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1

Poisson–Nernst–Planck equations for simulating biomolecular diffusion–reaction processes I: Finite element solutions

Benzhuo Lu, Michael J. Holst, J. Andrew McCammon, Y.C. Zhou

Journal:

Journal of Computational Physics

Year:

2010

Language:

english

File:

PDF, 1009 KB

english, 2010

2

A parallel finite element simulator for ion transport through three-dimensional ion channel systems

Tu, Bin, Chen, Minxin, Xie, Yan, Zhang, Linbo, Eisenberg, Bob, Lu, Benzhuo

Journal:

Journal of Computational Chemistry

Year:

2013

Language:

english

File:

PDF, 1.27 MB

english, 2013

3

A Multi-Time-Step Finite Element Algorithm for 3-D Simulation of Coupled Drift-Diffusion Reaction Process in Total Ionizing Dose Effect

Xu, Jingjie, Ma, Zhaocan, Li, Hongliang, Song, Yu, Zhang, Linbo, Lu, Benzhuo

Journal:

IEEE Transactions on Semiconductor Manufacturing

Year:

2018

Language:

english

File:

PDF, 1.42 MB

english, 2018

4

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

Liu, Xuejiao, Qiao, Yu, Lu, Benzhuo

Journal:

SIAM Journal on Applied Mathematics

Year:

2018

Language:

english

File:

PDF, 565 KB

english, 2018

5

A Finite Element Solution of Lateral Periodic Poisson–Boltzmann Model for Membrane Channel Proteins

Ji, Nan, Liu, Tiantian, Xu, Jingjie, Shen, Longzhu, Lu, Benzhuo

Journal:

International Journal of Molecular Sciences

Year:

2018

Language:

english

File:

PDF, 1.77 MB

english, 2018

6

A decoupling two-grid method for the time-dependent Poisson-Nernst-Planck equations

Shen, Ruigang, Shu, Shi, Yang, Ying, Lu, Benzhuo

Journal:

Numerical Algorithms

Year:

2019

Language:

english

File:

PDF, 2.45 MB

english, 2019

7

Direct estimation of entropy loss due to reduced translational and rotational motions upon molecular binding

Benzhuo Lu, Chung F. Wong

Journal:

Year:

2005

Language:

english

File:

PDF, 119 KB

english, 2005

8

E230Q mutation of the catalytic subunit of cAMP-dependent protein kinase affects local structure and the binding of peptide inhibitor

Man-Un Ung, Benzhuo Lu, J. A. McCammon

Journal:

Year:

2006

Language:

english

File:

PDF, 484 KB

english, 2006

9

Solutions to a reduced Poisson–Nernst–Planck system and determination of reaction rates

Bo Li, Benzhuo Lu, Zhongming Wang, J. Andrew McCammon

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

2010

Language:

english

File:

PDF, 1.29 MB

english, 2010

10

AFMPB: An adaptive fast multipole Poisson–Boltzmann solver for calculating electrostatics in biomolecular systems

Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, J. Andrew McCammon

Journal:

Computer Physics Communications

Year:

2010

Language:

english

File:

PDF, 491 KB

english, 2010

11

Molecular surface-free continuum model for electrodiffusion processes

Benzhuo Lu, J. Andrew McCammon

Journal:

Chemical Physics Letters

Year:

2008

Language:

english

File:

PDF, 348 KB

english, 2008

12

“New-version-fast-multipole-method” accelerated electrostatic calculations in biomolecular systems

Benzhuo Lu, Xiaolin Cheng, J. Andrew McCammon

Journal:

Journal of Computational Physics

Year:

2007

Language:

english

File:

PDF, 1.62 MB

english, 2007

13

Kinetics of diffusion-controlled enzymatic reactions with charged substrates

Benzhuo Lu, J Andrew McCammon

Journal:

Year:

2010

Language:

english

File:

PDF, 224 KB

english, 2010

14

A simulation method of combinding boundary element method with generalized Langevin dynamics

Weizu Chen, Benzhuo Lu, Cunxin Wang

Journal:

Chinese Science Bulletin

Year:

2000

Language:

english

File:

PDF, 365 KB

english, 2000

15

Salt and pH-dependent properties of native and mutant insulin

Xiaohui Ma, Chunhua Li, Benzhuo Lu, Weizu Chen, Cunxin Wang, Xiaojie Xu

Journal:

Chinese Science Bulletin

Year:

2002

Language:

english

File:

PDF, 118 KB

english, 2002

16

Channel Opening Motion of α7 Nicotinic Acetylcholine Receptor as Suggested by Normal Mode Analysis

Xiaolin Cheng, Benzhuo Lu, Barry Grant, Richard J. Law, J. Andrew McCammon

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 1.05 MB

english, 2006

17

Free Energy for the Permeation of Na + and Cl − Ions and Their Ion-Pair through a Zwitterionic Dimyristoyl Phosphatidylcholine Lipid Bilayer by Umbrella Integration with Harmonic Fourier Beads

Khavrutskii, Ilja V., Gorfe, Alemayehu A., Lu, Benzhuo, McCammon, J. Andrew

Journal:

Journal of the American Chemical Society

Year:

2009

Language:

english

File:

PDF, 1.60 MB

english, 2009

18

Enzymatic Activity versus Structural Dynamics: The Case of Acetylcholinesterase Tetramer

Gorfe, Alemayehu A., Lu, Benzhuo, Yu, Zeyun, McCammon, J. Andrew

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 496 KB

english, 2009

19

Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes II: Size Effects on Ionic Distributions and Diffusion-Reaction Rates

Lu, Benzhuo, Zhou, Y.C.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 942 KB

english, 2011

20

Triangulated manifold meshing method preserving molecular surface topology

Chen, Minxin, Tu, Bin, Lu, Benzhuo

Journal:

Journal of Molecular Graphics and Modelling

Year:

2012

Language:

english

File:

PDF, 1.39 MB

english, 2012

21

Release of ADP from the catalytic subunit of protein kinase A: A molecular dynamics simulation study

Benzhuo Lu, Chung F. Wong, J. Andrew McCammon

Journal:

Protein Science

Year:

2005

Language:

english

File:

PDF, 403 KB

english, 2005

22

Advances in biomolecular surface meshing and its applications to mathematical modeling

MinXin Chen, BenZhuo Lu

Journal:

Chinese Science Bulletin

Year:

2013

Language:

english

File:

PDF, 838 KB

english, 2013

23

VCMM: A visual tool for continuum molecular modeling

Bai, Shiyang, Lu, Benzhuo

Journal:

Journal of Molecular Graphics and Modelling

Year:

2014

Language:

english

File:

PDF, 2.04 MB

english, 2014

24

AFMPB: An adaptive fast multipole Poisson–Boltzmann solver for calculating electrostatics in biomolecular systems

Lu, Benzhuo, Cheng, Xiaolin, Huang, Jingfang, McCammon, J. Andrew

Journal:

Computer Physics Communications

Year:

2013

Language:

english

File:

PDF, 318 KB

english, 2013

25

A Software Platform for Finite Element Simulation of Ion Permeation in Ion Channel Systems

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 61 KB

english, 2014

26

Continuum electromechanical modeling of protein-membrane interactions

Zhou, Y. C., Lu, Benzhuo, Gorfe, Alemayehu A.

Journal:

Physical Review E

Year:

2010

Language:

english

File:

PDF, 2.90 MB

english, 2010

27

An Adaptive Fast Multipole Boundary Element Method for Poisson−Boltzmann Electrostatics

Lu, Benzhuo, Cheng, Xiaolin, Huang, Jingfang, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 1.14 MB

english, 2009

28

Improved Boundary Element Methods for Poisson−Boltzmann Electrostatic Potential and Force Calculations

Lu, Benzhuo, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2007

Language:

english

File:

PDF, 688 KB

english, 2007

29

Prediction of Binding Affinities between the Human Amphiphysin-1 SH3 Domain and Its Peptide Ligands Using Homology Modeling, Molecular Dynamics and Molecular Field Analysis

Hou, Tingjun, McLaughlin, William, Lu, Benzhuo, Chen, Ken, Wang, Wei

Journal:

Journal of Proteome Research

Year:

2006

Language:

english

File:

PDF, 642 KB

english, 2006

30

TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique

Chen, Minxin, Lu, Benzhuo

Journal:

Journal of Chemical Theory and Computation

Year:

2011

Language:

english

File:

PDF, 3.45 MB

english, 2011

31

Continuum Simulations of Acetylcholine Consumption by Acetylcholinesterase: A Poisson−Nernst−Planck Approach †

Zhou, Y. C., Lu, Benzhuo, Huber, Gary A., Holst, Michael J., McCammon, J. Andrew

Journal:

Journal of Physical Chemistry B

Year:

2008

Language:

english

File:

PDF, 347 KB

english, 2008

32

An ionic concentration and size dependent dielectric permittivity Poisson-Boltzmann model for biomolecular solvation studies

Li, Hanlin, Lu, Benzhuo

Journal:

The Journal of Chemical Physics

Year:

2014

Language:

english

File:

PDF, 1.02 MB

english, 2014

33

Computation of electrostatic forces between solvated molecules determined by the Poisson–Boltzmann equation using a boundary element method

Lu, Benzhuo, Zhang, Deqiang, McCammon, J. Andrew

Journal:

The Journal of Chemical Physics

Year:

2005

Language:

english

File:

PDF, 320 KB

english, 2005

34

Ionic size effects to molecular solvation energy and to ion current across a channel resulted from the nonuniform size-modified PNP equations

Qiao, Yu, Tu, Bin, Lu, Benzhuo

Journal:

The Journal of Chemical Physics

Year:

2014

Language:

english

File:

PDF, 1008 KB

english, 2014

35

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

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

Journal:

The Journal of Chemical Physics

Year:

2005

Language:

english

File:

PDF, 348 KB

english, 2005

36

Stabilized finite element methods to simulate the conductances of ion channels

Tu, Bin, Xie, Yan, Zhang, Linbo, Lu, Benzhuo

Journal:

Computer Physics Communications

Year:

2015

Language:

english

File:

PDF, 1.43 MB

english, 2015

37

Parameterization for molecular Gaussian surface and a comparison study of surface mesh generation

Liu, Tiantian, Chen, Minxin, Lu, Benzhuo

Journal:

Journal of Molecular Modeling

Year:

2015

Language:

english

File:

PDF, 2.31 MB

english, 2015

38

Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy

Zhang, Bo, Peng, Bo, Huang, Jingfang, Pitsianis, Nikos P., Sun, Xiaobai, Lu, Benzhuo

Journal:

Computer Physics Communications

Year:

2015

Language:

english

File:

PDF, 991 KB

english, 2015

39

Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain

Hou, Tingjun, Chen, Ken, McLaughlin, William A., Lu, Benzhuo, Wang, Wei

Journal:

PLoS Computational Biology

Year:

2006

Language:

english

File:

PDF, 270 KB

english, 2006

40

Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution

Lu, Benzhuo, Zhou, Y. C., Huber, Gary A., Bond, Stephen D., Holst, Michael J., McCammon, J. Andrew

Journal:

The Journal of Chemical Physics

Year:

2007

Language:

english

File:

PDF, 2.53 MB

english, 2007

41

A computational study of ion conductance in the KcsA K[sup +] channel using a Nernst–Planck model with explicit resident ions

Jung, Yong-Woon, Lu, Benzhuo, Mascagni, Michael

Journal:

The Journal of Chemical Physics

Year:

2009

Language:

english

File:

PDF, 1.37 MB

english, 2009

42

Parallel Adaptive Finite Element Algorithms for Solving the Coupled Electro-diffusion Equations

Xie, Yan, Cheng, Jie, Lu, Benzhuo, Zhang, Linbo

Journal:

Molecular Based Mathematical Biology

Year:

2013

Language:

english

File:

PDF, 5.46 MB

english, 2013

43

A Local Approximation of Fundamental Measure Theory Incorporated into Three Dimensional Poisson–Nernst–Planck Equations to Account for Hard Sphere Repulsion Among Ions

Qiao, Yu, Liu, Xuejiao, Chen, Minxin, Lu, Benzhuo

Journal:

Journal of Statistical Physics

Year:

2016

Language:

english

File:

PDF, 873 KB

english, 2016

44

Charged Substrate and Product Together Contribute Like a Nonreactive Species to the Overall Electrostatic Steering in Diffusion-Reaction Processes

Xu, Jingjie, Xie, Yan, Lu, Benzhuo, Zhang, Linbo

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 1.45 MB

english, 2016

45

Automated Parallel and Body-Fitted Mesh Generation in Finite Element Simulation of Macromolecular Systems

Xie, Yan, Liu, Tiantian, Tu, Bin, Lu, Benzhuo, Zhang, Linbo

Journal:

Communications in Computational Physics

Year:

2016

Language:

english

File:

PDF, 1.36 MB

english, 2016

46

Membrane-Channel Protein System Mesh Construction for Finite Element Simulations

Liu, Tiantian, Bai, Shiyang, Tu, Bin, Chen, Minxin, Lu, Benzhuo

Journal:

Molecular Based Mathematical Biology

Year:

2015

Language:

english

File:

PDF, 1.77 MB

english, 2015

47

An Error Analysis for the Finite Element Approximation to the Steady-State Poisson-Nernst-Planck Equations

Yang, Ying, Lu, Benzhuo

Journal:

Advances in Applied Mathematics and Mechanics

Year:

2013

Language:

english

File:

PDF, 196 KB

english, 2013

48

An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data

Jianbo Lu,Guoliang Xu,Shihua Zhang,Benzhuo Lu

Journal:

Algorithms for Molecular Biology

Year:

2016

Language:

english

File:

PDF, 1.26 MB

english, 2016

49

A Fast Direct Solver for a Class of 3-D Elliptic Partial Differential Equation with Variable Coefficient

Huang, Beibei, Tu, Bin, Lu, Benzhuo

Journal:

Communications in Computational Physics

Year:

2012

Language:

english

File:

PDF, 228 KB

english, 2012

50

channels

Liu, Xuejiao, Lu, Benzhuo

Journal:

Physical Review E

Year:

2017

Language:

english

File:

PDF, 1.35 MB

english, 2017

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