Literature DB >> 23521306

Hamiltonian adaptive resolution simulation for molecular liquids.

Raffaello Potestio1, Sebastian Fritsch, Pep Español, Rafael Delgado-Buscalioni, Kurt Kremer, Ralf Everaers, Davide Donadio.   

Abstract

Adaptive resolution schemes allow the simulation of a molecular fluid treating simultaneously different subregions of the system at different levels of resolution. In this work we present a new scheme formulated in terms of a global Hamiltonian. Within this approach equilibrium states corresponding to well-defined statistical ensembles can be generated making use of all standard molecular dynamics or Monte Carlo methods. Models at different resolutions can thus be coupled, and thermodynamic equilibrium can be modulated keeping each region at desired pressure or density without disrupting the Hamiltonian framework.

Mesh:

Year:  2013        PMID: 23521306     DOI: 10.1103/PhysRevLett.110.108301

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  19 in total

1.  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

2.  Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics.

Authors:  Nikolai D Petsev; L Gary Leal; M Scott Shell
Journal:  J Chem Phys       Date:  2015-01-28       Impact factor: 3.488

Review 3.  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

Review 4.  From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.

Authors:  Matías R Machado; Ari Zeida; Leonardo Darré; Sergio Pantano
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

5.  Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations.

Authors:  Maziar Heidari; Robinson Cortes-Huerto; Kurt Kremer; Raffaello Potestio
Journal:  Eur Phys J E Soft Matter       Date:  2018-05-23       Impact factor: 1.890

6.  Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.

Authors:  Melanie P Muller; Tao Jiang; Chang Sun; Muyun Lihan; Shashank Pant; Paween Mahinthichaichan; Anda Trifan; Emad Tajkhorshid
Journal:  Chem Rev       Date:  2019-04-12       Impact factor: 60.622

7.  Mesoscopic Adaptive Resolution Scheme toward Understanding of Interactions between Sickle Cell Fibers.

Authors:  Lu Lu; He Li; Xin Bian; Xuejin Li; George Em Karniadakis
Journal:  Biophys J       Date:  2017-07-11       Impact factor: 4.033

Review 8.  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

9.  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 10.  Recent advances in transferable coarse-grained modeling of proteins.

Authors:  Parimal Kar; Michael Feig
Journal:  Adv Protein Chem Struct Biol       Date:  2014-08-24       Impact factor: 3.507

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