Kinetic Theory Modeling and Efficient Numerical Simulation of Gene Regulatory Networks Based on Qualitative Descriptions
Article dans une revue 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.
Showing items related by title, author, creator and subject.
Article dans une revue avec comité de lectureAMMAR, Amine; MAGNIN, Morgan; ROUX, Olivier; CUETO, Elias; CHINESTA, 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 ...
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 lectureCHACELLOR, 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, ...
On the effective conductivity and the apparent viscosity of a thin rough polymer interface using PGD‐based separated representations Article dans une revue avec comité de lectureAMMAR, Amine; GHNATIOS, Chady; DELPLACE, Frank; BARASINSKI, Anais; DUVAL, Jean-Louis; CUETO, Elias; CHINESTA, Francisco (Wiley, 2020)Composite manufacturing processes usually proceed from preimpregnated preforms that are consolidated by simultaneously applying heat and pressure, so as to ensure a perfect contact compulsory for making molecular diffusion ...
Communication avec acteNASRI, 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 ...
Article dans une revue avec comité de lectureAMMAR, Amine; CHINESTA, Francisco; CUETO, Elias; DOBLARÉ, Manuel (Wiley, 2012)Models encountered in computational mechanics could involve many time scales. When these time scales cannot be separated, one must solve the evolution model in the entire time interval by using the finest time step that ...