Coarse-graining molecular systems by spectral matching

The Journal of Chemical Physics
Feliks NüskeCecilia Clementi

Abstract

Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale systems become computationally tractable. While significant progress has been made in tuning thermodynamic properties of reduced models, it remains a key challenge to ensure that relevant kinetic properties are retained by coarse-grained dynamical systems. In this study, we focus on data-driven methods to preserve the rare-event kinetics of the original system and make use of their close connection to the low-lying spectrum of the system's generator. Building on work by Crommelin and Vanden-Eijnden [Multiscale Model. Simul. 9, 1588 (2011)], we present a general framework, called spectral matching, which directly targets the generator's leading eigenvalue equations when learning parameters for coarse-grained models. We discuss different parametric models for effective dynamics and derive the resulting data-based regression problems. We show that spectral matching can be used to learn effective potentials which retain the slow dynamics but also to correct the dynamics induced by existing techniques,...Continue Reading

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Citations

Feb 25, 2020·Annual Review of Physical Chemistry·Frank NoéCecilia Clementi
Nov 22, 2020·The Journal of Chemical Physics·Brooke E HusicCecilia Clementi
Nov 4, 2020·The Journal of Chemical Physics·Jurgis RuzaRafael Gómez-Bombarelli
Mar 10, 2021·The Journal of Chemical Physics·Jiang WangCecilia Clementi
Mar 12, 2021·Chemical Reviews·Oliver T UnkeKlaus-Robert Müller
Mar 18, 2021·Journal of Chemical Theory and Computation·Stefan DoerrGianni De Fabritiis
Nov 14, 2020·Proceedings of the National Academy of Sciences of the United States of America·Jayvee R AbellaLydia E Kavraki
May 5, 2021·The Journal of Chemical Physics·Jiang WangCecilia Clementi
Dec 29, 2020·The Journal of Physical Chemistry. B·Nicholas E Jackson
Sep 3, 2021·The Journal of Chemical Physics·Yaoyi ChenFrank Noé

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