Experimental and empirical work in the field of nano-scale, functional multilayer coatings produced by physical (PVD) or chemical (CVD) vapor deposition are currently an object of international research. The research results have already been implemented in industrial products, however, the atomistic understanding of the underlying processes still incomplete. In particular the correlation between the deposition parameters and the resulting coating structure needs further attention. To overcome the heuristic stage of the coating development and to facilitate targeted and efficient optimization of the coating structure and the resulting mechanical properties, a deeper understanding of the correlation between the substrate temperature, deposition rate and energy onto the growing coating structure is necessary. The aim of this work is the combination and mutual validation of modern atomistic simulations methods with experimental investigations of physical vapor deposition in order to deposit silicon and silicon-based protective coatings with targeted microstructure and desired mechanical properties.