Extending dissipative particle dynamics (DPD) with chemical reactions, we have developed an integrated, spatially resolved, qualitative model of the Los Alamos protocell that allows to study systemic issues of the protocellular design over the entire life-cycle of the protocell. We have used this model to study container and genome replication of the aggregate as well as the mutual coupling between the subsystems. Key issues of the protocellular life-cycle have been identified. In particular, product inhibition of gene templates due to high relative concentration on the aggregate surface was been identified as the biggest problem in the toy model implementation of the system.
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