Curriculum Vitae For Benzhuo Lu

Benzhuo Lu

   Professor, Academy of Mathematics and Systems Science, Chinese Academy of Sciences.

Affiliation:

State Key Laboratory of Scientific/Engineering Computing

Institute of Computational Mathematics and Scientific/Engineering Computing,
National Center for Mathematics and Interdisciplinary Sciences (Mathematics and Biomedical division)

OFFICE ADDRESS

Academy of Mathematics and Systems Science
Chinese Academy of Sciences
Beijing 100190, China
Tel:0086-10-82541904
Fax: 0086-10-62542285
email:
http://lsec.cc.ac.cn/~lubz， and academic webpage: www.continuummodel.org

 

WORK EXPERIENCE

    Professor, Institute of Computational Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 2008.10 - present

    Research associate, Howard Hughes Medical Institute, University of California at San Diego, 2006 - 2008.

    Postdoc researcher, Chem. & Biochem. Dept of University of California at San Diego, 2003 - 2006.

    Visiting Student, the International Center for Theoretical Physics (ICTP), Trieste, Italy, 1999.6-1999.9

    Instructor, Yunnan Agriculture University, Kunming, China, 1993-1997.

EDUCATION

1997 - 2002, PhD in Biochemistry and Molecular Biology. University of Science and Technology of China, Hefei, China
1989 - 1993, B.S. in Physics. East China Normal University, Shanghai, China

 

RESEARCH

Biophysical/chemical Computation, modeling  and simulation. Current focuses are on continuum modeling

of biomolecular system/processes and solvation phenomena, numerical methods and software development,

and molecular dynamics simulation studies of proteins.


PROFESSIONAL ACTIVITIES

Editorial board/Editorial Advisory Board:

Commun. in Comput. Phys.

Computational Science & Discovery

Molecular Based Mathematical Biology

Journal of Applied Mathematics

数值计算与计算机应用 (J Numerical Methods and Computer Applications)

 


Reviews:
For journals: Nature Communications, Plos Comput Biology, Journal of Computational Physics, Biophysical Journal, Bioinformatics, Communications in Mathematical Sciences, Soft Matter, FEBS, Nonlinear Analysis Series B: Real World Applications, International J. Numerical Methods in Biomedical Engineering, Computational Science & Discovery, Physical Chemistry Chemical Physics, Journal of Chem. Phys., Communications in Computational Physics, Journal of Phys. Chem. A, B., J Chem Theory and Computation, J. Comput. Chem., Comput Phys. Commun, J. Neurophysiology, Scientific Reports, Molecular Based Mathematical Biology, Interdisciplinary Sciences- Computational Life Sciences，Chinese Science Bulletin, Current Medicinal Chemistry, and some other journals.

Reviewer of Mathematical Reviews/MathSciNet

For funding proposals: French National Research Agency (ANR) funding, NSFC and so on.

Member:

the American Chemical Society, Biophysical Society, and Protein Society, Beijing Society of Computational Mathematics, Chinese Computer Federation，CSIAM （China Society for Industrial and Applied Mathematics）...

Conferences/Symposiums/Sessions Organized

Program committee Co-Chair and Conference Co-Chair, International Workshop on Continuum Modeling of Biomolecules (WCMB), September 14-16, 2009, Beijing, China.

Advisory board, the 2nd Annual World Bio-Soft Forum (Bio-Soft 2010)，June 23-25，2010, Dalian，China

Conference Co-organizer, Workshop and Summer School on Coulomb Many-body Systems, Summer School: June 6-10, 2012, Workshop:June 12-14, 2012, Shanghai, China

Conference Co-organizer，Workshop on Meshing and Visualization in Scientific Computing，December 27-28，2012，Beijing

 

TEACHING EXPERIENCE
Taught courses:

general physics and calculus (for undergraduate students)

Biomolecular modeling and Computation (for Ph.D graduate students)

　

TALKS ON CONFERENCE, WORKSHOP, OR SEMINAR

 

  1. August 2014, 248th ACS National Meeting, San Francisco, Symposium "Modeling the effects of water and solvation in biological systems: Developments, August 10-14, 2014, US

  2. July 2014, Transport of Ionic Particles in Biological Environments, Workshop 4, University of Toronto campus in Toronto, Ontario, July 28-August 1, 2014, Canada

  3. August 2014, minisyposium of the SIAM Conference on the Life Sciences, August 4 - 7, 2014, Charlotte, NC, US

  4. July 2014, Protein Electrostatics – satellite meeting of EBEC 2014, 8-11 July, Lisbon, Portugal.

  5. March 2014, The 247th ACS National Meeting & Exposition, Dallas, ENFL: Division of Energy and Fuels, SESSION: Electrolyte Systems and Interfacial Processes in Energy Storage and Conversion, March 16-20, 2014, US

  6. 2013 复杂体系计算统计力学研讨会, 2013 年10月25－27日，复旦大学，China
  7. Oct. 24, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 10/24/2013，Shanghai
  8. Oct. 22, 第十二届全国计算（机）化学学术会议，2013年10月21-24日,苏州大学，中国
  9. Oct. 19, 2013, 2013第十二届全国高校计算数学年会，2013年10月19-23日，湖南长沙
  10. Oct. 14, 2013，Beijing International Center for Mathematical Research (BICMR)，（北京国际数学研究中心），Beijing, China
  11. Sept. 28, The 3rd Annual World Congress of Nano-S&T 2013, September 26-28, 2013, Xi'an, China
  12. Sept. 24，2013 Northeast Asian Symposium on High Performance Computing Methods Modeling （2013年东北亚高性能计算的方法和建模学术研讨会），Sept 22－25，2013，Chengdu，China
  13. July 17, 2013, Institute of High Energy Physics， CAS （科学院高能物理研究所），Beijing, China
  14. June 7, 2013， Univ of Wisconsin, Milwaukee, Math Dept，Milwaukee，US
  15. “Simulation of ion channel: PDE model, numerical calculation, and software development”，colloquium, Feb. 25, 2013，Alabama Univ., Math Dept，Alabama，US
  16. Advanced Molecular Simulation Methods in the Physical Sciences , Jun 10 – Jul 5, 2013, Kavli Institute for Theoretical Physics China (KITPC), Beijing, China
  17. 纳米技术与生物信息学前沿技术学术研讨会，May 10-11，2013, 北京工业大学，中国
  18. Workshop on Mathematical Modeling of Molecular Biology, May 28, 2013, Soochow University, Suzhou, China
  19. “Biomolecular surface/volume meshing and visualization for mathematical modeling”，CTW: Mathematical Challenges in Biomolecular/Biomedical Imaging and Visualization, February 18-22, 2013, Mathematical Biosciences Institute, The Ohio State University, Columbus, OH, US
  20. Workshop on Meshing and Visualization in Scientific Computing (面向大规模科学计算的网格生成和可视化技术研讨会)，国家数学与交叉科学中心（National Center for Mathematics and Interdisciplinary Sciences(NCMIS), CAS），中国科学院计算数学所（The Institute of Computational Mathematics and Scientific/Engineering Computing，CAS），2012年10月27-28日, Beijing
  21. Dec. 24, 2012，Hunan Normal Univerty. Physics Dept，Hunan，China
  22. Dec. 6, 2012，"ion channel simulation: PDE models, numerical computation, and software development"，Beijing University of Technolegy. Coll of Life Science，Beijing，China
  23. Nov. 15, 2012，Yunnan Normal Univerty. Math Dept，Kunming，China
  24. Nov. 13, 2012，Chongqing Univ. Math Dept，Chongqing，China
  25. Nov. 9, 2012，Tsinghua Univ. Math Dept，Beijing，China
  26. Workshop on Computational Statistical Mechanics of Complex Systems（复杂体系计算统计力学研讨会），2012 年10月26－31日，中国科大，合肥，China
  27. 华北-西南地区计算与应用数学交流会，北京大学，北京，2012年9月28-29
  28. “分子连续模型中的一些问题”，优化与应用研究中心“数学与生物交叉研讨会”, 科学院数学与系统科学研究院，北京，2012年5月7-8日
  29. 244th ACS National Meeting, Philadelphia, PA-COMP-Sessions, Program: Continuum Solvation Modeling in Biological Systems: Developments and Applications, August 19-23, 2012, Philadelphia, Pennsylvania, US
  30. Workshop and Summer School on Coulomb Many-body Systems, Summer School: June 6-10, 2012, Workshop:June 12-14, 2012, Shanghai, China?
  31. 北航—中科院数学院学科交叉研讨会, 3月31日—4月1日, 2012, 怀柔，北京
  32. “求解生物分子静电PB方程的边界元方法及其加速”，稠密矩阵方程的快速计算方法研讨会,河海大学工程与科学数值模拟软件中心, Nanjing, China，10.8, 2011
  33. “Modeling non-uniform particle size effects in electro-diffusion framework”，Minisymposium on Mathematics in Materials Science, National Center for Mathematics and Interdisciplinary Sciences, Beijing, China，9.19, 2011
  34. May 29, 2011, School of Physics and Technology, Wuhan Univ. Wuhan, China
  35. May 2, 2011, Department of Mathematical Sciences, Delaware State Univesity, Dover, USA
  36. CTW: Modeling and computation of biomolecular structure and dynamics, April 25-29, 2011, Mathematical Biosciences Institute, The Ohio State University, USA
  37. Joint symposium of National Center for Mathematical and Biomedical Interdisciplinary Research --- CAS-Max Planck Partner Institute for Computational Biology, Dec. 28-30, 2010，Shanghai, China
  38. Zhiyuan School, Shanghai Jiaotong University, 12/17/2010，Shanghai, China
  39. “Model and computations of ionic size effects in biomolecular solution”, Symposium of statistical physics and complex systems, organized by the Institute of Theoretical Physics, Dec. 5-8, 2010, Beijing
  40. Soochow University, System biology Research Center, 11/18/2010，Suzhou, China
  41. The 2nd Annual International Conference on Computational and Systems Biology (ICCSB2010), Oct. 22-24, 2010, Hangzhou, China
  42. The 2nd Annual World Bio-Soft Forum (Bio-Soft 2010)，June 23-25，2010, Dalian，China
  43. "Practice-driven mathematics—some examples in molecular modeling"，Yong investigator Association Seminar，Academy of Mathematics and System Sciences, Chinese Academy of Sciences, May 28, 2010, Beijing
  44. "Poisson-Boltzmann electrostatic calculations", Soochow University，4/7/2010，Suzhou, China

  45. International Workshop on Continuum Modeling of Biomolecules, Institute of Computational Mathematics and Scientific/Engineering Computing, Sep. 14-17, 2009, Beijing Workshop on "Frontiers in Computational and Applied Mathematics", August 9-10, 2009, Tsinghua University, Beijing. August 9, 2009.

  46. Continuum modeling of electrodiffusion around single molecule, KITPC Workshop on "Dynamics and Biomolecular Machinery", Jul 29-Aug 10, 2009, Kavli Institute for Theoretical Physics China at the Chinese Academy of Sciences, July 29, 2009.

  47. 2009 SIAM Annual Meeting, July 6-10, Denver, Colorado, July 10, 2009.

  48. “Free energy calculation methods in Molecular modeling”，Beijing Institute of Genomics, Chinese Academy of Science, Beijing, China. May 8, 2009.

  49. School of Mathematical Sciences, Peking University, Beijing, China. March 17, 2009.

  50. Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing, China. Dec. 15, 2008.

  51. Lecture series (I, II, III), Institute of Computational Mathematics, Chinese Academy of Sciences,Beijing, China. Dec. 8, 11, 17, 2008.

  52. "Modelling of Electrostatics and Diffusion Processes in Biological Systems", Frontiers in Science (FIS) program -- Integrated Physics, Biology, Chemistry, Mathematics and Computer Science, a CTBP-CSUSM Seminar Series, California State University San Marcos, Sept. 25, 2008.

  53. "Fully-continuum diffusion -- the Poisson-Nernst-Planck model and some extensions" at the 2008 CTBP Summer School, Coarse-Grained Physical Modeling of Biological Systems: Advanced Theory and Methods, San Diego, CA, August 11-15, 2008.

  54. "Continuum modeling of electrodiffusion: from equilibrium to nonequilibrium states"，Dept. of Molecular Biology & Biochemistry, University of California at Irvine, 4/25/08.

  55. Informal Seminars on Mathematics and Biochemistry-Biophysics, "Boundary integral methods for electrostatics in biomolecules. Part I: An overview", 4/8/08,

  56.  Spring quarter, 2008; And "Electrodiffusion", 10/2/07, Summer and Fall quarter, 2007. Department of Mathematics, UCSD.　

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

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

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

  60. 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).

  61. "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.

  62. "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.

  63. "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.

  64. "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.

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

 

　

Poster Presentations

  1. Integral Equation Methods, Fast Algorithms and Applications, IMA Hot Topics Workshop, August 2-5, 2010,Minneapolis, US
  2. "An adaptive fast multipole algorithm for electrostatic interactions in biomolecular systems" on Dec. 8-12, 2008 at Institute for Mathematics and Its Applications (IMA) Annual Program Year Workshop: Solvation, Minnesota.
  3. "Solutions to a Model Poisson-Nernst-Planck system and the Determination of Reaction Rates”on Dec. 8-12, 2008 at Institute for Mathematics and Its Applications (IMA) Annual Program Year Workshop: Solvation, Minnesota.
  4. ``Finite element Poisson-Nernst-Planck approach for electrodiffusion and reaction processes in biomolecular systems" 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.
  5. ``A calculation method of Poisson-Boltzmann forces between solvated macromolecules" on Biophysical Society 50th Annual Meeting, February 18-22, 2006, Salt Lake city, Utah.
  6. 　``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
  7. 　``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.