Multicellular tumor spheroids are realistic in-vitro systems in radiation biology research to study the effect of anticancer drugs or to evaluate the resistance of cancer cells within specific conditions. When combining the modeling of spheroids together with the simulation of radiation therapy treatments using Monte Carlo methods, one could estimate cell and DNA damage to be compared with experimental endpoints. We developed a Cell Population (CPOP) modeler combined to Geant4 simulations in order to tackle how energy depositions are allocated to cells, especially when enhancing radiation outcomes using high-Z nanoparticles.