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Study of Conditions for the Emergence of Cellular Communication Using Self-Adaptive Multi-Agent Systems Sebastien Maignan

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Study of Conditions for the Emergence of Cellular Communication Using Self-Adaptive Multi-Agent Systems Sebastien Maignan Study of conditions for the emergence of cellular communication using self-adaptive multi-agent systems Sebastien Maignan To cite this version: Sebastien Maignan. Study of conditions for the emergence of cellular communication using self- adaptive multi-agent systems. Artificial Intelligence [cs.AI]. Université Paul Sabatier - Toulouse III, 2018. English. NNT : 2018TOU30094. tel-02094368 HAL Id: tel-02094368 https://tel.archives-ouvertes.fr/tel-02094368 Submitted on 9 Apr 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Délivré par l'Université Toulouse 3 Paul Sabatier (UT3 Paul Sabatier) Sébastien Maignan Le 30 août 2018 Study of conditions for the emergence of cellular communication using self-adaptive multi-agent systems École doctorale et discipline ou spécialité ED MITT : Domaine STIC : Intelligence Artificielle Unité de recherche Institut de Recherche en Informatique de Toulouse Directrice(s) ou Directeur(s) de Thèse Pierre Glize, Carole Bernon Jury Marie BEURTON-AIMAR Maître de Conférences, HdR, Université de Bordeaux Rapporteur Vincent RODIN Professeur des Universités, Université de Bretagne Occidentale Rapporteur Arnaud DUCRUIX Professeur Emérite, Université Paris Descartes Examinateur Bernard FRANCÈS Professeur Emérite, Université de Toulouse Examinateur Marie-Pierre GLEIZES Professeur des Universités, Université de Toulouse Examinatrice Guillaume HUTZLER Maître de Conférences, HdR, Université d'Evry Examinateur Carole BERNON Maître de Conférences, Université de Toulouse Co-Directrice Pierre GLIZE Ingénieur d'Etude, HdR, CNRS Directeur Jean-Pierre MANO Data Scientist, Brennus Analytics Invité Délivré par l'Université Toulouse 3 Paul Sabatier (UT3 Paul Sabatier) Sébastien Maignan Le 30 août 2018 Study of conditions for the emergence of cellular communication using self-adaptive multi-agent systems École doctorale et discipline ou spécialité ED MITT : Domaine STIC : Intelligence Artificielle Unité de recherche Institut de Recherche en Informatique de Toulouse Directrice(s) ou Directeur(s) de Thèse Pierre Glize, Carole Bernon Jury Marie BEURTON-AIMAR Maître de Conférences, HdR, Université de Bordeaux Rapporteur Vincent RODIN Professeur des Universités, Université de Bretagne Occidentale Rapporteur Arnaud DUCRUIX Professeur Emérite, Université Paris Descartes Examinateur Bernard FRANCÈS Professeur Emérite, Université de Toulouse Examinateur Marie-Pierre GLEIZES Professeur des Universités, Université de Toulouse Examinatrice Guillaume HUTZLER Maître de Conférences, HdR, Université d'Evry Examinateur Carole BERNON Maître de Conférences, Université de Toulouse Co-Directrice Pierre GLIZE Ingénieur d'Etude, HdR, CNRS Directeur Jean-Pierre MANO Data Scientist, Brennus Analytics Invité Remerciements Tout d’abord je souhaiterai remercier les membres du jury Marie Beurton-Aimar, Vincent Rodin, Arnaud Ducruix, Bernard Francès, Guillaume Hutzler et Jean-Pierre Mano d’avoir accepté d’évaluer ce travail. Je voudrais remercier Marie-Pierre Gleizes de m’avoir accueilli chez SMAC bien que mon sujet sortait un peu de la thématique du laboratoire ainsi que de sa gentillesse. Je tiens à remercier Pierre Glize et Carole Bernon qui ont accepté de me guider pendant cette thèse. Je me souviendrais toujours de nos sessions de travail où nous essayions d’imaginer les « motivations » des cellules primitives. J’aimerais aussi remercier mon épouse Marie-José et mes enfants Julien, Karine et Alexandre de leur soutien inconditionnel. Enfin je voudrais exprimer ma gratitude à tous les membres de l’équipe SMAC. Ces quelques années passées en votre compagnie ont été une expérience inoubliable à bien des égards. Que ce soit pour les discussions scientifiques, philosophiques ou pour la bonne humeur permanente, j’en ai apprécié chaque seconde. Cependant comme je ne suis pas certain de trouver les mots justes pour vous tous, j’ai trouvé une boite usagée mais magique qui contient le remerciement parfait pour chacun d’entre vous. Elle possède des trous d’aérations car à une époque il est dit qu’elle a contenu un mouton… . Table of contents CHAPTER 1. Introduction ..................................................................................................................... 1 CHAPTER 2. Context and State of the Art ........................................................................................... 9 2.1 DNA is Information but the Rest of the Cell too ..................................................................... 9 2.2 Is DNA the Programming Language of the Cell? ................................................................... 11 2.3 Optimization in Nature: Combination as a Way to Improve Biological Processes ................ 14 2.4 Simulating the Emergence of Structured Communication ................................................... 16 2.5 Complex Systems ................................................................................................................... 17 2.6 Emergence ............................................................................................................................. 18 2.7 Biological Background ........................................................................................................... 20 2.7.1 Generalities ................................................................................................................... 20 2.7.2 Complexity and Emergence in Biological Systems ........................................................ 23 2.7.3 Emergence of Multicellularity ....................................................................................... 26 2.7.4 Cell-cell Communication Systems.................................................................................. 28 2.7.5 Paracrine Signalling ....................................................................................................... 30 2.7.6 Summary of Biological Features Important for Simulation ........................................... 30 2.8 Experimental Support of the Structured Communication Hypothesis ................................. 31 2.8.1 Neovascularization Therapy .......................................................................................... 32 2.8.2 Reprogramming Malignant Cells into Normal Cells using Paracrine Signals ................. 32 2.8.3 Cytokine Combination Protect from Viral Infection ...................................................... 33 2.8.4 Calcium Signaling Associated with Pairwise Agonist Scanning ..................................... 33 2.8.5 Macrophage Cytokine Release ...................................................................................... 34 2.8.6 Monocytes Impacts the Cytokine Environment ............................................................ 34 2.8.7 Conclusion on Experimental Biology ............................................................................. 34 2.9 Computational Methods ....................................................................................................... 35 2.9.1 Models ........................................................................................................................... 35 2.9.2 Computer Simulation .................................................................................................... 35 2.9.3 Models and Techniques Used in Cell Simulation Systems ............................................ 36 2.9.4 Summary of Required Computational Features ............................................................ 45 2.10 Software for Cellular Simulation ........................................................................................... 45 2.10.1 Netlogo .......................................................................................................................... 45 2.10.2 CompuCell3D ................................................................................................................. 46 2.10.3 The Virtual Cell .............................................................................................................. 46 2.10.4 CellSys ............................................................................................................................ 47 2.10.5 Cell-based Chaste .......................................................................................................... 47 2.10.6 EPISIM ............................................................................................................................ 48 i 2.10.7 Morpheus ...................................................................................................................... 48 2.10.8 LBIBCell .......................................................................................................................... 49 2.10.9 Onko3D .......................................................................................................................... 50 2.10.10 NetBioDyn.................................................................................................................. 50 2.10.11 PhysiCell ....................................................................................................................
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