A Coarse-Grained Simulation Model for Self-Assembly of Liquid Droplets Featuring Explicit Mobile Binders

TL;DR

This paper introduces a coarse-grained simulation model for self-assembly of liquid droplets with mobile binders, enabling detailed study of valence control, folding pathways, and experimental optimization in colloidomer systems.

Contribution

It presents an open-source CGMD platform with dynamic bonding to simulate and analyze self-assembly and folding of colloidomers with explicit mobile binding sites.

Findings

Optimized parameters for high-yield linear colloidomer chains

Observed folding into all possible rigid structures in simulations

Validated model against recent experimental results

Abstract

Colloidal particles with mobile binding molecules constitute a powerful platform for probing the physics of self-assembly. Binding molecules are free to diffuse and rearrange on the surface, giving rise to spontaneous control over the number of droplet-droplet bonds, i.e., valence, as a function of the concentration of binders. This type of valence control has been realized experimentally by tuning the interaction strength between DNA-coated emulsion droplets. Optimizing for valence two yields droplet polymer chains, termed `colloidomers', which have recently been used to probe the physics of folding. To understand the underlying self-assembly mechanisms, here we present a coarse-grained molecular dynamics (CGMD) model to study the self-assembly of this class of systems using explicit representations of mobile binding sites. We explore how valence of assembled structures can be tuned through kinetic control in the strong binding limit. More specifically, we optimize experimental control parameters to obtain the highest yield of long linear colloidomer chains. Subsequently tuning the dynamics of binding and unbinding via a temperature-dependent model allows us to observe the heptamer chain collapse into all possible rigid structures, in good agreement with recent folding experiments. Our CGMD platform and dynamic bonding model (implemented as an open-source custom plugin to HOOMD-Blue) reveal the molecular features governing the binding patch size and valence control, and opens the study of pathways in colloidomer folding. This model can therefore guide programmable design in experiments.