We have investigated the atomistic mechanism behind the irradiation-induced amorphization in Si using molecular dynamics simulation techniques. The microscopic description of the process is based on the defect known as bond defect or IV pair. IV pairs recombine very fast when isolated, but if they interact to each other they survive longer times and thus accumulate giving rise to amorphization. This fact accounts for the superlinear behavior of the accumulated damage with dose and the different activation energies for recrystallization observed in the experiments. The molecular dynamics results have been used to define an atomistic model for amorphization and recrystallization which has been implemented in a kinetic Monte Carlo code. The model is able to reproduce quantitatively the dependence of the critical crystal-amorphous transition on the irradiation parameters.