Modeling of the production processes of layered materials can be done by molecular dynamics on the basis of an appropriate choice of interacting potentials of Tersoff-type, whose parameters are determined by ab initio methods. In particular, we analyze the ion beam assisted deposition of thin cubic boron nitride films and the co-deposition of fullerenes on silicon substrates. Numerical integration of the equation of motion is done by a parallel version of the Stoermer-Verlet scheme using a particle-in-cell method in addition to the nearest neighbor concept. Visualizations of the numerical simulations reveal a transition from hexagonal lattice to cubic crystallographic structures of the boron nitride layer, as observed in experiment. We also analyze in detail the fullerene-silicon substrate interaction by varying the impact energy and the angular speed of the fullerene molecule and the temperature of the system.