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DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture 期刊论文
COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 2019, 卷号: 25, 期号: 4, 页码: 1235-1258
作者:  Zhang, Bo;  DeBuhr, Jackson;  Niedzielski, Drake;  Mayolo, Silvio;  Lu, Benzhuo;  Sterling, Thomas
收藏  |  浏览/下载：189/0  |  提交时间：2019/03/05
Poisson-Boltzmann equation  boundary element method  DASHMM  distributed computing  
A Finite Element Solution of Lateral Periodic Poisson-Boltzmann Model for Membrane Channel Proteins 期刊论文
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2018, 卷号: 19, 期号: 3, 页码: 17
作者:  Ji, Nan;  Liu, Tiantian;  Xu, Jingjie;  Shen, Longzhu Q.;  Lu, Benzhuo
收藏  |  浏览/下载：178/0  |  提交时间：2018/07/30
laterally periodic Poisson-Boltzmann model  finite element method  membrane channel proteins  pore region  solvation  
Introducing Membrane Transport Energy into the Design of Sustainable Chemicals against Cytotoxicity 期刊论文
ACS SUSTAINABLE CHEMISTRY & ENGINEERING, 2018, 卷号: 6, 期号: 2, 页码: 2055-2061
作者:  Shen, Longzhu Q.;  Nan, Ji;  Lu, Benzhuo
收藏  |  浏览/下载：152/0  |  提交时间：2018/07/30
DFT  Cytotoxicity  Membrane  Finite element  Poisson Boltzmann  Geometry  Sustainability  
ANALYSIS OF THE MEAN FIELD FREE ENERGY FUNCTIONAL OF ELECTROLYTE SOLUTION WITH NONHOMOGENOUS BOUNDARY CONDITIONS AND THE GENERALIZED PB/PNP EQUATIONS WITH INHOMOGENEOUS DIELECTRIC PERMITTIVITY 期刊论文
SIAM JOURNAL ON APPLIED MATHEMATICS, 2018, 卷号: 78, 期号: 2, 页码: 1131-1154
作者:  Liu, Xuejiao;  Qiao, Yu;  Lu, Benzhou
收藏  |  浏览/下载：172/0  |  提交时间：2018/07/30
free energy functional  electrolyte  boundary conditions  variable dielectric  generalized Poisson-Nernst-Planck/Poisson-Boltzmann equations  energy law  
Incorporating Born solvation energy into the three-dimensional Poisson-Nernst-Planck model to study ion selectivity in KcsA K+ channels 期刊论文
PHYSICAL REVIEW E, 2017, 卷号: 96, 期号: 6, 页码: 10
作者:  Liu, Xuejiao;  Lu, Benzhuo
收藏  |  浏览/下载：160/0  |  提交时间：2018/07/30
A Local Approximation of Fundamental Measure Theory Incorporated into Three Dimensional Poisson-Nernst-Planck Equations to Account for Hard Sphere Repulsion Among Ions 期刊论文
JOURNAL OF STATISTICAL PHYSICS, 2016, 卷号: 163, 期号: 1, 页码: 156-174
作者:  Qiao, Yu;  Liu, Xuejiao;  Chen, Minxin;  Lu, Benzhuo
收藏  |  浏览/下载：151/0  |  提交时间：2018/07/30
Hard sphere repulsion  Three dimensional fundamental measure theory  Poisson-Nernst-Planck equations  Size-modified PNP  Equation of state  
Automated Parallel and Body-Fitted Mesh Generation in Finite Element Simulation of Macromolecular Systems 期刊论文
COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 2016, 卷号: 19, 期号: 3, 页码: 582-602
作者:  Xie, Yan;  Liu, Tiantian;  Tu, Bin;  Lu, Benzhuo;  Zhang, Linbo
收藏  |  浏览/下载：118/0  |  提交时间：2018/07/30
Parallel mesh generation  body-fitted  PHG  biomolecules  finite element simulation  
Continuum electromechanical modeling of protein-membrane interactions 期刊论文
PHYSICAL REVIEW E, 2010, 卷号: 82, 期号: 4, 页码: 5
作者:  Zhou, Y. C.;  Lu, Benzhuo;  Gorfe, Alemayehu A.
收藏  |  浏览/下载：99/0  |  提交时间：2018/07/30
AFMPB: An adaptive fast multipole, Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems 期刊论文
COMPUTER PHYSICS COMMUNICATIONS, 2010, 卷号: 181, 期号: 6, 页码: 1150-1160
作者:  Lu, Benzhuo;  Cheng, Xiaolin;  Huang, Jingfang;  McCammon, J. Andrew
收藏  |  浏览/下载：144/0  |  提交时间：2018/07/30
Poisson-Boltzmann equation  Boundary integral equation  Node-patch method  Krylov subspace methods  Fast multipole methods  Diagonal translations