Theory and Computer Simulations of Molecular Kinetics. Molecular-level understanding of virtually any process that occurs in the cellular environment requires a kinetic description as well as the ability to measure and/or compute the associated timescales, making the subject of molecular kinetics essential in biochemistry and systems biology. Yet this material is not commonly taught by most graduate programs in Chemistry, Biochemistry, or Biophysics. Indeed, while rudimentary concepts of chemical kinetics are commonly covered in Physical Chemistry and Biochemistry courses and some ideas from chemical kinetics are covered as part of advanced non-equilibrium statistical mechanics (when available), no courses that cover the subject in a systematic manner usually exist. We believe that this shortcoming cannot be simply addressed by curriculum development in a usual university setting because the topic of molecular kinetics has recently seen rapid development, with many computational techniques as well as fundamental theoretical concepts emerging over the last decade. As a result, no systematic and up-to-date textbooks covering this subject currently exist. Moreover, qualified lecturers (who would have to be active researchers in the field) are not necessarily available at most institutions.
List of topics:
(i) Stochastic processes: Langevin dynamics, Fokker-Planck Equation, Path Integral formulation, Generalized Langevin Equation, Dominant Paths (Orland)
(ii) Crossing barriers: Correlation function expressions for the rate, Transition State Theory, Transmission Coefficient, Kramers’ equation, Grote-Hynes and Langer theories, Quantum effects on barrier crossing rates (Makarov)
(iii) Simulation techniques: Kinetic Monte Carlo, Molecular Dynamics, Umbrella Sampling and Generalized Ensembles (Elber, Makarov, Orland)
(iv) Enhanced Sampling Techniques for Kinetics: Transition Interface Sampling, Forward Flux, Weighted Ensembles, and Milestoning (Elber)
(v) Analyzing the results of simulations: Committors, Markov State Models, Transition Path Theory and Milestoning graphs, and Maxflux pathways (Elber)
(vi) Application to biomolecular folding and action (Orland, Makarov, Elber)