Multiscale Modeling and Computation

Contact: Yang Cao

2008
Wang, P., R. Randhawa, C. A. Shaffer, Y. Cao, and W. T. Baumann, "Converting Macromolecular Regulatory Models from Deterministic to Stochastic Formulation", Proceedings of High Performance Computing and Simulation 2008 (HPCS 2008), pp. 385–392, April, 2008.
Cao, Y., and L. Petzold, "Slow Scale Tau-leaping Method", Computer Methods in Applied Mechanics and Engineering, 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.
Cao, Y., and Z. Liu, "The detailed comparison between StochSim and SSA", The first q-bio conference on cellular information processing, Santa Fe, New Mexico, August, 2007.
Cao, Y., "The adaptive explicit-implicit tau-leap method", SCICADE (International Conference on SCIenti c Computation And Di erential Equations), Santa Malo, France, July, 2007.
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.
Cao, Y., D. Gillespie, and L. Petzold, "Efficient Stepsize Selection for the Tau-Leaping Method", J. Chem. Phys., 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.
2005
Cao, Y., D. Gillespie, and L. Petzold, "Avoiding Negative Populations in Explicit Tau Leaping", J. Chem. Phys., 2005.
Cao, Y., D. Gillespie, and L. Petzold, "Accelerated Stochastic Simulation of the Sti Enzyme-Substrate Reaction", J. Chem. Phys., 2005.
Gunawan, R., Y. Cao, L. Petzold, and D. F. III, "Sensitivity analysis of discrete stochastic systems", Biophys. J., 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.
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., 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, "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., 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.
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., 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, "A posteriori error estimation and global error control for rrdinary di erential equations by the adjoint method", SIAM J. Scienti c Computing, 2004.
Cao, Y., and L. Petzold, "An error estimate for matrix equations", Applied Numerical Mathematics, 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.
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.
Cao, Y., and L. Petzold, "A subspace error estimate for linear systems", SIAM J. Mat. Anal. Appl., 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.
Petzold, L., Y. Cao, S. Li, and R. Serban, "Adaptive numerical methods for sensitivity analysis of di erential-algebraic equations and partial di erential equations", Proceedings,Workshop on Modeling and Simulation in Chemical Engineering, Coimbra, Portugal, 2003.
2002
Cao, Y., S. Li, L. Petzold, and R. Serban, "Adjoint sensitivity analysis for di erential-algebraic equations: the adjoint DAE system and its numerical solution", SIAM J. Sci. Comput., 2002.
Cao, Y., S. Li, and L. Petzold, "Adjoint sensitivity analysis for di erential-algebraic equations: algorithms and software", J. Comp. Appl. Math., 2002.
2001
Petzold, L., R. Serban, S. Li, S. Raha, and Y. Cao, "sensitivity analysis and design optimization of di erential-algebraic equation systems", NATO Advanced Research Workshop on Computational Aspects of Nonlinear Structural Systems with Large Rigid Body Motion, 2001.
2000
Cao, Y., and Q. Li, "Multistep discretization of index 3 DAEs", ICMSEC Chinese Acd. Sci, 2000.
Cao, Y., S. Li, and L. Petzold, "Adjoint sensitivity analysis for DAE systems", NSF-KDI/IGPP W orkshop 2000 on Accurate Simulation and Modelling of Physical Systems, San Diego, 2000.
1999
Cao, Y., and Q. Li, "Predictor-corrector formula for solving index-2 di erential-algebraic equations", Mathematica Numerica Sinica,, 1999.
1998
Cao, Y., and Q. Li, "A-stable explicit nonlinear Runge-Kutta methods", Tsinghua Science & Technoloty, 1998.
Cao, Y., and Q. Li, "Nonlinear Runge-Kutta methods for solving di erential-algebraic equations", Chinese J. Numer. Math., April, 1998.