Nanopore-Based DNA Sequencing and DNA Motion Control - Nanopores: Sensing and Fundamental Biological Interactions - page 280

molecule are represented by solid circles. The thicknesses W and S are in units of
the intercharge distance of the DNA, d (assumed to be ~0.7 nm for stretched
ssDNA). Voltage bias V 0 is applied on the middle metal layer while the two
other metal layers are grounded. If we ignore the distortion of the electrical field
inside the nanopore, then the electric field inside the nanopore is 0 at the area with
metal wall (metal zone) and takes a constant value E TR ¼V 0 /( Sd )or V 0 /( Sd ) at the
area with dielectric wall (dielectric zone). The net force on the DNA will be
F net ¼ q *( N R - N L )* V 0 /( Sd ), q * is the effective charge on each phosphate group of
the DNA backbone (about 0.5 e) according to [ 34 ], N R is the number of charges on
the DNA that are in the right dielectric zone and N L is the number of charges on the
DNA that are in the left dielectric zone.
As shown in Fig. 11.29a , assuming the dielectric layer thickness S is a half
integer, and the metal layer thickness W is slightly (

e ) larger than integer length, the

Fig. 11.29 For the case that the thickness of the dielectric layer S is a half integer and the
thickness of the metal layer W is slightly larger than an integer: (a) Schematic of forces on
the charges of the DNA at different displacements of the DNA (relative to the nanopore). The force
on each charge of the DNA is represented by a white arrow , pointing the direction of the force.
(b) Schematic of the net force on the DNA vs. the displacement of the DNA d (relative to the

nanopore). (c) The potential associated with the force depicted in (b). DE TR is the effective

trapping barrier. (Adapted from [ 45 ])