Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Zechner, Christoph, Koeppl, Heinz
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
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
_version_ 1782347523446276096
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
work_keys_str_mv AT zechnerchristoph uncoupledanalysisofstochasticreactionnetworksinfluctuatingenvironments
AT koepplheinz uncoupledanalysisofstochasticreactionnetworksinfluctuatingenvironments