Literature DB >> 24982246

Concurrent multiscale modelling of atomistic and hydrodynamic processes in liquids.

Anton Markesteijn1, Sergey Karabasov2, Arturs Scukins3, Dmitry Nerukh3, Vyacheslav Glotov4, Vasily Goloviznin4.   

Abstract

Fluctuations of liquids at the scales where the hydrodynamic and atomistic descriptions overlap are considered. The importance of these fluctuations for atomistic motions is discussed and examples of their accurate modelling with a multi-space-time-scale fluctuating hydrodynamics scheme are provided. To resolve microscopic details of liquid systems, including biomolecular solutions, together with macroscopic fluctuations in space-time, a novel hybrid atomistic-fluctuating hydrodynamics approach is introduced. For a smooth transition between the atomistic and continuum representations, an analogy with two-phase hydrodynamics is used that leads to a strict preservation of macroscopic mass and momentum conservation laws. Examples of numerical implementation of the new hybrid approach for the multiscale simulation of liquid argon in equilibrium conditions are provided.
© 2014 The Author(s) Published by the Royal Society. All rights reserved.

Entities:  

Keywords:  Landau–Lifshitz fluctuating hydrodynamics equations; hybrid atomistic–continuum methods; hydrodynamic analogy; molecular dynamics; multiscale modelling; nanofluidics

Year:  2014        PMID: 24982246      PMCID: PMC4084524          DOI: 10.1098/rsta.2013.0379

Source DB:  PubMed          Journal:  Philos Trans A Math Phys Eng Sci        ISSN: 1364-503X            Impact factor:   4.226


  15 in total

1.  Protein denaturation and protein:drugs interactions from intrinsic protein fluorescence measurements at the nanolitre scale.

Authors:  Matthieu Gaudet; Nina Remtulla; Sophie E Jackson; Ewan R G Main; Daniel G Bracewell; Gabriel Aeppli; Paul A Dalby
Journal:  Protein Sci       Date:  2010-08       Impact factor: 6.725

2.  Molecular dynamics study of orientational cooperativity in water.

Authors:  Pradeep Kumar; Giancarlo Franzese; Sergey V Buldyrev; H Eugene Stanley
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2006-04-10

3.  Multiscale modeling of liquids with molecular specificity.

Authors:  G De Fabritiis; R Delgado-Buscalioni; P V Coveney
Journal:  Phys Rev Lett       Date:  2006-09-25       Impact factor: 9.161

4.  Fluctuating hydrodynamic modeling of fluids at the nanoscale.

Authors:  G De Fabritiis; M Serrano; R Delgado-Buscalioni; P V Coveney
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2007-02-08

5.  A unified model of protein dynamics.

Authors:  Hans Frauenfelder; Guo Chen; Joel Berendzen; Paul W Fenimore; Helén Jansson; Benjamin H McMahon; Izabela R Stroe; Jan Swenson; Robert D Young
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-27       Impact factor: 11.205

6.  Bridging fluctuating hydrodynamics and molecular dynamics simulations of fluids.

Authors:  Nikolaos K Voulgarakis; Jhih-Wei Chu
Journal:  J Chem Phys       Date:  2009-04-07       Impact factor: 3.488

7.  Canonical dynamics: Equilibrium phase-space distributions.

Authors: 
Journal:  Phys Rev A Gen Phys       Date:  1985-03

8.  Biotechnology at low Reynolds numbers.

Authors:  J P Brody; P Yager; R E Goldstein; R H Austin
Journal:  Biophys J       Date:  1996-12       Impact factor: 4.033

9.  Solvent flow patterns fluctuating largely around a protein and correlation with solvent density fluctuations: A molecular dynamics study.

Authors:  Koji Umezawa; Ryota Morikawa; Haruki Nakamura; Junichi Higo
Journal:  J Chem Phys       Date:  2010-04-21       Impact factor: 3.488

10.  Water-Peptide Dynamics during Conformational Transitions.

Authors:  Dmitry Nerukh; Sergey Karabasov
Journal:  J Phys Chem Lett       Date:  2013-02-25       Impact factor: 6.475

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  2 in total

1.  Multiscale modelling: approaches and challenges.

Authors:  Sergey Karabasov; Dmitry Nerukh; Alfons Hoekstra; Bastien Chopard; Peter V Coveney
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2014-08-06       Impact factor: 4.226

2.  All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid's Stability.

Authors:  Elvira Tarasova; Vladimir Farafonov; Reza Khayat; Noriaki Okimoto; Teruhisa S Komatsu; Makoto Taiji; Dmitry Nerukh
Journal:  J Phys Chem Lett       Date:  2017-02-01       Impact factor: 6.475

  2 in total

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