Paper Citing NAMD - Abstract
Zhao, Xiongce; Payne, Christina M.; Cummings, Peter T.; Lee, James W.
Single-strand DNA molecule translocation through nanoelectrode gaps
NANOTECHNOLOGY, 18 Art. No. 424018, OCT 24 2007
Molecular dynamics simulations were performed to investigate the translocation of single-strand DNA through nanoscale electrode gaps under the action of a constant driving force. The application behind this theoretical study is a proposal to use nanoelectrodes as a screening gap as part of a rapid genomic sequencing device. Preliminary results from a series of simulations using various gap widths and driving forces suggest that the narrowest electrode gap that a single-strand DNA can pass is similar to 1.5 nm. The minimum force required to initiate the translocation within nanoseconds is similar to 0.3 nN. Simulations using DNA segments of various lengths indicate that the minimum initiation force is insensitive to the length of DNA. However, the average threading velocity of DNA varies appreciably from short to long DNA segments. We attribute such variation to the different nature of drag force experienced by the short and long DNA segments in the environment. It is found that DNA molecules deform significantly to fit in the shape of the nanogap during the translocation.
