Complex networks, comprised of individual elements that interact with each other through
reaction channels, are ubiquitous across many scientific and engineering disciplines …

A review of the physical principles that are the ground of the stochastic formulation of
chemical kinetics is presented along with a survey of the algorithms currently used to …

Active matter systems, and in particular the cell cytoskeleton, exhibit complex
mechanochemical dynamics that are still not well understood. While prior computational …

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 …

We propose a new exact stochastic rejection-based simulation algorithm for biochemical
reactions and extend it to systems with delays. Our algorithm accelerates the simulation by …

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 …

Nowadays, mathematical modeling is playing a key role in many different research fields. In
the context of system biology, mathematical models and their associated computer …

Biological circuits and systems within even a single cell need to be represented by large-
scale feedback networks of nonlinear, stochastic, stiff, asynchronous, non-modular coupled …

Molecular discreteness is apparent in small-volume chemical systems, such as biological
cells, leading to stochastic kinetics. Here we present a theoretical framework to understand …