‘ENVIRONMENT’: a stochastic simulation platform to study protocell dynamics

In this paper we describe the main features of a new computational platform, 'ENVIRONMENT', which has been developed with the aim to simulate stochastically the dynamics and stability of chemically reacting (proto-)cellular systems. Real biochemical reactions always take place in the context of compartments, which naturally involve other types of processes, like self-assembly, diffusion, flip-flop or transport. However, these processes have been traditionally neglected by artificial chemistry models, conceived in abstract, homogeneous spaces and typically focused on the formation or evolution of pure reaction networks. In contrast, our stochastic kinetics approach is meant to study the time evolution of chemistries in heterogeneous conditions, particularly in the case when aqueous and lipidic phases (micelles, vesicles, etc.) coexist, providing a much more complex and dynamic environment to host reactions. In this way, we hope to contribute to bring together theoretical and experimental research on protocell or minimal artificial cell systems, as illustrated with two concrete examples at the end, where we simulate real experiments with oleic acid and POPC vesicles.