Kinetic Theory Modeling and Efficient Numerical Simulation of Gene Regulatory Networks Based on Qualitative Descriptions
TypeArticles dans des revues avec comité de lecture
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 a kinetic theory framework. The last equation is efficiently solved by considering a separated representation within the proper generalized decomposition framework that allows circumventing the so-called curse of dimensionality. Finally, model parameters can be added as extra-coordinates in order to obtain a parametric solution of the model.
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AMMAR, Amine; MAGNIN, Morgan; ROUX, Olivier; CUETO, Elias; CHINESTA, Francisco (2016)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 ...
Linking Discrete and Stochastic Models: The Chemical Master Equation as a Bridge between Process Hitting and Proper Generalized Decomposition CHACELLOR, Courtney; AMMAR, Amine; CHINESTA, 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, ...
NASRI, Mohamed Aziz; AGUADO, Jose Vicente; AMMAR, Amine; CUETO, Elias; CHINESTA, Francisco; MOREL, Franck; ROBERT, Camille; EL AREM, Saber (Key Engineering Materials, 2015)Forming processes usually involve irreversible plastic transformations. The calculation in that case becomes cumbersome when large parts and processes are considered. Recently Model Order Reduction techniques opened new ...
CHINESTA, Francisco; LEYGUE, Adrien; BORDEU, Felipe; AGUADO, Jose Vicente; CUETO, Elias; GONZALEZ, David; ALFARO, Iciar; AMMAR, Amine; HUERTA, Antonio (Springer, 2013)In this paper we are addressing a new paradigm in the field of simulation-based engineering sciences (SBES) to face the challenges posed by current ICT technologies. Despite the impressive progress attained by simulation ...
Nonincremental proper generalized decomposition solution of parametric uncoupled models defined in evolving domains AMMAR, Amine; CUETO, Elias; CHINESTA, Francisco (Wiley, 2012)This work addresses the recurrent issue related to the existence of reduced bases related to the solution of parametric models defined in evolving domains. In this first part of the work, we address the case of decoupled ...