Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels

TL;DR: The Next Reaction Method is presented, an exact algorithm to simulate coupled chemical reactions that uses only a single random number per simulation event, and is also efficient.

Abstract: There are two fundamental ways to view coupled systems of chemical equations:  as continuous, represented by differential equations whose variables are concentrations, or as discrete, represented by stochastic processes whose variables are numbers of molecules. Although the former is by far more common, systems with very small numbers of molecules are important in some applications (e.g., in small biological cells or in surface processes). In both views, most complicated systems with multiple reaction channels and multiple chemical species cannot be solved analytically. There are exact numerical simulation methods to simulate trajectories of discrete, stochastic systems, (methods that are rigorously equivalent to the Master Equation approach) but these do not scale well to systems with many reaction pathways. This paper presents the Next Reaction Method, an exact algorithm to simulate coupled chemical reactions that is also efficient:  it (a) uses only a single random number per simulation event, and (b) ...