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
Date
2013Journal
Lecture Notes in Computer ScienceAbstract
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, we can exploit the advantages of each, widening the range of analysis possible for larger, more detailed models of gene regulatory networks. In this paper, we create just such a link between Process Hitting [6,7,8], a recently introduced discrete framework, and the Chemical Master Equation in such a way that allows the application of powerful numerical techniques, namely Proper Generalized Decomposition [1,2,3], to overcome the curse of dimensionality. With these tools in hand, one can exploit the formal analysis of discrete models without sacrificing the ability to obtain a full space state solution, widening the scope of analysis and interpretation possible. As a demonstration of the utility of this methodology, we have applied it here to the p53-mdm2 network [4,5], a widely studied biological regulatory network.
Files in this item
Related items
Showing items related by title, author, creator and subject.
-
Article dans une revue avec comité de lectureIn 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 ...
-
Article dans une revue avec comité de lecture
AMMAR, Amine; MAGNIN, Morgan; ROUX, Olivier;
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 ... -
Article dans une revue avec comité de lectureGRMELA, Miroslav; MAITREJEAN, Guillaume;
CHINESTA SORIA, Francisco;
AMMAR, Amine (Springer Verlag, 2013)
Smoluchowski kinetic equation governing the time evolution of the pair correlation function of rigid sphericalparticles suspended in a Newtonian fluid is extended to include particle migration. The extended kinetic equation ... -
Article dans une revue avec comité de lectureALFARO, Icíar; GONZALEZ, David; BORDEU, Felipe; LEYGUE, Adrien;
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 ... -
Article dans une revue avec comité de lectureAGHIGHI, Mohammad Saeid;
AMMAR, Amine; METIVIER, Christel; NORMANDIN, Magdeleine;
CHINESTA SORIA, Francisco (Elsevier, 2013)
This paper focuses on the non-incremental solution of transient coupled non-linear models, in particular the one related to the Rayleigh–Bénard flow problem that models natural thermal convection. For this purpose we are ...