Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm

On the rejection-based algorithm for simulation and analysis of large-scale reaction networks

(2015) Vo Hong Thanh et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays

(2014) Vo Hong Thanh et al.   JOURNAL OF CHEMICAL PHYSICS

On the stochastic SIS epidemic model in a periodic environment

(2014) Nicolas Bacaër   JOURNAL OF MATHEMATICAL BIOLOGY

Fast adaptive uniformisation of the chemical master equation

(2010) M. Mateescu et al.   IET Systems Biology

Reaction Factoring and Bipartite Update Graphs Accelerate the Gillespie Algorithm for Large-Scale Biochemical Systems

(2010) Sagar Indurkhya et al.   PLoS One

Efficient Formulations for Exact Stochastic Simulation of Chemical Systems

(2009) Sean Mauch et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit

(2009) Hong Li et al.   INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS

A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks

(2009) Rajesh Ramaswamy et al.   JOURNAL OF CHEMICAL PHYSICS

Discrete-time stochastic modeling and simulation of biochemical networks

(2008) Werner Sandmann   COMPUTATIONAL BIOLOGY AND CHEMISTRY

A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks

(2008) Alexander Slepoy et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient kinetic Monte Carlo simulation

(2007) Tim P. Schulze   JOURNAL OF COMPUTATIONAL PHYSICS