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 …

GillesPy is an open-source Python package for model construction and simulation of
stochastic biochemical systems. GillesPy consists of a Python framework for model building …

Biochemical reactions often occur at low copy numbers but at once in crowded and diverse
environments. Space and stochasticity therefore play an essential role in biochemical …

The last few decades have revealed the living cell to be a crowded spatially heterogeneous
space teeming with biomolecules whose concentrations and activities are governed by …

Biochemical reaction networks (BRNs) in a cell frequently consist of reactions with disparate
timescales. The stochastic simulations of such multiscale BRNs are prohibitively slow due to …

Biochemical systems consist of numerous elementary reactions governed by the law of
mass action. However, experimentally characterizing all the elementary reactions is nearly …

Necroptosis is a form of regulated cell death associated with degenerative disorders,
autoimmune and inflammatory diseases, and cancer. To better understand the biochemical …

During the last decade, a consensus has emerged that the stochastic triggering of an
excitable system drives pseudopod formation and subsequent migration of amoeboid cells …

Propensity functions of the Hill type are commonly used to model transcriptional regulation
in stochastic models of gene expression. This leads to an effective reduced master equation …

The chemical master equation (CME) is the exact mathematical formulation of chemical
reactions occurring in a dilute and well-mixed volume. The reaction-diffusion master …