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dc.contributor.advisorRen, Pengyu
dc.creatorXia, Zhen, active 2013en
dc.date.accessioned2013-10-31T20:06:33Zen
dc.date.issued2013-05en
dc.date.submittedMay 2013en
dc.identifier.urihttp://hdl.handle.net/2152/21875en
dc.descriptiontexten
dc.description.abstractBiological molecules are essential parts of organisms and participate in a variety of biological processes within cells. Understanding the relationship between sequence, structure, and function of biological molecules are of fundamental importance in life science and the health care industry. In this dissertation, a multi-scale approach was utilized to develop coarse-grained molecular models for protein and RNA simulations. By simplifying the atomistic representation of a biomolecular system, the coarse-grained approach enables the molecular dynamics simulations to reveal the biological processes, which occur on the time and length scales that are inaccessible to the all-atom models. For RNA, an "intermediate" coarse-grained model was proposed to provide both accuracy and efficiency for RNA 3D structure modeling and prediction. The overall potential parameters were derived based on structural statistics sampled from experimental structures. For protein, a general, transferable coarse-grain framework based on the Gay-Berne potential and electrostatic point multipole expansion was developed for polypeptide simulations. Next, an advanced atomistic model was developed to model electrostatic interaction with high resolution and incorporates electronic polarization effect that is ignored in conventional atomistic models. The last part of my thesis work involves applying all-atom molecular simulations to address important questions and problems in biophysics and structural biology. For example, the interaction between protein and miRNA, the recognition mechanism of antigen and antibody, and the structure dynamics of protein in mixed denaturants.en
dc.format.mimetypeapplication/pdfen
dc.language.isoen_USen
dc.subjectStructural modelingen
dc.subjectMolecular dynamicsen
dc.subjectProteinen
dc.subjectRNAen
dc.subjectCoarse-grained modelen
dc.subjectAtomistic modelen
dc.subjectRNA silencingen
dc.subjectInfluenzaen
dc.subjectPolarizable force fielden
dc.titleModeling the structure, dynamics, and interactions of biological moleculesen
dc.date.updated2013-10-31T20:06:33Zen
dc.description.departmentBiomedical Engineeringen
thesis.degree.departmentBiomedical Engineeringen
thesis.degree.disciplineBiomedical Engineeringen
thesis.degree.grantorThe University of Texas at Austinen
thesis.degree.levelDoctoralen
thesis.degree.nameDoctor of Philosophyen


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