Evolutionary Design of a DDPD Model of Ligation

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. 1 Evolutionary design of self-assembling chemical systems Many familiar examples of supramolecular self-assembly—such as micelles and vesicles—result solely from the dynamics of weak associative forces between molecules. Such structures contain strong intramolecular covalent bonds that are relatively fixed during the self-assembly process. Here we consider the selfassembly of supram...

• Type: Conference
• Year: 2005
• Where: AE
• Authors: Mark A. Bedau, Andrew Buchanan, Gianluca Gazzola, Martin M. Hanczyc, Thomas Maeke, John S. McCaskill, Irene Poli, Norman H. Packard
• Keywords: AE 2005, Dissipative Particle Dynamics, Strong Bonds, Weak Associative Forces