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. Author manuscript; available in PMC: 2011 Sep 9.
Published in final edited form as: Nanotechnology. 2010 Sep 1;21(39):395501. doi: 10.1088/0957-4484/21/39/395501

FIGURE 5. MD simulation of the nanopore trap.

FIGURE 5

(a,b) Snapshots of the simulated systems that include dsDNA and water and ions (not shown) as well as a 2.6nm×2.1nm-cross section (a) or a 2.0nm-diameter (b) pore. The dsDNA within the constriction is stretched beyond 0.34nm/base-pair by 0–9% (larger pore) or 20–30% (smaller pore) depending on the external bias voltage. (c,d) The number of base-pairs permeating through the larger (c) or the smaller (d) pore in four MD simulations carried out at different biases. The simulations predict a voltage threshold between 500mV and 1.0V in both cases. (Insets) Normalized histogram of the DNA displacement in the pore constriction under a 0V bias. The solid line shows the distribution expected for a particle restrained by a harmonic spring of a 3.0nN/nm (larger pore) or a 7.2 nN/nm (smaller pore) spring constant.