Paper Citing NAMD - Abstract
Cruz-Chu, Eduardo R.; Ritz, Thorsten; Siwy, Zuzanna S.; Schulten, Klaus
Molecular control of ionic conduction in polymer nanopores
FARADAY DISCUSSIONS, 143:47-62, 2009
Polymeric nanopores show unique transport properties and have attracted a great deal of scientific interest as a test system to study ionic and molecular transport at the nanoscale. By means of all-atom molecular dynamics, we simulated the ion dynamics inside polymeric polyethylene terephthalate nanopores. For this purpose, we established a protocol to assemble atomic models of polymeric material into which we sculpted a nanopore model with the key features of experimental devices, namely a conical geometry and a negative surface charge density. Molecular dynamics simulations of ion currents through the pore show that the protonation state of the carboxyl group of exposed residues have a considerable effect on ion selectivity, by affecting ionic densities and electrostatic potentials inside the nanopores. The role of high concentrations of Ca(2+) ions was investigated in detail.
