Figure 4
From: Subdiffusion in Membrane Permeation of Small Molecules
Voids within the membrane and their effect on methanol motion.
(A) Snapshot of a molecular dynamics simulation of methanol permeation with spontaneously appearing void regions highlighted in violet. (B) Overlay of the voids in 30 randomly selected snapshots extracted from simulations. (C) Fraction of empty volume as a function of z. The blue and red curves, respectively, were calculated from trajectories in the absence of methanol and with methanol in the interval −5 < z < 5 Å. (D) Evolution of three exemplary large voids in the membrane. The volume of each void is plotted as a function of time from its first appearance. (E) Volume of the void immediately surrounding the methanol molecule during a simulation in which the alcohol occupied the membrane. If there is no empty space adjacent to methanol, then the volume was recorded as zero. Methanol atoms were ignored in computing this volume. (F) Mean squared displacement of methanol along the permeation axis as a function the void size along this axis. The plot represents displacements with a lag time of Δt = 30 ps, averaged over four 1 ns simulations in which the alcohol diffused within the membrane and a bias was applied to yield a flat free-energy profile along z. This void size was calculated as the standard deviation of the positions of the voxels forming the void. The error bars represent standard errors.
