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dc.contributor.authorPu, Yangen_US
dc.date.accessioned2015-05-15T08:00:35Z
dc.date.available2015-05-15T08:00:35Z
dc.date.issued2015-05-14en_US
dc.identifier.othervt_gsexam:5117en_US
dc.identifier.urihttp://hdl.handle.net/10919/52347
dc.description.abstractIn this thesis we study modeling and simulation approaches for multiscale biochemical systems. The thesis addresses both modeling methods and simulation strategies. In the first part, we propose modeling methods to study the behavior of the insulin secretion pathway. We first expand the single cell model proposed by Bertram et. al. to model multiple cells. Synchronization among multiple cells is observed. Then an unhealthy cell model is proposed to study the insulin secretion failure caused by weakening of mitochondria function. By studying the interaction between the healthy and unhealthy cells, we find that the insulin secretion can be reinstated by increasing the glucokinase level. This new discovery sheds light on antidiabetic medication. In order to study the stochastic dynamics of the insulin secretion pathway, we first apply the hybrid method to model the discrete events in the insulin secretion pathway. Based on the hybrid model, a probability based measurement is proposed and applied to test the new antidiabetic remedy. In the second part, we focus on different simulation schemes for multiscale biochemical systems. We first propose a partitioning strategy for the hybrid method which leads to an efficient way of building stochastic cell cycle models. Then different implementation methods for the hybrid method are studied. A root finding method based on inverse interpolation is introduced to implement the hybrid method with three different ODE solvers. A detailed discussion of the performance of these three ODE solvers is presented. Last, we propose a new strategy to automatically detect stiffness and identify species that cause stiffness for the Tau-Leaping method, as well as two stiffness reduction methods. The efficiency is demonstrated by applying this new strategy on a stiff decaying dimerization model and a heat shock protein regulation model.en_US
dc.format.mediumETDen_US
dc.publisherVirginia Techen_US
dc.rightsThis Item is protected by copyright and/or related rights. Some uses of this Item may be deemed fair and permitted by law even without permission from the rights holder(s), or the rights holder(s) may have licensed the work for use under certain conditions. For other uses you need to obtain permission from the rights holder(s).en_US
dc.subjectInsulin secretion pathwayen_US
dc.subjectNumerical modelen_US
dc.subjectHybrid methoden_US
dc.subjectSSAen_US
dc.subjectQSSAen_US
dc.titleThe Art of Modeling and Simulation of Multiscale Biochemical 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 Science and Applicationsen_US
dc.contributor.committeechairCao, Yangen_US
dc.contributor.committeechairWatson, Layne T.en_US
dc.contributor.committeememberSandu, Adrianen_US
dc.contributor.committeememberBorggaard, Jeffrey T.en_US
dc.contributor.committeememberSamuels, David Charlesen_US


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