The course will explore physical models and computational approaches used for the simulations of Meso-Bio-Nano (MBN) systems and the investigation of their structure and dynamics at the atomic level of detail. The course is based on practical exercises with the universal computational package MBN Explorer and MBN Studio, as well as with the biophysical programs NAMD and VMD. In particular, the case studies of atomic clusters, nanoparticles, biomolecular systems, nanomaterials, composite materials and material interfaces, crystalline, liquid and gaseous systems, thermo-mechanical properties of materials, dynamical, collision, chemical and irradiation driven multiscale phenomena will be discussed. Relevant physical concepts, mathematical techniques and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics, and Monte Carlo simulations on parallel computers