In recent years the interaction between dynamical systems theory and non-equilibrium statistical mechanics has been enormous. The discovery of fluctuation theorems as a fundamental structure common to almost all non-equilibrium systems, and the connections with the free energy calculation methods of Jarzynski and Crooks, have excited both theorists and experimentalists. This graduate-level book charts the development and theoretical analysis of molecular dynamics as applied to equilibrium and non-equilibrium systems. Designed for both researchers in the field and graduate students of physics, it connects molecular dynamics simulation with the mathematical theory to understand non-equilibrium steady states. It also provides a link between the atomic, nano, and macro worlds. The book ends with an introduction to the use of non-equilibrium statistical mechanics to justify a thermodynamic treatment of non-equilibrium steady states, and gives a direction to further avenues of exploration.