Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

New Langevin and gradient thermostats for rigid body dynamics

(2015) R. L. Davidchack et al.   JOURNAL OF CHEMICAL PHYSICS

The small-voxel tracking algorithm for simulating chemical reactions among diffusing molecules

(2014) Daniel T. Gillespie et al.   JOURNAL OF CHEMICAL PHYSICS

Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems

(2014) Margaret E. Johnson et al.   Physical Review X

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

(2013) Johannes Schöneberg et al.   PLoS One

Membrane Clustering and the Role of Rebinding in Biochemical Signaling

(2012) Andrew Mugler et al.   BIOPHYSICAL JOURNAL

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

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

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

Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions

(2011) Jana Lipková et al.   SIAM JOURNAL ON APPLIED MATHEMATICS

Adaptive Multiscale Molecular Dynamics of Macromolecular Fluids

(2010) Steven O. Nielsen et al.   PHYSICAL REVIEW LETTERS

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