Perspective: Stochastic algorithms for chemical kinetics

Spatial stochastic modelling of the Hes1 gene regulatory network: intrinsic noise can explain heterogeneity in embryonic stem cell differentiation

(2013) M. Sturrock et al.   Journal of the Royal Society Interface

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

(2012) Brian Drawert et al.   BMC Systems Biology

Linear noise approximation is valid over limited times for any chemical system that is sufficiently large

(2012) E.W.J. Wallace et al.   IET Systems Biology

Coupled Mesoscopic and Microscopic Simulation of Stochastic Reaction-Diffusion Processes in Mixed Dimensions

(2012) Andreas Hellander et al.   MULTISCALE MODELING & SIMULATION

Reaction-diffusion master equation in the microscopic limit

(2012) Stefan Hellander et al.   PHYSICAL REVIEW E

An Efficient Finite Difference Method for Parameter Sensitivities of Continuous Time Markov Chains

(2012) David F. Anderson   SIAM JOURNAL ON NUMERICAL ANALYSIS

StochKit2: software for discrete stochastic simulation of biochemical systems with events

(2011) K. R. Sanft et al.   BIOINFORMATICS

Legitimacy of the stochastic Michaelis–Menten approximation

(2011) K.R. Sanft et al.   IET Systems Biology

An accelerated algorithm for discrete stochastic simulation of reaction–diffusion systems using gradient-based diffusion and tau-leaping

(2011) Wonryull Koh et al.   JOURNAL OF CHEMICAL PHYSICS

Automated estimation of rare event probabilities in biochemical systems

(2011) Bernie J. Daigle et al.   JOURNAL OF CHEMICAL PHYSICS

How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?

(2011) Ramon Grima et al.   JOURNAL OF CHEMICAL PHYSICS

State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events

(2011) Min K. Roh et al.   JOURNAL OF CHEMICAL PHYSICS

A new method for choosing the computational cell in stochastic reaction–diffusion systems

(2011) Hye-Won Kang et al.   JOURNAL OF MATHEMATICAL BIOLOGY

The two-regime method for optimizing stochastic reaction-diffusion simulations

(2011) M. B. Flegg et al.   Journal of the Royal Society Interface

The influence of volume exclusion by chromatin on the time required to find specific DNA binding sites by diffusion

(2011) S. A. Isaacson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Approximate Moment Dynamics for Chemically Reacting Systems

(2010) Abhyudai Singh et al.   IEEE TRANSACTIONS ON AUTOMATIC CONTROL

Accurate implementation of leaping in space: The spatial partitioned-leaping algorithm

(2010) Krishna A. Iyengar et al.   JOURNAL OF CHEMICAL PHYSICS

Intrinsic biochemical noise in crowded intracellular conditions

(2010) R. Grima   JOURNAL OF CHEMICAL PHYSICS

State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm

(2010) Min K. Roh et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks

(2010) Muruhan Rathinam et al.   JOURNAL OF CHEMICAL PHYSICS

The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation

(2010) Brian Drawert et al.   JOURNAL OF CHEMICAL PHYSICS

Spatio-temporal correlations can drastically change the response of a MAPK pathway

(2010) K. Takahashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stochastic reaction-diffusion kinetics in the microscopic limit

(2010) D. Fange et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient Formulations for Exact Stochastic Simulation of Chemical Systems

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

A diffusional bimolecular propensity function

(2009) Daniel T. Gillespie   JOURNAL OF CHEMICAL PHYSICS

The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems

(2009) Sotiria Lampoudi et al.   JOURNAL OF CHEMICAL PHYSICS

Refining the weighted stochastic simulation algorithm

(2009) Dan T. Gillespie et al.   JOURNAL OF CHEMICAL PHYSICS

Effect of excluded volume on 2D discrete stochastic chemical kinetics

(2009) Sotiria Lampoudi et al.   JOURNAL OF COMPUTATIONAL PHYSICS

An adaptive algorithm for simulation of stochastic reaction–diffusion processes

(2009) Lars Ferm et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Deterministic Limit of Stochastic Chemical Kinetics

(2009) Daniel T. Gillespie   JOURNAL OF PHYSICAL CHEMISTRY B

Reaction-diffusion master equation, diffusion-limited reactions, and singular potentials

(2009) Samuel A. Isaacson et al.   PHYSICAL REVIEW E

The Reaction-Diffusion Master Equation as an Asymptotic Approximation of Diffusion to a Small Target

(2009) Samuel A. Isaacson   SIAM JOURNAL ON APPLIED MATHEMATICS

Simulation of Stochastic Reaction-Diffusion Processes on Unstructured Meshes

(2009) Stefan Engblom et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

An efficient and exact stochastic simulation method to analyze rare events in biochemical systems

(2008) Hiroyuki Kuwahara et al.   JOURNAL OF CHEMICAL PHYSICS

Incorporating postleap checks in tau-leaping

(2008) David F. Anderson   JOURNAL OF CHEMICAL PHYSICS

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

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

Accelerated stochastic and hybrid methods for spatial simulations of reaction–diffusion systems

(2007) Diego Rossinelli et al.   CHEMICAL PHYSICS LETTERS