The dynamics of a model chain by constrained molecular dynamics

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dc.contributor.advisorHutchinson, John S.
dc.creatorChen, Kaiqi
dc.date.accessioned2009-06-04T00:02:54Z
dc.date.available2009-06-04T00:02:54Z
dc.date.issued1996
dc.description.abstractA new method for the treatment of holonomic constraints in molecular dynamics simulation has been developed. In this method, constraint forces are solved explicitly. The method explores the special mathematical property (sparse and symmetric positive definite) of an matrix inherent to the molecule under study. The method is especially useful when some bond angles are constrained. A lattice model for proteins is proposed. The connection between implicit-solvent model and explicit-solvent model has been established. The structural features of globular proteins are studied by the model. It is found that the proteins are driven to compact conformations by strong water-water interactions. The constrained molecular dynamics simulations are applied to a short chain in solvent to infer the possible move set for Monte Carlo simulations. It is found that the end monomers should be more mobile than the inner ones and that one and two-monomer moves are the integral part of the set of basic moves. The moves involving four or more monomers can be modeled as the result of several basic moves.
dc.format.extent65 p.en_US
dc.format.mimetypeapplication/pdf
dc.identifier.callnoTHESIS CHEM. 1996 CHEN
dc.identifier.citationChen, Kaiqi. "The dynamics of a model chain by constrained molecular dynamics." (1996) Master’s Thesis, Rice University. <a href="https://hdl.handle.net/1911/14041">https://hdl.handle.net/1911/14041</a>.
dc.identifier.urihttps://hdl.handle.net/1911/14041
dc.language.isoeng
dc.rightsCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.
dc.subjectPhysical chemistry
dc.subjectMolecular physics
dc.titleThe dynamics of a model chain by constrained molecular dynamics
dc.typeThesis
dc.type.materialText
thesis.degree.departmentChemistry
thesis.degree.disciplineNatural Sciences
thesis.degree.grantorRice University
thesis.degree.levelMasters
thesis.degree.nameMaster of Science
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