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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. 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)
   
2. 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)
   
3. 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 )
4. 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 )
5. 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 )
6. 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 )
7. 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.
8. 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.
9. 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 )
10. 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 )
11. 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 )
12. 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 )
13. 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)
    
14. 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 )
15. 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.
16. 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.
17. 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 )
18. 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.
19. 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.
20. 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.
21. 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.
22. 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 )
23. 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.
24. 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 )
25. 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.

Talks

• "Fully-continuum diffusion -- Poisson-Nernst-Planck Equation" (scheduled) at the 2008 CTBP Summer School, Coarse-Grained Physical Modeling of Biological Systems: Advanced Theory and Methods, San Diego, CA, August 11-15, 2008. Weblink: http://ctbp.ucsd.edu/summer_school08/apply2008.html.

• Dept. of Molecular Biology & Biochemistry, University of California at Irvine, 4/25/08.

• Informal Seminars on Mathematics and Biochemistry-Biophysics, "Boundary integral methods for electrostatics in biomolecules. Part I: An overview", 4/8/08, Spring quarter, 2008; And "Electrodiffusion", 10/2/07, Summer and Fall quarter, 2007. Department of Mathematics, UCSD.

• "Some developments, improvements, and applications in biomolecular modeling techniques", Dec. 11, 2007, at the Institute of Computational Mathematics and Scientific/Engineering Computations, Beijing.

• "Discrete and Continuum molecular modeling", Dec. 17, 2007, at the Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, China.

• "Toward more efficient and accurate continuum modeling", Dec. 22, 2007, Beijing University of Technology, Beijing.

• Cyberinfrastructure and multiscale modeling approaches , NBCR (National Biomedical Computation Resource) Summer Institute 2006, La Jolla, California, August 7-11 August, 2006, weblink: http://nbcr.net/si/2006/contact.php (Instructor).

• "Electrostatics, density distribution, and diffusion - A continuum modeling frame with realistic spatiotemporal resolution" on March 7, 2007 at the Biophysical Society 51st Annual Meeting . Baltimore, Maryland, MD, March 3-7, 2007.

• "Accelerating computations to order N for electrostatic interactions of biomolecular systems" on Sep. 11, 2006 at the 232nd ACS National Meeting, San Francisco, CA, September 10-14, 2006.

• "Molecular Simulations of Protein Kinase A: Release of ADP from the catalytic subunit of PKA: A MD simulation study" on July 12, 2005 at ICAM Frontiers of Science Symposium: Signal Transduction and Protein Phosphorylation, UC San Diego, CA.

• "A new minimization method for real protein folding prediction," presented on May. 30, 2002 at the Seventh Symposium on Life Science at Home and Abroad, the Academy of military medical sciences, Beijing, China.

• "Dynamics simulation for protein-protein interaction" at Proceedings of Chinese Biomedical Engineering 2001 (CBME), Wuhan, China.

Poster Presentations

• ``Finite element Poisson-Nernst-Planck approach for electrodiffusion and reaction processes in biomolecular systems" (to be attending) on January 4-8, 2008 at the Pacific Symposium on Biocomputing, session ``Multiscale Modeling and Simulation: from Molecules to Cells to Organisms", The Big Island of Hawaii, January 4-8, 2008.

• ``A calculation method of Poisson-Boltzmann forces between solvated macromolecules" on Biophysical Society 50th Annual Meeting, February 18-22, 2006, Salt Lake city, Utah.

• ``Rate constant calculation of ligand binding with solvation force determined by boundary elementary method" on Mar. 13, 2005 at the 229th American Chemical Society National Meeting & Exposition, San Diego, CA

• ``Effect of E230Q to the synergistic binding of ATP and PKI to the catalytic subunit of PKA" on July 30, 2005 at 19th Annual Symposium of The Protein Society: The Integration of the Cellular Protein Machinery: Complexes to Networks, Boston, Massachusetts.

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

"Quantum theory and the philosophy of art", (in Chinese) 1999, (might printed in 2002). (PDF)