کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
6932331 867728 2014 16 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
ترجمه فارسی عنوان
طرح های تجزیه و راه حل های جدید برای بهینه سازی معادله پواسون-بولتزمن در محاسبه الکترواستاتیک بیوموکلئال
موضوعات مرتبط
مهندسی و علوم پایه مهندسی کامپیوتر نرم افزارهای علوم کامپیوتر
چکیده انگلیسی
The Poisson-Boltzmann equation (PBE) is one widely-used implicit solvent continuum model in the calculation of electrostatic potential energy for biomolecules in ionic solvent, but its numerical solution remains a challenge due to its strong singularity and nonlinearity caused by its singular distribution source terms and exponential nonlinear terms. To effectively deal with such a challenge, in this paper, new solution decomposition and minimization schemes are proposed, together with a new PBE analysis on solution existence and uniqueness. Moreover, a PBE finite element program package is developed in Python based on the FEniCS program library and GAMer, a molecular surface and volumetric mesh generation program package. Numerical tests on proteins and a nonlinear Born ball model with an analytical solution validate the new solution decomposition and minimization schemes, and demonstrate the effectiveness and efficiency of the new PBE finite element program package.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Computational Physics - Volume 275, 15 October 2014, Pages 294-309
نویسندگان
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