Ppsim: A Software Package for Efficiently Simulating and Visualizing Population Protocols

We introduce ppsim [], a software package for efficiently simulating population protocols, widely-studied subclass of chemical reaction networks (CRNs) in which all reactions have two reactants and products. Each step the dynamics involves picking uniform random pair from n molecules to collide (potentially null) reaction. In recent breakthrough, Berenbrink, Hammer, Kaaser, Meyer, Penschuck, Tran [] discovered protocol simulation algorithm quadratically faster than naïve algorithm, \(\varTheta (\sqrt{n})\) constant time (independently n, though scales with number species), while preserving exact stochastic dynamics.ppsim implements this tightly optimized Cython implementation that can exactly simulate hundreds billions seconds. It dynamically switches CRN Gillespie efficiency gains when applicable configuration becomes small. As Python library, also includes many useful tools data visualization Jupyter notebooks, allowing robust such as histogram plots at snapshots averaging repeated trials.Finally, we give framework takes any only bimolecular (2 reactant, 2 product) or unimolecular (1 1 reactions, arbitrary rate constants, compiles it into continuous-time protocol. This lets sample master equation (unlike approximate heuristics \(\tau \)-leaping LNA), achieving asymptotic running time. linked demonstrate efficacy tool on some protocols interest molecular programming, including majority models DNA strand displacement reactions.