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Slack reactants: A state-space truncation framework to estimate quantitative behavior of the chemical master equation

State space truncation methods are widely used to approximate solutions of the chemical master equation. While most methods of this kind focus on truncating the state space directly, in this work, we propose modifying the underlying chemical reaction network by introducing slack reactants that indir...

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Detalles Bibliográficos
Autores principales: Kim, Jinsu, Dark, Jason, Enciso, German, Sindi, Suzanne
Formato: Online Artículo Texto
Lenguaje:English
Publicado: AIP Publishing LLC 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8729884/
https://www.ncbi.nlm.nih.gov/pubmed/32770905
http://dx.doi.org/10.1063/5.0013457
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author Kim, Jinsu
Dark, Jason
Enciso, German
Sindi, Suzanne
author_facet Kim, Jinsu
Dark, Jason
Enciso, German
Sindi, Suzanne
author_sort Kim, Jinsu
collection PubMed
description State space truncation methods are widely used to approximate solutions of the chemical master equation. While most methods of this kind focus on truncating the state space directly, in this work, we propose modifying the underlying chemical reaction network by introducing slack reactants that indirectly truncate the state space. More specifically, slack reactants introduce an expanded chemical reaction network and impose a truncation scheme based on desired mass conservation laws. This network structure also allows us to prove inheritance of special properties of the original model, such as irreducibility and complex balancing. We use the network structure imposed by slack reactants to prove the convergence of the stationary distribution and first arrival times. We then provide examples comparing our method with the stationary finite state projection and finite buffer methods. Our slack reactant system appears to be more robust than some competing methods with respect to calculating first arrival times.
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spelling pubmed-87298842022-01-12 Slack reactants: A state-space truncation framework to estimate quantitative behavior of the chemical master equation Kim, Jinsu Dark, Jason Enciso, German Sindi, Suzanne J Chem Phys ARTICLES State space truncation methods are widely used to approximate solutions of the chemical master equation. While most methods of this kind focus on truncating the state space directly, in this work, we propose modifying the underlying chemical reaction network by introducing slack reactants that indirectly truncate the state space. More specifically, slack reactants introduce an expanded chemical reaction network and impose a truncation scheme based on desired mass conservation laws. This network structure also allows us to prove inheritance of special properties of the original model, such as irreducibility and complex balancing. We use the network structure imposed by slack reactants to prove the convergence of the stationary distribution and first arrival times. We then provide examples comparing our method with the stationary finite state projection and finite buffer methods. Our slack reactant system appears to be more robust than some competing methods with respect to calculating first arrival times. AIP Publishing LLC 2020-08-07 2020-08-05 /pmc/articles/PMC8729884/ /pubmed/32770905 http://dx.doi.org/10.1063/5.0013457 Text en © 2020 Author(s). 0021-9606/2020/153(5)/054117/20/$0.00 https://creativecommons.org/licenses/by/4.0/All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle ARTICLES
Kim, Jinsu
Dark, Jason
Enciso, German
Sindi, Suzanne
Slack reactants: A state-space truncation framework to estimate quantitative behavior of the chemical master equation
title Slack reactants: A state-space truncation framework to estimate quantitative behavior of the chemical master equation
title_full Slack reactants: A state-space truncation framework to estimate quantitative behavior of the chemical master equation
title_fullStr Slack reactants: A state-space truncation framework to estimate quantitative behavior of the chemical master equation
title_full_unstemmed Slack reactants: A state-space truncation framework to estimate quantitative behavior of the chemical master equation
title_short Slack reactants: A state-space truncation framework to estimate quantitative behavior of the chemical master equation
title_sort slack reactants: a state-space truncation framework to estimate quantitative behavior of the chemical master equation
topic ARTICLES
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8729884/
https://www.ncbi.nlm.nih.gov/pubmed/32770905
http://dx.doi.org/10.1063/5.0013457
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