Discontinuous Bubble Immersed Finite Element Method for Poisson-Boltzmann Equation

被引:14
|
作者
Kwon, In [1 ]
Kwak, Do Y. [1 ]
机构
[1] Korea Adv Inst Sci & Technol, Dept Math Sci, 291 Daehak Ro,373-1 Guseong Dong, Daejeon 305701, South Korea
关键词
Biomolecular electrostatics; Poisson-Boltzmann equation; immersed finite element method; discontinuous bubble function; linearization; MATCHED INTERFACE; ELLIPTIC-EQUATIONS; ELECTROSTATICS; APPROXIMATION; SIMULATIONS; JUMP;
D O I
10.4208/cicp.OA-2018-0014
中图分类号
O4 [物理学];
学科分类号
0702 ;
摘要
We develop a numerical scheme for nonlinear Poisson-Boltzmann equation. First, we regularize the solution of PBE to remove the singularity. We introduce the discontinuous bubble function to treat the nonhomogeneous jump conditions of the regularized solution. Next, starting with an initial guess, we apply linearization to treat the nonlinearity. Then, we discretize the discontinuous bubble and the bilinear form of PBE. Finally, we solve the discretized linear problem by IFEM. This process is repeated by updating the previous approximation. We carry out numerical experiments. We observe optimal convergence rate for all examples.
引用
收藏
页码:928 / 946
页数:19
相关论文
共 50 条
  • [41] Asymptotic analysis of the Poisson-Boltzmann equation in biological membrane channels
    El Jarroudi, Mustapha
    Brillard, Alain
    MATHEMATICAL BIOSCIENCES, 2013, 243 (01) : 46 - 56
  • [42] A Deep Neural Network Based on ResNet for Predicting Solutions of Poisson-Boltzmann Equation
    Kwon, In
    Jo, Gwanghyun
    Shin, Kwang-Seong
    ELECTRONICS, 2021, 10 (21)
  • [43] Efficient mesh refinement for the Poisson-Boltzmann equation with boundary elements
    Ramm, Vicente
    Chaudhry, Jehanzeb H.
    Cooper, Christopher D.
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2021, 42 (12) : 855 - 869
  • [44] Regularization methods for the Poisson-Boltzmann equation: Comparison and accuracy recovery
    Lee, Arum
    Geng, Weihua
    Zhao, Shan
    JOURNAL OF COMPUTATIONAL PHYSICS, 2021, 426
  • [45] Weak formulations of the nonlinear Poisson-Boltzmann equation in biomolecular electrostatics
    Iglesias, Jose A.
    Nakov, Svetoslav
    JOURNAL OF MATHEMATICAL ANALYSIS AND APPLICATIONS, 2022, 511 (01)
  • [46] Analytical solutions of the nonlinear Poisson-Boltzmann equation in mixture of electrolytes
    Liu, Xinmin
    Li, Hang
    Li, Rui
    Tian, Rui
    SURFACE SCIENCE, 2013, 607 : 197 - 202
  • [47] A POSTERIORI ANALYSIS AND EFFICIENT REFINEMENT STRATEGIES FOR THE POISSON-BOLTZMANN EQUATION
    Chaudhry, Jehanzeb H.
    SIAM JOURNAL ON SCIENTIFIC COMPUTING, 2018, 40 (04): : A2519 - A2542
  • [48] Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems
    Baker, N
    Holst, M
    Wang, F
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2000, 21 (15) : 1343 - 1352
  • [49] Assessment of Linear Finite-Difference Poisson-Boltzmann Solvers
    Wang, Jun
    Luo, Ray
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2010, 31 (08) : 1689 - 1698
  • [50] Fast solution of the linearized Poisson-Boltzmann equation with nonaffine parametrized boundary conditions using the reduced basis method
    Kweyu, Cleophas
    Feng, Lihong
    Stein, Matthias
    Benner, Peter
    COMPUTING AND VISUALIZATION IN SCIENCE, 2020, 23 (1-4) : 1 - 4