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Title: Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes

The Saffman-Delbrück hydrodynamic model for lipid-bilayer membranes is modified to account for the periodic boundary conditions commonly imposed in molecular simulations. Predicted lateral diffusion coefficients for membrane-embedded solid bodies are sensitive to box shape and converge slowly to the limit of infinite box size, raising serious doubts for the prospects of using detailed simulations to accurately predict membrane-protein diffusivities and related transport properties. Estimates for the relative error associated with periodic boundary artifacts are 50% and higher for fully atomistic models in currently feasible simulation boxes. MARTINI simulations of LacY membrane protein diffusion and LacY dimer diffusion in DPPC membranes and lipid diffusion in pure DPPC bilayers support the underlying hydrodynamic model.
Authors:
 [1] ;  [2] ;  [3] ;  [2] ;  [4] ;  [5] ;  [2]
  1. Center for Theoretical Biological Physics and Department of Physics, University of California, San Diego, California 92093 (United States)
  2. (United States)
  3. Department of Physics and Astronomy, Earlham College, Richmond, Indiana 47374 (United States)
  4. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892 (United States)
  5. Department of Physics, University of California, Santa Barbara, California 93106 (United States)
Publication Date:
OSTI Identifier:
22493365
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 143; Journal Issue: 24; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; BOUNDARY CONDITIONS; COMPUTERIZED SIMULATION; DIFFUSION; DIMERS; ERRORS; HYDRODYNAMICS; LAYERS; LIPIDS; MEMBRANE PROTEINS; MEMBRANES; SOLIDS; THERMAL DIFFUSIVITY