Literature DB >> 25637963

Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics.

Nikolai D Petsev1, L Gary Leal1, M Scott Shell1.   

Abstract

We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.

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Year:  2015        PMID: 25637963      PMCID: PMC5848718          DOI: 10.1063/1.4905720

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  25 in total

1.  Transport coefficients of the Lennard-Jones model fluid. I. Viscosity.

Authors:  Karsten Meier; Arno Laesecke; Stephan Kabelac
Journal:  J Chem Phys       Date:  2004-08-22       Impact factor: 3.488

2.  Transport coefficients of the Lennard-Jones model fluid. III. Bulk viscosity.

Authors:  Karsten Meier; Arno Laesecke; Stephan Kabelac
Journal:  J Chem Phys       Date:  2005-01-01       Impact factor: 3.488

3.  Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly.

Authors:  Matej Praprotnik; Luigi Delle Site; Kurt Kremer
Journal:  J Chem Phys       Date:  2005-12-08       Impact factor: 3.488

4.  Embedding molecular dynamics within fluctuating hydrodynamics in multiscale simulations of liquids.

Authors:  R Delgado-Buscalioni; G De Fabritiis
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2007-09-25

5.  Multiscale modeling with smoothed dissipative particle dynamics.

Authors:  Pandurang M Kulkarni; Chia-Chun Fu; M Scott Shell; L Gary Leal
Journal:  J Chem Phys       Date:  2013-06-21       Impact factor: 3.488

6.  Coupling atomistic and continuum hydrodynamics through a mesoscopic model: application to liquid water.

Authors:  Rafael Delgado-Buscalioni; Kurt Kremer; Matej Praprotnik
Journal:  J Chem Phys       Date:  2009-12-28       Impact factor: 3.488

7.  Smoothed particle hydrodynamic model for viscoelastic fluids with thermal fluctuations.

Authors:  Adolfo Vázquez-Quesada; Marco Ellero; Pep Español
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-05-22

8.  Hamiltonian adaptive resolution simulation for molecular liquids.

Authors:  Raffaello Potestio; Sebastian Fritsch; Pep Español; Rafael Delgado-Buscalioni; Kurt Kremer; Ralf Everaers; Davide Donadio
Journal:  Phys Rev Lett       Date:  2013-03-05       Impact factor: 9.161

9.  Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model.

Authors:  Asim Okur; Lauren Wickstrom; Melinda Layten; Raphäel Geney; Kun Song; Viktor Hornak; Carlos Simmerling
Journal:  J Chem Theory Comput       Date:  2006-03       Impact factor: 6.006

10.  Consistent scaling of thermal fluctuations in smoothed dissipative particle dynamics.

Authors:  Adolfo Vázquez-Quesada; Marco Ellero; Pep Español
Journal:  J Chem Phys       Date:  2009-01-21       Impact factor: 3.488

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  5 in total

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Journal:  Biophys J       Date:  2018-04-09       Impact factor: 4.033

Review 2.  SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids.

Authors:  Julija Zavadlav; Siewert J Marrink; Matej Praprotnik
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

3.  Homogeneous nucleation: Patching the way from the macroscopic to the nanoscopic description.

Authors:  Detlef Lohse; Andrea Prosperetti
Journal:  Proc Natl Acad Sci U S A       Date:  2016-11-21       Impact factor: 11.205

4.  Communication: Adaptive boundaries in multiscale simulations.

Authors:  Jason A Wagoner; Vijay S Pande
Journal:  J Chem Phys       Date:  2018-04-14       Impact factor: 3.488

5.  Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics.

Authors:  Nikolai D Petsev; L Gary Leal; M Scott Shell
Journal:  J Chem Phys       Date:  2016-02-28       Impact factor: 3.488

  5 in total

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