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

Colloidal particles with mobile binding moities constitute a powerful platform for probing the physics of self-assembly, because the valence of the particles arises naturally depending on the number of available neighbors. This has been realized experimentally with DNA-coated oil emulsion droplets, where it has been shown that valence control can be tuned through the concentration of DNA on the surface as well as the strength of the binding or unbinding interactions. Moreover, chains of these droplets termed `colloidomers' can be used to probe the physics of polymer folding. Here, we present a coarse-grain (CG) molecular dynamics simulation model to study the self-assembly of this class of systems using explicit representations of mobile binding sites. Using this model, we explore how valence and assembled structures can be tuned both with these thermodynamic factors, as well as through kinetic control in the strong binding limit. As example uses of our framework, we show that we can determine principles that allow us to optimize conditions in which colloidomer chains are preferred, and our model exhibits folding behavior of colloidomers commensurate with recent work on this topic. A crucial element of our simulation framework is a model for dynamic binding and unbinding where kinetics are tunable, and can depend on external factors such as temperature. This dynamic binding is implemented as an open-source custom plugin to HOOMD-Blue which allows us to study our model on relatively large scales. Our CG platform lays the groundwork for future studies of this class of systems, including pathways for colloidomer folding, and the mechanical factors governing binding patch size, both of which have been explored in recent experimental studies.