Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane - Nanopores: Sensing and Fundamental Biological Interactions - page 171

9 10 11 12 13 14 15 16

t(ns)

Fig. 7.13 Electric responses of the C 3 AC 7 strand ( black solid line ) and its 11 fragments
( grey dashed line ), each translocating independently through the nanopore, computed on the
upper electrode

the whole C 3 AC 7 strand and 205 m V for the backbone, while the maximum voltage

for a single base is about 35 V. For the sake of comparison, we show on Fig. 7.12b

the voltage traces computed by the multi-scale approach of Gracheva et al. [ 19 , 31 ].
Note that we display voltage trace versus time as Gracheva et al. plot their trace
versus position, which are equivalent given the constant velocity v ¼

m

2 m/s used in
both models. Our results feature a good qualitative agreement regarding the shape
of the curves. There is however a major discrepancy in the magnitude of the signal
which is due to the fact that Gracheva et al. compute the voltage signal over a ring
located at the inner constriction of the nanopore by 3D self-consistent Poisson
Solver, while our SPICE model, which computes the voltage signal on the overall
electrode (Fig. 7.2 ), accounts for the circuit losses in the membrane leading to a
significant reduction of the signal amplitude read by an external observer. More-
over, the response greatly depends on the parasitic capacitors connected in parallel
on the output as they act as a capacitor divider. As a consequence, these parasitic
capacitors should be minimized as much as possible.
As mentioned earlier, we show in Fig. 7.13 , the simulation of the 11 molecular
fragments of the single-stranded C 3 AC 7 molecule, each translocating indepen-
dently through the nanopore-capacitor. Each fragment is composed of a sugar
ring, a phosphate group and a base (except the first one which does not include
the phosphate group) and results in a voltage dip. These voltage dips look quite
similar and overlap significantly. Moreover the fourth trace related to the fragment
containing the A base is not significantly different from the C base signatures.
As discussed above, the first fragment signature exhibits a short positive shoulder.
Our qualitative observations are consistent with the analysis of Gracheva et al. [ 31 ]
as their corresponding simulation features the same characteristics such as the 11