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Application of Finite Element Method in Protein Normal Mode Analysis

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dc.contributor.advisorByung H. Kim
dc.contributor.authorHsu, Chiung-fang
dc.contributor.departmentUniversity of Massachusetts Amherst
dc.contributor.departmentMechanical Engineering
dc.date2023-09-23T07:34:31.000
dc.date.accessioned2024-04-26T20:34:53Z
dc.date.available2012-11-24T00:00:00Z
dc.date.issued2013-01-01
dc.date.submittedFebruary
dc.description.abstractThis study proposed a finite element procedure for protein normal mode analysis (NMA). The finite element model adopted the protein solvent-excluded surface to generate a homogeneous and isotropic volume. A simplified triangular approximation of coarse molecular surface was generated from the original surface model by using the Gaussian-based blurring technique. Similar to the widely adopted elastic network model, the finite element model holds a major advantage over standard all-atom normal mode analysis: the computationally expensive process of energy minimization that may distort the initial protein structure has been eliminated. This modification significantly increases the efficiency of normal mode analysis. In addition, the finite element model successfully brings out the capability of normal mode analysis in low-frequency/high collectivity molecular motion by capturing protein shape properties. Fair results from six protein models in this study have fortified the capability of the finite element model in protein normal mode analysis.
dc.description.degreeMaster of Science in Mechanical Engineering (M.S.M.E.)
dc.identifier.doihttps://doi.org/10.7275/3399947
dc.identifier.urihttps://hdl.handle.net/20.500.14394/44440
dc.relation.urlhttps://scholarworks.umass.edu/cgi/viewcontent.cgi?article=2088&context=theses&unstamped=1
dc.source.statuspublished
dc.subjectprotein normal mode analysis
dc.subjectfinite element analysis
dc.subjectprotein elastic network model
dc.subjectApplied Mechanics
dc.subjectBiomechanical Engineering
dc.subjectComputer-Aided Engineering and Design
dc.titleApplication of Finite Element Method in Protein Normal Mode Analysis
dc.typeopen
dc.typearticle
dc.typethesis
digcom.contributor.authorisAuthorOfPublication|email:chiungfa@engin.umass.edu|institution:University of Massachusetts Amherst|Hsu, Chiung-fang
digcom.date.embargo2012-11-24T00:00:00-08:00
digcom.identifiertheses/1014
digcom.identifier.contextkey3399947
digcom.identifier.submissionpaththeses/1014
dspace.entity.typePublication
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