The spatiotemporal master equation: Approximation of reaction-diffusion dynamics via Markov state modeling

Reaction rates for mesoscopic reaction-diffusion kinetics

(2015) Stefan Hellander et al.   PHYSICAL REVIEW E

Simulation tools for particle-based reaction-diffusion dynamics in continuous space

(2014) Johannes Schöneberg et al.   BMC Biophysics

Markov State Models for Rare Events in Molecular Dynamics

(2013) Marco Sarich et al.   Entropy

A convergent reaction-diffusion master equation

(2013) Samuel A. Isaacson   JOURNAL OF CHEMICAL PHYSICS

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

(2013) Johannes Schöneberg et al.   PLoS One

Hybrid Stochastic--Deterministic Solution of the Chemical Master Equation

(2012) Stephan Menz et al.   MULTISCALE MODELING & SIMULATION

Reaction-diffusion master equation in the microscopic limit

(2012) Stefan Hellander et al.   PHYSICAL REVIEW E

Markov state models based on milestoning

(2011) Christof Schütte et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

On the Approximation Quality of Markov State Models

(2010) Marco Sarich et al.   MULTISCALE MODELING & SIMULATION

Using generalized ensemble simulations and Markov state models to identify conformational states

(2009) Gregory R. Bowman et al.   METHODS

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