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Some corrections

　

　

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 .

　

Research Articles

  1. 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. (in print)

    2. ( * FEM solution of PNP equations, condition number issues)

  2. 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)

    3. (Has been selected for Faculty of 1000 Biology: evaluations for Lu B et al Comput Phys Commun 2010 181 :1150-60 http://f1000biology.com/article/id/3242956/evaluation )

    (* For AFMPB package description and release )

  3. 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)
  4. Benzhuo Lu, and Andrew McCammon. Kinetics of diffusion-controlled enzymatic reactions with charged substrates. PMC Biophysics, 3:1, 2010. (PDF)
  5. 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.
  6. 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.
  7. 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.
  8. 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)
  9. 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)
  10. 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)
  11. 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 )
  12. 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 )
  13. 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 )
  14. 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 )
  15. 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.
  16. 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.
  17. 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 )
  18. 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 )
  19. 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 )
  20. 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 )
  21. 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)
  22. 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 )
  23. 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.
  24. 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.
  25. 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 )
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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 )
  31. 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.
  32. 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 )
  33. 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, (might printed in 2002). (PDF)

Ben-Zhuo Lu 2007-10-13