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.‎