کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
8051728 | 1519375 | 2018 | 15 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference
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کلمات کلیدی
موضوعات مرتبط
مهندسی و علوم پایه
سایر رشته های مهندسی
مکانیک محاسباتی
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چکیده انگلیسی
The size-modified Poisson-Boltzmann equation (SMPBE) is one important variant of the popular dielectric model, the Poisson-Boltzmann equation (PBE), to reflect ionic size effects in the prediction of electrostatics for a biomolecule in an ionic solvent. In this paper, a new SMPBE hybrid solver is developed using a solution decomposition, Schwartz's overlapped domain decomposition, finite element, and finite difference. It is then programmed as a software package in C, Fortran, and Python based on the state-of-the-art finite element library DOLFIN from the FEniCS project. This software package is well validated on a Born ball model with analytical solution and a dipole model with known physical properties. Numerical results on six proteins with different net charges demonstrate its high performance. Finally, this new SMPBE hybrid solver is shown to be numerically stable and convergent in the calculation of electrostatic solvation free energy for 216 biomolecules and binding free energy for a DNA-drug complex.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Applied Mathematical Modelling - Volume 58, June 2018, Pages 166-180
Journal: Applied Mathematical Modelling - Volume 58, June 2018, Pages 166-180
نویسندگان
Jinyong Ying, Dexuan Xie,