Yang Cao 

Department of Computer Science 
Phone: (805)893-5728 (O)
University of California
Fax:    (805)893-5435 
Santa Barbara
CA 93106
Note: I have moved to Virginia Tech!
Detailed CV

Education:
 


Research:


Publications:
  1. (pdf file) Y. Cao, D. Gillespie and L. Petzold, Efficient Stepsize Selection for the Tau-Leaping Method, to appear, J. Chem. Phys. 2006.
  2. (pdf file) Y. Cao and L. Petzold, Accuracy Limitations and the Measurement of Errors in the Stochastic Simulation of Chemically Reacting Systems,  Journal of Computational Physics,  Volume 212, Issue 1 , Pages 6-24, 10 February 2006.
  3. (pdf file) Y. Cao , D. Gillespie and L. Petzold, Avoiding Negative Populations in Explicit Tau Leaping, J. Chem. Phys. 123, 054104 (2005).
  4. (pdf file) Y. Cao, D. Gillespie and L. Petzold, Accelerated Stochastic Simulation of the Stiff Enzyme-Substrate Reaction, J. Chem. Phys., 123(14), 144917, 08 Oct 2005.
  5. (pdf file) Y. Cao and L. Petzold, Trapezoidal tau-lepaing formula for the stochastic simulation of biochemical systems, Proceedings of Foundations of Systems Biology in Engineering (FOSBE 2005), Pages 149-152.
  6. (pdf file) Y. Cao, D. Gillespie and L. Petzold, Multiscale Stochastic Simulation Algorithm with Stochastic Partial Equilibrium Assumption for Chemically Reacting Systems, J. Comput. Phys., Volume 206, Issue 2, 1 July 2005, Pages 395-411. (Journal Link)
  7. (pdf file) R. Gunawan, Y. Cao, L. Petzold and F. Doyle III, Sensitivity analysis of discrete stochastic systems, Biophys. J. 88: 2530-2540, 2005.
  8. (pdf file) M. Rathinam,  L. Petzold, Y. Cao, D. Gillespie, Consistency and stability of tau leaping schemes for chemical reaction systems, SIAM Multiscale Modeling and Simulation, vol 4, 867-895, 2005. 
  9. (pdf file) Y. Cao, D. Gillespie and L. Petzold, The slow-scale stochastic simulation algorithm, J. Chem. Phys., 122(1), 014116, 2005.
  10. (pdf file) Y. Cao, L. Petzold, M. Rathinam, D. Gillespie, The numerical stability of leaping methods for stochastic simulation of chemically reacting systems, J. Chem. Phys. 121(24), 12169-12178, 2004. 
  11. (pdf file) Y. Cao, H. Li and L. Petzold, Efficient formulation of the stochastic simulation algorithm for chemically reacting system, J. Chem. Phys. 121(9), pp. 4059-4067, 2004. 
  12. (pdf file)Yang Cao and Linda Petzold,  A Posteriori Error Estimation and Global Error Control for Ordinary Differential Equations by the Adjoint Method, SIAM J. Scientific Computing, 26(2), 359-374, 2004.  
  13. Yang Cao and Linda Petzold, An error estimate for matrix equations(PostScript file), Applied Numerical Mathematics, 50(3-4),  395-407, 2004.  
  14. (pdf file) M. Rathinam, Y. Cao, L. Petzold, D. Gillespie, Stiffness in Stochastic Chemically Reacting Systems: The Implicit Tau-Leaping Method, J. Chemical Physics, 119(24), p12784-94, 2003.
  15. (pdf file) Adaptive Numerical Methods for Sensitivity Analysis of Differential-Algebraic Equations and Partial Differential Equations L. Petzold, Y. Cao, S. Li and R. Serban, Proceedings, Workshop on Modelling and Simulation in Chemical Engineering, Coimbra, Portugal, 2003. 
  16. Yang Cao and Linda Petzold, A subspace error estimate for linear systems(PS file), SIAM J. Mat. Anal. Appl., 24(3), 787-801, 2003.  
  17. (pdf file)Yang Cao, Shengtai Li, Linda Petzold and Radu Serban, Adjoint sensitivity analysis for differential-algebraic equations: the adjoint DAE system and its numerical solution, SIAM J. Sci. Comput. 24(3), 1076--1089, 2002, 
  18. (pdf file)Yang Cao, Shengtai Li and Linda Petzold, Adjoint Sensitivity Analysis for Differential-Algebraic Equations: Algorithms and Software, J. Comp. Appl. Math. 149 (1), 171--191, 2002.                 
  19. Sensitivity Analysis and Design Optimization of Differential-Algebraic Equation Systems(PS file). L. Petzold, R. Serban, S. Li, S. Raha and Y. Cao, Proc. NATO Advanced Research Workshop on Computational Aspects of Nonlinear Structural Systems with Large Rigid Body Motion, 2001.
  20. Yang Cao, Qing-Yang Li, Multistep discretization of Index 3 DAEs. Journal of Computational Mathematics, vol.18, (no.3), ICMSEC Chinese Acd. Sci, May 2000. p.325-36.  
  21. Yang Cao, Qingyang Li, Predictor-corrector formula for solving index-2 differential-algebraic equations. Mathematica Numerica Sinica, vol.21, (no.1), Math. Numerica Sinica, China, 1999. p.65-74. 
  22. Yang Cao and Qingyang Li, Highest order multistep formula for solving index-2 differential algebraic equations, BIT, vol 38, no.4, 1998  
  23. Yang Cao and Qingyang Li, A-stable explicit nonlinear Runge-Kutta methods, Tsinghua Science & Technoloty, 1998  
  24. Yang Cao and Qingyang Li, Nonlinear Runge-Kutta methods for solving differential-algebraic equations. Chinese J. Numer. Math. Appl. 20, 1998, p.75--85.

Award:
  • Parsons Foundation Fellowship in 1998-1999

My Homepage at VT