Hybrid multiscale simulation reveals focusing of a diffusing peptide molecule by parallel shear flow in water
Hybrid multiscale simulation reveals focusing of a diffusing peptide molecule by parallel shear flow in water
The hybrid Molecular Dynamics - Fluctuating Hydrodynamics model is extended for multi-resolution simulations of molecular diffusion in water under a steady shear flow. Cases of water self-diffusion and a small protein diffusion in water are considered. For the switched-off flow effect, the model is validated in comparison with the reference all-atom equilibrium molecular dynamics solution. With the flow effect included, the multiscale model correctly captures the mean flow velocity distribution as well as the difference between mean square deviations in different directions with respect to the flow in accordance with the diffusion theory. Results of the simulations are analysed in the context of using hydrodynamic flow gradients for molecular diffusion focusing.
Couette flow, Diffusion, Molecular dynamics, Multi-scale modelling, Soft matter, Two-phase flow analogy
285-297
Hu, J.
bc03f2c8-b504-4720-81f6-5ccd3f9a36e3
Korotkin, I. A.
1ca96363-075e-41d9-a0c1-153c8c0cc31a
Karabasov, S. A.
8c5764f1-8325-47c0-8db7-4565ac15685d
15 April 2019
Hu, J.
bc03f2c8-b504-4720-81f6-5ccd3f9a36e3
Korotkin, I. A.
1ca96363-075e-41d9-a0c1-153c8c0cc31a
Karabasov, S. A.
8c5764f1-8325-47c0-8db7-4565ac15685d
Hu, J., Korotkin, I. A. and Karabasov, S. A.
(2019)
Hybrid multiscale simulation reveals focusing of a diffusing peptide molecule by parallel shear flow in water.
Journal of Molecular Liquids, 280, .
(doi:10.1016/j.molliq.2019.01.152).
Abstract
The hybrid Molecular Dynamics - Fluctuating Hydrodynamics model is extended for multi-resolution simulations of molecular diffusion in water under a steady shear flow. Cases of water self-diffusion and a small protein diffusion in water are considered. For the switched-off flow effect, the model is validated in comparison with the reference all-atom equilibrium molecular dynamics solution. With the flow effect included, the multiscale model correctly captures the mean flow velocity distribution as well as the difference between mean square deviations in different directions with respect to the flow in accordance with the diffusion theory. Results of the simulations are analysed in the context of using hydrodynamic flow gradients for molecular diffusion focusing.
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More information
Accepted/In Press date: 28 January 2019
e-pub ahead of print date: 1 February 2019
Published date: 15 April 2019
Additional Information:
Funding Information:
The work of JH was supported by China Scholarship Council (CSC). IK gratefully acknowledges the funding under the Marie Skłodowska-Curie Individual Fellowship Grant H2020-MSCA-IF-2015-700276 (HIPPOGRIFFE). This research utilised Queen Mary's Apocrita HPC facility, supported by QMUL Research-IT [ 65 ]. The authors are grateful to Drs Dmitry Nerukh and Anton Markesteijn for helpful discussions on the two-phase flow analogy method. All method developments discussed in the present work have been implemented as internal procedures of the GROningen Machine for Chemical Simulations (GROMACS) software [ 66 ].
Publisher Copyright:
© 2019 Elsevier B.V.
Keywords:
Couette flow, Diffusion, Molecular dynamics, Multi-scale modelling, Soft matter, Two-phase flow analogy
Identifiers
Local EPrints ID: 468112
URI: http://eprints.soton.ac.uk/id/eprint/468112
ISSN: 0167-7322
PURE UUID: d7ec8bd1-3701-4776-975a-c07d8f304210
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Date deposited: 02 Aug 2022 17:08
Last modified: 18 Mar 2024 03:50
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Author:
J. Hu
Author:
S. A. Karabasov
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