Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane - Nanopores: Sensing and Fundamental Biological Interactions - page 151

Chapter 7
Simulation of Electronic Sensing of Biomolecules
in Translocation Through a Nanopore
in a Semiconductor Membrane
Maria E. Gracheva, Amandine Leroux, Jacques Destin ´ ,
and Jean-Pierre Leburton
Abstract A two-level computational model for simulation of the electric signal
detected on the electrodes of a Semiconductor-Oxide-Semiconductor (SOS) capac-
itor forming a nanoscale artificial membrane, and containing a nanopore with
translocating DNA are presented. At the device level, a three-dimensional self-
consistent scheme involving snapshots of the DNA charge distribution, as well as
the electrolytic charge and the charge in the semiconductor membrane compute the
electrostatic potential over the whole solid-liquid system. With this numerical
approach we investigate the possibility of resolving individual nucleotides as well
as their types in the absence of conformational disorder. At the system level, we
develop a circuit-element model for the SOS semiconductor membrane where the
membrane is discretized into interconnected elementary circuit elements to assess
the response of the DNA away from the pore. The model is tested on the transloca-
tion of 11 base single-stranded C 3 AC 7 DNA molecule, for which the electric signal
shows good qualitative agreement with the multi-scale device approach of
Gracheva et al. also described in the first part of this chapter (Gracheva et al.,
Nanotech. 17, 622-633, 2006), while quantifying the low-pass filtering in the
membrane. 1
Keywords DNA sequencing • Solid-state nanopore • Poisson equation •
Multi-scale approach • Circuit modeling • SPICE simulation