  Cross-reactions and other systematic issues generated by the coupling of
functional chemical subsystems pose the largest challenge for assembling a
viable protocell in the laboratory. Our current work seeks to identify and
clarify such key issues as we represent and analyze in simulation a full
implementation of a minimal protocell. Using a 3D dissipative particle dynamics
(DPD) simulation method we are able to address the coupled diffusion,
self-assembly, and chemical reaction processes, required to model a full life
cycle of the protocell, the protocell being composed of coupled genetic,
metabolic, and container subsystems. Utilizing this minimal structural and
functional representation of the constituent molecules, their interactions, and
their reactions, we identify and explore the nature of the many linked
processes for the full protocellular system.
