Identification of simple reaction coordinates from complex dynamics
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.
- Publication:
-
Journal of Chemical Physics
- Pub Date:
- January 2017
- DOI:
- 10.1063/1.4974306
- arXiv:
- arXiv:1602.08776
- Bibcode:
- 2017JChPh.146d4109M
- Keywords:
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- Condensed Matter - Statistical Mechanics;
- Quantitative Biology - Biomolecules;
- Quantitative Biology - Quantitative Methods
- E-Print:
- 18 pages, 10 figures