Figure 1.
The sketch on the left represents the chemical structure of a water molecule. The corresponding ELBA model is depicted on the right; the arrow represents an electrical point dipole.
Table 1.
Parameters of the ELBA water model.
Table 2.
Water physical properties.
Figure 2.
The sketch on the left represented the chemical structure of a DOPC lipid. The corresponding CG model is depicted on the right. CG electrostatics are highlighted; they comprise positive (“+” sign) and negative (“−” sign) point charges in the headgroups, and point dipoles (arrows) in the glycerol and ester sites.
Table 3.
Parameters of the ELBA force field.
Table 4.
Summary of simulations of preassembled bilayer systems.
Figure 3.
DOPC electron density profiles.
The distributions calculated from simulations of the ELBA model are superimposed on the experimental profile obtained by Liu and Nagle [101]. The simulation curves refer to runs A, B and C.
Figure 4.
Simulation snapshots: a) run A (128 lipids+4232 waters), b) run B (512 lipids+16810 waters), c) run C (1058 lipids+34848 waters). Choline and phosphate sites are red, glycerol and ester sites are yellow, tail sites are green and water sites are transparent blue.
Table 5.
Structural parameters of fluid-phase DOPC bilayers at full hydration.
Table 6.
Structural parameters of DOPE bilayers, 9 waters/lipid, .
Figure 5.
Final snapshots from a simulation of a DSPC lipids bilayer at (run G).
Figure 6.
DSPC electron density profiles.
The “gel phase” curve refers to the simulation at (run G), while the “fluid phase” curve refers to the simulation at
(run H).
Table 7.
Structural parameters of DSPC bilayers.
Table 8.
Gel-to-fluid ratios for elastic properties of DSPC bilayers.
Figure 7.
DOPC lateral pressure profiles.
The curves refer to runs A (128 lipids), B (512 lipids) and C (1058 lipids).
Figure 8.
DOPE lateral pressure profiles.
The curves refer to runs D (128 lipids), E (512 lipids) and F (1058 lipids).
Figure 9.
DSPC lateral pressure profiles.
The “gel phase” curve refers to the simulation at (run G), while the “fluid phase” curve refers to the simulation at
(run H).
Table 9.
Curvature elastic parameters of fluidmphase DOPC bilayers at full hydration.
Table 10.
Curvature elastic parameters of DOPE bilayers, 9 waters/lipid, .
Table 11.
Curvature elastic parameters of DSPC bilayers.
Table 12.
Dipole potential.
Figure 10.
DOPC electrostatic potential profile.
The total transmembrane potential is plotted together with the individual contributions of the various charged species in the system. The data were obtained from run A.
Table 13.
Water permeability coefficient [
m/s].
Figure 11.
Self-assembly simulation snapshots.
Trajectory snapshots from a self-assembly simulation of 128 DOPC lipid molecules and 4232 water sites.
Figure 12.
Self-assembly simulation snapshots.
Trajectory snapshots from a DOPE-water system. To facilitate interpretation, each panel was prepared by juxtaposing four replicas of the main simulation region through their periodic boundaries. The main simulation region comprises 512 DOPE lipid molecules and 10890 water sites.