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Literature DB >> 26723598

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

Brian A Camley¹, Michael G Lerner², Richard W Pastor³, Frank L H Brown⁴.

Abstract

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.

Entities: Chemical

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Year: 2015 PMID： 26723598 PMCID： PMC4608966 DOI： 10.1063/1.4932980

Source DB: PubMed Journal: J Chem Phys ISSN： 0021-9606 Impact factor: 3.488

56 in total

1. Molecular-dynamics investigation of tracer diffusion in a simple liquid: test of the Stokes-Einstein law.

Authors: F Ould-Kaddour; D Levesque
Journal: Phys Rev E Stat Nonlin Soft Matter Phys Date: 2000-12-21

2. Mobility of extended bodies in viscous films and membranes.

Authors: Alex J Levine; T B Liverpool; F C MacKintosh
Journal: Phys Rev E Stat Nonlin Soft Matter Phys Date: 2004-02-19

3. Hybrid elastic and discrete-particle approach to biomembrane dynamics with application to the mobility of curved integral membrane proteins.

Authors: Ali Naji; Paul J Atzberger; Frank L H Brown
Journal: Phys Rev Lett Date: 2009-04-03 Impact factor: 9.161

4. Perturbative path-integral study of active- and passive-tracer diffusion in fluctuating fields.

Authors: Vincent Démery; David S Dean
Journal: Phys Rev E Stat Nonlin Soft Matter Phys Date: 2011-07-29

5. Beyond the creeping viscous flow limit for lipid bilayer membranes: theory of single-particle microrheology, domain flicker spectroscopy, and long-time tails.

Authors: Brian A Camley; Frank L H Brown
Journal: Phys Rev E Stat Nonlin Soft Matter Phys Date: 2011-08-04

6. Contributions to membrane-embedded-protein diffusion beyond hydrodynamic theories.

Authors: Brian A Camley; Frank L H Brown
Journal: Phys Rev E Stat Nonlin Soft Matter Phys Date: 2012-06-25

7. Tunable generic model for fluid bilayer membranes.

Authors: Ira R Cooke; Kurt Kremer; Markus Deserno
Journal: Phys Rev E Stat Nonlin Soft Matter Phys Date: 2005-07-26

8. Lipid bilayer domain fluctuations as a probe of membrane viscosity.

Authors: Brian A Camley; Cinzia Esposito; Tobias Baumgart; Frank L H Brown
Journal: Biophys J Date: 2010-09-22 Impact factor: 4.033

9. Intermonolayer friction and surface shear viscosity of lipid bilayer membranes.

Authors: W K den Otter; S A Shkulipa
Journal: Biophys J Date: 2007-04-27 Impact factor: 4.033

10. Subdiffusion and lateral diffusion coefficient of lipid atoms and molecules in phospholipid bilayers.

Authors: Elijah Flenner; Jhuma Das; Maikel C Rheinstädter; Ioan Kosztin
Journal: Phys Rev E Stat Nonlin Soft Matter Phys Date: 2009-01-14

34 in total

1. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.

Authors: Giray Enkavi; Matti Javanainen; Waldemar Kulig; Tomasz Róg; Ilpo Vattulainen
Journal: Chem Rev Date: 2019-03-12 Impact factor: 60.622

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

1. Molecular-dynamics investigation of tracer diffusion in a simple liquid: test of the Stokes-Einstein law.

2. Mobility of extended bodies in viscous films and membranes.

3. Hybrid elastic and discrete-particle approach to biomembrane dynamics with application to the mobility of curved integral membrane proteins.

4. Perturbative path-integral study of active- and passive-tracer diffusion in fluctuating fields.

5. Beyond the creeping viscous flow limit for lipid bilayer membranes: theory of single-particle microrheology, domain flicker spectroscopy, and long-time tails.

6. Contributions to membrane-embedded-protein diffusion beyond hydrodynamic theories.

7. Tunable generic model for fluid bilayer membranes.

8. Lipid bilayer domain fluctuations as a probe of membrane viscosity.

9. Intermonolayer friction and surface shear viscosity of lipid bilayer membranes.

10. Subdiffusion and lateral diffusion coefficient of lipid atoms and molecules in phospholipid bilayers.

1. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.

Review 2. Molecular Dynamics Simulations of Membrane Permeability.

3. The Plasma Membrane as a Competitive Inhibitor and Positive Allosteric Modulator of KRas4B Signaling.

4. Surface Shear Viscosity and Interleaflet Friction from Nonequilibrium Simulations of Lipid Bilayers.

5. Toward Hydrodynamics with Solvent Free Lipid Models: STRD Martini.

6. Molecular Dynamics Analysis of Cardiolipin and Monolysocardiolipin on Bilayer Properties.

7. Spatially Resolving the Condensing Effect of Cholesterol in Lipid Bilayers.

8. Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales.

9. Molecular dynamics simulations of lipid nanodiscs.

10. Molecular dynamics simulations of ethanol permeation through single and double-lipid bilayers.