The biophysical mechanism of liquid-liquid phase separation (LLPS) has emerged as an attractive idea to explain the formation and function of membrane-less organelles, such as nuclear bodies. Our aim is to simulate the genesis of promyelocytic leukemia nuclear bodies (PML-NBs) at the molecular level using computer models in order to gain insight on LLPS within PML-NBs. To this end, we have generated a computer model of PML-NB assembly which uncovers molecular details of their genesis and a spatial map of its LLPS-driving elements. Model predictions can be exploited to test new hypotheses of PML-NB structure in the wet lab in an iterative process. The established computer model may be expanded to other membrane-less organelles to reveal their structural details.