Investigations of polymerization-induced self assembly in emulsion were conducted using molecular dynamics simulations. Using umbrella sampling and the weighted histogram analysis method algorithm, we calculated the interaction free energy between different self-assembled copolymer aggregates. In the presence of poly(ethylene glycol) (PEG) side chains at 80 degrees C, an attractive interaction between the copolymer micelles is observed. This attractive well is followed, in some case, by a repulsive barrier depending on the position of the PEG side chains. The strength of this repulsive barrier controls the aggregation kinetics: a strong repulsive barrier leads to slower aggregation rate and thus larger and denser clusters (i.e., reaction-limited cluster aggregation). These clusters then coalesce into large vesicles due to the presence of interstitial water molecules in the cluster. Inversely, a weak repulsive barrier causes rapid aggregation, which gives loose and ramified clusters (i.e., diffusion-limited cluster aggregation) that coalesce after swelling with a hydrophobic monomer, leading to tubular nanostructures and small vesicles. This new mechanism approach can explain the change of morphology from spheres to fibers and vesicles depending on the polymer architecture in the case of polymerization-induced self-assembly (PISA) in emulsion.