Abstract Computer-aided simulations are valuable research tools for investigation of the properties of nuclear materials at atomic scale. This is because in principle, comparing with the experimental techniques, any system could be computed, including the experimentally challenging radiotoxic materials, and the only limitation is the availability and performance of the supercomputing resources and the approximate character of computational methods. Here we present an overview of our research activities on atomistic simulations of materials related to nuclear waste management. We discuss various structural, chemical, energetic, thermodynamic and radiation damage resistance properties of phosphate-based ceramic waste forms and nuclear graphite. Emphasis is put on selecting a reliable computational methodology. Our atomistic modeling effort complements the relevant experimental studies. We demonstrate that the combined atomistic modeling and experimental studies result in superior characterization of the investigated nuclear materials.