Biblio

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2009
Gillespie, D., Y. Cao, K. Sanft, and L. Petzold, "The subtle business of model reduction for stochastic chemical kinetics", J. Chem. Phys. , 2009.
2008
Li, H., Y. Cao, L. Petzold, and D. Gillespie, "Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems", Biotechnology Progress, vol. 24, no. 1, 2008.
Cao, Y., and L. Petzold, "Slow Scale Tau-leaping Method", Computer Methods in Applied Mechanics and Engineering, 2008.
2007
Cao, Y., D. Gillespie, and L. Petzold, "The adaptive explicit-implicit tau-leaping method with automatic tau selection", J. Chem. Phys., 2007.
2006
Cao, Y., L. Petzold, and D. Gillespie, "Adaptive tau-leaping method for biochemical systems", minisymposium talk in SIAM Annual Meeting 2006, Boston, Massachusetts, July, 2006.
Cao, Y., and L. Petzold, "Accuracy Limitations and the Measurement of Errors in the Stochastic Simulation of Chemically Reacting Systems", J. Comput. Phys., 2006.
Cao, Y., D. Gillespie, and L. Petzold, "Efficient Stepsize Selection for the Tau-Leaping Method", J. Chem. Phys., 2006.
Petzold, L., S. T. Li, Y. Cao, and R. Serban, "Sensitivity analysis of di erential-algebraic equations and partial di erential equations", COMPUTERS & CHEMICAL ENGINEERING, 2006.
2005
Cao, Y., A. Hall, L. H, and L. Petzold, "StochKit, a new stochastic simulation toolkit", Sixth International Conference on Systems Biology, Boston, Massachusetts, October, 2005.
Cao, Y., and L. Petzold, "Measurement of error in stochastic simulation: when the mean and the variance are not enough", 4th SIAM conference on Computational Science and Engineering, February, 2005.
Cao, Y., S. Lampoudi, H. Li, and L. Petzold, "A software package for discrete stochastic simulation of chemically reacting systems", 4th SIAM conference on Computational Science and Engineering, February, 2005.
Cao, Y., and L. Petzold, "Trapezoidal tau-lepaing formula for the stochastic simulation of biochemical systems", Proceedings of Foundations of Systems Biology in Engineering (FOSBE 2005), pp. pp 149- 152, August, 2005.
Cao, Y., D. Gillespie, and L. Petzold, "Accelerated Stochastic Simulation of the Sti Enzyme-Substrate Reaction", J. Chem. Phys., 2005.
Cao, Y., D. Gillespie, and L. Petzold, "Avoiding Negative Populations in Explicit Tau Leaping", J. Chem. Phys., 2005.
Rathinam, M., L. Petzold, Y. Cao, and D. Gillespie, "Consistency and stability of tau leaping schemes for chemical reaction systems", SIAM Multiscale Modeling and Simulation, 2005.
Cao, Y., L. Petzold, and D. Gillespie, "Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems", J. Comput. Phys., 2005.
Gunawan, R., Y. Cao, L. Petzold, and D. F. III, "Sensitivity analysis of discrete stochastic systems", Biophys. J., 2005.
Cao, Y., D. Gillespie, and L. Petzold, "The slow-scale stochastic simulation algorithm", J. Chem. Phys., 2005.
2004
Cao, Y., H. Li, and L. Petzold, "Efficient formulation of the stochastic simulation algorithm for chemically reacting systems", the 5th International Conference on Systems Biology, October, 2004.
Gunawan, R., Y. Cao, S. Lampoudi, L. Petzold, and D. F. III, "Stochastic sensitivity analysis of a circadian gene network", the 5th International Conference on Systems Biology, Heidelberg, Germany, October, 2004.
Cao, Y., H. Li, and L. Petzold, "Efficient formulation of the stochastic simulation algorithm for chemically reacting systems", J. Chem. Phys., 2004.
Cao, Y., and L. Petzold, "An error estimate for matrix equations", Applied Numerical Mathematics, 2004.
Cao, Y., L. Petzold, M. Rathinam, and D. Gillespie, "The numerical stability of leaping methods for stochastic simulation of chemically reacting systems", J. Chem. Phys., 2004.
Cao, Y., and L. Petzold, "A posteriori error estimation and global error control for rrdinary di erential equations by the adjoint method", SIAM J. Scienti c Computing, 2004.
2003
Cao, Y., L. Petzold, and D. Gillespie, "Towards the multiscale simulation of biochemical systems", the workshop of U.S. Army Research Oce, Institute for Collaborative Biotechnologies site visit, UCSB, July, 2003.