A modified Next Reaction Method for simulating chemical systems with time dependent propensities and delays

TL;DR

This paper introduces a modified Next Reaction Method that efficiently simulates chemical systems with time-dependent propensities and delays, improving upon existing exact simulation techniques for discrete jump Markov processes.

Contribution

The paper develops a new version of the Next Reaction Method that handles time-dependent propensities and delays, enhancing simulation efficiency for chemical reaction systems.

Findings

Efficient exact simulation of systems with time-dependent propensities.

Extension of the method to include delays in reactions.

Improved computational performance over previous algorithms.

Abstract

Chemical reaction systems with a low to moderate number of molecules are typically modeled as discrete jump Markov processes. These systems are oftentimes simulated with methods that produce statistically exact sample paths such as the Gillespie Algorithm or the Next Reaction Method. In this paper we make explicit use of the fact that the initiation times of the reactions can be represented as the firing times of independent, unit rate Poisson processes with internal times given by integrated propensity functions. Using this representation we derive a modified Next Reaction Method and, in a way that achieves efficiency over existing approaches for exact simulation, extend it to systems with time dependent propensities as well as to systems with delays.