A software tool for the compact solution of the chemical master equation

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dc.citation.epage316en_US
dc.citation.spage312en_US
dc.citation.volumeNumber10740en_US
dc.contributor.authorDayar Tuğrulen_US
dc.contributor.authorOrhan, M. C.en_US
dc.coverage.spatialErlangen, Germanyen_US
dc.date.accessioned2019-02-21T16:03:50Z
dc.date.available2019-02-21T16:03:50Z
dc.date.issued2018en_US
dc.departmentDepartment of Computer Engineeringen_US
dc.descriptionConference name: 19th International GI/ITG Conference, MMB 2018en_US
dc.descriptionDate of Conference: February 26-28, 2018en_US
dc.description.abstractThe problem of computing the transient probability distribution of countably infinite multidimensional continuous-time Markov chains (CTMCs) arising in systems of stochastic chemical kinetics is addressed by a software tool. Starting from an initial probability distribution, time evolution of the probability distribution associated with the CTMC is described by a system of linear first-order ordinary differential equations, known as the chemical master equation (CME). The solver for the CME uses the time stepping implicit backward differentiation formulae (BDF). Solution vectors in BDF can be stored compactly during transient analysis in one of the Hierarchical Tucker Decomposition, Quantized Tensor Train, or Transposed Quantized Tensor Train formats.
dc.description.provenanceMade available in DSpace on 2019-02-21T16:03:50Z (GMT). No. of bitstreams: 1 Bilkent-research-paper.pdf: 222869 bytes, checksum: 842af2b9bd649e7f548593affdbafbb3 (MD5) Previous issue date: 2018en
dc.description.sponsorshipAcknowledgement. Part of this work is supported by the Alexander von Humboldt Foundation through the Research Group Linkage Programme. The research of M. Can Orhan is carried out during his PhD studies at Bilkent University and supported by The Scientific and Technological Research Council of Turkey under grant 2211-A. We thank the referees whose comments led to an improved manuscript.
dc.identifier.doi10.1007/978-3-319-74947-1_24
dc.identifier.doi10.1007/978-3-319-74947-1en_US
dc.identifier.eissn1611-3349en_US
dc.identifier.isbn9783319749464
dc.identifier.issn0302-9743
dc.identifier.urihttp://hdl.handle.net/11693/50139
dc.language.isoEnglish
dc.publisherSpringer, Cham
dc.relation.isversionofhttps://doi.org/10.1007/978-3-319-74947-1_24
dc.relation.isversionofhttps://doi.org/10.1007/978-3-319-74947-1en_US
dc.relation.projectBilkent Üniversitesi - Alexander von Humboldt-Stiftung - 2211-A
dc.source.titleMeasurement, Modelling and Evaluation of Computing Systemsen_US
dc.subjectBackward differentiationen_US
dc.subjectChemical master equationen_US
dc.subjectCompact vectoren_US
dc.subjectContinuous-time Markov chainen_US
dc.subjectKronecker decompositionen_US
dc.titleA software tool for the compact solution of the chemical master equationen_US
dc.typeConference Paperen_US

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