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 …

We introduce Catalyst. jl, a flexible and feature-filled Julia library for modeling and high-
performance simulation of chemical reaction networks (CRNs). Catalyst supports simulating …

Stochastic simulation has been widely used to model the dynamics of biochemical reaction
networks. Several algorithms have been proposed that are exact solutions of the chemical …

We introduce Catalyst. jl, a flexible and feature-filled Julia library for modeling and high
performance simulation of chemical reaction networks (CRNs). Catalyst acts as both a …

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 …

Background Hybrid simulation of (computational) biochemical reaction networks, which
combines stochastic and deterministic dynamics, is an important direction to tackle future …

This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a
new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical …

In this paper, we present a novel method to estimate chemical reaction and diffusion rates
for biochemical reaction–diffusion dynamics from a time series of observations. Our …

Exact stochastic simulation is an indispensable tool for a quantitative study of biochemical
reaction networks. The simulation realizes the time evolution of the model by randomly …