Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane - Nanopores: Sensing and Fundamental Biological Interactions - page 156

7.3.1 Computational Approach

We assume a quasi-static behavior of electrical response, and consider a step-by-step
motion of DNA through the nanopore. An atomic-level description of the DNA
strand with its charge distribution has been computed by using the NAMD code as
described in [ 24 ]. In this method, a molecular system is approximated by an
ensemble of atoms interacting with each other according to a molecular force field
that has been developed and calibrated to reproduce quantitatively physical proper-
ties of the simulated system [ 17 , 27 ]. For each DNA position in the nanopore we
compute the voltage response on the capacitor electrodes self-consistently by a 3D
Poisson Solver (PS) incorporating the charge variation in the electrolytic solution as
well as in the semiconductor materials and the oxide [ 19 ].

7.3.2 3D Self-Consistent Modeling of the Capacitor Response

By tracking the motion of every atom in the DNA strand during its translocation,
molecular dynamics provides the temporal charge distribution of the polymer in the
nanopore. In this work we use the molecular charge distribution for a “snapshot” of
the DNA conformations in a continuum charge model of the electrolyte and the
solid state materials to compute the electrostatic potential in the whole region, and
specifically in the Si layers to obtain the voltage response due to DNA translocation.
Here, we assume the snapshot of the initial DNA charge distribution moves rigidly
through the pore. In the future we can analyze the behavior of a succession of such
“snapshots”.

7.3.2.1 Charge Model of the Buffer Solution

At room temperature, we assume that all KCl molecules in the electrolyte solution
are fully dissociated. Hence, in the absence of external potential, there is an equal
number of K + and Cl - ions when the electrolyte solution is at equilibrium:

½K þ 0 ¼½Cl 0 ¼ c (7.1)

where c is the concentration of the buffer solution, which is assumed to be constant.
See Appendix for details.
In the presence of an electrostatic potential

f

(r), the ion concentrations in

solution obey the Boltzmann statistics [ 28 ]:

;

qfð Þ

r

½K þ ð Þ¼½K þ 0 exp

r (7.2)

kT