Inexact methods for the chemical master equation with constant or time-varying propensities, and application to parameter inference

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dc.contributorHadji, Layachi
dc.contributorHalpern, David
dc.contributorMarquez Lago, Tatiana T.
dc.contributorSun, Min
dc.contributor.advisorSidje, Roger B.
dc.contributor.authorDinh, Khanh Ngoc
dc.contributor.otherUniversity of Alabama Tuscaloosa
dc.date.accessioned2018-07-11T16:49:09Z
dc.date.available2018-07-11T16:49:09Z
dc.date.issued2018
dc.descriptionElectronic Thesis or Dissertationen_US
dc.description.abstractComplex reaction networks arise in molecular biology and many other different fields of science such as ecology and social study. A familiar approach to modeling such problems is to find their master equation. In systems biology, the equation is called the chemical master equation (CME), and solving the CME is a difficult task, because of the curse of dimensionality. The goal of this dissertation is to alleviate this curse via the use of the finite state projection (FSP), in both cases where the CME matrix is constant (if the reaction rates are time-independent) or time-varying (if the reaction rates change over time). The work includes a theoretical characterization of the FSP truncation technique by showing that it can be put in the framework of inexact Krylov methods that relax matrix-vector products and compute them expediently by trading accuracy for speed. We also examine practical applications of our work in delay CME and parameter inference through local and global optimization schemes.en_US
dc.format.extent160 p.
dc.format.mediumelectronic
dc.format.mimetypeapplication/pdf
dc.identifier.otheru0015_0000001_0002943
dc.identifier.otherDinh_alatus_0004D_13456
dc.identifier.urihttp://ir.ua.edu/handle/123456789/3628
dc.languageEnglish
dc.language.isoen_US
dc.publisherUniversity of Alabama Libraries
dc.relation.hasversionborn digital
dc.relation.ispartofThe University of Alabama Electronic Theses and Dissertations
dc.relation.ispartofThe University of Alabama Libraries Digital Collections
dc.rightsAll rights reserved by the author unless otherwise indicated.en_US
dc.subjectApplied mathematics
dc.titleInexact methods for the chemical master equation with constant or time-varying propensities, and application to parameter inferenceen_US
dc.typethesis
dc.typetext
etdms.degree.departmentUniversity of Alabama. Department of Mathematics
etdms.degree.disciplineMathematics
etdms.degree.grantorThe University of Alabama
etdms.degree.leveldoctoral
etdms.degree.namePh.D.
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