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dc.contributor.authorFleming, R M T
dc.contributor.authorThiele, I
dc.date.accessioned2015-06-05T13:23:12Zen
dc.date.available2015-06-05T13:23:12Zen
dc.date.issued2012-12-07en
dc.identifier.citationJ. Theor. Biol. 2012, 314:173-81en
dc.identifier.issn1095-8541en
dc.identifier.pmid22947275en
dc.identifier.doi10.1016/j.jtbi.2012.08.021en
dc.identifier.urihttp://hdl.handle.net/2336/556459en
dc.descriptionTo access publisher's full text version of this article click on the hyperlink at the bottom of the pageen
dc.description.abstractLiving systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to mimic this forcing. We provide a general formulation to force an arbitrary large kinetic model in a manner that is still consistent with the existence of a non-equilibrium steady state. We can guarantee the existence of a non-equilibrium steady state assuming only two conditions; that every reaction is mass balanced and that continuous kinetic reaction rate laws never lead to a negative molecule concentration. These conditions can be verified in polynomial time and are flexible enough to permit one to force a system away from equilibrium. With expository biochemical examples we show how reversible, mass balanced perpetual reaction(s), with thermodynamically infeasible kinetic parameters, can be used to perpetually force various kinetic models in a manner consistent with the existence of a steady state. Easily testable existence conditions are foundational for efforts to reliably compute non-equilibrium steady states in genome-scale biochemical kinetic models.
dc.description.sponsorshipU.S. Department of Energy (Offices of Advanced Scientific Computing Research & Biological and Environmental Research) as part of the Scientific Discovery Through Advanced Computing program DE-SC0002009 info:eu-repo/grantAgreement/EC/FP7/249261en
dc.language.isoenen
dc.publisherAcademic Press Ltd- Elsevier Scienceen
dc.relationinfo:eu-repo/grantAgreement/EC/FP7/249261en
dc.relation.urlhttp://dx.doi.org/ 10.1016/j.jtbi.2012.08.021en
dc.relation.urlhttp://arxiv.org/pdf/1109.4498.pdfen
dc.rightsopenAccessen
dc.subject.meshAnaerobiosisen
dc.subject.meshEnzymesen
dc.subject.meshGlycolysisen
dc.subject.meshKineticsen
dc.subject.meshModels, Biologicalen
dc.subject.meshMolecular Weighten
dc.subject.meshThermodynamicsen
dc.subject.meshTrypanosoma brucei bruceien
dc.titleMass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration.en
dc.typearticleen
dc.contributor.department[ 1 ] Univ Iceland, Ctr Syst Biol, IS-101 Reykjavik, Iceland [ 2 ] Univ Iceland, Fac Med, Dept Biochem & Mol Biol, IS-101 Reykjavik, Iceland [ 3 ] Univ Iceland, Fac Ind Engn Mech Engn & Comp Sci, IS-101 Reykjavik, Icelanden
dc.identifier.journalJournal of theoretical biologyen
dc.rights.accessOpen Access - Opinn aðganguren
html.description.abstractLiving systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to mimic this forcing. We provide a general formulation to force an arbitrary large kinetic model in a manner that is still consistent with the existence of a non-equilibrium steady state. We can guarantee the existence of a non-equilibrium steady state assuming only two conditions; that every reaction is mass balanced and that continuous kinetic reaction rate laws never lead to a negative molecule concentration. These conditions can be verified in polynomial time and are flexible enough to permit one to force a system away from equilibrium. With expository biochemical examples we show how reversible, mass balanced perpetual reaction(s), with thermodynamically infeasible kinetic parameters, can be used to perpetually force various kinetic models in a manner consistent with the existence of a steady state. Easily testable existence conditions are foundational for efforts to reliably compute non-equilibrium steady states in genome-scale biochemical kinetic models.


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