Simplified Simulations for Studying Self-Assembling Terminal Structures

We develop models of "patchy" particles for use in molecular dynamics simulations of self-assembly. These models are inspired by virus capsids, whose building blocks reliably arrange themselves into "terminal" structures - configurations that have many copies of identical building blocks but which stop growing once they are the right size. We specify the shapes of modeled building blocks and which components of them are attracted to which other components and perform molecular dynamics simulations to test our hypotheses about which structures are thermodynamically stable. Our results show how sensitive the assembly of two-dimensional triangular capsids are to attractive site placement and strength. This work is a first step towards building more complex models of "smart" particle assembly that can be used to test hypotheses about the theoretical limits of self-assembly.