Slicing and Dicing: Optimal Coarse-Grained Representation to Preserve Molecular Kinetics

The aim of molecular coarse-graining approaches is to recover relevant physical properties of the molecular system via a lower-resolution model that can be more efficiently simulated. Ideally, the lower resolution still accounts for the degrees of freedom necessary to recover the correct physical behavior. The selection of these degrees of freedom has often relied on the scientist's chemical and physical intuition. In this article, we make the argument that in soft matter contexts desirable coarse-grained models accurately reproduce the long-time dynamics of a system by correctly capturing the rare-event transitions. We propose a bottom-up coarse-graining scheme that correctly preserves the relevant slow degrees of freedom, and we test this idea for three systems of increasing complexity. We show that in contrast to this method existing coarse-graining schemes such as those from information theory or structure-based approaches are not able to recapitulate the slow time scales of the system.

Automated summary

The aim of molecular coarse-graining approaches is to simulate the physical properties of a molecular system more efficiently using a lower-resolution model. In this article, we argue that accurate coarse-grained models in soft matter contexts should accurately capture rare-event transitions to reproduce the system's long-time dynamics. We propose a bottom-up coarse-graining scheme that preserves the relevant slow degrees of freedom, and demonstrate its effectiveness in three systems of increasing complexity.