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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:11/0  |  Submit date:2019/03/05
Poisson-Boltzmann equation  boundary element method  DASHMM  distributed computing  
A DECOUPLING TWO-GRID METHOD FOR THE STEADY-STATE POISSON-NERNST-PLANCK EQUATIONS 期刊论文
JOURNAL OF COMPUTATIONAL MATHEMATICS, 2019, 卷号: 37, 期号: 4, 页码: 556-578
Authors:  Yang, Ying;  Lu, Benzhuo;  Xie, Yan
Favorite  |  View/Download:6/0  |  Submit date:2020/05/24
Poisson-Nernst-Planck equations  Two-grid finite element method  Decoupling method  Error analysis  Gummel iteration  
Frontiers in biomolecular mesh generation and molecular visualization systems 期刊论文
Visual Computing for Industry, Biomedicine, and Art, 2018, 卷号: 1, 期号: 1
Authors:  Gui,Sheng;  Khan,Dawar;  Wang,Qin;  Yan,Dong-Ming;  Lu,Ben-Zhuo
Favorite  |  View/Download:14/0  |  Submit date:2018/10/07
Biomolecular mesh generation  Remeshing  BEM  FEM  Molecular visualization  
Conic shapes have higher sensitivity than cylindrical ones in nanopore DNA sequencing 期刊论文
SCIENTIFIC REPORTS, 2018, 卷号: 8, 页码: 11
Authors:  Tu, Bin;  Bai, Shiyang;  Lu, Benzhuo;  Fang, Qiaojun
Favorite  |  View/Download:11/0  |  Submit date:2018/07/30
Molecular Surface Remeshing with Local Region Refinement 期刊论文
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2018, 卷号: 19, 期号: 5, 页码: 20
Authors:  Khan, Dawar;  Yan, Dong-Ming;  Gui, Sheng;  Lu, Benzhuo;  Zhang, Xiaopeng
Favorite  |  View/Download:12/0  |  Submit date:2018/07/30
molecular surface mesh  molecular simulation  meshing quality  finite element method  
A Time-Dependent Finite Element Algorithm for Simulations of Ion Current Rectification and Hysteresis Properties of 3D Nanopore System 期刊论文
IEEE TRANSACTIONS ON NANOTECHNOLOGY, 2018, 卷号: 17, 期号: 3, 页码: 513-519
Authors:  Xu, Jingjie;  Lu, Benzhuo;  Zhang, Linbo
Favorite  |  View/Download:13/0  |  Submit date:2018/07/30
3D nanopore  analytical test  backward Euler  FEM  ICR  numerical simulation  PNP equations  varying voltage  
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:18/0  |  Submit date: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
Authors:  Shen, Longzhu Q.;  Nan, Ji;  Lu, Benzhuo
Favorite  |  View/Download:10/0  |  Submit date:2018/07/30
DFT  Cytotoxicity  Membrane  Finite element  Poisson Boltzmann  Geometry  Sustainability  
A Multi-Time-Step Finite Element Algorithm for 3-D Simulation of Coupled Drift-Diffusion Reaction Process in Total Ionizing Dose Effect 期刊论文
IEEE TRANSACTIONS ON SEMICONDUCTOR MANUFACTURING, 2018, 卷号: 31, 期号: 1, 页码: 183-189
Authors:  Xu, Jingjie;  Ma, Zhaocan;  Li, Hongliang;  Song, Yu;  Zhang, Linbo;  Lu, Benzhuo
Favorite  |  View/Download:14/0  |  Submit date:2018/07/30
Drift-diffusion reaction  ELDRS  finite element method  multi-time-step algorithm  TID  
EFFICIENT AND QUALIFIED MESH GENERATION FOR GAUSSIAN MOLECULAR SURFACE USING ADAPTIVE PARTITION AND PIECEWISE POLYNOMIAL APPROXIMATION 期刊论文
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 2018, 卷号: 40, 期号: 2, 页码: B507-B527
Authors:  Liu, Tiantian;  Chen, Minxin;  Lu, Benzhuo
Favorite  |  View/Download:15/0  |  Submit date:2018/07/30
surface mesh generation  Gaussian surface  triangulation  adaptive partition  trilinear polynomial