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dc.contributor.authorZwolak, Jason Walteren_US
dc.date.accessioned2014-03-14T20:21:12Z
dc.date.available2014-03-14T20:21:12Z
dc.date.issued2004-12-15en_US
dc.identifier.otheretd-12282004-101753en_US
dc.identifier.urihttp://hdl.handle.net/10919/30274
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_US
dc.publisherVirginia Techen_US
dc.relation.haspartthesis.pdfen_US
dc.rightsI hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to Virginia Tech or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.en_US
dc.subjectmolecular networksen_US
dc.subjectcell cycleen_US
dc.subjectComputational biologyen_US
dc.subjectglobal optimizationen_US
dc.titleComputational Tools for Molecular Networks in Biological Systemsen_US
dc.typeDissertationen_US
dc.contributor.departmentComputer Scienceen_US
dc.description.degreePh. D.en_US
thesis.degree.namePh. D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen_US
thesis.degree.disciplineComputer Scienceen_US
dc.contributor.committeememberSible, Jill C.en_US
dc.contributor.committeememberHeath, Lenwood S.en_US
dc.contributor.committeememberShaffer, Clifford A.en_US
dc.identifier.sourceurlhttp://scholar.lib.vt.edu/theses/available/etd-12282004-101753/en_US
dc.contributor.committeecochairWatson, Layne T.en_US
dc.contributor.committeecochairTyson, John J.en_US
dc.date.sdate2004-12-28en_US
dc.date.rdate2005-01-07
dc.date.adate2005-01-07en_US


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