Hong Li

email:

hongli ~At~ engr -dot- ucsb -dot- edu

address:

Department of Computer Science
University of California at Santa Barbara
Santa Barbara, CA, 93106



About me

I am an Assistant Researcher in Department of Computer Sience, University of California at Santa Barbara, USA, working with Professor Linda Petzold in the Computational Science & Engineering research group.

I received my Ph.D. and M.S. Degree from the Department of Computer Sience, University of California at Santa Barbara, USA, and my B.S. from the Department of Computing Science and Technology , Peking University, China.

Research Interests

Multiscale algorithms and software for biochemical systems
High Performance Stochastic Simulation Methods For Chemically React- ing Systems, including accelerating the performance by sequential algorithms and by parallel on special hardware (General Purpose Graphics Processing Unit, clusters and others) 

My Erdos number is 4, Erdos -> Amnon B. Barak -> Paul E. Saylor -> Linda Petzold -> me
Erdos number calculator

Publications

  • H. Li and L. Petzold: "Efficient Parallelization of Stochastic Simulation Algorithm for Chemically Reacting Systems on the Graphics Processing Unit," Accepted, International Journal of High Performance Computing, 2009.
  • Kolpas, H. Li, Ian Couzin, J. Moehlis and L. Petzold: "Spatial Position and Information Transfer in a Schooling Model," submitted, 2008.
  • H. Li, A. Kolpas, L. Petzold and J. Moehlis: Efficient Parallel Simulation of an Individual-Based Fish Schooling Model on a Graphics Processing Unit," to appear, Grace Hopper Celebration of Women in Computing, 2008.
  • (pdf file)H. Li, A. Kolpas, L. Petzold and J. Moehlis: "Accelerating Simulation of an Individual-Based Fish Schooling Model on a Graphics Processing Unit," NVISION, 2008.
  • (pdf file)H. Li and L. Petzold: "Efficient Parallel Simulation for Stochastic Simulation of Biochemical Systems on the Graphics Processing Unit," 13th SIAM Conference on Parallel Processing for Scientific Computing, Atlanta, Georgia, 2008.
  • H. Li, Y. Cao, L. Petzold and D. Gillespie: "Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems," Biotechnology Progress, 24, 56-61, 2008.
  • H. Li, A. Kolpas, L. Petzold and J. Moehlis: "Parallel Simulation for a Fish Schooling Model on a General-Purpose Graphics Processing Unit," to appear, Concurrency and Computation: Practice and Experience journal, 2007.
  • H. Li and L. Petzold: StochKit : A Stochastic Simulation Toolkit, ICB Army-Industry Collaboration Conference, May, 2006
  • H. Li and L. Petzold: "Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems," Technical Report, 2006.
  • (pdf file)Hong Li, Linda R. Petzold, Stochastic Simulation Toolkit for Chemically Reacting Systems, feedback and dynamics in nature, October, 2006, San Diego, California
  • (pdf file)H. Li and Linda Petzold, "StochKit in a Nutshell - Introduction and Use", http://www.engr.ucsb.edu/~cse/
  • (pdf file)Y. Cao, Andrew Hall, Hong Li and Sotiria Lampoudi, "User's Guide for StochKit", http://www.engr.ucsb.edu/~cse/
  • (pdf file) H. Li, Y. Cao and L. Petzold: "StochKit -- A Stochastic Simulation Toolkit," Harvey Mudd Mathematics Conference on Scientific Computing, Claremont, California, November 2005.
  • Y. Cao, S. Lampoundi, H. Li and L. Petzold: "A Software Package for Discrete Stochastic Simulation of Chemically Reacting Systems," 4th SIAM conference on Computational Science and Engineering, Orlando, Florida, February 2005.
  • (pdf file)Y. Cao, H. Li and L. Petzold: "Efficient Formulation of the Stochastic Simulation Algorithm for Chemically Reacting System," 5th International Conference on Systems Biology (ICSB 2004), Heidelberg, Germany, October 2004.
  • Y. Cao, H. Li and L. R. Petzold: "Efficient Formulation of the Stochastic Simulation Algorithm for Chemically Reacting Systems," Journal of Chemical Physics, 121 (9), 4059-4067, 2004.
  • H. Li, Kevin Sanft, and L. Petzold: "Optimal Static Heap for Discrete Stochastic Simulation of Chemically Reacting Systems," in preparation, 2008.
  • Parent, kid: http://www.gosoude.com
    kid journal: http://www.gosoude.com/category/kidseducate/bjournal/bstorytelling/
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