It is clear that system-level computer simulations of the protocell cannot be performed at the same resolution than simulations of individual subsystems and their molecular components: the duration of the protocellular life-cycle which is expected to fall in the range of miilliseconds, missing knowledge of precise molecular details, and lack of theory for chemical reactions on the molecular level render atomistic simulation approaches like Molecular Dynamics (MD) impossible. Given the time scale of the system, coarse-grained simulation techniques appear more suitable for system-level computer simulations — the resulting model is understood as a toy-model that does not allow for predictive modelling but a systemic understanding of the system.
Our model is based on the dissipative particle dynamics (DPD) technique [8,9] which we have extended by a stochastic process that models chemical reactions based on the Smoluchoskwi model for diffusion limited reactions [1]. The precise algorithm for chemical reactions has been adopted from Ref. [10]. It allows for formation and breaking of chemical bonds, bead type transformation, and rate enhancement by nearby catalysts. Similar extensions to DPD have been developed in Ref. [6]. Functional groups of molecules are represented by connected point particles (beads) on a coarse level: e.g. one bead represents an amphiphilic head group or a base in the nuckeic acid strand. In total, the model employs 5 different bead types with interaction parameters taken from published comparable models [7] and are choosen such that phase-diagrams of surfactant-water and surfactant-oil-water systems can be recovered [5,12].