Paper Citing NAMD - Abstract
Cruz-Chu, Eduardo R.; Schulten, Klaus
Computational Microscopy of the Role of Protonable Surface Residues in Nanoprecipitation Oscillations
ACS NANO, 4:4463-4474, AUG 2010
A novel phenomenon has recently been reported in polymeric nanopores. This phenomenon, so-called nanoprecipitation, is characterized by the transient formation of precipitates in the nanopore lumen, producing a sequence of low and high conductance states in the ionic current through the pore. By means of all-atom molecular dynamics simulations, we studied nanoprecipitation for polyethylene terephthalate nanopore immersed in electrolytic solution containing calcium phosphate, covering a total simulation time of 1.24 mu s. Our results suggest that protonable surface residues at the nanopore surface, namely carboxyl groups, trigger the formation of precipitates that strongly adhere to the surface, blocking the pore and producing the low conductance state. On the basis of the simulations, we propose a mechanism for the formation of the high conductance state; the mechanism involves detachment of the precipitate from the surface due to reprotonation of carboxyl groups and subsequent translocation of the precipitate out of the pore.
