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Despite the importance of non-equilibrium statistical mechanics in modernphysics and related fields, the topic is often omitted from undergraduate andcore-graduate curricula. Key aspects of non-equilibrium physics, however, canbe understood with a minimum of formalism based on a rigorous trajectorypicture. The fundamental object is the ensemble of trajectories, a set ofindependent time-evolving systems that easily can be visualized or simulated(for protein folding, e.g.), and which can be analyzed rigorously in analogy toan ensemble of static system configurations. The trajectory picture provides astraightforward basis for understanding first-passage times, "mechanisms" incomplex systems, and fundamental constraints the apparent reversibility ofcomplex processes. Trajectories make concrete the physics underlying thediffusion and Fokker-Planck partial differential equations. Last but not least,trajectory ensembles underpin some of the most important algorithms which haveprovided significant advances in biomolecular studies of protein conformationaland binding processes.

A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applications