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Some corrections

Book chapter

  1. Benzhuo Lu, Poisson-Nernst-Planck equation, in book: Encyclopedia of Applied and Computational Mathematics, edited by Bjorn Engquist, Publisher: Springer-Verlag: Berlin Heidelberg, 2013.
  2. Benzhuo Lu, Finite Element Modeling of Biomolecular Systems in Ionic Solution,in book:Image-Based Geometric Modeling and Mesh Generation. Publisher:Springer Berlin Heidelberg, 2013, XI, p271.
  3. Minxin Chen, Bin Tu,and Benzhuo Lu,Surface Triangular Mesh and Volume Tetrahedral Mesh Generations for Biomolecular Modelling,in book:Image-Based Geometric Modeling and Mesh Generation. Publisher:Springer Berlin Heidelberg, 2013, XI, p85-106.


Invited Review

  1. B. Z. Lu, Y. C. Zhou, Michael J. Holst, and J. A. McCammon. Recent progress in numerical methods for the Poisson-Boltzmann equation in biophysical applications. Commun. in Comput. Phys., 3(5):973-1009, 2008. (PDF), link to the Journal webpage .

( Top 10 most cited paper of this journal [till 05/2010], see the journal webpage)

  1. Minxin Chen, and B. Z. Lu, Advances in biomolecular surface meshing and its applications to mathematical modeling, Chinese Science Bulletin, 58(16):1843-1849, 2013 (PDF)
  2. 彭波,李翰林,卢本卓,生物分子模拟中的静电计算,计算物理,2:127-159, 2015. (PDF)
  3. Qiao Yu, and Lu Ben-Zhuo, Improvements in continuum modeling for biomolecular systems, Chinese Physics B, 25(1): 018705, 2016
  4. 张林波, 郑伟英, 卢本卓, 崔涛, 冷伟,林灯,并行自适应有限元软件平台 PHG 及其应用,中国科学: 信息科学 46:1442, 2016.(PDF)


Research Articles

  1. Longzhu Shen, Nan Ji, Benzhuo Lu, Introducing Membrane Transport Energy into the Design of Sustainable Chemicals against Cytotoxicity, 
    ACS Sustainable Chemistry & Engineering, (submitted) 2017.
  2. Ying Yang, Benzhuo Lu, Yan Xie, A Decoupling Two-Grid Method for the Steady-State Poisson-Nernst-Planck Equations, (submitted) 2016
  3. Jingjie Xu, Zhaocan Ma, Hongliang Li, Yu Song, Linbo Zhang, and Benzhuo Lu, A Multi-Time-Step Finite Element Algorithm for 3D Simulation of Coupled Drift-Diffusion-Reaction Process in Total Ionizing Dose Effect (sumitted), 2017
  4. Liu T, Chen M, Song Y, Li H, Lu B, Quality improvement of surface triangular mesh using a modified Laplacian smoothing approach avoiding intersection. PLoS ONE, 12(9): e0184206, 2017. (PDF)
  5. B. Zhang, J. DeBuhr, D. Niedzielski, S. Mayolo, B. Lu, T. Sterling, DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture, Computer Phys Commun. (submitted), 2017
  6. Zhaocan Ma, Jingjie Xu, Hongliang Li, Song Yu, Linbo Zhang, and Benzhuo Lu, 3D Simulation of the Defect Generation by Hydrogen at Si-SiO2 Interface, Proceedings of the International Conference on Computational Methods, Vol.4,610, 2017
  7. Xuejiao Liu, Yu Qiao, and Benzhuo Lu, Analysis of the Mean Field Free Energy Functional of Electrolyte Solution with Non-homogenous Boundary Conditions and the Generalized PB/PNP Equations with Inhomogeneous Dielectric Permittivity, 2016,
  8. Tiantian Liu, M.X. Chen, and B.Z. Lu, Efficient and qualified mesh generation for Gaussian molecular surface using adaptive partition and piecewise polynomial approximation, 2016,
  9. Jianbo Lu, Guoliang Xu, Shihua Zhang, and Benzhuo Lu, An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data, Algorithms for Molecular Biology, 11:18, 2016. (PDF)
  10. Jingjie Xu, Yan Xie, Benzhuo Lu, and Linbo Zhang, Charged Substrate and Product Together Contribute Like a Nonreactive Species to the Overall Electrostatic Steering in Diffusion-Reaction Processes, J. Phys. Chem. B, 120: 8147-8153, 2016. (PDF)
  11. (* Explain: why the charged substrate and product are not explicitly considered in the Debyle-Huckel limiting law )

  12. Yu Qiao, Xuejiao Liu, Minxin Chen, Benzhuo Lu, A Local Approximation of Fundamental Measure Theory Incorporated into Three Dimensional Poisson–Nernst–Planck Equations to Account for Hard Sphere Repulsion Among Ions, Journal of Statistical Physics, 163(1): 156-174, 2016. (PDF)
  13. (* FMT + PNP, size effects, Monte Carlo simulation, equation of state)

  14. 许竞劼, 谢妍, 卢本卓, 一个基于PHG平台的并行有限元生物分子模拟解法器, 数值计算与计算机应用, 37(1):67-82, 2016. (PDF)
  15. Yan Xie,Tiantian Liu,Bin Tu, Benzhuo Lu, Linbo Zhang, Automated Parallel and Body-fitted Mesh Generation in Finite Element Simulation of Macromolecular Systems, Commun. in Comput. Phys.,19: 582-602, 2016. (PDF)
  16. Tiantian Liu, Shiyang Bai, Bin Tu, Minxin Chen, Benzhuo Lu, Mesh Construction for Membrane-Channel Protein System for Finite Element Simulations, Molecular Based Mathematical Biology, 3(1):2299-3266, 2015. (pdf)
  17. T.T. Liu, M.X. Chen, B.Z. Lu, Parameterization for molecular Gaussian surface and a comparison study of surface mesh generation, J. Molecular Modeling, 21(5):113, 2015. (PDF)
  18. Bo Zhang, Bo Peng, Jingfang Huang, Nikos P. Pitsianis, Xiaobai Sun, Benzhuo Lu, Parallel AFMPB solver with automatic surface meshing for calculations of molecular solvation free energy, Computer Physics Communications, 190: 173–181, 2015. (PDF)
  19. ( * Parallel AFMPB using Cilk Plus, C and fortran mixed, total solvation energy calculation, automeshing (VDW surface) as an option )

  20. Bin Tu, Yan Xie, Linbo Zhang, Benzhuo Lu, Stabilized finite element methods to simulate the conductances of ion channels, Computer Physics Communications, 188: 131-139, 2015 (PDF).
  21. Hanlin Li and Benzhuo Lu, An ionic concentration and size dependent dielectric permittivity Poisson-Boltzmann model for biomolecular solvation studies, J. Chem. Phys. 141: 024115, 2014 (PDF)
  22. ( * a variable dielectric PB model (VDPB) )

  23. Yu Qiao, Bin Tu and Benzhuo Lu, Ionic size effects to molecular solvation energy and to ion current across a channel resulted from the nonuniform size-modified PNP equations, J. Chem. Phys. 140: 174102, 2014 (PDF)
  24. B Tu, S Y Bai, M X Chen, Y Xie, L B Zhang and B Z Lu,A software platform for continuum modeling of ion channels based on unstructured mesh, Computational Science & Discovery, 7:014002, 2014 (PDF)
  25. Shiyang Bai, Benzhuo Lu, VCMM: A visual tool for continuum molecular modeling, Journal of Molecular Graphics and Modelling, 50: 44-49, 2014. (PDF)
    (*Visualize and analyze molecule, mesh (both unstructured and structured), and simulation data; Interface for solvers and tools)
  26. Xie Y, Tu B, Lu BZ, Zhang LB. Poisson-Boltzmann 方程的并行有限元求解及网格自适应生成,软件学报,2013,24(Suppl.(2)):110-117。(PDF
  27. Bin Tu, Minxin Chen, Yan Xie, Linbo Zhang, Bob Eisenberg, and Benzhuo Lu, A Parallel Finite Element Simulator for Ion Transport through Three-dimensional Ion Channel Systems, J. Comput. Chem. 34(24): 2065-2078, 2013. (PDF)

  28. Selected as Inside Cover image of JCC (Volume 34, Issue 24).

    ( * Parallel finite element method, ion channel simulation, mesh generation for channel protein and membrane system, comparison with Brownian dynamics simulation and experimental results )

  29. Minxin Chen, Bin Tu, Benzhuo Lu, Triangulated Manifold Meshing Method Preserving Molecular Surface Topology, Journal of Molecular Graphics and Modelling, 38: 411-418, 2012 (PDF).
  30. ( * An improverd version of TMSmesh, aiming to make the generated molecular surface mesh to be a manifold mesh )

  31. Yan Xie, Jie Cheng, Benzhuo Lu, Linbo Zhang, Parallel Adaptive Finite Element Algorithms for Solving the Coupled Electro-diffusion Equations, Molecular Based Mathematical Biology, 1: 90-108, 2013 (pdf).
  32. Ying Yang, B.Z. Lu, An Error Bounds Analysis for the Finite Element Approximation to the Steady-state Poisson-Nernst-Planck equations, Advances in Applied Mathematics and Mechanics, 5(1): 113-130, 2013. (pdf)
  33. Bo Zhang, Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, Nikos P. Pitsianis, Xiaobai Sun, and J. Andrew McCammon, Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver, Commun. in Comput. Phys. 13(1): 107-128, 2013 (PDF).
  34. Beibei Huang, Bin Tu, Benzhuo Lu, A fast direct solver for a class of 3-D elliptic PDE with variable coefficient, Commun. in Comput. Phys. 12(4): 1148-1162, 2012.
  35. Benzhuo Lu, Yongcheng Zhou, Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes II: Size Effects on Ionic Distributions and Diffusion-reaction Rates, Biophysical J. 100(10):2475-2485, 2011 (PDF)
  36. ( * Size-Modified PB, Size-modified Poisson-Nernst-Planck equations, arbitrarily non-uniform sizes, finite size effects on diffusion-reaction rate)

  37. Minxin Chen, Benzhuo Lu, TMSmesh: A robust method for molecular surface mesh generation using a trace technique, J. Chem. Theory Comput., 7:203-212, 2011 (PDF)
  38. ( * Molecular surface meshing tool, being capable of generating mesh for arbitrarily large molecule with good quality in terms of topological correctness, faithfulness to original molecular surface, and uniformness.)

  39. Y. C. Zhou, Benzhuo Lu, and Alemayehu A. Gorfe, Continuum electromechanical modeling of a protein-membrane interaction, Phys. Rev. E 82, 041923 (2010) [5 pages] (PDF)
  40. ( * Electrostatic-elastic (membrane) model, electrostatic force induced membrane curvature )

  41. Benzhuo Lu, Michael J. Holst, J. Andraw McCammon, and Y. C. Zhou. Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions, J. Comput. Phys. 2010. 229:6979-6994. (PDF)
  42. ( * FEM solution of PNP equations, condition number issues)

  43. B. Z. Lu, X. Cheng, J. Huang, J. A. McCammon. AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems, Computer Physics Communications, 181: 1150–1160, 2010. (PDF)
  44. (Has been selected for Faculty of 1000 Biology: evaluations for Lu B et al Comput Phys Commun. 2010, 181:1150-60 )

    (* For AFMPB package description and release )

  45. Bo Li, Benzhuo Lu, Zhongming Wang, J. Andrew McCammon, Solutions to a Reduced Poisson–Nernst–Planck System and Determination of Reaction Rates. Physica A, 389:1329-1345, 2010. (PDF)
  46. Benzhuo Lu, and Andrew McCammon. Kinetics of diffusion-controlled enzymatic reactions with charged substrates. PMC Biophysics, 3:1, 2010. (PDF)
  47. Yong-Woon Jung, Benzhuo Lu, Michael Mascagni. A computational study of ion conductance in the KcsA K+ channel using a Nernst-Planck model with explicit resident ions. J. Chem. Phys. 131, 215101, 2009. (PDF), (jcp link). The article has been selected for the December 2009 issue of JCP: BioChemical Physics. and for the December 15, 2009 issue of the Virtual Journal of Biological Physics Research.
  48. Alemayehu A. Gorfe*, Benzhuo Lu*, Zeyun Yu, and J. Andrew McCammon. Enzymatic Activity versus Structural Dynamics: The Case of Acetylcholinesterase Tetramer. Biophysical Journal., 97(3), 897-905, 2009.(PDF), link to journal.
  49. B. Z. Lu, X. Cheng, J. Huang, J. A. McCammon, An adaptive fast multipole boundary element method for Poisson-Boltzmann electrostatics. J. Chem. Theory Comput., 5(6):1692-1699, 2009. (PDF), link.
  50. Ilja V. Khavrutskii, Alemayehu A. Gorfe, Benzhuo Lu, J. Andrew McCammon. Free Energy for the Permeation of Na+ and Cl- Ions and their Ion-Pair through Zwitterionic Dimyristoyl Phosphatidylcholine Lipid Bilayer by Umbrella Integration with Harmonic Fourier Beads. J. Am. Chem. Soc., 131(5):1706-1716, 2009. (PDF)
  51. B. Z. Lu and J. A. McCammon. Molecular surface-free continuum model for electrodiffusion processes. Chem. Phys. Lett., 451(4-6):282-286, 2008. (PDF)
  52. Y. C. Zhou, B. Z. Lu, Gary A. Huber, Michael J. Holst, and J. A. McCammon. Continuum simulations of acetylcholine consumption by acetylcholinesterase: A Poisson-Nernst-Planck approach. J. Phys. Chem. B, 112(2):270-275, 2008. (PDF)
  53. B. Z. Lu, Y. C. Zhou, Gary A. Huber, Stephen D. Bond, Michael J. Holst, and J. Andrew McCammon. Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. J. Chem. Phys., 127(13):135102, 2007. (PDF)
    Also selected for October 15, 2007 issue of Virtual Journal of Biological Physics Research. link
    (* A solver for Poisson-Nernst-Planck, Poisson-Boltzmann, Smoluchowski equations, and realistic spatiotemporal diffusion-reaction problem; hybrid FEM/BEM, surface and volume mesh generation; a bunch of examples )
  54. B. Z. Lu, X. L. Cheng, and J. A. McCammon. "New-Version-Fast-Multipole Method" Accelerated Electrostatic Calculations in Biomolecular Systems. J. Comput. Phys., 226(2):1348-1366, 2007. (PDF)
    (* FMM BEM, technical details )
  55. B. Z. Lu and J. A. McCammon. Improved boundary element methods for Poisson-Boltzmann electrostatic potential and force calculations. J. Chem. Theory. Comput., 3(3):1134-1142, 2007. (PDF)
    (** A "node patch" boundary element method --- the third low order BEM, mesh geometry correction, force calculation )
  56. B. Z. Lu, X. L. Cheng, J. F. Huang, and J. A. McCammon. Order N algorithm for computation of electrostatic interactions in biomolecular systems. Proc. Natl. Acad. Sci. U. S. A., 103(51):19314-19319, 2006. (PDF)
    ( * Fast multipole, well-conditioned boundary integral equations, multidomains )
  57. T. J. Hou, K. Chen, W. McLaughlin, B. Z. Lu, and W. Wang. Computational analysis and prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 domain. PLoS Computational Biology, 2(1):e1, 2006.
  58. T. J. Hou, W. McLaughlin, B. Z. Lu, K. Chen, and W. Wang. Prediction of Binding Affinities between the Human Amphiphysin-1 SH3 Domain and Its Peptide Ligands Using Homology Modeling, Molecular dynamics and Molecular Field Analysis. J. Proteome research, 5(1):32-43, 2006. (PDF)
  59. X. L. Cheng, B. Z. Lu, B. Grant, R. Law, and J. A. McCammon. Channel opening motion of \alpha 7 nicotinic acetylcholine receptor as suggested by normal mode analysis. J. Mol. Biol., 355(2):310-324, 2006. (PDF)
    ( * nAChR, normal model analysis, channel gating )
  60. M. U. Ung, B. Z. Lu*, and J. A. McCammon. E230Q mutation of the catalytic subunit of cAMP-dependent protein kinase affects local structure and the binding of peptide inhibitor. Biopolymers, 81(6):428-439, 2006. (PDF)
    ( * PKA, E230Q mutation effect, peptide binding )
  61. B. Z. Lu, X. L. Cheng, T. J. Hou, and J. A. McCammon. Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals. J. Chem. Phys., 123(8):084904, 2005. (PDF)
    Also selected for the September 15, 2005 issue of Virtual Journal of Biological Physics Research. link
    ( * Maxwell stress tensor, strong singular and hypersingular integrals, BEM, PB force and torque )
  62. B. Z. Lu, D. Q. Zhang, and J. A. McCammon. Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. J. Chem. Phys., 122(21):214102, 2005. (PDF)
    Also selected for the June 1, 2005 issue of Virtual Journal of Biological Physics Research. link
    ( * A set of boundary integral equations derived from energy variation principle for calculations of the PB forces between biomolecules )
  63. B. Z. Lu, C. F. Wong, and J. A. McCammon. Release of ADP from the catalytic subunit of protein kinase A: A molecular dynamics simulation study. Protein Sci., 14(1):159-168, 2005. (PDF)
  64. B. Z. Lu and C. F. Wong. Direct calculation of entropy loss due to reduced translational and rotational motions upon molecular binding. Biopolymers, 79:277-285, 2005. (PDF)
    ( * Entropy calculation, formulations, entropy loss of bound water molecules and ATP )
  65. Y. H. Yu, B. Z. Lu*, J. G. Han, and P. F. Zhang. Scoring the protein-protein docked structures based on the balance and tightness of binding. J. Comput. Aided Mol. Des, 18(4):251-260, 2004.
  66. J. G. Han, Z. Y. Ren, and B. Z. Lu. Geometries and stabilities of re-doped si-n (n=1-12) clusters: a density functional investigation. J. Phys. Chem. A, 108(23):5100-5110, 2004.
  67. B. Z. Lu, B. H. Wang, W. Z. Chen, and C. X. Wang. A new computational approach for real protein folding prediction. Protein Eng., 16(9):659-663, 2003. (PDF)
    ( * Relative entropy, protein folding )
  68. Y. H. Yu, C. H. Li, B. Z. Lu, W. Z. Chen, and C. X. Wang. A new method to select the near-native conformations from the docked structures. Acta Phys.-Chim. Sin. (in Chinese), 19(8):757-761, 2003.
  69. B. Z. Lu, C. X. Wang, and B. H. Wang. A new minimization method for real protein folding prediction. Chin. J. Chem. Phys. (in Chinese), 16(2):117-121, 2003.
  70. W. Y. Wang, B. Z. Lu, W. Z. Chen, and C. X. Wang. Study on the stability of insulin hexamer in solution by molecular dynamics simulations. Acta Chim. Sin. (in Chinese), 60(12):2129-2134, 2002.
  71. W. Y. Wang, B. Z. Lu, W. Z. Chen, and C. X. Wang. The study on the flexibility of insulin hexamer in solution by molecular dynamics simulations. Acta Biophysica Sinica (in Chinese), (19):35-40, 2003.
  72. B. Z. Lu, W. Z. Chen, C. X. Wang, and X. J. Xu. Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation. Proteins, 48(3):497-504, 2002. (PDF)
    ( * Finite difference Poisson-Boltzmann molecular dynamics simulation )
  73. X. H. Ma, C. H. Li, B. Z. Lu, W. Z. Chen, C. X. Wang, and X. J. Xu. Salt and pH-dependent properties of native and mutant insulin. Chin. Sci. Bull., 47(6):464-466, 2002.
  74. B. Z. Lu, C. X. Wang, W. Z. Chen, S. Z. Wan, and Y. Y. Shi. A stochastic dynamics simulation study associated with hydration force and friction memory effect. J. Phys. Chem. B, 104(29):6877-6883, 2000. (PDF)
    ( * Generalized Langevin dynamics, friction memory, boundary element method Poisson-Boltzmann force )
  75. B. Z. Lu, W. Z. Chen, and C. X. Wang. The generalized Langevin dynamics associated with boundary element method. Chinese Science Bulletin, 45:1482-1486, 2000.



Others (published in my notebook, disappeared journal, or somewhere in an old mountain and forest you may not reach :) )

“量子原理与艺术哲学”(Quantum theory and the philosophy of art), (in Chinese中文) 1999, (maybe printed in 2002). (PDF)
( * 艺术中的不确定性,及量化评价的可能性? )

Ben-Zhuo Lu 2012-4-24