The authors present a concurrent Monte Carlo (MC)-molecular dynamics (MD) approach to modeling matter response to excitation of its electronic system at nanometric scales. The two methods are combined on-the-fly at each time step in one code, TREKIS-4. The MC model describes the arrival of irradiation (a photon, an electron, or a fast ion). It traces induced cascades of secondary electrons and holes, and their energy exchange with atoms due to scattering. The excited atomic system is simulated with an MD model. An efficient way is proposed to account for nonthermal effects in the electron-atom energy transfer in covalent materials via the conversion of the potential energy of the electronic ensemble into the kinetic energy of atoms. Such a combined MC-MD approach enables a time-resolved tracing of the excitation kinetics of both, the electronic and atomic systems, and their simultaneous response to a deposited dose. As a proof-of-principle, it is shown that the proposed method describes atomic dynamics after X-ray irradiation in good agreement with tight-binding MD. The model also allows gaining insights into the atomic system behavior during the energy deposition from a nonequilibrium electronic system excited by an ion impact.