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Issue 8, 2019
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Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study

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Abstract

In recent years, a massive increase has been observed in the number of published articles describing accurate and reliable molecular dynamics simulations of lipid bilayers. This is due to several reasons, including the development of fast and efficient methods for treating long-range electrostatic interactions, significant progress in computer hardware, progress in atomistic simulation algorithms and the development of well-validated empirical molecular mechanical force fields. Although molecular dynamics is an effective approach for investigating different aspects of lipid bilayers, to the best of our knowledge, there is no review in the literature that explains the different analyses that can be carried out with membrane simulation. This review gives an overview about the some of the most important possible analyses, technical challenges, and existing protocols that can be performed on the biological membrane by molecular dynamics simulation. The reviewed analyses include the degree of membrane disruption, average area per lipid, probability distributions for the area per lipid molecule, membrane thickness, membrane area compressibility, lateral diffusion, rotational diffusion, order parameters, head group tilt, electron density profile, mass density profile, electrostatic potential profile, ordering of vicinity waters, number of hydrogen bonds, and radial distribution function.

Graphical abstract: Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study

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Publication details

The article was received on 11 Oct 2018, accepted on 16 Jan 2019 and first published on 06 Feb 2019


Article type: Review Article
DOI: 10.1039/C8RA08441F
RSC Adv., 2019,9, 4644-4658
  • Open access: Creative Commons BY license
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    Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study

    S. Moradi, A. Nowroozi and M. Shahlaei, RSC Adv., 2019, 9, 4644
    DOI: 10.1039/C8RA08441F

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