Figure 1. Workflow in Simulation and ReaDDy Code Design.

A: Typical workflow and interplay between file input, file output and modules of ReaDDy. The left side of part A describes input and output functionalities of ReaDDy (sketched files) and how they interplay with code modules (squares). Among these modules, white drawn squares have access to both the particle level but also to information how particles are formed to groups. Grey squares are only based on particles to guarantee high computational efficiency. Modules communicate via interfaces, making them exchangeable. Currently two ReaDDy Core implementations exist, a Brownian dynamics based BD Core and a Monte Carlo based MC Core. The design is intended to encourage the incorporation of third party software to play the Core-role in the ReaDDy framework. B: Detailed view of the interplay between Group/Reaction Module (Gr/Rk Module), the Core module and their submodules during the main iteration loop. Most of the simulation time is spend on incrementing particle positions. As a result, the algorithm will circle between Particle Configuration, Neighbor List and Diffusion Engine (thick black arrows) to propagate diffusing particles. If a possible reaction event between two particle arises, this information is passed to the Gr/Rk Module module and is handled there before according changes of the Particle Configuration end that cycle (dashed arrows).