Identification of simple reaction coordinates from complex dynamics

• Main Authors: McGibbon, Robert T, Husic, Brooke E, Pande, Vijay S
• Format: Journal Article
• Language: English
• Published: 06-01-2017
• Subjects: Physics - Statistical Mechanics; Quantitative Biology - Biomolecules; Quantitative Biology - Quantitative Methods
• DOI: 10.48550/arxiv.1602.08776

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
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.