I am not sure if MD is really the appropriate tool because of accessible length scales. I know that the group of Jens Harting at Eindhoven Technical University used lattice Boltzmann simulations with functionalized particles which then formed pickering emulsions etc.
Frijters, S.C.J., Günther, F.S. & Harting, J.D.R. (2014). Domain and droplet sizes in emulsions stabilized by colloidal particles. Physical Review E, 90(4), 042307-1/8. in Web of Science Cited 2 times
Günther, F.S., Frijters, S.C.J. & Harting, J.D.R. (2014). Timescales of emulsion formation caused by anisotropic particles. Soft Matter, 10(27), 4977-4989. in Web of Science Cited 9 times