Figure 1
From: Subdiffusion in Membrane Permeation of Small Molecules
(A) Snapshot of a portion of the simulation system. Methanol is depicted as spheres, with H, C, and O atoms colored respectively in white, green, and red. The lipids are shown as sticks, with C, N, O, and P atoms in gray, blue, red and gold. Lipid hydrogen atoms are not shown. Although the simulation included explicit water molecules, here, for clarity, water is represented as a translucent turquoise surface. (B) Free-energy profile for the translocation of methanol across a fully hydrated palmitoyl-oleoyl-phosphatidylcholine bilayer. The transition coordinate, z, is the distance between the mid-plane of the bilayer and the center of mass of the methanol molecule. The raw free-energy profile (magenta curve) and that obtained from the antisymmetrized gradient (black curve), taking advantage of the symmetry of the pure bilayer, are compared. The error bars represent the estimated uncertainty (see Methods) of the free-energy for moving the methanol molecule from a position far from the membrane to the position z.
