Solid State Nanopores for Selective Sensing of DNA - Nanopores: Sensing and Fundamental Biological Interactions - page 114

variable polymer composition at the surface. The monomer pressure ranged
from 40 mTorr to 160 mTorr and peak powers ranged between 100-150 W. They
controlled the permeability of O 2 and CO 2 through these membranes and found
the permeation rate of the gases as a function of pore diameter and polymer chemistry.
5.3 DNA-Nanopore Interactions by Molecular Dynamics
To achieve optimal design of SSNs for Deoxyribonucleic acid (DNA) analysis,
we need to understand DNA translocation dynamics under different applied volt-
ages and electrolytic solution conditions. During translocation, it is essential to
understand the effect of different forces which influence the DNA movement
through the SSN. Due to the smaller lengths of DNA strands and SSN channels,
DNA dynamics during translocation are still not precisely understood.
Cross et al. demonstrated the effect of SSN diameter on DNAmobility [ 25 ]. They
concluded that in order to understand the molecular dynamics, the SSN diameter
should be comparable to the size of the translocating species. The dependence
of DNA kinetics on temperature has also been reported [ 26 ]. Iqbal and co-workers
have developed a molecular dynamics model where they considered the effect of
ion accumulation at the entrance of the SSNs [ 27 ]. In their simulations, they showed
that higher voltages could compensate for the effects of ion accumulation. They
used nano-scale molecular dynamics NAND for their simulations [ 28 ].
A CHARMM force field was used for DNA-SSNs interaction [ 29 ]. Si 3 N 4
nanopores of different diameters ranging from 1.5 nm to 4 nm were used for
simulations at room temperature as shown in Fig. 5.4 . The supercomputer cluster
POPEL was used for all the simulations. They simulated the effect of SSN diameter
and applied voltage on DNA translocation kinetics.
Fig. 5.4 Figure shows DNA translocation through the nanopore with different diameter: (a) 1.5 nm,
(b)2nm,(c) 3 nm and (d) 4 nm [ 27 ]. Reprinted by permission from New World Publishing
International: American Journal of Biomedical Sciences, copyright (2009)