Skip to Main content Skip to Navigation
Journal articles

Beyond the chemical master equation: stochastic chemical kinetics coupled with auxiliary processes

Abstract : The chemical master equation and its continuum approximations are indispensable tools in the modeling of chemical reaction networks. These are routinely used to capture complex nonlinear phenomena such as multimodality as well as transient events such as first-passage times, that accurately characterise a plethora of biological and chemical processes. However, some mechanisms, such as heterogeneous cellular growth or phenotypic selection at the population level, cannot be represented by the master equation and thus have been tackled separately. In this work, we propose a unifying framework that augments the chemical master equation to capture such auxiliary dynamics, and we develop and analyse a numerical solver that accurately simulates the system dynamics. We showcase these contributions by casting a diverse array of examples from the literature within this framework, and apply the solver to both match and extend previous studies. Analytical calculations performed for each example validate our numerical results and benchmark the solver implementation.
Complete list of metadata

https://hal.inria.fr/hal-02991103
Contributor : Davin Lunz Connect in order to contact the contributor
Submitted on : Tuesday, September 14, 2021 - 10:18:55 AM
Last modification on : Thursday, September 16, 2021 - 3:39:05 AM

File

PLOS_lunz.pdf
Files produced by the author(s)

Identifiers

Citation

Davin Lunz, Gregory Batt, Jakob Ruess, Joseph Frédéric Bonnans. Beyond the chemical master equation: stochastic chemical kinetics coupled with auxiliary processes. PLoS Computational Biology, Public Library of Science, 2021, ⟨10.1371/journal.pcbi.1009214⟩. ⟨hal-02991103v2⟩

Share

Metrics

Record views

29

Files downloads

83