Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane - Nanopores: Sensing and Fundamental Biological Interactions - page 153

Fig. 7.1 ( Center panel ) Schematic of a novel biosensor consisting of a nanopore in a capacitor
membrane. ( Right panel ) High resolution TEM through the capacitor membrane structure.
( Left panel ) High resolution lattice image of a nanopore sputtered into the capacitor membrane.
Reproduced from [ 19 ] with permission
methods for measuring fine signals with nanopore sensors are being developed
[ 18 , 20 - 23 ], the theoretical resolution of such measurements can be estimated
through computation.
Following a preliminary experimental demonstration, we have developed a
computational model that simulates the electrical response of DNA translocation
through a nanopore in a SiO 2 membrane sandwiched between two conducting
layers of heavily doped Si [Fig. 7.1 (center panel)] [ 19 ]. In this approach, the
DNA translocation through the nanopore is simulated by using “snapshots” of
the molecular charge distribution obtained from atomistic modeling [ 19 , 24 ]
while the voltage response in the solid-state capacitor is modeled by a 3D self-
consistent Poisson Solver (PS). We evaluate the possibility of resolving individual
nucleotides as well as their types. We show that the new device has the potential to
identify DNA molecules by using the voltage induced on the electrodes without
utilizing the signal of ionic current fluctuations.
In addition, to account for the ohmic and capacitive loading in the membrane
and to assess the magnitude of the signal on a detector far from the nanopore
we developed a simple membrane-nanopore model based on a circuit-element
approach to assess the electric response of a DNA translocation along the membrane.
In this approach, the electrostatic induction from each of the charges in the DNA
strand moving through the pore and felt by the semiconductor membranes is
modeled as a current source, while the membrane equivalent circuit is simulated
by SPICE to assess the voltage traces collected on the remote electrodes of the
nanopore-capacitor.
This chapter is organized as follows: Section 7.2 describes the structure of the
membrane. Section 7.3 describes the computational model to simulate the electrical
response of the solid-state capacitor to a DNA translocating through the nanopore.
The model of the DNA translocation and the elements of the equivalent electric
circuit are detailed respectively in Section 7.5 . Sections 7.4 and 7.6 present and
discuss the results obtained by our models.