Speed and accuracy tradeoffs in molecular electrostatic computation

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dc.contributor.advisorBajaj, Chandrajiten
dc.contributor.committeeMemberArikan, Okanen
dc.contributor.committeeMemberDhillon, Inderjiten
dc.contributor.committeeMemberRossky, Peteren
dc.contributor.committeeMemberYing, Lexingen
dc.creatorChen, Shun-Chuan, 1979-en
dc.date.accessioned2010-08-20T19:50:18Zen
dc.date.accessioned2010-08-20T19:50:26Zen
dc.date.accessioned2017-05-11T22:20:04Z
dc.date.available2010-08-20T19:50:18Zen
dc.date.available2010-08-20T19:50:26Zen
dc.date.available2017-05-11T22:20:04Z
dc.date.issued2009-12en
dc.date.submittedDecember 2009en
dc.date.updated2010-08-20T19:50:26Zen
dc.descriptiontexten
dc.description.abstractIn this study, we consider electrostatics contributed from the molecules in the ionic solution. It plays a significant role in determining the binding affinity of molecules and drugs. We develop the overall framework of computing electrostatic properties for three-dimensional molecular structures, including potential, energy, and forces. These properties are derived from Poisson-Boltzmann equation, a partial differential equation that describes the electrostatic behavior of molecules in ionic solutions. In order to compute these properties, we derived new boundary integral equations and designed a boundary element algorithm based on the linear time fast multipole method for solving the linearized Poisson-Boltzmann equation. Meanwhile, a higher-order parametric formulation called algebraic spline model is used for accurate approximation of the unknown solution of the linearized Poisson-Boltzmann equation. Based on algebraic spline model, we represent the normal derivative of electrostatic potential by surrounding electrostatic potential. This representation guarantees the consistent relation between electrostatic potential and its normal derivative. In addition, accurate numerical solution and fast computation for electrostatic energy and forces are also discussed. In addition, we described our hierarchical modeling and parameter optimization of molecular structures. Based on this technique, we can control the scalability of molecular models for electrostatic computation. The numerical test and experimental results show that the proposed techniques offer an efficient and accurate solution for solving the electrostatic problem of molecules.en
dc.format.mimetypeapplication/pdfen
dc.identifier.urihttp://hdl.handle.net/2152/ETD-UT-2009-12-598en
dc.language.isoengen
dc.subjectPoisson-Boltzmann equationen
dc.subjectBoundary element methoden
dc.subjectFast multipole methoden
dc.subjectCoarse-grained techniquesen
dc.titleSpeed and accuracy tradeoffs in molecular electrostatic computationen
dc.type.genrethesisen

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