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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
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 | ||||||
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| Subjects: | Q Science > QA Mathematics Q Science > QP Physiology |
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| 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: |
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| Date of first compliant deposit: | 3 December 2018 | ||||||
| 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: |
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