Modeling chemical environments is an important step to understanding the diversity of prebiotic systems that may have formed on the early earth or potentially can occur on other worlds. By using the modern Earth as a test case, these models predict scenarios with systems more conducive to the formation of the organic molecules that are important to life. Here we use the equilibrium thermodynamic modeling program HSC Chem to investigate prebiotic environments. This program uses the raw material that the user inputs into the system in order to calculate the change in amounts of chemical species forming as a function of temperature and pressure using equilibrium (batch reactor) chemistry. Our results show that that ferrous ion (Fe2+), which may be important in the early formation of organic molecules on Earth, is most abundant in the aqueous phase where the atmosphere contains carbon dioxide as a major constituent. A pure methane atmosphere exhibits the lowest concentrations of this ion, and mixtures tend to end up in between the two extremes. Additionally, we have determined the pH of early oceans, which has implications for biomineralization, chemical reactions, and mineral chemistry. We see that the CO2 atmosphere, and to some extent, the mixtures and CH4 atmospheres, exhibit near neutral pHs. These results allow prediction of processes that might have taken place and could have impacted the development of life on the early earth.

A synthetic proto-organism could be self-assembled by integrating a lipid proto-container with a proto-metabolic subsystem and a proto-genetic subsystem. This three-component system can use energy and nutrients by means of either redox or photo-chemical reactions, evolve its proto-genome by means of template directed replication, and ultimately die. The evolutionary dynamics of the proto-organism depends crucially on the chemical kinetics of its sub-systems and on their interplay. In this work the template replication kinetics is investigated and it is found that the product inhibition inherent in the ligation-like replication process allows for coexistence of unrelated self-replicating proto-genes in the lipid surface layer. The combined catalytic effects from the proto-genes on the metabolic production rates determine the fate of the strain protocell.