This chapter gives an overview of Irradiation-Driven MolecularDynamics (IDMD)-the novel computational technique enabling atomistic simulations of the irradiation-driven transformations of complex Meso-Bio-Nano (MBN) systems exposed to various radiation modalities.Within the IDMD framework, various quantum processes occurring in irradiated systems are treated as random, fast, and local transformations incorporated into the classical MD framework in a stochastic manner with the probabilities elaborated on the basis of quantum mechanics. Major transformations of irradiated molecular systems (such as topological changes, redistribution of atomic partial charges, alteration of interatomic interactions) and possible paths of their further reactive transformations can be simulated bymeans of MD with reactive force fields, particularly with the reactive CHARMM (rCHARMM) force field implemented in the MBN Explorer software package. This chapter provides several exemplary case studies illustrating the utilization of IDMD. Particular examples include irradiation-induced chemical transformations (including fragmentation) of organic and biomolecular systems and controlled fabrication of nanostructures using the Focused Electron Beam-Induced Deposition (FEBID) technique.