ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics

Publishing date: 2019-04-11

Published on: PLOS Computational Biology

summary: Interacting-particle reaction dynamics (iPRD) combines the simulation of dynamical trajectories of interacting particles as in molecular dynamics (MD) simulations with reaction kinetics, in which particles appear, disappear, or change their type and interactions based on a set of reaction rules. Here the authors introduce the iPRD software ReaDDy 2, which provides a Python interface in which the simulation environment, particle interactions and reaction rules can be conveniently defined and the simulation can be run, stored and analyzed. A C++ interface is available to enable deeper and more flexible interactions with the framework.

authors: Moritz Hoffmann, Christoph Fröhner, Frank Noé

link to paper: 10.1371/journal.pcbi.1006830

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