Identification of simple reaction coordinates from complex dynamics.

Identification of simple reaction coordinates from complex dynamics.

J Chem Phys. 2017 01 28;146(4):044109

Authors: McGibbon RT, Husic BE, Pande VS

Abstract
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.

PMID: 28147508 [PubMed – indexed for MEDLINE]