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Systematic derivation of hybrid coarse-grained models

Di Pasquale, Nicodemo; Hudson, Thomas; Icardi, Matteo


Nicodemo Di Pasquale

Thomas Hudson


Molecular dynamics represents a key enabling technology for applications ranging from biology to the development of new materials. However, many real-world applications remain inaccessible to fully-resolved simulations due their unsustainable computational costs and must therefore rely on semi-empirical coarse-grained models. Significant efforts have been devoted in the last decade towards improving the predictivity of these coarse-grained models and providing a rigorous justification of their use, through a combination of theoretical studies and data-driven approaches. One of the most promising research effort is the (re)discovery of the Mori-Zwanzig projection as a generic, yet systematic, theoretical tool for deriving coarse-grained models. Despite its clean mathematical formulation and generality, there are still many open questions about its applicability and assumptions. In this work, we propose a detailed derivation of a hybrid multi-scale system, generalising and further investigating the approach developed in [Español, P., EPL, 88, 40008 (2009)]. Issues such as the general coexistence of atoms (fully-resolved degrees of freedom) and beads (larger coarse-grained units), the role of the fine-to-coarse mapping chosen, and the approximation of effective potentials are discussed. The theoretical discussion is supported by numerical simulations of a monodimen-sional nonlinear periodic benchmark system with an open-source parallel Julia code, easily extensible to arbitrary potential models and fine-to-coarse mapping functions. The results presented highlight the importance of introducing, in the macroscopic model, non-constant fluctuating and dissipative terms, given by the Mori-Zwanzig approach, to correctly reproduce the reference fine-grained results, without requiring ad-hoc calibration of interaction potentials and thermostats.


Di Pasquale, N., Hudson, T., & Icardi, M. (2019). Systematic derivation of hybrid coarse-grained models. Physical Review E, 99(1), Article 013303.

Journal Article Type Article
Acceptance Date Dec 13, 2018
Online Publication Date Jan 7, 2019
Publication Date Jan 7, 2019
Deposit Date Jan 7, 2019
Publicly Available Date Jan 8, 2019
Journal Physical Review E
Print ISSN 2470-0045
Electronic ISSN 1550-2376
Publisher American Physical Society
Peer Reviewed Peer Reviewed
Volume 99
Issue 1
Article Number 013303
Keywords Chemical Physics
Public URL
Publisher URL
Additional Information ©2019 American Physical Society


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