Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.

The simulation of complex biochemical systems, consisting of intertwined subsystems, is a challenging task in computational biology. The complex biochemical organization of the cell is effectively modeled by the minimal cell model called chemoton, proposed by Gánti. Since the chemoton is a system co...

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Autores principales:	István Zachar, Anna Fedor, Eörs Szathmáry
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/850fe270319d4be9b0df46e504c04eff
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spelling	oai:doaj.org-article:850fe270319d4be9b0df46e504c04eff2021-11-18T06:49:59ZTwo different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.1932-620310.1371/journal.pone.0021380https://doaj.org/article/850fe270319d4be9b0df46e504c04eff2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21818258/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The simulation of complex biochemical systems, consisting of intertwined subsystems, is a challenging task in computational biology. The complex biochemical organization of the cell is effectively modeled by the minimal cell model called chemoton, proposed by Gánti. Since the chemoton is a system consisting of a large but fixed number of interacting molecular species, it can effectively be implemented in a process algebra-based language such as the BlenX programming language. The stochastic model behaves comparably to previous continuous deterministic models of the chemoton. Additionally to the well-known chemoton, we also implemented an extended version with two competing template cycles. The new insight from our study is that the coupling of reactions in the chemoton ensures that these templates coexist providing an alternative solution to Eigen's paradox. Our technical innovation involves the introduction of a two-state switch to control cell growth and division, thus providing an example for hybrid methods in BlenX. Further developments to the BlenX language are suggested in the Appendix.István ZacharAnna FedorEörs SzathmáryPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 7, p e21380 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q István Zachar Anna Fedor Eörs Szathmáry Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.
description	The simulation of complex biochemical systems, consisting of intertwined subsystems, is a challenging task in computational biology. The complex biochemical organization of the cell is effectively modeled by the minimal cell model called chemoton, proposed by Gánti. Since the chemoton is a system consisting of a large but fixed number of interacting molecular species, it can effectively be implemented in a process algebra-based language such as the BlenX programming language. The stochastic model behaves comparably to previous continuous deterministic models of the chemoton. Additionally to the well-known chemoton, we also implemented an extended version with two competing template cycles. The new insight from our study is that the coupling of reactions in the chemoton ensures that these templates coexist providing an alternative solution to Eigen's paradox. Our technical innovation involves the introduction of a two-state switch to control cell growth and division, thus providing an example for hybrid methods in BlenX. Further developments to the BlenX language are suggested in the Appendix.
format	article
author	István Zachar Anna Fedor Eörs Szathmáry
author_facet	István Zachar Anna Fedor Eörs Szathmáry
author_sort	István Zachar
title	Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.
title_short	Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.
title_full	Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.
title_fullStr	Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.
title_full_unstemmed	Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.
title_sort	two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/850fe270319d4be9b0df46e504c04eff
work_keys_str_mv	AT istvanzachar twodifferenttemplatereplicatorscoexistinginthesameprotocellstochasticsimulationofanextendedchemotonmodel AT annafedor twodifferenttemplatereplicatorscoexistinginthesameprotocellstochasticsimulationofanextendedchemotonmodel AT eorsszathmary twodifferenttemplatereplicatorscoexistinginthesameprotocellstochasticsimulationofanextendedchemotonmodel
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Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.

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