Molecular dynamics simulation of reversibly self-assembling shells in solution using trapezoidal particles

TL;DR

This study uses molecular dynamics to simulate the reversible self-assembly of polyhedral shells from trapezoidal particles, revealing detailed growth pathways, intermediate states, and the role of reversible bonding in achieving high-yield complete shells.

Contribution

It introduces a new simulation model for shell assembly from trapezoidal particles, highlighting the effects of particle shape and reversible bonding on assembly accuracy and efficiency.

Findings

High yield of complete shells achieved in simulations

Reversible bonding prevents incorrect assembly

Growth pathways resemble virus capsid formation

Abstract

The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the capsid of a T=1 virus. Growth occurs in the presence of an atomistic solvent and, under suitable conditions, achieves a high yield of complete shells. The simulations provide details of the structure and lifetime of the particle clusters that appear as intermediate states along the growth pathway, and the nature of the transitions between them. In certain respects the growth of size-60 shells from trapezoidal particles resembles the growth of icosahedral shells from triangular particles studied previously, with reversible bonding playing a major role in avoiding incorrect assembly, although the details differ due to particle shape and bond organization. The strong preference for maximal bonding exhibited by the triangular particle clusters is also apparent for trapezoidal particles, but this is now confined to early growth, and is less pronounced as shells approach completion along a variety of pathways.