Identification of simple reaction coordinates from complex dynamics

• Published in: The Journal of chemical physics Vol. 146; no. 4; p. 044109
• Main Authors: McGibbon, Robert T, Husic, Brooke E, Pande, Vijay S
• Format: Journal Article
• Language: English
• Published: United States 28.01.2017
• Subjects: Animals; Biphenyl Compounds - chemistry; Cattle; Molecular Dynamics Simulation; Protease Inhibitors - chemistry; Protease Inhibitors - pharmacology; Small Molecule Libraries - chemistry; Trypsin - metabolism
• DOI: 10.1063/1.4974306

Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems, as a maximally predictive one-dimensional projection. We then show that this criterion is uniquely satisfied by a dominant eigenfunction of an integral operator associated with the ensemble dynamics. We present a new sparse estimator for these eigenfunctions which can search through a large candidate pool of structural order parameters and build simple, interpretable approximations that employ only a small number of these order parameters. Example applications with a small molecule's rotational dynamics and simulations of protein conformational change and folding show that this approach can filter through statistical noise to identify simple reaction coordinates from complex dynamics.