Literature DB >> 16164327

Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals.

Benzhuo Lu1, Xiaolin Cheng, Tingjun Hou, J Andrew McCammon.   

Abstract

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.

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Year:  2005        PMID: 16164327     DOI: 10.1063/1.2008252

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  6 in total

1.  ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION.

Authors:  Michael Holst; James Andrew McCammon; Zeyun Yu; Youngcheng Zhou; Yunrong Zhu
Journal:  Commun Comput Phys       Date:  2012       Impact factor: 3.246

2.  Exploring accurate Poisson-Boltzmann methods for biomolecular simulations.

Authors:  Changhao Wang; Jun Wang; Qin Cai; Zhilin Li; Hong-Kai Zhao; Ray Luo
Journal:  Comput Theor Chem       Date:  2013-11-15       Impact factor: 1.926

3.  Dielectric Boundary Force in Molecular Solvation with the Poisson-Boltzmann Free Energy: A Shape Derivative Approach.

Authors:  Bo Li; Xiaoliang Cheng; Zhengfang Zhang
Journal:  SIAM J Appl Math       Date:  2011       Impact factor: 2.080

4.  An efficient second-order poisson-boltzmann method.

Authors:  Haixin Wei; Ray Luo; Ruxi Qi
Journal:  J Comput Chem       Date:  2019-02-18       Impact factor: 3.376

5.  Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations.

Authors:  Yuhui Cheng; Jason K Suen; Deqiang Zhang; Stephen D Bond; Yongjie Zhang; Yuhua Song; Nathan A Baker; Chandrajit L Bajaj; Michael J Holst; J Andrew McCammon
Journal:  Biophys J       Date:  2007-02-16       Impact factor: 4.033

6.  Improved Poisson-Boltzmann Methods for High-Performance Computing.

Authors:  Haixin Wei; Aaron Luo; Tianyin Qiu; Ray Luo; Ruxi Qi
Journal:  J Chem Theory Comput       Date:  2019-09-30       Impact factor: 6.006

  6 in total

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