Controlling Fragment Competition on Pathways to Addressable Self-Assembly

TL;DR

This paper introduces a 'completability' algorithm to analyze and mitigate fragment competition in addressable self-assembly, optimizing pathways for better efficiency and yield in forming target structures.

Contribution

The study presents a novel algorithm to quantify fragment competition and offers principles for designing bonding networks that suppress incompatibility in self-assembly.

Findings

Competition arises from loops in bonding networks.

Careful network design reduces fragment competition.

Semi-hierarchical pathways improve assembly success.

Abstract

Addressable self-assembly is the formation of a target structure from a set of unique molecular or colloidal building-blocks, each of which occupies a defined location in the target. The requirement that each type of building-block appears exactly once in each copy of the target introduces severe restrictions on the combinations of particles and on the pathways that lead to successful self-assembly. These restrictions can limit the efficiency of self-assembly and the final yield of the product. In particular, partially formed fragments may compete with each other if their compositions overlap, since they cannot be combined. Here, we introduce a "completability" algorithm to quantify competition between self-assembling fragments and use it to deduce general principles for suppressing the effects of fragment incompatibility in the self-assembly of small addressable clusters. Competition originates from loops in the bonding network of the target structure, but loops may be needed to provide structural rigidity and thermodynamic stability. An optimal compromise can be achieved by careful choice of bonding networks and by promoting semi-hierarchical pathways that rule out competition between early fragments. These concepts are illustrated in simulations of self-assembly in two contrasting addressable targets of 20 unique components each.