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J Chem Phys. 2017 Jan 28;146(4):044109. doi: 10.1063/1.4974306.

Identification of simple reaction coordinates from complex dynamics.

Author information

1
Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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
PMCID:
PMC5272828
DOI:
10.1063/1.4974306
[Indexed for MEDLINE]
Free PMC Article

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