Atomistic process models are beginning to play an important role as direct simulation approaches for front-end processes and materials, and also as a pathway to improve continuum modeling. Detailed insight into the underlying physics using ab-initio methods and classical molecular dynamics simulations will be needed for understanding the kinetics of reduced thermal budget processes and the role of impurities. However, the limited sizes and time scales accessible for detailed atomistic techniques usually lead to the difficult task of relating the information obtained from simulations to experimental data. The solution consists of the use of a hierarchical simulation scheme: more fundamental techniques are employed to extract parameters and models that are then feed into less detailed simulators which allow direct comparison with experiments. This scheme will be illustrated with the atomistic modeling of the ion-beam induced amorphization and recrystallization of silicon. The model is based on the bond defect or IV pair, which is used as the building block of the amorphous phase. It is shown that the recombination of this defect depends on the surrounding bond defects, which accounts for the cooperative nature of the amorphization and recrystallization processes. The implementation of this model in a kinetic Monte Carlo code allows extracting data directly comparable with experiments.