Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes.

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 characte...

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Autores principales:	Davin Lunz, Gregory Batt, Jakob Ruess, J Frédéric Bonnans
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/4b872ddcf3104a8c8a77ca4519d77ae8
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id	oai:doaj.org-article:4b872ddcf3104a8c8a77ca4519d77ae8
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spelling	oai:doaj.org-article:4b872ddcf3104a8c8a77ca4519d77ae82021-12-02T19:57:22ZBeyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes.1553-734X1553-735810.1371/journal.pcbi.1009214https://doaj.org/article/4b872ddcf3104a8c8a77ca4519d77ae82021-07-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009214https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The 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 applying the solver to both match and extend previous studies. Analytical calculations performed for each example validate our numerical results and benchmark the solver implementation.Davin LunzGregory BattJakob RuessJ Frédéric BonnansPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 7, p e1009214 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Davin Lunz Gregory Batt Jakob Ruess J Frédéric Bonnans Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes.
description	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 applying the solver to both match and extend previous studies. Analytical calculations performed for each example validate our numerical results and benchmark the solver implementation.
format	article
author	Davin Lunz Gregory Batt Jakob Ruess J Frédéric Bonnans
author_facet	Davin Lunz Gregory Batt Jakob Ruess J Frédéric Bonnans
author_sort	Davin Lunz
title	Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes.
title_short	Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes.
title_full	Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes.
title_fullStr	Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes.
title_full_unstemmed	Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes.
title_sort	beyond the chemical master equation: stochastic chemical kinetics coupled with auxiliary processes.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/4b872ddcf3104a8c8a77ca4519d77ae8
work_keys_str_mv	AT davinlunz beyondthechemicalmasterequationstochasticchemicalkineticscoupledwithauxiliaryprocesses AT gregorybatt beyondthechemicalmasterequationstochasticchemicalkineticscoupledwithauxiliaryprocesses AT jakobruess beyondthechemicalmasterequationstochasticchemicalkineticscoupledwithauxiliaryprocesses AT jfredericbonnans beyondthechemicalmasterequationstochasticchemicalkineticscoupledwithauxiliaryprocesses
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Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes.

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