Sat, 05 Jul 2008 03:54:23 BST CiteULike: matthewhflamm ssa http://www.citeulike.org/user/matthewhflamm/tag/ssa CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/matthewhflamm/article/2903017 <i>The Journal of Chemical Physics, Vol. 128, No. 15. (2008)</i><br /><br />View this record in Web of Science Unbiased tau-leap methods for stochastic simulation of chemically reacting systems Zhouyi Xu Xiaodong Cai The Journal of Chemical Physics, Vol. 128, No. 15. (2008) 2008-06-17T19:07:13-00:00 2008 The Journal of Chemical Physics 128 15 AIP ssa tau-leap http://www.citeulike.org/user/matthewhflamm/article/781026 <i>Journal of Physical Chemistry, Vol. 81, No. 25. (15 December 1977), pp. 2340-2361.</i> Exact stochastic simulation of coupled chemical reactions Daniel Gillespie Journal of Physical Chemistry, Vol. 81, No. 25. (15 December 1977), pp. 2340-2361. 2006-07-31T14:43:56-00:00 1977 Journal of Physical Chemistry 81 25 2340 2361 ssa http://www.citeulike.org/user/matthewhflamm/article/782029 <i>Journal of Computational Physics, Vol. 22, No. 4. (December 1976), pp. 403-434.</i><br /><br />An exact method is presented for numerically calculating, within the framework of the stochastic formulation of chemical kinetics, the time evolution of any spatially homogeneous mixture of molecular species which interreact through a specified set of coupled chemical reaction channels. The method is a compact, computer-oriented, Monte Carlo simulation procedure. It should be particularly useful for modeling the transient behavior of well-mixed gas-phase systems in which many molecular species participate in many highly coupled chemical reactions. For “ordinary” chemical systems in which fluctuations and correlations play no significant role, the method stands as an alternative to the traditional procedure of numerically solving the deterministic reaction rate equations. For nonlinear systems near chemical instabilities, where fluctuations and correlations may invalidate the deterministic equations, the method constitutes an efficient way of numerically examining the predictions of the stochastic master equation. Although fully equivalent to the spatially homogeneous master equation, the numerical simulation algorithm presented here is more directly based on a newly defined entity called “the reaction probability density function.” The purpose of this article is to describe the mechanics of the simulation algorithm, and to establish in a rigorous, a priori manner its physical and mathematical validity; numerical applications to specific chemical systems will be presented in subsequent publications. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions Daniel Gillespie doi:10.1016/0021-9991(76)90041-3 Journal of Computational Physics, Vol. 22, No. 4. (December 1976), pp. 403-434. 2006-08-01T23:42:26-00:00 1976 Journal of Computational Physics 22 4 403 434 ssa http://www.citeulike.org/user/matthewhflamm/article/1775523 <i>The Journal of Chemical Physics, Vol. 115, No. 4. (2001), pp. 1716-1733.</i><br /><br />The stochastic simulation algorithm (SSA) is an essentially exact procedure for numerically simulating the time evolution of a well-stirred chemically reacting system. Despite recent major improvements in the efficiency of the SSA, its drawback remains the great amount of computer time that is often required to simulate a desired amount of system time. Presented here is the "-leap" method, an approximate procedure that in some circumstances can produce significant gains in simulation speed with acceptable losses in accuracy. Some primitive strategies for control parameter selection and error mitigation for the -leap method are described, and simulation results for two simple model systems are exhibited. With further refinement, the -leap method should provide a viable way of segueing from the exact SSA to the approximate chemical Langevin equation, and thence to the conventional deterministic reaction rate equation, as the system size becomes larger. Approximate accelerated stochastic simulation of chemically reacting systems Daniel Gillespie doi:10.1063/1.1378322 The Journal of Chemical Physics, Vol. 115, No. 4. (2001), pp. 1716-1733. 2007-10-16T16:59:42-00:00 2001 The Journal of Chemical Physics 115 4 1716 1733 AIP ssa tau-leap http://www.citeulike.org/user/matthewhflamm/article/2798716 <i>The Journal of Chemical Physics, Vol. 119, No. 16. (2003), pp. 8229-8234.</i><br /><br />View This Record in Scopus Improved leap-size selection for accelerated stochastic simulation Daniel Gillespie Linda Petzold The Journal of Chemical Physics, Vol. 119, No. 16. (2003), pp. 8229-8234. 2008-05-14T13:29:59-00:00 2003 The Journal of Chemical Physics 119 16 8229 8234 AIP ssa tau-leap http://www.citeulike.org/user/matthewhflamm/article/782020 <i>J. Phys. Chem. A, Vol. 104, No. 9. (9 March 2000), pp. 1876-1889.</i> Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels MA Gibson J Bruck doi:10.1021/jp993732q J. Phys. Chem. A, Vol. 104, No. 9. (9 March 2000), pp. 1876-1889. 2006-08-01T23:16:10-00:00 2000 J. Phys. Chem. A 104 9 1876 1889 ssa http://www.citeulike.org/user/matthewhflamm/article/2552523 <i>The Journal of Chemical Physics, Vol. 127, No. 9. (2007)</i><br /><br />View this record in Web of Science Two classes of quasi-steady-state model reductions for stochastic kinetics Ethan Mastny Eric Haseltine James Rawlings The Journal of Chemical Physics, Vol. 127, No. 9. (2007) 2008-03-18T19:10:09-00:00 2007 The Journal of Chemical Physics 127 9 AIP qssa ssa