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Chemical Master Equation Empirical Moment Closure

Article dans une revue avec comité de lecture
Auteur
ccAMMAR, Amine
211916 Laboratoire Angevin de Mécanique, Procédés et InnovAtion [LAMPA]
MAGNIN, Morgan
21439 Institut de Recherche en Communications et en Cybernétique de Nantes [IRCCyN]
ROUX, Olivier
ccCUETO, Elias
161327 Aragón Institute of Engineering Research [Zaragoza] [I3A]
ccCHINESTA SORIA, Francisco
10921 Institut de Recherche en Génie Civil et Mécanique [GeM]

URI
http://hdl.handle.net/10985/11391
DOI
10.4172/2329-6577.1000155
Date
2016
Journal
Biological Systems: Open Access

Résumé

The numerical solution of the Chemical Master Equation (CME) governing gene regulatory networks and cell signaling processes remains a challenging task due to its complexity, exponentially growing with the number of species involved. When considering separated representations of the probability distribution function within the Proper Generalized Decomposition-PGD-frame-work the complexity of the CME grows only linearly with the number of state space dimensions. In order to speed up calculations moment-based descriptions are usually preferred, however these descriptions involve the necessity of using closure relations whose impact on the calculated solution is most of time unpredictable. In this work we propose an empirical closure, fitted from the solution of the chemical master equation, the last solved within the PGD framework.

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  • Laboratoire Angevin de Mécanique, Procédés et InnovAtion (LAMPA)

Documents liés

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  • Kinetic Theory Modeling and Efficient Numerical Simulation of Gene Regulatory Networks Based on Qualitative Descriptions 
    Article dans une revue avec comité de lecture
    ccCHINESTA SORIA, Francisco; MAGNIN, Morgan; ROUX, Olivier; ccAMMAR, Amine; ccCUETO, Elias (MDPI, 2015)
    In this work, we begin by considering the qualitative modeling of biological regulatory systems using process hitting, from which we define its probabilistic counterpart by considering the chemical master equation within ...
  • Linking Discrete and Stochastic Models: The Chemical Master Equation as a Bridge between Process Hitting and Proper Generalized Decomposition 
    Article dans une revue avec comité de lecture
    CHANCELLOR, Courtney; ccAMMAR, Amine; ccCHINESTA SORIA, Francisco; MAGNIN, Morgan; ROUX, Olivier (Springer, 2013)
    Modeling frameworks bring structure and analysis tools to large and non-intuitive systems but come with certain inherent assumptions and limitations, sometimes to an inhibitive extent. By building bridges in existing models, ...
  • Real-time in silico experiments on gene regulatory networks and surgery simulation on handheld devices 
    Article dans une revue avec comité de lecture
    ALFARO, Icíar; GONZALEZ, David; BORDEU, Felipe; LEYGUE, Adrien; ccAMMAR, Amine; ccCUETO, Elias; ccCHINESTA SORIA, Francisco (Springer Verlag, 2014)
    Simulation of all phenomena taking place in a surgical procedure is a formidable task that involves, when possible, the use of supercomputing facilities over long time periods. However, decision taking in the operating ...
  • Towards a high-resolution numerical strategy based on separated representations 
    Article dans une revue avec comité de lecture
    ccCUETO, Elias; GONZALEZ, David; ccAMMAR, Amine; ccCHINESTA SORIA, Francisco (Springer Link, 2008)
    Many models in Science and Engineering are defined in spaces (the so-called conformation spaces) of high dimensionality. In kinetic theory, for instance, the micro scale of a fluid evolves in a space whose number of ...
  • Reduction of the chemical master equation for gene regulatory networks using proper generalized decompositions 
    Article dans une revue avec comité de lecture
    ccAMMAR, Amine; ccCUETO, Elias; ccCHINESTA SORIA, Francisco (John Wiley and Sons, 2012)
    The numerical solution of the chemical master equation (CME) governing gene regulatory networks and cell signaling processes remains a challenging task owing to its complexity, exponentially growing with the number of ...

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