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Simulation and optimization of dynamic flux balance analysis models using an interior point method reformulation

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dc.contributor.authorScott, F
dc.contributor.authorWilson, P
dc.contributor.authorConejeros, R
dc.contributor.authorVassiliadis, VS
dc.contributor.orcidConejeros, R [0000-0002-1273-535X]
dc.contributor.orcidVassiliadis, VS [0000-0002-5415-7551]
dc.date.accessioned2018-11-16T00:31:13Z
dc.date.available2018-11-16T00:31:13Z
dc.date.issued2018
dc.description.abstractThis work presents a novel, differentiable, way of solving dynamic Flux Balance Analysis (dFBA) problems by embedding flux balance analysis of metabolic network models within lumped bulk kinetics for biochemical processes. The proposed methodology utilizes transformation of the bounds of the embedded linear programming problem of flux balance analysis via a logarithmic barrier (interior point) approach. By exploiting the first-order optimality conditions of the interior-point problem, and with further transformations, the approach results in a system of implicit ordinary differential equations. Results from four case studies, show that the CPU and wall-times obtained using the proposed method are competitive with existing state-of-the-art approaches for solving dFBA simulations, for problem sizes up to genome-scale. The differentiability of the proposed approach allows, using existing commercial packages, its application to the optimal control of dFBA problems at a genome-scale size, thus outperforming existing formulations as shown by two dynamic optimization case studies.
dc.description.sponsorship• R. Conejeros would like to thank CONICYT’s research grant FONDECYT 1151295 for funding this research. • F. Scott gratefully acknowledges financial support from CONICYT (Proyectos REDES ETAPA INICIAL, Convocatoria 2017, REDI170254).
dc.identifier.doi10.17863/CAM.32518
dc.identifier.eissn1873-4375
dc.identifier.issn0098-1354
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/285147
dc.language.isoeng
dc.publisherElsevier BV
dc.publisher.urlhttp://dx.doi.org/10.1016/j.compchemeng.2018.08.041
dc.subjectDynamic flux balance analysis
dc.subjectOrdinary differential equations with
dc.subjectembedded optimization
dc.subjectLinear programming
dc.subjectGenome-scale metabolic network
dc.titleSimulation and optimization of dynamic flux balance analysis models using an interior point method reformulation
dc.typeArticle
dcterms.dateAccepted2018-08-30
prism.endingPage170
prism.publicationDate2018
prism.publicationNameComputers and Chemical Engineering
prism.startingPage152
prism.volume119
rioxxterms.licenseref.startdate2018-11-02
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.typeJournal Article/Review
rioxxterms.versionAM
rioxxterms.versionofrecord10.1016/j.compchemeng.2018.08.041

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