Computational Tools for Molecular Networks in Biological Systems

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dc.contributor.authorZwolak, Jason W.en
dc.contributor.committeecochairWatson, Layne T.en
dc.contributor.committeecochairTyson, John J.en
dc.contributor.committeememberSible, Jill C.en
dc.contributor.committeememberHeath, Lenwood S.en
dc.contributor.committeememberShaffer, Clifford A.en
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2014-03-14T20:21:12Zen
dc.date.adate2005-01-07en
dc.date.available2014-03-14T20:21:12Zen
dc.date.issued2004-12-15en
dc.date.rdate2005-01-07en
dc.date.sdate2004-12-28en
dc.description.abstractTheoretical molecular biologists try to understand the workings of cells through mathematics. Some theoreticians use systems of ordinary differential equations (ODEs) as the basis for mathematical modelling of molecular networks. This thesis develops algorithms for estimating molecular reaction rate constants within those mathematical models by fitting the models to experimental data. An additional step is taken to fit non-timecourse experimental data (e.g., transformations must be performed on the ODE solutions before the experimental and simulation data are similar, and therefore, comparable). VTDIRECT is used to perform (a deterministic direct search) global estimation and ODRPACK is used to perform (a trust region Levenberg-Marquardt based) local estimation of rate constants. One such transformation performed on the ODE solutions determines the value of the steady state of the ODE solutions. A new algorithm was developed that finds all steady state solutions of the ODE system given that the system has a special structure (e.g., the right hand sides of the ODEs are rational functions). Also, since the rate constants in the models cannot be negative and may have other restrictions on the values, ODRPACK was modified to address this problem of bound constraints. The new Fortran 95 version of ODRPACK is named ODRPACK95.en
dc.description.degreePh. D.en
dc.identifier.otheretd-12282004-101753en
dc.identifier.sourceurlhttp://scholar.lib.vt.edu/theses/available/etd-12282004-101753/en
dc.identifier.urihttp://hdl.handle.net/10919/30274en
dc.publisherVirginia Techen
dc.relation.haspartthesis.pdfen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectmolecular networksen
dc.subjectcell cycleen
dc.subjectComputational biologyen
dc.subjectglobal optimizationen
dc.titleComputational Tools for Molecular Networks in Biological Systemsen
dc.typeDissertationen
thesis.degree.disciplineComputer Scienceen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.leveldoctoralen
thesis.degree.namePh. D.en

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