The Los Alamos protocell [11] consists of three replicating subsystems — container, metabolism, and genome — that are coupled by stoichiometric and catalytic interactions. It is envisioned that the protocell would spontaneously self-assemble out of its components, produce its building blocks from precursor molecules via a light-driven metabolism, self-reproduce, and eventually evolve. More precisely, amphiphiles are employed to form an aggregate that can be loaded with hydrophobic precursor molecules. The metabolic turnover of these precursors into additional amphiphiles is performed by a photo-sensitizer molecule. This sensitizer is covalently bond to a nucleic acid strand. By the choice of appropriate bases, the metabolic turnover rate is envisioned to depend on the actual base sequence — effectively turning it into a genome that is directly coupled to the metabolism. Additional sensitizers and nucleic acid oligomers are synthesized by the same metabolic reaction from other precursor molecules. Replication of the genome is envisioned by template directed ligation and melting of the resulting double-strand in a temperature cycle.
Even if container, metabolism and genome work independently, numerous issues are expected to emerge when integrating the subsystems into a functional whole. This motivates integrated computer simulations of system-level processes of the protocell over its entire life-cycle.