COAST: Controllable approximative stochastic reaction algorithm.
We present an approximative algorithm for stochastic simulations of chemical reaction systems, called COAST, based on three different modeling levels: for small numbers of particles an exact stochastic model; for intermediate numbers an approximative, but computationally more efficient stochastic model based on discrete Gaussian distributions; and for large numbers the deterministic reaction kinetics. In every simulation time step, the subdivision of the reaction channels into the three different modeling levels is done automatically, where all approximations applied can be controlled by a single error parameter for which an appropriate value can easily be found. Test simulations show that the results of COAST simulations agree well with the outcomes of exact algorithms; however, the asymptotic run times of COAST are asymptotically proportional to smaller powers of the particle numbers than exact algorithms.
Wagner
Holger
H
FSPM, Bielefeld University, Postfach 100131, 33501 Bielefeld, Germany.
Möller
Mark
M
Prank
Klaus
K
D000465:Algorithms; D003198:Computer Simulation; D003205:Computing Methodologies; D008954:Models, Biological; D008962:Models, Theoretical; D013269:Stochastic Processes; D013997:Time Factors