Fig. 7: MD simulation of Lsi1 with silicic acid.
From: Structural basis for high selectivity of a rice silicon channel Lsi1
Distribution of Si atoms of silicic acid (a) and its overlay with modeled Si(OH)4 molecules (Si1-Si8) (b), and distribution of Si atoms as well as oxygen atoms of silicic acid (c), or oxygen atoms of water (d) in the 0−300 ns MD simulation. In a, structural bottlenecks found in the channel are indicated by red arrows. In d, Wat3, Wat9, and Wat17 locations are indicated by blue arrows. Distributions of (c) and (d) are merged in (e). f The MD trajectory of the silicic acid permeation during the 100−420 ns. Positions of silicic acid (black), Wat3 (green), Wat9 (blue), and Wat17 (red) in the channel are plotted. Enlarged views of (f) and the distributions of Si(OH)4 molecules at the beginning and end of the simulation are provided in Supplementary Fig. 11.
