Robust self-assembly of nonconvex shapes in 2D

Abstract

We present fast simulation methods for the self-assembly of complex shapes in two dimensions. The shapes are modeled via a general boundary curve and interact via a standard volume term promoting overlap and an interpenetration penalty. To efficiently realize the Gibbs measure on the space of possible configurations we employ the hybrid Monte Carlo algorithm together with a careful use of signed distance functions for energy evaluation. Motivated by the self-assembly of identical coat proteins of the tobacco mosaic virus which assemble into a helical shell, we design a particular nonconvex 2D model shape and demonstrate its robust self-assembly into a unique final state. Our numerical experiments reveal two essential prerequisites for this self-assembly process: blocking and matching (i.e., local repulsion and attraction) of different parts of the boundary; and nonconvexity and handedness of the shape.