Evolutionary design of a DDPD model of ligation

Authors:
Mark A. Bedau;Andrew Buchanan;Gianluca Gazzola;Martin Hanczyc;Thomas Maeke;John McCaskill;Irene Poli;Norman H. Packard
Affiliations:
Protolife S.r.l., Marghera, Venezia, Italy;Protolife S.r.l., Marghera, Venezia, Italy;Protolife S.r.l., Marghera, Venezia, Italy;Protolife S.r.l., Marghera, Venezia, Italy;European Center for Living Technology, Venezia, Italy;European Center for Living Technology, Venezia, Italy;European Center for Living Technology, Venezia, Italy;Protolife S.r.l., Marghera, Venezia, Italy
Venue:
EA'05 Proceedings of the 7th international conference on Artificial Evolution
Year:
2005

Citing 1
Cited 3

Chemical genetic algorithms: coevolution between codes and code translation

ICAL 2003 Proceedings of the eighth international conference on Artificial life

Life Cycle of a Minimal Protocell---A Dissipative Particle Dynamics Study

Artificial Life
Catalysis by self-assembled structures in emergent reaction networks

ECAL'07 Proceedings of the 9th European conference on Advances in artificial life
Chemical computing

UPP'04 Proceedings of the 2004 international conference on Unconventional Programming Paradigms

Quantified Score

Hi-index	0.00

Visualization

Abstract

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.