Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals.
نویسندگان
چکیده
The electrostatic interaction among molecules solvated in ionic solution is governed by the Poisson-Boltzmann equation (PBE). Here the hypersingular integral technique is used in a boundary element method (BEM) for the three-dimensional (3D) linear PBE to calculate the Maxwell stress tensor on the solvated molecular surface, and then the PB forces and torques can be obtained from the stress tensor. Compared with the variational method (also in a BEM frame) that we proposed recently, this method provides an even more efficient way to calculate the full intermolecular electrostatic interaction force, especially for macromolecular systems. Thus, it may be more suitable for the application of Brownian dynamics methods to study the dynamics of protein/protein docking as well as the assembly of large 3D architectures involving many diffusing subunits. The method has been tested on two simple cases to demonstrate its reliability and efficiency, and also compared with our previous variational method used in BEM.
منابع مشابه
Improved Boundary Element Methods for Poisson-Boltzmann Electrostatic Potential and Force Calculations.
A patch representation differing from the traditional treatments in the boundary element method (BEM) is presented, which we call the constant "node patch" method. Its application to solving the Poisson-Boltzmann equation (PBE) demonstrates considerable improvement in speed compared with the constant element and linear element methods. In addition, for the node-based BEMs, we propose an efficie...
متن کاملDielectrophoretic effect of nonuniform electric fields on the protoplast cell
In recent years, dielectrophoresis based microfluidics systems have been used to manipulate colloids, inert particles, and biological microparticles, such as red blood cells, white blood cells, platelets, cancer cells, bacteria, yeast, microorganisms, proteins, DNA, etc. In the current study the governing electric potential equations have been solved in the presence of cell for the purpose of ...
متن کاملElectrostatic analysis of the charged surface in a solution via the finite element method: The Poisson-Boltzmann theory
Electrostatic potential as well as the local volume charge density are computed for a macromolecule by solving the Poisson-Boltzmann equation (PBE) using the finite element method (FEM). As a verification, our numerical results for a one dimensional PBE, which corresponds to an infinite-length macromolecule, are compared with the existing analytical solution and good agreement is found. As a ma...
متن کاملA treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
We present a treecode-accelerated boundary integral (TABI) solver for electrostatics of solvated biomolecules described by the linear Poisson-Boltzmann equation. The method employs a wellconditioned boundary integral formulation for the electrostatic potential and its normal derivative on the molecular surface. The surface is triangulated and the integral equations are discretized by centroid c...
متن کاملLattice Boltzmann Simulation of Deformation and Breakup of a Droplet under Gravity Force Using Interparticle Potential Model
Abstract In this paper interparticle potential model of the lattice Boltzmann method (LBM) is used to simulate deformation and breakup of a falling droplet under gravity force. First this model is applied to ensure that the surface tension effect is properly implemented in this model. Two tests have been considered. First, it has been checked an initial square drop in a 2D domain can freely def...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- The Journal of chemical physics
دوره 123 8 شماره
صفحات -
تاریخ انتشار 2005