Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane - Nanopores: Sensing and Fundamental Biological Interactions - page 169

Fig. 7.11 Chart diagram of
the proposed electric circuit
approach to compute the
response of a DNA strand
translocation through a
nanopore
to each SiO 2 layer by a symbolic single capacitor, connected to both resistor
networks in the case of the intermediate layer and to one resistor network and the
electrolyte solution in the case of the external layers. Finally we introduce two
parasitic capacitors connected in parallel with the output of both electrodes; they
account for the capacitors that will inevitably appear with the connection to any
measurement device such as instrumentation amplifiers, and for which we assumed
a fixed value of 0.01 pF.
The whole approach is depicted in Fig. 7.11 . The atomistic charge distribution of
the DNA strand obtained from the NAMD [ 24 ] is mapped on our grid in order to
calculate the electrostatic induction of the strand. Then we use our SPICE circuit
model and simulate the translocation of the ssDNA molecule to obtain the electrical
signature of the strand.
7.6 Results and Discussion of the SPICE Model
7.6.1 DNA Strand Translocation
In Fig. 7.12a we show the calculated electrical response (solid line) on the upper
electrode of a 11 bases ssDNA sequence, 5 0 - CCCACCCCCCC -3 0 (C 3 AC 7 ).