Literature DB >> 18361557

Concurrent triple-scale simulation of molecular liquids.

Rafael Delgado-Buscalioni1, Kurt Kremer, Matej Praprotnik.   

Abstract

We present a triple-scale simulation of a molecular liquid, in which the atomistic, coarse-grained, and continuum descriptions of the liquid are concurrently coupled. The presented multiscale approach, which covers the length scales ranging from the micro- to macroscale, is a combination of two dual-scale models: a particle-based adaptive resolution scheme (AdResS), which couples the atomic and mesoscopic scales, and a hybrid continuum-molecular dynamics scheme (HybridMD). The combined AdResS-HybridMD scheme successfully sorts out the problem of large molecule insertion in the hybrid particle-continuum simulations of molecular liquids. The combined model is shown to correctly describe the hydrodynamics within a hybrid particle-continuum framework. The presented approach opens up the possibility to perform efficient grand-canonical molecular dynamics simulations of truly open molecular liquid systems.

Year:  2008        PMID: 18361557     DOI: 10.1063/1.2890729

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


  11 in total

1.  Comparative atomistic and coarse-grained study of water: what do we lose by coarse-graining?

Authors:  Han Wang; Christoph Junghans; Kurt Kremer
Journal:  Eur Phys J E Soft Matter       Date:  2009-01-14       Impact factor: 1.890

2.  Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution.

Authors:  Julija Zavadlav; Jurij Sablić; Rudolf Podgornik; Matej Praprotnik
Journal:  Biophys J       Date:  2018-04-09       Impact factor: 4.033

Review 3.  Adaptive resolution simulations of biomolecular systems.

Authors:  Julija Zavadlav; Staš Bevc; Matej Praprotnik
Journal:  Eur Biophys J       Date:  2017-09-13       Impact factor: 1.733

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

Review 5.  Bottom-up Coarse-Graining: Principles and Perspectives.

Authors:  Jaehyeok Jin; Alexander J Pak; Aleksander E P Durumeric; Timothy D Loose; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2022-09-07       Impact factor: 6.578

6.  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

7.  Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations.

Authors:  Mark B Flegga; Stefan Hellander; Radek Erban
Journal:  J Comput Phys       Date:  2015-05-15       Impact factor: 3.553

8.  Path Integral Molecular Dynamics of Liquid Water in a Mean-Field Particle Reservoir.

Authors:  Antonios Evangelakis; Sara Panahian Jand; Luigi Delle Site
Journal:  ChemistryOpen       Date:  2022-02-25       Impact factor: 2.630

9.  Dissipative Particle Dynamics Simulations for Phospholipid Membranes Based on a Four-To-One Coarse-Grained Mapping Scheme.

Authors:  Xiaoxu Li; Lianghui Gao; Weihai Fang
Journal:  PLoS One       Date:  2016-05-03       Impact factor: 3.240

Review 10.  From adaptive resolution to molecular dynamics of open systems.

Authors:  Robinson Cortes-Huerto; Matej Praprotnik; Kurt Kremer; Luigi Delle Site
Journal:  Eur Phys J B       Date:  2021-09-23       Impact factor: 1.500

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