Zhenli Xu,Wei Cai,Xiaolin Cheng
Zhenli Xu
A multiple-image method is proposed to approximate the reaction-field potential of a source charge inside a finite length cylinder due to the electric polarization of the surrounding membrane and bulk water. When applied to a hybrid ion-cha...
Xiaodong Pang,Huan-Xiang Zhou
Xiaodong Pang
The Poisson-Boltzmann equation is widely used for modeling the electrostatics of biomolecules, but the calculation results are sensitive to the choice of the boundary between the low solute dielectric and the high solvent dielectric. The de...
Songming Hou,Zhilin Li,Liqun Wang et al.
Songming Hou et al.
Solving elasticity equations with interfaces is a challenging problem for most existing methods. Nonetheless, it has wide applications in engineering and science. An accurate and efficient method is desired. In this paper, an efficient non-...
An Adaptive Mesh Refinement Strategy for Immersed Boundary/Interface Methods [0.03%]
一种自适应网格加密的浸入式边界/界面方法策略
Zhilin Li,Peng Song
Zhilin Li
An adaptive mesh refinement strategy is proposed in this paper for the Immersed Boundary and Immersed Interface methods for two-dimensional elliptic interface problems involving singular sources. The interface is represented by the zero lev...
ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION [0.03%]
泊松-玻尔兹曼方程的自适应有限元方法技术
Michael Holst,James Andrew McCammon,Zeyun Yu et al.
Michael Holst et al.
We consider the design of an effective and reliable adaptive finite element method (AFEM) for the nonlinear Poisson-Boltzmann equation (PBE). We first examine the two-term regularization technique for the continuous problem recently propose...
Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules [0.03%]
适用于生物分子三介电层混合溶剂化的像电荷法
Peihua Qin,Zhenli Xu,Wei Cai et al.
Peihua Qin et al.
This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the Poisson-Boltzmann equation. In this model, an interior spherical cavity will contain the sol...
Fast Spectral Collocation Method for Surface Integral Equations of Potential Problems in a Spheroid [0.03%]
势问题椭球面积分方程的快速谱配置方法
Zhenli Xu,Wei Cai
Zhenli Xu
This paper proposes a new technique to speed up the computation of the matrix of spectral collocation discretizations of surface single and double layer operators over a spheroid. The layer densities are approximated by a spectral expansion...
Free Energy Calculations for DNA Near Surfaces Using an Ellipsoidal Geometry [0.03%]
基于椭圆几何的DNA分子在表面附近自由能计算
J Ambia-Garrido,B Montgomery Pettitt
J Ambia-Garrido
The change in some thermodynamic quantities such as Gibbs' free energy, entropy and enthalpy of the binding of two DNA strands (forming a double helix), while one is tethered to a surface and are analytically calculated. These particles are...