Lateral migration of peptides in transversely sheared flows in water: an atomistic-scale-resolving simulation

For atomistic scale-resolving simulations of peptide diffusion, which are representative of molecular sorting in micro-fluidic device, a hybrid Fluctuating Hydrodynamics - Molecular Dynamics (FH/MD) model is implemented based on the two-phase flow analogy framework. Thanks to the used framework, in comparison with existing simulations in the literature, the suggested model captures inter-atomic forces between the peptides and the surrounding shell of water atoms at atomistic resolution while concurrently taking into account the non-uniform flow effect. In comparison with previous applications of the hybrid two-phase flow analogy method, multiple moving atomic-resolution zones are implemented for the first time here. The moving zones comprise one and two peptides solvated in water with a Poiseuille flow applied, where each diffusing peptide and the surrounding water shell are dynamically resolved. The models are validated in comparison with the pure all-atom molecular dynamics simulations for the no flow case and then used to investigate how the flow rate and the starting location of peptides in the parabolic flow profile affect their lateral migration over a range of flow Reynolds numbers. It is estimated that for the Poiseuille flows considered, the FH/MD model is 2–20 times faster in comparison with the conventional all-atom non-equilibrium molecular dynamics simulations.

Diffusion, Flow protein, Hybrid Fluctuating Hydrodynamics - Molecular Dynamics model, Poiseuille

10.1016/j.molliq.2021.116111

0167-7322

116111

Li, Fan

55b2ae6a-88d8-4194-92b7-1493c14c765e

Korotkin, Ivan

1ca96363-075e-41d9-a0c1-153c8c0cc31a

Farafonov, Vladimir

207a6c3e-4af2-4f1e-8a8c-7db7dc00ed17

Karabasov, Sergey A.

8c5764f1-8325-47c0-8db7-4565ac15685d

1 September 2021

Li, Fan

55b2ae6a-88d8-4194-92b7-1493c14c765e

Korotkin, Ivan

1ca96363-075e-41d9-a0c1-153c8c0cc31a

Farafonov, Vladimir

207a6c3e-4af2-4f1e-8a8c-7db7dc00ed17

Karabasov, Sergey A.

8c5764f1-8325-47c0-8db7-4565ac15685d

Li, Fan, Korotkin, Ivan, Farafonov, Vladimir and Karabasov, Sergey A. (2021) Lateral migration of peptides in transversely sheared flows in water: an atomistic-scale-resolving simulation. Journal of Molecular Liquids, 337, 116111. (doi:10.1016/j.molliq.2021.116111).

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Accepted/In Press date: 5 April 2021

e-pub ahead of print date: 18 May 2021

Published date: 1 September 2021

Additional Information: Funding Information: The work of F.L. was supported by the China Scholarship Council (CSC). I.A.K. and S.A.K. gratefully acknowledge the funding under the European Commission Marie Skłodowska-Curie Individual Fellowship Grant No. H2020-MSCA-IF-2015-700276 (HIPPOGRIFFE). V. F. thanks Ministry of Education and Science of Ukraine for financial support in the frame of project “Novel nanomaterials based on the lyophilic self-assembled systems: theoretical prediction, experimental investigation and biomedical applications” (0120U101064). The work was also supported by European Commission in the framework of the RISE program, Grant No. H2020-MSCA-RISE-2018-824022-ATM2BT and utilised Queen Mary’s Apocrita HPC facility, supported by QMUL Research-IT [59] . Funding Information: The work of F.L. was supported by the China Scholarship Council (CSC). I.A.K. and S.A.K. gratefully acknowledge the funding under the European Commission Marie Sk?odowska-Curie Individual Fellowship Grant No. H2020-MSCA-IF-2015-700276 (HIPPOGRIFFE). V. F. thanks Ministry of Education and Science of Ukraine for financial support in the frame of project ?Novel nanomaterials based on the lyophilic self-assembled systems: theoretical prediction, experimental investigation and biomedical applications? (0120U101064). The work was also supported by European Commission in the framework of the RISE program, Grant No. H2020-MSCA-RISE-2018-824022-ATM2BT and utilised Queen Mary's Apocrita HPC facility, supported by QMUL Research-IT [59]. The authors are greatful to Dr Dmitry Nerkuh from Aston University, UK for helpuful comments and discussion. The data that support the findings of this study are available from the corresponding author upon reasonable request. Publisher Copyright: © 2021 Elsevier B.V. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

Keywords: Diffusion, Flow protein, Hybrid Fluctuating Hydrodynamics - Molecular Dynamics model, Poiseuille