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

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.

The FLAME-accelerated signalling tool (FaST) for facile parallelisation of flexible agent-based models of cell signalling

“…However, such an inclusion would increase the amount of computation due to the increased binding radius and in most circumstances, this is unlikely to significantly change outcomes in the simulation. In very crowded environments, alternative simulators such as LAMMPS or ReaDDY may be more appropriate as they include more detailed particle-particle interactions that become prominent under these circumstances 43,44 . However, with all simulations, inclusion of increased detail leads to a greater computational burden that restricts their usage to the sort of time scales (seconds/minutes) that are less relevant in biology.…”

Minimal coarse-grained models for molecular self-organisation in biology

“…A promising way to approach such complex processes is via combining particle-based reaction-diffusion frameworks with coarse-grained molecular dynamics simulations. This can be addressed by interacting-particle reaction dynamics, as introduced with the software package ReaDDy/ReaDDy2 [86][87][88] in which chemical reactions are explicitly incorporated (Fig. 2).…”

Surface reaction-diffusion kinetics on lattice at the microscopic scale

“…In the former, the reaction occurs either immediately or with a probability of reflection when the distance between reactants equals to a predefined reaction radius, whereas in the Doi model, the reaction occurs with a fixed probability per unit time when the reactants are closer than the radius. Off-lattice SCK methods that support surface reactions include Smoldyn [48,49], CDS [50] and eGFRD [51], while the Doi model is adopted by MCell [52], ReaDDy [53,54] and SpringSaLaD [55]. Smoldyn also recently included the option to support the Doi model.…”