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On the proper calculation of electrostatic interactions in solid-supported bilayer systems
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10.1063/1.3548836
/content/aip/journal/jcp/134/5/10.1063/1.3548836
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/5/10.1063/1.3548836

Figures

Image of FIG. 1.
FIG. 1.

A snapshot from the simulation of a quartz/water interface embedded in vacuum. The blue box represents the unit simulation cell with a box length in the z-direction (L z ) of 100 Å. The simulation cell is repeated periodically in all three directions. Water is in contact with the hydrophilic side of the quartz (011). Empty space (vacuum) is used to separate water and the other side of the quartz crystal in the z-direction.

Image of FIG. 2.
FIG. 2.

A snapshot from the simulation of a hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayer deposited on a quartz crystal surface. The blue box represents the unit simulation cell with L z of 200 Å. The simulation cell is repeated periodically in all three directions.

Image of FIG. 3.
FIG. 3.

Structural properties of the quartz/water interface. (a) Distributions of mass density of water under different electrostatic boundary conditions. (b) Average values of cosine of the angle between the water dipole and the z-axis (〈cos θdipole, z 〉) across the interface.

Image of FIG. 4.
FIG. 4.

Electrostatic properties of the quartz/water interface. (a) and (b) Profiles of electrostatic potential [ϕ(z)] and electric field [E(z)], respectively, calculated by applying Eqs. (13) and (14) suitable for the planar vacuum boundary condition to simulation data generated under the conducting periodic boundary condition (EW3D). (c) and (d) The same profiles are calculated by applying Eqs. (11) and (12), i.e., applying the consistent conducting periodic boundary condition to both the simulation (EW3D) and the calculation of electrostatic properties. All results from simulations performed and analyzed using the planar vacuum boundary condition with the periodic boundary condition correction (EW3DC) are shown as solid lines and were obtained by using Eqs. (13) and (14).

Image of FIG. 5.
FIG. 5.

Structural properties of the quartz-supported DMPC lipid bilayer. (a) d PP, the average distance between phosphate atoms in upper and lower leaflets, as a function of time. Circles and squares represent 10-ns block averages for simulations with the EW3D and EW3DC methods, respectively. Dashed and solid lines represent cumulative averages for the EW3D and EW3DC methods, respectively. (b) Distributions of mass density contributed by the DMPC lipid bilayer and water molecules calculated from simulations with the EW3D (dashed lines) and EW3DC (solid lines) methods. (c) Comparison of 〈cos θdipole, z 〉 values obtained from simulations with the EW3D (dashed lines) and EW3DC (solid lines) methods.

Image of FIG. 6.
FIG. 6.

Electrostatic properties of the quartz-supported DMPC lipid bilayer. (a) and (b) Profiles of ϕ(z) and E(z) with the EW3D (dashed lines) and EW3DC (solid lines) methods.

Image of FIG. 7.
FIG. 7.

Comparison of DMPC lipid bilayers in solution (dashed lines) and with the quartz/water interface (solid lines) with a larger system size having 176 lipids. Dotted-dashed lines represent the results with the original system size having 44 lipids. Distributions with the quartz/water interface were shifted with respect to the membrane center to coincide with the free solvated bilayer. (a) Distributions of mass density contributed by DMPC lipids and water molecules. (b) 〈cos θdipole, z 〉 values across the interface. (c) ϕ(z) values. (d) E(z) values. (e) Order parameter of acyl chain sn-1 calculated by S CD = , where θ is the angle between the C–H vector and the z-axis. Circles and squares represent results with a larger system size for DMPC bilayers in solution and with the quartz/water interface, respectively. Pluses represent the results with the original system size.

Image of FIG. 8.
FIG. 8.

Structural and electrostatic properties of the quartz/water interface in bulk solution without vacuum interfaces. Results with the EW3D and EW3DC methods are shown by the dashed and solid lines, respectively. Distributions were calculated with respect to the center of the quartz crystal. (a) Distributions of mass density contributed by water molecules. (b) 〈cos θdipole, z 〉 values across the interface. (c) ϕ(z) values. (d) E(z) values. The inset in C shows a magnified view of ϕ(z) profiles in the bulklike region of the water phase.

Tables

Generic image for table
Table I.

Values of 〈cos θdipole, z 〉 and the average mass density at the bulklike region (10 Å < z <15 Å) of water in the quartz/water interface as a function of different electrostatic boundary conditions and box size variations in the z-direction (L z ).

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/content/aip/journal/jcp/134/5/10.1063/1.3548836
2011-02-04
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: On the proper calculation of electrostatic interactions in solid-supported bilayer systems
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/5/10.1063/1.3548836
10.1063/1.3548836
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