The tutorial is designed for graduate students and postdoctoral researchers in computational and/or bio/nanophysical and chemical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational bio/nanophysics and chemistry. The hands-on tutorial will explore physical models and computational approaches used for the simulation of bio/nano systems and the investigation of their function at an atomic level. The course will be based on several practical exercises to be done with a universal computational package MesoBioNano (MBN) Explorer (www.mbnexplorer.com). In particular, the case studies of atomic clusters, nanoparticles, biomolecular systems, nanomaterials, composite materials, hybrid molecular systems, crystalline systems, thermo-mechanical properties of materials, and 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.