Modelling non-Markovian dynamics in biochemical reactions

Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Vega, Carlos Alberto Olarte; Torella, Luca

Modelling non-Markovian dynamics in biochemical reactions

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dc.contributor.author	Chiarugi, Davide
dc.contributor.author	Falaschi, Moreno
dc.contributor.author	Hermith, Diana
dc.contributor.author	Vega, Carlos Alberto Olarte
dc.contributor.author	Torella, Luca
dc.date.accessioned	2020-07-30T19:43:41Z
dc.date.available	2020-07-30T19:43:41Z
dc.date.issued	2015
dc.description.resumo	Background Biochemical reactions are often modelled as discrete-state continuous-time stochastic processes evolving as memoryless Markov processes. However, in some cases, biochemical systems exhibit non-Markovian dynamics. We propose here a methodology for building stochastic simulation algorithms which model more precisely non-Markovian processes in some specific situations. Our methodology is based on Constraint Programming and is implemented by using Gecode, a state-of-the-art framework for constraint solving. Results Our technique allows us to randomly sample waiting times from probability density functions that not necessarily are distributed according to a negative exponential function. In this context, we discuss an important case-study in which the probability density function is inferred from single-molecule experiments that describe the distribution of the time intervals between two consecutive enzymatically catalysed reactions. Noticeably, this feature allows some types of enzyme reactions to be modelled as non-Markovian processes. Conclusions We show that our methodology makes it possible to obtain accurate models of enzymatic reactions that, in specific cases, fit experimental data better than the corresponding Markovian models	pt_BR
dc.identifier.citation	CHIARUGI, Davide; FALASCHI, Moreno; HERMITH, Diana; OLARTE, Carlos; TORELLA, Luca. Modelling non-Markovian dynamics in biochemical reactions. BMC Systems Biology, v. 9, p. S8, 2015. Disponível em: https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-9-S3-S8. Acesso em: 29 jul. 2020. https://doi.org/10.1186/1752-0509-9-S3-S8	pt_BR
dc.identifier.doi	10.1186/1752-0509-9-S3-S8
dc.identifier.issn	1752-0509
dc.identifier.uri	https://repositorio.ufrn.br/jspui/handle/123456789/29763
dc.language	en	pt_BR
dc.publisher	BMC	pt_BR
dc.subject	Non-Markovian dynamics	pt_BR
dc.subject	Constraint programming	pt_BR
dc.subject	Biochemical reactions	pt_BR
dc.title	Modelling non-Markovian dynamics in biochemical reactions	pt_BR
dc.type	article	pt_BR