An efficient method for computing steady state solutions with Gillespie's direct method
- Creators
- Mauch, S.
- Stalzer, M.
Abstract
Gillespie's direct method is a stochastic simulation algorithm that may be used to calculate the steady state solution of a chemically reacting system. Recently the all possible states method was introduced as a way of accelerating the convergence of the simulations. We demonstrate that while the all possible states (APS) method does reduce the number of required trajectories, it is actually much slower than the original algorithm for most problems. We introduce the elapsed time method, which reformulates the process of recording the species populations. The resulting algorithm yields the same results as the original method, but is more efficient, particularly for large models. In implementing the elapsed time method, we present robust methods for recording statistics and empirical probability distributions. We demonstrate how to use the histogram distance to estimate the error in steady state solutions.
Additional Information
© 2010 American Institute of Physics. Received 8 May 2010; accepted 25 August 2010; published online 12 October 2010. This project was supported by Grant No. R01EB007511 from the National Institute of Biomedical Imaging and Bioengineering. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of Biomedical Imaging and Bioengineering or the National Institutes of Health. The authors gratefully acknowledge Dan Gillespie, Linda Petzold and her research group at UCSB, Michael Hucka, and John McCorquodale for many useful conversations and comments.Attached Files
Published - Mauch2010p11665The_Journal_of_chemical_physics.pdf
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Additional details
- Eprint ID
- 20585
- Resolver ID
- CaltechAUTHORS:20101028-112349899
- R01EB007511
- National Institute of Biomedical Imaging and Bioengineering
- Created
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2010-11-19Created from EPrint's datestamp field
- Updated
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2021-11-09Created from EPrint's last_modified field