A lot of discoveries in modern science and technology, in particular, recent progress in nanotechnologies, are inseparably linked with the use of computer molecular simulation methods. Today, molecular simulation is one of the basic instruments in exploring the properties of nano- and biostructures. Molecular simulation is a practical tool for the development of new materials and new drugs, as well as for performing large-scale calculations on molecular complexes of hundreds of thousands or multi-million particle systems. In this book, original papers are collected that demonstrate efficient uses of molecular dynamics (MD) simulation for studying nanoscale phenomena in a number of models from material and life sciences.