecology between those favoring simple aggregated mathematical models contain... more There is a debate in ecology between those favoring simple aggregated mathematical models containing only a few equations expressing a small number of general principles and those preferring complex individual-based models that are more structurally realistic with a more detailed representation of the basic processes and interactions at the level of the individuals. In this thesis we attempt to bridge these two approaches by deriving deterministic moment approximation models of microbial individual-based models. We illustrate the approach on the example of biofilm growth with immotile and motile bacteria. We show that moment model can capture the main features of spatial pattern that arise in simplified biofilm individual-based models. Finally we assess the limitation of the moment models in capturing the effect of local fluctuations of the individuals environment.(trad auto)Il y a un débat en écologie entre ceux qui favorisent les modèles mathématiques agrégés simples ne contenant ...
Les équipes du projet collaborent à plusieurs modèles individus-centrés dans une démarche commune... more Les équipes du projet collaborent à plusieurs modèles individus-centrés dans une démarche commune au projet DISCO: ces modèles individus-centrés sont confrontés à la fois à des modèles de type équations aux dérivées partielles ou équations différentielles ordinaires (démarche de "double modélisation") et à des observations venant de démarches expérimentales spécifiques. Cette démarche permet d'identifier clairement les effets spécifiques de l'introduction d'un modèle à partir d'individus. Les modèles individus-centrés donnent lieu aussi dans certains cas à l'émergence de structures spatiales (dans les deux exemples de modèles 2 D) qui étaient difficilement prédictibles initialement. Nous cherchons ensuite à comprendre les mécanismes donnant lieu à ces structures, notamment en définissant des modèles plus simples. Ce rapport présente ces modèles de manière très condensée, le lecteur intéressé pourra trouver les détails dans les documents cités dans les r...
Recent experimental observations of Pseudomonas aeruginosa, a model bacterium in biofilm research... more Recent experimental observations of Pseudomonas aeruginosa, a model bacterium in biofilm research, reveal that, under specific growth conditions, bacterial cells form patterns of interconnected microcolonies. In the present work, we use an individual-based model to assess the involvement of bacteria motility and self-produced extracellular substance in the formation of these patterns. In our simulations, the pattern of interconnected microcolonies appears only when bacteria motility is reduced by excreted extracellular macromolecules. Immotile bacteria form isolated microcolonies and constantly motile bacteria form flat biofilms. Based on experimental data and computer simulations we suggest a mechanism that could be responsible for these interconnected microcolonies.
Bacteria growth, detachment and surface-associated motility are recongnized to play an important ... more Bacteria growth, detachment and surface-associated motility are recongnized to play an important role in microbial biofilm formation. In this paper we we investigate using an individual-based model how these processes interplay to yield complex biofilm spatial patterns.
Page 1. Chapter 6 Viability and Resilience of a Bacterial Biofilm Individual-Based Model Nabil Ma... more Page 1. Chapter 6 Viability and Resilience of a Bacterial Biofilm Individual-Based Model Nabil Mabrouk, Jean-Denis Mathias, and Guillaume Deffuant 6.1 Introduction In many industrial applications, bacteria are cultivated in ...
2009 Fourth International Multi-Conference on Computing in the Global Information Technology, 2009
We consider a 2D individual-based model of biofilm, in which bacteria can generate a polymeric su... more We consider a 2D individual-based model of biofilm, in which bacteria can generate a polymeric substance (EPS), The coupling between polymer generation and bacteria creates a variety of biofilm structures. Then, we derive the equations of first and second moment evolution for the bacteria and EPS particle population sizes. This approximation of the dynamics is much lighter to compute than
... Biosystems, 91(1):126145, January 2008. [8] FL Hellweger and V. Bucci. A bunch of tiny indiv... more ... Biosystems, 91(1):126145, January 2008. [8] FL Hellweger and V. Bucci. A bunch of tiny individuals - individual-based modeling for microbes. Ecological Modelling, 220:822, 2009. [9] OP Judson. The rise of the individual-based model in ecology. ...
Recent experimental observations of Pseudomonas aeruginosa, a model bacterium in biofilm research... more Recent experimental observations of Pseudomonas aeruginosa, a model bacterium in biofilm research, reveal that, under specific growth conditions, bacterial cells form patterns of interconnected microcolonies. In the present work, we use an individual-based model to assess the involvement of bacteria motility and self-produced extracellular substance in the formation of these patterns. In our simulations, the pattern of interconnected microcolonies appears only when bacteria motility is reduced by excreted extracellular macromolecules. Immotile bacteria form isolated microcolonies and constantly motile bacteria form flat biofilms. Based on experimental data and computer simulations we suggest a mechanism that could be responsible for these interconnected microcolonies.
There is a debate in ecology between those favoring simple aggregated mathematical models contain... more There is a debate in ecology between those favoring simple aggregated mathematical models containing only a few equations expressing a small number of general principles and those preferring complex individual-based models that are more structurally realistic with a more detailed representation of the basic processes and interactions at the level of the individuals. In this thesis we attempt to bridge these two approaches by deriving deterministic moment approximation models of microbial individual-based models. We illustrate the approach on the example of biofilm growth with immotile and motile bacteria. We show that moment model can capture the main features of spatial pattern that arise in simplified biofilm individual-based models. Finally we assess the limitation of the moment models in capturing the effect of local fluctuations of the individuals environment.(trad auto)Il y a un débat en écologie entre ceux qui favorisent les modèles mathématiques agrégés simples ne contenant ...
Les équipes du projet collaborent à plusieurs modèles individus-centrés dans une démarche commune... more Les équipes du projet collaborent à plusieurs modèles individus-centrés dans une démarche commune au projet DISCO: ces modèles individus-centrés sont confrontés à la fois à des modèles de type équations aux dérivées partielles ou équations différentielles ordinaires (démarche de "double modélisation") et à des observations venant de démarches expérimentales spécifiques. Cette démarche permet d'identifier clairement les effets spécifiques de l'introduction d'un modèle à partir d'individus. Les modèles individus-centrés donnent lieu aussi dans certains cas à l'émergence de structures spatiales (dans les deux exemples de modèles 2 D) qui étaient difficilement prédictibles initialement. Nous cherchons ensuite à comprendre les mécanismes donnant lieu à ces structures, notamment en définissant des modèles plus simples. Ce rapport présente ces modèles de manière très condensée, le lecteur intéressé pourra trouver les détails dans les documents cités dans les r...
Recent experimental observations of Pseudomonas aeruginosa, a model bacterium in biofilm research... more Recent experimental observations of Pseudomonas aeruginosa, a model bacterium in biofilm research, reveal that, under specific growth conditions, bacterial cells form patterns of interconnected microcolonies. In the present work, we use an individual-based model to assess the involvement of bacteria motility and self-produced extracellular substance in the formation of these patterns. In our simulations, the pattern of interconnected microcolonies appears only when bacteria motility is reduced by excreted extracellular macromolecules. Immotile bacteria form isolated microcolonies and constantly motile bacteria form flat biofilms. Based on experimental data and computer simulations we suggest a mechanism that could be responsible for these interconnected microcolonies.
Bacteria growth, detachment and surface-associated motility are recongnized to play an important ... more Bacteria growth, detachment and surface-associated motility are recongnized to play an important role in microbial biofilm formation. In this paper we we investigate using an individual-based model how these processes interplay to yield complex biofilm spatial patterns.
Page 1. Chapter 6 Viability and Resilience of a Bacterial Biofilm Individual-Based Model Nabil Ma... more Page 1. Chapter 6 Viability and Resilience of a Bacterial Biofilm Individual-Based Model Nabil Mabrouk, Jean-Denis Mathias, and Guillaume Deffuant 6.1 Introduction In many industrial applications, bacteria are cultivated in ...
2009 Fourth International Multi-Conference on Computing in the Global Information Technology, 2009
We consider a 2D individual-based model of biofilm, in which bacteria can generate a polymeric su... more We consider a 2D individual-based model of biofilm, in which bacteria can generate a polymeric substance (EPS), The coupling between polymer generation and bacteria creates a variety of biofilm structures. Then, we derive the equations of first and second moment evolution for the bacteria and EPS particle population sizes. This approximation of the dynamics is much lighter to compute than
... Biosystems, 91(1):126145, January 2008. [8] FL Hellweger and V. Bucci. A bunch of tiny indiv... more ... Biosystems, 91(1):126145, January 2008. [8] FL Hellweger and V. Bucci. A bunch of tiny individuals - individual-based modeling for microbes. Ecological Modelling, 220:822, 2009. [9] OP Judson. The rise of the individual-based model in ecology. ...
Recent experimental observations of Pseudomonas aeruginosa, a model bacterium in biofilm research... more Recent experimental observations of Pseudomonas aeruginosa, a model bacterium in biofilm research, reveal that, under specific growth conditions, bacterial cells form patterns of interconnected microcolonies. In the present work, we use an individual-based model to assess the involvement of bacteria motility and self-produced extracellular substance in the formation of these patterns. In our simulations, the pattern of interconnected microcolonies appears only when bacteria motility is reduced by excreted extracellular macromolecules. Immotile bacteria form isolated microcolonies and constantly motile bacteria form flat biofilms. Based on experimental data and computer simulations we suggest a mechanism that could be responsible for these interconnected microcolonies.
Uploads
Papers by Nabil Mabrouk