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dc.contributor.authorRué, Pau
dc.contributor.authorVillà-Freixa, Jordi
dc.contributor.authorBurrage, Kevin
dc.date.accessioned2020-10-28T13:38:29Z
dc.date.available2020-10-28T13:38:29Z
dc.date.issued2010
dc.identifier.citationRué, Pau; Villà-Freixa, Jordi; Burrage, Kevin. Simulation methods with extended stability for stiff biochemical Kinetics. BMC Systems Biology, 2010, 4, p. 1-13. Disponible en: <https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-4-110>. Fecha de acceso: 28 oct. 2020. DOI: 10.1186/1752-0509-4-110ca
dc.identifier.issn1752-0509ca
dc.identifier.urihttp://hdl.handle.net/20.500.12328/1697
dc.description.abstractBackground: With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (bio)chemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA). The key quantity is the step size, or waiting time, τ, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where τ can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called τ-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as τ grows. Results: In this paper we extend Poisson τ-leap methods to a general class of Runge-Kutta (RK) τ-leap methods. We show that with the proper selection of the coefficients, the variance of the extended τ-leap can be wellbehaved, leading to significantly larger step sizes. Conclusions: The benefit of adapting the extended method to the use of RK frameworks is clear in terms of speed of calculation, as the number of evaluations of the Poisson distribution is still one set per time step, as in the original τ-leap method. The approach paves the way to explore new multiscale methods to simulate (bio) chemical systems.ca
dc.format.extent13ca
dc.language.isoengca
dc.publisherSpringer Natureca
dc.relation.ispartofBMC Systems Biologyca
dc.relation.ispartofseries4;
dc.rights© 2010 Rué et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.ca
dc.rights.urihttps://creativecommons.org/licenses/by/2.0/
dc.subject.otherCinètica químicaca
dc.subject.otherReaccions químiques
dc.subject.otherBioquímica
dc.subject.otherCinética química
dc.subject.otherReacciones químicas
dc.subject.otherBioquímica
dc.subject.otherChemical kinetics
dc.subject.otherChemical reactions
dc.subject.otherBiochemistry
dc.titleSimulation methods with extended stability for stiff biochemical Kineticsca
dc.typeinfo:eu-repo/semantics/articleca
dc.description.versioninfo:eu-repo/semantics/publishedVersionca
dc.rights.accessLevelinfo:eu-repo/semantics/openAccess
dc.embargo.termscapca
dc.relation.projectIDinfo:eu-repo/grantAgreement/ES/3PN/CTQ2008-00755/BQU
dc.subject.udc57ca
dc.identifier.doihttps://dx.doi.org/10.1186/1752-0509-4-110ca


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© 2010 Rué et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Except where otherwise noted, this item's license is described as https://creativecommons.org/licenses/by/2.0/