Jump to main content
Jump to site search

Volume 169, 2014
Previous Article Next Article

Methodologies for the analysis of instantaneous lipid diffusion in md simulations of large membrane systems

Author affiliations

Abstract

Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic and structural properties of biological membranes. Molecular dynamics (MD) simulations provide a valuable tool for studying membrane models, complementing experimental approaches. It is now possible to simulate large membrane systems, such as simplified models of bacterial and viral envelope membranes. Consequently, there is a pressing need to develop tools to visualize and quantify the dynamics of these immense systems, which typically comprise millions of particles. To tackle this issue, we have developed visual and quantitative analyses of molecular positions and their velocity field using path line, vector field and streamline techniques. This allows us to highlight large, transient flow-like movements of lipids and to better understand crowding within the lipid bilayer. The current study focuses on visualization and analysis of lipid dynamics. However, the methods are flexible and can be readily applied to e.g. proteins and nanoparticles within large complex membranes. The protocols developed here are readily accessible both as a plugin for the molecular visualization program VMD and as a module for the MDAnalysis library.

Back to tab navigation
Please wait while Download options loads

Supplementary files

Publication details

The article was received on 16 Dec 2013, accepted on 20 Feb 2014 and first published on 21 Feb 2014


Article type: Paper
DOI: 10.1039/C3FD00145H
Citation: Faraday Discuss., 2014,169, 455-475
  •   Request permissions

    Methodologies for the analysis of instantaneous lipid diffusion in md simulations of large membrane systems

    M. Chavent, T. Reddy, J. Goose, A. C. E. Dahl, J. E. Stone, B. Jobard and M. S. P. Sansom, Faraday Discuss., 2014, 169, 455
    DOI: 10.1039/C3FD00145H

Search articles by author