Chapter 4 Evolutionary Design of a Model of Self-Assembling Chemical Structures

Abstract We introduce a new variant of dissipative particle dynamics (DPD) models that include the possibility of dynamically forming and breaking strong bonds. This model exhibits different forms of self-assembly processes; some like micelle formation involve only weak bonds, and others like the ligation of oligomers involve both weak and strong bonds. Complex self-assembly processes are notoriously difficult to design and program. We empirically demonstrate an evolutionary algorithm that optimizes self-assembly processes like micelle formation and template-directed ligation.

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