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

Moritz Hoffmann, Christoph Fröhner and Frank Noé

PLOS Computational Biology, 2019, vol. 15, issue 2, 1-26

Abstract: 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. This combination facilitates the simulation of reaction kinetics in crowded environments, involving complex molecular geometries such as polymers, and employing complex reaction mechanisms such as breaking and fusion of polymers. iPRD simulations are ideal to simulate the detailed spatiotemporal reaction mechanism in complex and dense environments, such as in signalling processes at cellular membranes, or in nano- to microscale chemical reactors. Here we 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. The main computational work of ReaDDy 2 is done in hardware-specific simulation kernels. While the version introduced here provides single- and multi-threading CPU kernels, the architecture is ready to implement GPU and multi-node kernels. We demonstrate the efficiency and validity of ReaDDy 2 using several benchmark examples. ReaDDy 2 is available at the https://readdy.github.io/ website.Author summary: Biological cells are not well-mixed reaction containers. Cellular signaling strongly depends on crowding, space exclusion, association and dissociation of proteins and other macromolecules. These are often confined to complex geometries and cell compartments. Understanding the mechanisms is challenging, as experiments can only achieve either high spatial resolution or high temporal resolution. Computer simulations on the other hand can capture these levels of detail. In particular, reaction-diffusion simulations can describe processes in a cell on a mesoscopic scale.

Date: 2019
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1006830

DOI: 10.1371/journal.pcbi.1006830

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