Paper Citing NAMD - Abstract
Gracheva, M.E.; Xiong, A.L.; Aksimentiev, A.; Schulten, K.; Timp, G.; Leburton, J.P.
Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor
NANOTECHNOLOGY, 17:622-633, FEB 14 2006
A multi-scale/multi-material computational model for simulation of the electric signal detected on the electrodes of a metal-oxide-semiconductor (MOS) capacitor forming a nanoscale artificial membrane, and containing a nanopore with translocating DNA, is presented. The multi-scale approach is based on the incorporation of a molecular dynamics description of a translocating DNA molecule in the nanopore within a three-dimensional Poisson equation self-consistent scheme involving, electrolytic and semiconductor charges for the electrostatic potential calculation. The voltage signal obtained from the simulation supports the possibility for single nucleotide resolution with a nanopore device. The electric signal predicted on the capacitor electrodes complements ongoing experiments exploring the use of nanopores in a MOS capacitor membrane for DNA sequencing.
DOI:10.1088/0957-4484/17/3/002
