Single molecule simulations in complex geometries with embedded dynamic one-dimensional structures

Hybrid spatial Gillespie and particle tracking simulation

(2012) Michael Klann et al.   BIOINFORMATICS

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

(2012) Brian Drawert et al.   BMC Systems Biology

Efficient Sampling in Event-Driven Algorithms for Reaction-Diffusion Processes

(2012) Mohammad Hossein Bani-Hashemian et al.   Communications in Computational Physics

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

The lac Repressor Displays Facilitated Diffusion in Living Cells

(2012) P. Hammar et al.   SCIENCE

Flexible single molecule simulation of reaction–diffusion processes

(2011) Stefan Hellander et al.   JOURNAL OF COMPUTATIONAL PHYSICS

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

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

A First-Passage Kinetic Monte Carlo algorithm for complex diffusion–reaction systems

(2010) Aleksandar Donev et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Algorithm for generating a Brownian motion on a sphere

(2010) Tobias Carlsson et al.   Journal of Physics A-Mathematical and Theoretical

Incorporating Active Transport of Cellular Cargo in Stochastic Mesoscopic Models of Living Cells

(2010) Andreas Hellander et al.   MULTISCALE MODELING & SIMULATION

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

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

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

STEPS: Modeling and simulating complex reaction-diffusion systems with Python

(2009) Stefan Wils   Frontiers in Neuroinformatics

Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces

(2008) Rex A. Kerr et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING