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...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Pastor, Richard W [verfasserIn] |
|---|
| Format: |
Artikel |
|---|---|
| Sprache: |
Englisch |
| Erschienen: |
2015 |
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| Übergeordnetes Werk: |
Enthalten in: The journal of chemical physics - Melville, NY : AIP, 1933, 143(2015), 24 |
|---|---|
| Übergeordnetes Werk: |
volume:143 ; year:2015 ; number:24 |
| Links: |
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| DOI / URN: |
10.1063/1.4932980 |
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OLC1969413069 |
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| 520 | |a 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. | ||
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10.1063/1.4932980 doi PQ20160211 (DE-627)OLC1969413069 (DE-599)GBVOLC1969413069 (PRQ)c816-61f69e9fb9d74a5a3eb4b5345f15d0dce091ddbac54f1f00c4d1013c9333a2800 (KEY)0048355920150000143002400000stronginfluenceofperiodicboundaryconditionsonlater DE-627 ger DE-627 rakwb eng 540 530 DNB Pastor, Richard W verfasserin aut Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes 2015 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier 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. Brown, Frank L H oth Camley, Brian A oth Lerner, Michael G oth Enthalten in The journal of chemical physics Melville, NY : AIP, 1933 143(2015), 24 (DE-627)129079049 (DE-600)3113-6 (DE-576)014411660 0021-9606 nnns volume:143 year:2015 number:24 http://dx.doi.org/10.1063/1.4932980 Volltext http://www.ncbi.nlm.nih.gov/pubmed/26723598 GBV_USEFLAG_A SYSFLAG_A GBV_OLC SSG-OLC-PHY SSG-OLC-CHE SSG-OLC-PHA SSG-OLC-DE-84 GBV_ILN_21 GBV_ILN_59 GBV_ILN_70 GBV_ILN_2016 GBV_ILN_2279 AR 143 2015 24 |
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Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes |
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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. |
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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. |
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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. |
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