Paper Citing NAMD - Abstract
Gracheva, Maria E.; Leroux, Amandine; Destine, Jacques; Leburton, Jean-Pierre
Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane
NANOPORES: SENSING AND FUNDAMENTAL BIOLOGICAL INTERACTIONS, 151-175, 2011
A two-level computational model for simulation of the electric signal detected on the electrodes of a Semiconductor-Oxide-Semiconductor (SOS) capacitor 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 translocation 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.
