Graphene Sculpturene Nanopores for DNA Nucleobase Sensing

Abstract

To demonstrate the potential of nanopores in bilayer graphene for DNA sequencing, we computed the current-voltage characteristics of a bilayer graphene junction containing a nanopore and found that they change significantly when nucleobases are transported through the pore. To demonstrate the sensitivity and selectivity of example devices, we computed the probability distribution PX(β) of the quantity β representing the change in the logarithmic current through the pore due to the presence of a nucleobase X (X = adenine, thymine, guanine, or cytosine). We quantified the selectivity of the bilayer-graphene nanopores by showing that PX(β) exhibits distinct peaks for each base X. To demonstrate that such discriminating sensing is a general feature of bilayer nanopores, the well-separated positions of these peaks were shown to be present for different pores, with alternative examples of electrical contacts.

Graphene nanodevices for DNA sequencing

“…Similar results were obtained from various theoretical calculations, where electronic transport was studied using DFT and NEGF for different types of ribbons (width ∼3 nm and pore diameter ∼1.5nm) in the absence and presence of each of the four DNA nucleobases [72][73][74][75][76][77][78][79].…”

“…Theoretical studies show that an armchair ribbon will be semiconducting [66][67][68][69] and that a zigzag-edged ribbon is metallic with a current profile that peaks at the edges [66,[69][70][71]. Both armchair and zigzag nanoribbons have been proposed to present promising platforms for DNA sequencing in a large number of theoretical reports [72][73][74][75][76][77][78][79], and experimentalists have begun to explore this approach [80][81][82][83][84][85].…”

“…These point contacts were found to exhibit a greater sensitivity than armchair edged ribbons provided that the carrier density is enhanced, for example by gating [76]. Another more complex device, consisting of a two nanoribbons stacked on top of one another to form a small overhang (∼3 nm) with a nanopore (∼1.5 nm) [78], yielded again base discrimination.…”

Enhancing the thermoelectric figure of merit in engineered graphene nanoribbons

“…To find the optimized geometry and ground state Hamiltonian of the structure analogously as described in [9], we employed the SIESTA [13] implementation of DFT using the generalized gradient approximation (GGA) of the exchange and correlation functional with the Perdew-Burke-Ernzerhof parameterization (PBE) [14] a double zeta polarized basis set, a real-space grid defined with a plane wave cut-off energy of 250 Ry and a maximum force tolerance of 40 meV/Å. From the converged DFT calculation, the underlying mean-field Hamiltonian was combined with the GOLLUM [12] implementation of the nonequilibrium Greens function (NEGF) method.…”

“…In what follows, we explore the electrical conductance, thermal conductance, and Seebeck and Peltier coefficients of the range of structures shown in Figure 1. These engineered graphene ribbons include: a zigzag monolayer graphene nanoribbon with hydrogen terminated edges (Figure 1a), a monolayer graphene nanopore with hydrogen terminated edges (Figure 1b), an AA-bilayer graphene nanoribbon (Figure 1c), an engineered bilayer graphene nanopore (Figure 1d), an AA-bilayer graphene with monolayer lead, in which the transport takes place from the top layer to the bottom layer (Figure 1e), an engineered bilayer graphene nanopore with monolayer leads and either hydrogen termination [9] (Figure 1f) or oxygen termination (Figure 1g) inside the pore. The ribbon lengths (L) and widths (W) in all cases are almost equal (L ≈ 6 nm, W ≈ 3 nm) and the pores sizes are about 1.3 nm.…”