A new computationally facile approximation of electrostatic potential suitable for macromolecules

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dc.contributor.authorGordon, John Carrollen
dc.contributor.committeechairOnufriev, Alexey V.en
dc.contributor.committeememberSandu, Adrianen
dc.contributor.committeememberHeath, Lenwood S.en
dc.contributor.committeememberMurali, T. M.en
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2014-03-14T20:31:44Zen
dc.date.adate2007-03-29en
dc.date.available2014-03-14T20:31:44Zen
dc.date.issued2007-02-01en
dc.date.rdate2010-10-27en
dc.date.sdate2007-02-12en
dc.description.abstractThe electrostatic properties of a molecule are often essential in determining its behavior; as such, the ability to approximate these electrostatic potentials computationally is often essential to obtaining a full understanding of how these molecules function. An approximate, analytical solution to the (linearized) Poisson-Boltzmann equation is proposed that is suitable for realistic biomolecules of virtually any size. A comparison with accepted numerical approaches on a large test set of biomolecular structures shows that the proposed method is considerably less expensive computationally, yet accurate enough to be considered as a possible alternative. The utility of the approach is demonstrated by computing and analyzing the electrostatic potential generated by full capsid of the tobacco ringspot virus (half a million atoms) at atomic resolution. The details of the potential distribution on the molecular surface sheds light on the mechanism behind the high selectivity of the capsid to the viral RNA. These results are generated with the modest computational power of a desktop PC. The applicability of the analytical approximation as an initial guess for traditional numerical methods as a means of improving the convergence of iterative solutions is investigated and found to be quite promising.en
dc.description.degreeMaster of Scienceen
dc.identifier.otheretd-02122007-135819en
dc.identifier.sourceurlhttp://scholar.lib.vt.edu/theses/available/etd-02122007-135819/en
dc.identifier.urihttp://hdl.handle.net/10919/31216en
dc.publisherVirginia Techen
dc.relation.haspartgordon_thesis.pdfen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectVirusen
dc.subjectMacromoleculeen
dc.subjectGEMen
dc.subjectAPLBen
dc.subjectPoisson-Boltzmannen
dc.subjectElectrostatic potentialen
dc.titleA new computationally facile approximation of electrostatic potential suitable for macromoleculesen
dc.typeThesisen
thesis.degree.disciplineComputer Scienceen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.levelmastersen
thesis.degree.nameMaster of Scienceen

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