Journal
MULTISCALE MODELING & SIMULATION
Volume 6, Issue 4, Pages 1146-1168Publisher
SIAM PUBLICATIONS
DOI: 10.1137/060678154
Keywords
chemical master equation; stochastic simulation algorithm; systems biology
Funding
- Australian Research Council (ARC)
Ask authors/readers for more resources
We present numerical methods for both the direct solution and simulation of the chemical master equation (CME), and, compared to popular methods in current use, such as the Gillespie stochastic simulation algorithm (SSA) and tau-Leap approximations, this new approach has the advantage of being able to detect when the system has settled down to equilibrium. This improved performance is due to the incorporation of information from the associated CME, a valuable complementary approach to the SSA that has often been felt to be too computationally inefficient. Hybrid methods, that combine these complementary approaches and so are able to detect equilibrium while maintaining the efficiency of the leap methods, are also presented. Amongst CME-solvers the recently suggested finite state projection algorithm is especially well suited to this purpose and has been adapted here for the task, leading to a type of exact tau-Leap. It is also observed that a CME-solver is often more efficient than an SSA or even a tau-Leap approach for computing moments of the solution such as the mean and variance. These techniques are demonstrated on a test suite of five biologically inspired models, namely, stochastic models of the genetic toggle, receptor oligomerization, the Schlogl reactions, Goutsias' model of regulated gene transcription, and a decaying-dimerizing reaction set. For the gene toggle it is observed that important experimentally measurable traits such as the percentage of cells that undergo so-called switching may also be more efficiently approximated via a CME-based approach.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available