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arXiv · 2309.05878

Reaction coordinate flows for model reduction of molecular kinetics

Hao Wu·Frank Noé
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Abstract

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.

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Hao Wu, Frank Noé. 2023-09-11. Reaction coordinate flows for model reduction of molecular kinetics. https://arxiv.org/abs/2309.05878

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