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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2021-07-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1009214 |
| _version_ | 1830449295597240320 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-21T07:52:20Z |
| format | Article |
| id | doaj.art-4b872ddcf3104a8c8a77ca4519d77ae8 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-21T07:52:20Z |
| publishDate | 2021-07-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-4b872ddcf3104a8c8a77ca4519d77ae82022-12-21T19:11:03ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582021-07-01177e100921410.1371/journal.pcbi.1009214Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes.Davin LunzGregory BattJakob RuessJ Frédéric BonnansThe 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.https://doi.org/10.1371/journal.pcbi.1009214 |
| spellingShingle | Davin Lunz Gregory Batt Jakob Ruess J Frédéric Bonnans Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes. PLoS Computational Biology |
| title | 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_short | 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 |
| url | https://doi.org/10.1371/journal.pcbi.1009214 |
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