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Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments
The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as, for instance, the fluctuations in ribosome copy numbers for a gene regulatory network. While several recent studies demonstrate the importance of accounting for...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256010/ https://www.ncbi.nlm.nih.gov/pubmed/25473849 http://dx.doi.org/10.1371/journal.pcbi.1003942 |
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author | Zechner, Christoph Koeppl, Heinz |
author_facet | Zechner, Christoph Koeppl, Heinz |
author_sort | Zechner, Christoph |
collection | PubMed |
description | The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as, for instance, the fluctuations in ribosome copy numbers for a gene regulatory network. While several recent studies demonstrate the importance of accounting for such extrinsic components, the resulting models are typically hard to analyze. In this work we develop a general mathematical framework that allows to uncouple the network from its dynamic environment by incorporating only the environment's effect onto the network into a new model. More technically, we show how such fluctuating extrinsic components (e.g., chemical species) can be marginalized in order to obtain this decoupled model. We derive its corresponding process- and master equations and show how stochastic simulations can be performed. Using several case studies, we demonstrate the significance of the approach. |
format | Online Article Text |
id | pubmed-4256010 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-42560102014-12-11 Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments Zechner, Christoph Koeppl, Heinz PLoS Comput Biol Research Article The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as, for instance, the fluctuations in ribosome copy numbers for a gene regulatory network. While several recent studies demonstrate the importance of accounting for such extrinsic components, the resulting models are typically hard to analyze. In this work we develop a general mathematical framework that allows to uncouple the network from its dynamic environment by incorporating only the environment's effect onto the network into a new model. More technically, we show how such fluctuating extrinsic components (e.g., chemical species) can be marginalized in order to obtain this decoupled model. We derive its corresponding process- and master equations and show how stochastic simulations can be performed. Using several case studies, we demonstrate the significance of the approach. Public Library of Science 2014-12-04 /pmc/articles/PMC4256010/ /pubmed/25473849 http://dx.doi.org/10.1371/journal.pcbi.1003942 Text en © 2014 Zechner, Koeppl http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Zechner, Christoph Koeppl, Heinz Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments |
title | Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments |
title_full | Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments |
title_fullStr | Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments |
title_full_unstemmed | Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments |
title_short | Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments |
title_sort | uncoupled analysis of stochastic reaction networks in fluctuating environments |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256010/ https://www.ncbi.nlm.nih.gov/pubmed/25473849 http://dx.doi.org/10.1371/journal.pcbi.1003942 |
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