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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
Authors:  Zhang, Bo;  DeBuhr, Jackson;  Niedzielski, Drake;  Mayolo, Silvio;  Lu, Benzhuo;  Sterling, Thomas
Favorite  |  View/Download:68/0  |  Submit date:2019/03/05
Poisson-Boltzmann equation  boundary element method  DASHMM  distributed computing  
Stability of Nonlinear Wave Patterns to the Bipolar Vlasov-Poisson-Boltzmann System 期刊论文
ARCHIVE FOR RATIONAL MECHANICS AND ANALYSIS, 2018, 卷号: 228, 期号: 1, 页码: 39-127
Authors:  Li, Hailiang;  Wang, Yi;  Yang, Tong;  Zhong, Mingying
Favorite  |  View/Download:91/0  |  Submit date:2018/07/30
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
Authors:  Ji, Nan;  Liu, Tiantian;  Xu, Jingjie;  Shen, Longzhu Q.;  Lu, Benzhuo
Favorite  |  View/Download:74/0  |  Submit date:2018/07/30
laterally periodic Poisson-Boltzmann model  finite element method  membrane channel proteins  pore region  solvation  
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
Authors:  Liu, Xuejiao;  Qiao, Yu;  Lu, Benzhou
Favorite  |  View/Download:62/0  |  Submit date:2018/07/30
free energy functional  electrolyte  boundary conditions  variable dielectric  generalized Poisson-Nernst-Planck/Poisson-Boltzmann equations  energy law  
TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique 期刊论文
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2011, 卷号: 7, 期号: 1, 页码: 203-212
Authors:  Chen, Minxin;  Lu, Benzhuo
Favorite  |  View/Download:32/0  |  Submit date: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
Authors:  Lu, Benzhuo;  Cheng, Xiaolin;  Huang, Jingfang;  McCammon, J. Andrew
Favorite  |  View/Download:47/0  |  Submit date:2018/07/30
Poisson-Boltzmann equation  Boundary integral equation  Node-patch method  Krylov subspace methods  Fast multipole methods  Diagonal translations  
Two-scale finite element Green's function approximations with applications to electrostatic potential computation 期刊论文
JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY, 2010, 卷号: 23, 期号: 1, 页码: 177-193
Authors:  Yang, Ying;  Zhou, Aihui
Favorite  |  View/Download:34/0  |  Submit date:2018/07/30
Error analysis  finite element  Green's function  Poisson-Boltzmann equation  two-scale  
Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules 期刊论文
COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 2009, 卷号: 6, 期号: 5, 页码: 955-977
Authors:  Qin, Peihua;  Xu, Zhenli;  Cai, Wei;  Jacobs, Donald
Favorite  |  View/Download:38/0  |  Submit date:2018/07/30
Image charge methods  distance-dependent dielectric permittivity  hybrid implicit/explicit model  reaction field  Poisson-Boltzmann equation  protein  
An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics 期刊论文
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2009, 卷号: 5, 期号: 6, 页码: 1692-1699
Authors:  Lu, Benzhuo;  Cheng, Xiaolin;  Huang, Jingfang;  McCammon, J. Andrew
Favorite  |  View/Download:43/0  |  Submit date:2018/07/30
A finite element recovery approach to Green's function approximations with applications to electrostatic potential computation 期刊论文
JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS, 2009, 卷号: 225, 期号: 1, 页码: 202-212
Authors:  Yang, Ying;  Zhou, Aihui
Favorite  |  View/Download:34/0  |  Submit date:2018/07/30
Finite element  Green's function  Recovery approach  Three dimensions  Electrostatic potential  Poisson-Boltzmann equation