title: A hierarchical exact accelerated stochastic simulation algorithm.
abstract: A new algorithm, "HiER-leap" (hierarchical exact reaction-leaping), is derived which improves on the computational properties of the ER-leap algorithm for exact accelerated simulation of stochastic chemical kinetics. Unlike ER-leap, HiER-leap utilizes a hierarchical or divide-and-conquer organization of reaction channels into tightly coupled "blocks" and is thereby able to speed up systems with many reaction channels. Like ER-leap, HiER-leap is based on the use of upper and lower bounds on the reaction propensities to define a rejection sampling algorithm with inexpensive early rejection and acceptance steps. But in HiER-leap, large portions of intra-block sampling may be done in parallel. An accept/reject step is used to synchronize across blocks. This method scales well when many reaction channels are present and has desirable asymptotic properties. The algorithm is exact, parallelizable and achieves a significant speedup over the stochastic simulation algorithm and ER-leap on certain problems. This algorithm offers a potentially important step towards efficient in silico modeling of entire organisms.
authors.affiliation: Department of Computer Science, University of California, Irvine, California 92697, USA.
authors.forename: David
authors.initials: D
authors.lastname: Orendorff
authors.forename: Eric
authors.initials: E
authors.lastname: Mjolsness
mesh_terms: D000465:Algorithms; D007700:Kinetics; D008390:Markov Chains; D008956:Models, Chemical; D015203:Reproducibility of Results; D013269:Stochastic Processes