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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
AIP Publishing LLC
2020
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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. |
format | Online Article Text |
id | pubmed-8729884 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | AIP Publishing LLC |
record_format | MEDLINE/PubMed |
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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