Kinetic Theory Modeling and Efficient Numerical Simulation of Gene Regulatory Networks Based on Qualitative Descriptions
Article dans une revue avec comité de lecture
Auteur
CHINESTA SORIA, FranciscoMAGNIN, MorganROUX, Olivier AMMAR, Amine CUETO, EliasRésumé
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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Article dans une revue avec comité de lectureAMMAR, Amine; ; ; CUETO, Elias; CHINESTA SORIA, Francisco (Omics Publishing Group, 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 ...
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Article dans une revue avec comité de lecture;AMMAR, Amine; CHINESTA SORIA, Francisco; ; (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, ...
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Article dans une revue avec comité de lecture; ; ; ;AMMAR, Amine; CUETO, Elias; CHINESTA 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 ...
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Article dans une revue avec comité de lectureCUETO, Elias; ; AMMAR, Amine; CHINESTA 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 ...
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Article dans une revue avec comité de lectureAMMAR, Amine; CUETO, Elias; CHINESTA 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 ...