A Coarse-Grained Simulation Model for Self-Assembly of DNA-Coated Emulsion Droplets

DNA-coated emulsion droplets constitute a promising experimental platform for self-assembly because of thermo-reversible binding interactions between the complementary strands of sticky DNA on adjacent droplets. The DNA are mobile and can freely diffuse on the surface of these droplets and the valence of the droplets naturally emerges as a consequence of the concentration of DNA on the surface as well as the strength of the binding or unbinding interactions. We have designed a coarse-grained molecular dynamics simulation model to study the self-assembly of these DNA-coated emulsion droplets. Using this model we show, in accordance with experiment, that ‘colloidomer’ chains can be formed under conditions where the preferred valence is two. We also study the behavior of these colloidomers in solution. The crucial element of our simulation model is temperature-dependent dynamic binding and unbinding between beads representing the DNA-coated droplets. This dynamic binding is implemented as a custom plugin to HOOMD-Blue which allows us to incorporate and study its effect on the self-assembly process. This platform opens the path for the study of thermodynamic valence control and folding of emulsion droplets.