A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks.

A, Slepoy; AP, Thompson; SJ, Plimpton

doi:10.1063/1.2919546

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A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks.

Shared by NobleBlocks on May 1, 2008 • 12:00 AM UTC

Authors:

Slepoy A

Thompson AP

Plimpton SJ

Abstract

The time evolution of species concentrations in biochemical reaction networks is often modeled using the stochastic simulation algorithm (SSA) [Gillespie, J. Phys. Chem. 81, 2340 (1977)]. The computational cost of the original SSA scaled linearly with the number of reactions in the network. Gibson a...

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