Extracting bulk properties of self-assembling systems from small simulations

TL;DR

This paper discusses how to accurately estimate bulk properties of self-assembling systems from small simulations, addressing finite-size effects and proposing methods for better yield predictions and multiple object formation.

Contribution

It introduces new methods to estimate bulk yields from small system simulations and extends umbrella sampling for multiple finite-sized objects.

Findings

Finite-size effects significantly impact yield calculations.

Proposed methods improve bulk property estimations from small simulations.

Extended umbrella sampling enables modeling multiple assemblies.

Abstract

For systems that self assemble into finite-sized objects, it is sometimes convenient to compute the thermodynamics for a small system where a single assembly can form. However, we show that in the canonical ensemble the use of small systems can lead to significant finite-size effects due to the suppression of concentration fluctuations. We introduce methods to estimate the bulk-yields from simulations of small systems and to follow the convergence of yields with system size, under the assumptions that the various species behave ideally. We also propose an extension to the umbrella sampling technique that allows the formation of multiple finite-sized objects.