Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes
- Center for Theoretical Biological Physics and Department of Physics, University of California, San Diego, California 92093 (United States)
- Department of Physics and Astronomy, Earlham College, Richmond, Indiana 47374 (United States)
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892 (United States)
- Department of Physics, University of California, Santa Barbara, California 93106 (United States)
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.
- OSTI ID:
- 22493365
- Journal Information:
- Journal of Chemical Physics, Vol. 143, Issue 24; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA); ISSN 0021-9606
- Country of Publication:
- United States
- Language:
- English
Similar Records
Regulation of channel function due to physical energetic coupling with a lipid bilayer
Fluctuating hydrodynamics of multicomponent membranes with embedded proteins