Paper Citing NAMD - Abstract
Titov, Alexey V.; Wang, Boyang; Sint, Kyaw; Kral, Petr
Controllable Synthetic Molecular Channels: Biomimetic Ammonia Switch
JOURNAL OF PHYSICAL CHEMISTRY B, 114:1174-1179, JAN 21 2010
We use molecular dynamics simulations combined with iterative screening to test if one can design mechanically controllable and selective molecular pores. The first model pore is formed by two stacked carbon nanocones connected by aliphatic chains at their open tips, in analogy to aquaporins. It turns out that when one nanocone is gradually rotated with respect to the other, the molecular chains alter the size of the nanopore formed at the cone tips and control the flow rates of liquid pentane through it. The second model pore is formed by two carbon nanotubes joined by a cylindrical structure of antiparallel peptides. By application of a torque to one of the nanotubes, while holding the other, we can reversibly fold the peptides into forward or backward-twisted barrels. We have modified the internal residues in these barrels to make these pores selective and controllable. Eventually, we found a nanopore that in the two folded configurations has very different transmission rates for hydrated NH(3) molecules.
