The microscopic spatial kinetic Monte Carlo (KMC) method has been employed extensively
in materials modeling. In this review paper, we focus on different traditional and multiscale …

Monte Carlo methods are heuristic algorithms that use probabilities to select an outcome
among several possible events in a given process. Monte Carlo methods are useful in …

BioNetGen is an open-source software package for rule-based modeling of complex
biochemical systems. Version 2.2 of the software introduces numerous new features for both …

We outline our perspective on stochastic chemical kinetics, paying particular attention to
numerical simulation algorithms. We first focus on dilute, well-mixed systems, whose …

This review provides a pedagogic and self-contained introduction to master equations and
to their representation by path integrals. Since the 1930s, master equations have served as …

Computer simulations have become an invaluable tool to study the sometimes
counterintuitive temporal dynamics of (bio-) chemical systems. In particular, stochastic …

Spatial stochastic simulation is a valuable technique for studying reactions in biological
systems. With the availability of high‐performance computing (HPC), the method is poised to …

Abstract Models of chemical kinetics that incorporate both stochasticity and diffusion are an
increasingly common tool for studying biology. The variety of competing models is vast, but …

We address the problem of simulating biochemical reaction networks with time-dependent
rates and propose a new algorithm based on our rejection-based stochastic simulation …

The dynamics of molecular systems is an essential tool of systems biology. It helps figuring
out what is the effect of the perturbation of a system, or what is the best dose for a drug or …