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Systematic derivation of hybrid coarse-grained models

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Di Pasquale, Nicodemo, Hudson, Thomas E. (Edward) and Icardi, Matteo (2019) Systematic derivation of hybrid coarse-grained models. Physical Review E, 99 . 013303. doi:10.1103/PhysRevE.99.013303

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Official URL: https://doi.org/10.1103/PhysRevE.99.013303

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Abstract

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 monodimensional 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.

Item Type: Journal Article
Subjects: Q Science > QA Mathematics
Q Science > QP Physiology
Divisions: Faculty of Science > Mathematics
Library of Congress Subject Headings (LCSH): Molecular dynamics -- Simulation methods , Mathematical models
Journal or Publication Title: Physical Review E
Publisher: American Physical Society
ISSN: 1539-3755
Official Date: 7 January 2019
Dates:
DateEvent
7 January 2019Published
1 December 2018Accepted
Volume: 99
Article Number: 013303
DOI: 10.1103/PhysRevE.99.013303
Status: Peer Reviewed
Publication Status: Published
Publisher Statement: © 2019 American Physical Society
Access rights to Published version: Restricted or Subscription Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
UNSPECIFIEDLeverhulme Trusthttp://dx.doi.org/10.13039/501100000275
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