Reaction coordinate flows for model reduction of molecular kinetics
This work addresses the challenge of model reduction in molecular kinetics for researchers in computational chemistry and biophysics, offering a novel method but with incremental improvements over existing techniques.
The authors tackled the problem of discovering low-dimensional kinetic models for molecular systems by introducing a flow-based machine learning approach called reaction coordinate flow, which effectively produces interpretable and accurate representations from simulation data.
In this work, we introduce a flow based machine learning approach, called reaction coordinate (RC) flow, for discovery of low-dimensional kinetic models of molecular systems. The RC flow utilizes a normalizing flow to design the coordinate transformation and a Brownian dynamics model to approximate the kinetics of RC, where all model parameters can be estimated in a data-driven manner. In contrast to existing model reduction methods for molecular kinetics, RC flow offers a trainable and tractable model of reduced kinetics in continuous time and space due to the invertibility of the normalizing flow. Furthermore, the Brownian dynamics-based reduced kinetic model investigated in this work yields a readily discernible representation of metastable states within the phase space of the molecular system. Numerical experiments demonstrate how effectively the proposed method discovers interpretable and accurate low-dimensional representations of given full-state kinetics from simulations.