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.
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., D. Gillespie, and L. Petzold, "Efficient Stepsize Selection for the Tau-Leaping Method", J. Chem. Phys., 2006.
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.
Cao, Y., D. Gillespie, and L. Petzold, "The slow-scale stochastic simulation algorithm", J. Chem. Phys., 2005.
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.
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.
Rathinam, M., L. Petzold, Y. Cao, and D. Gillespie, "Sti ness in stochastic chemically reacting systems: The implicit tau-leaping method", J. Chem. Phys., 2003.