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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
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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
Authors:  Ji, Nan;  Liu, Tiantian;  Xu, Jingjie;  Shen, Longzhu Q.;  Lu, Benzhuo
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laterally periodic Poisson-Boltzmann model  finite element method  membrane channel proteins  pore region  solvation  
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
Authors:  Liu, Xuejiao;  Lu, Benzhuo
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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
Authors:  Xie, Yan;  Liu, Tiantian;  Tu, Bin;  Lu, Benzhuo;  Zhang, Linbo
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Parallel mesh generation  body-fitted  PHG  biomolecules  finite element simulation  
An Algebraic Spline Model of Molecular Surfaces for Energetic Computations 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2011, 卷号: 8, 期号: 6, 页码: 1458-1467
Authors:  Zhao, Wenqi;  Xu, Guoliang;  Bajaj, Chandrajit
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Polynomial splines  molecular surfaces  prismatic scaffolds  Bernstein-Bezier basis  solvation energetics  error bounds  rate of convergence  
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
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Continuum electromechanical modeling of protein-membrane interactions 期刊论文
PHYSICAL REVIEW E, 2010, 卷号: 82, 期号: 4, 页码: 5
Authors:  Zhou, Y. C.;  Lu, Benzhuo;  Gorfe, Alemayehu A.
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Testing a Hybrid Solvation Model with a Transition Layer Via Molecular Dynamics Simulation 期刊论文
BIOPHYSICAL JOURNAL, 2010, 卷号: 98, 期号: 3, 页码: 575A-575A
Authors:  Song, Wei;  Qin, Peihua;  Lin, Yuchun;  Baumketner, Andriy;  Cai, Wei;  Jacobs, Donald
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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
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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
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