Complete virus capsid at all-atom resolution:simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function

Tarasova, Elvira, Korotkin, Ivan, Farafonov, Volodymyr, Karabasov, Sergey and Nerukh, Dmitry (2017). Complete virus capsid at all-atom resolution:simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function. Journal of Molecular Liquids, in pre ,

Abstract

Simulations of complete virus capsid at atomistic details have been performed using standard Molecular Dynamics as well as original hybrid Molecular Dynamics/hydrodynamics methodologies. The results show that the capsid is stable in water solution at room temperature and ions composition similar to physiological conditions. Detailed analysis of the flow of water molecules and ions through the capsid’s wall is performed. It demonstrates that ions do not cross the capsid shell, while water exhibits substantial flows in both directions. This behaviour can be classified as a semipermeable membrane and may play a role in mechanical properties of the virus particle.

Publication DOI: https://doi.org/10.1016/j.molliq.2017.06.124
Dataset DOI: https://doi.org/10.17036/researchdata.aston.ac.uk.00000213
Divisions: Engineering & Applied Sciences > Systems analytics research institute (SARI)
Engineering & Applied Sciences > Mathematics
Additional Information: © 2017, Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/
Uncontrolled Keywords: all-atom simulation of viruses,hybrid molecular dynamics/hydrodynamics,multiscale simulations,Electronic, Optical and Magnetic Materials,Atomic and Molecular Physics, and Optics,Condensed Matter Physics,Spectroscopy,Physical and Theoretical Chemistry,Materials Chemistry
Published Online Date: 2017-06-29
Authors: Tarasova, Elvira
Korotkin, Ivan
Farafonov, Volodymyr
Karabasov, Sergey
Nerukh, Dmitry ( 0000-0001-9005-9919)

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