Bedau, Mark A., Andrew Buchanan, Gianluca Gazzola, Martin Hanczyc, Thomas Maeke, John McCaskill, Irene Poli, and Norman H. Packard. “Evolutionary design of a DDPD model of ligation.” In International Conference on Artificial Evolution (Evolution Artificielle) , pp. 201-212. Springer, Berlin, Heidelberg, 2005.
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Ligation is a form of chemical self-assembly that involves dynamic formation of strong covalent bonds in the presence of weak associative forces. We study an extremely simple form of ligation by means of a dissipative particle dynamics (DPD) model extended to include the dynamic making and breaking of strong bonds, which we term dynamically bonding dissipative particle dynamics (DDPD). Then we use a chemical genetic algorithm (CGA) to optimize the model’s parameters to achieve a limited form of ligation of trimers—a proof of principle for the evolutionary design of self-assembling chemical systems.