Understanding molecular and cellular processes using statistical physics

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dc.contributor.authorWu, Zhanghanen
dc.contributor.committeechairXing, Jianhuaen
dc.contributor.committeememberCao, Yangen
dc.contributor.committeememberCimini, Danielaen
dc.contributor.committeememberWalker, Richard A.en
dc.contributor.departmentGenetics, Bioinformatics, and Computational Biologyen
dc.date.accessioned2014-03-14T20:12:08Zen
dc.date.adate2011-06-13en
dc.date.available2014-03-14T20:12:08Zen
dc.date.issued2011-05-04en
dc.date.rdate2011-06-13en
dc.date.sdate2011-05-16en
dc.description.abstractUsing statistical physics principles to solve problems in biology is one of the most promising directions due to the complexity and non-equilibrium fluctuations in biological systems. In this work, we try to describe the dynamics at both cellular and molecular levels. Microtubule dynamics and dynamic disorder of enzyme proteins are two of the examples we investigated. The dynamics of microtubules and the mechanical properties of these polymers are essential for many key cellular processes. However, critical discrepancies between experimental observations and existing models need to be resolved before further progress towards a complete model can be made. We carried out computational studies to compare the mechanical properties of two alternative models, one corresponding to the existing, conventional model, and the other considering an additional type of tubulin lateral interaction described in a cryo-EM structure of a proposed trapped intermediate in the microtubule assembly process. Our work indicates that a class of sheet structures is transiently trapped as an intermediate during the assembly process in physiological conditions. In the second part of the work, we analyzed enzyme slow conformational changes in the context of regulatory networks. A single enzymatic reaction with slow conformational changes can serve as a basic functional motif with properties normally discussed with larger networks in the field of systems biology. The work on slow enzyme dynamics fills the missing gap between studies on intramolecular and network dynamics. We also showed that enzyme fluctuations could be amplified into fluctuations in phosphorylation networks. This can be used as a novel biochemical "reporter" for measuring single enzyme conformational fluctuation rates.en
dc.description.degreePh. D.en
dc.identifier.otheretd-05162011-105041en
dc.identifier.sourceurlhttp://scholar.lib.vt.edu/theses/available/etd-05162011-105041/en
dc.identifier.urihttp://hdl.handle.net/10919/27745en
dc.publisherVirginia Techen
dc.relation.haspartWU_Zhanghan_D_2011.pdfen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectMicrotubule Dynamicsen
dc.subjectMathematical Modelingen
dc.subjectEnzyme Conformational Changesen
dc.subjectSingle Molecular Fluctuationsen
dc.titleUnderstanding molecular and cellular processes using statistical physicsen
dc.typeDissertationen
thesis.degree.disciplineGenetics, Bioinformatics, and Computational Biologyen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.leveldoctoralen
thesis.degree.namePh. D.en

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