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• W2127434 abstract "The Poisson–Nernst–Planck (PNP) theory is a simplified continuum model for a wide variety of chemical, physical and biological applications. Its ability of providing quantitative explanation and increasingly qualitative predictions of experimental measurements has earned itself much recognition in the research community. Numerous computational algorithms have been constructed for the solution of the PNP equations. However, in the realistic ion-channel context, no second-order convergent PNP algorithm has ever been reported in the literature, due to many numerical obstacles, including discontinuous coefficients, singular charges, geometric singularities, and nonlinear couplings. The present work introduces a number of numerical algorithms to overcome the abovementioned numerical challenges and constructs the first second-order convergent PNP solver in the ion-channel context. First, a Dirichlet to Neumann mapping (DNM) algorithm is designed to alleviate the charge singularity due to the protein structure. Additionally, the matched interface and boundary (MIB) method is reformulated for solving the PNP equations. The MIB method systematically enforces the interface jump conditions and achieves the second order accuracy in the presence of complex geometry and geometric singularities of molecular surfaces. Moreover, two iterative schemes are utilized to deal with the coupled nonlinear equations. Furthermore, extensive and rigorous numerical validations are carried out over a number of geometries, including a sphere, two proteins and an ion channel, to examine the numerical accuracy and convergence order of the present numerical algorithms. Finally, application is considered to a real transmembrane protein, the Gramicidin A channel protein. The performance of the proposed numerical techniques is tested against a number of factors, including mesh sizes, diffusion coefficient profiles, iterative schemes, ion concentrations, and applied voltages. Numerical predictions are compared with experimental measurements." @default.
• W2127434 created "2016-06-24" @default.
• W2127434 creator A5038778212 @default.
• W2127434 creator A5047294643 @default.
• W2127434 creator A5076050916 @default.
• W2127434 date "2011-06-01" @default.
• W2127434 modified "2023-10-12" @default.
• W2127434 title "Second-order Poisson–Nernst–Planck solver for ion transport" @default.
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• W2127434 doi "https://doi.org/10.1016/j.jcp.2011.03.020" @default.
• W2127434 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3087981" @default.
• W2127434 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/21552336" @default.
• W2127434 hasPublicationYear "2011" @default.
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