Abstract
We derive an explicit formula for the propensity function (stochastic reaction rate) of a generic bimolecular chemical reaction in which the reactant molecules move about by diffusion, as solute molecules in a bath of much smaller and more numerous solvent molecules. Our derivation assumes that the solution is macroscopically well stirred and dilute in the solute molecules. It effectively extends the physical rationale for the chemical master equation and the stochastic simulation algorithm from well-stirred dilute gases to well-stirred dilute solutions, with the former becoming a limiting case of the latter. This extension is important for cellular systems, where the solvent molecules are typically water and the solute (reactant) molecules are much larger organic structures, whose relatively low populations often require a discrete-stochastic formalism. In the course of our derivation, we illuminate some limitations on the ability of the classical diffusion equation to accurately describe how a diffusing molecule moves on spatial and temporal scales that are relevant to collision-induced chemical reactions.