Time dependent solution for acceleration of tau-leaping

The tau-leaping method is often effective for speeding up discrete stochastic simulation of chemically reacting systems. However, when fast reactions are involved, the speed-up for this method can be quite limited. One way to address this is to apply a stochastic quasi-steady state assumption. However we must be careful when using this assumption. If the fast subsystem cannot reach a steady distribution fast enough, the quasi-steady-state assumption will propagate error into the simulation. To avoid these errors, we propose to use the time dependent solution rather than the quasi-steady-state. Generally speaking, the time dependent solution is not easy to derive for an arbitrary network. However, for some common motifs we do have time dependent solutions. We derive the time dependent solutions for these motifs, and then show how they can be used with tau-leaping to achieve substantial speed-ups, including for a realistic model of blood coagulation. Although the method is complicated, we have automated it.

J. Fu, S. Wu, and L. R. Petzold
Journal of Computational Physics
Volume: 235
Pages: 446–457
Date: February, 2013
ICB Affiliated Authors: Linda R Petzold