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dc.contributor.authorReznik, Eden_US
dc.contributor.authorKaper, Tasso J.en_US
dc.contributor.authorSegre, Danielen_US
dc.date.accessioned2020-01-29T18:15:45Z
dc.date.available2020-01-29T18:15:45Z
dc.date.issued2013-03-01
dc.identifierhttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000316950900032&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=6e74115fe3da270499c3d65c9b17d654
dc.identifier.citationEd Reznik, Tasso J Kaper, Daniel Segre. 2013. "The dynamics of hybrid metabolic-genetic oscillators." CHAOS, Volume 23, Issue 1, 013132. https://doi.org/10.1063/1.4793573
dc.identifier.issn1054-1500
dc.identifier.urihttps://hdl.handle.net/2144/39200
dc.description.abstractThe synthetic construction of intracellular circuits is frequently hindered by a poor knowledge of appropriate kinetics and precise rate parameters. Here, we use generalized modeling (GM) to study the dynamical behavior of topological models of a family of hybrid metabolic-genetic circuits known as "metabolators." Under mild assumptions on the kinetics, we use GM to analytically prove that all explicit kinetic models which are topologically analogous to one such circuit, the "core metabolator," cannot undergo Hopf bifurcations. Then, we examine more detailed models of the metabolator. Inspired by the experimental observation of a Hopf bifurcation in a synthetically constructed circuit related to the core metabolator, we apply GM to identify the critical components of the synthetically constructed metabolator which must be reintroduced in order to recover the Hopf bifurcation. Next, we study the dynamics of a re-wired version of the core metabolator, dubbed the "reverse" metabolator, and show that it exhibits a substantially richer set of dynamical behaviors, including both local and global oscillations. Prompted by the observation of relaxation oscillations in the reverse metabolator, we study the role that a separation of genetic and metabolic time scales may play in its dynamics, and find that widely separated time scales promote stability in the circuit. Our results illustrate a generic pipeline for vetting the potential success of a circuit design, simply by studying the dynamics of the corresponding generalized model.en_US
dc.description.sponsorshipE.R. and D. S. were supported by grants from the Office of Science (BER), U.S. Department of Energy (DE-SC0004962), and National Science Foundation NSF DMS-0602204 EMSW21-RTG Biodynamics at Boston University. T.J.K. was supported in part by NSF Grant No. DMS-1109587. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. E. R. would like to acknowledge the kind support of the Santa Fe Institute while studying the metabolator at the 2011 Summer School. (DE-SC0004962 - Office of Science (BER), U.S. Department of Energy; DMS-0602204 EMSW21-RTG - National Science Foundation NSF; DMS-1109587 - NSF; Santa Fe Institute)en_US
dc.format.extent14 p.en_US
dc.languageEnglish
dc.language.isoen_US
dc.publisherAMER INST PHYSICSen_US
dc.relation.ispartofCHAOS
dc.rights© 2013 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Ed Reznik, Tasso J Kaper, Daniel Segre. 2013. "The dynamics of hybrid metabolic-genetic oscillators." Chaos, Volume 23, Issue 1, 013132 and may be found at https://doi.org/10.1063/1.4793573.en_US
dc.subjectScience & technologyen_US
dc.subjectPhysical sciencesen_US
dc.subjectMathematics, applieden_US
dc.subjectPhysics, mathematicalen_US
dc.subjectMathematicsen_US
dc.subjectPhysicsen_US
dc.subjectNetworksen_US
dc.subjectStabilityen_US
dc.subjectModelsen_US
dc.subjectEnergy metabolismen_US
dc.subjectEscherichia coli K12en_US
dc.subjectGene expression regulation, bacterialen_US
dc.subjectGene regulatory networksen_US
dc.subjectKineticsen_US
dc.subjectModels, biologicalen_US
dc.subjectModels, geneticen_US
dc.subjectOscillometryen_US
dc.subjectSynthetic biologyen_US
dc.subjectSystems integrationen_US
dc.subjectApplied mathematicsen_US
dc.subjectNumerical and computational mathematicsen_US
dc.subjectFluids & plasmasen_US
dc.titleThe dynamics of hybrid metabolic-genetic oscillatorsen_US
dc.typeArticleen_US
dc.description.versionPublished versionen_US
dc.identifier.doi10.1063/1.4793573
pubs.elements-sourceweb-of-scienceen_US
pubs.notesEmbargo: Not knownen_US
pubs.organisational-groupBoston Universityen_US
pubs.organisational-groupBoston University, College of Arts & Sciencesen_US
pubs.organisational-groupBoston University, College of Arts & Sciences, Department of Biologyen_US
pubs.organisational-groupBoston University, College of Arts & Sciences, Department of Mathematics & Statisticsen_US
pubs.publication-statusPublisheden_US
dc.identifier.orcid0000-0003-4859-1914 (Segre, Daniel)
dc.identifier.mycv33071


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