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Exploring the Augmented Immersed Interface Method (IIM) to solve the Poisson Equations for Biomolecular Simulation

Posted on:2013-12-20Degree:M.SType:Thesis
University:University of California, IrvineCandidate:Liu, XingpingFull Text:PDF
GTID:2450390008469777Subject:Biology
Abstract/Summary:
As in typical applications, a piecewise-constant dielectric scheme was used to model different solution regions, i.e., solute and solvent. The dielectric interface is absent upon introduction of the surface charge concept. The immersed interface method then is used to set up the linear system of equations of the discretized Poisson equations with the introduced surface charge boundary condition. The GMRES algorithm is applied to compute the imaged surface charge so that the original flux relations can be satisfied. Numerical results along with analysis and comparison with other approaches for problems with on spherical interfaces are also presented.
Keywords/Search Tags:Interface, Equations
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