The interior of cells contains numerous components that need to be carefully organized in space to fulfill a wide range of biological functions. The most widespread form of intracellular compartments completely lack membranes. In the place of membranes, these compartments—so called biomolecular condensates—are sustained and segregated in space via phase separation. Molecular modeling and simulations complement experiments by providing close-up views that elucidate the physicochemical principles shaping biomolecular condensates. Within the paradigm of phase separation, I will discuss our efforts at developing quantitatively accurate submolecular-resolution computer models for studying biomolecular condensates. Additionally, I will demonstrate how these approaches can be leveraged for engineering intracellular compartments.