Local current analysis on defective zigzag graphene nanoribbons devices for biosensor material applications

Abstract

In this contribution, we aim at investigating the mechanism of biosensing in graphene-based materials from first principles. Inspired by recent experiments, we construct an atomistic model composed of a pyrene molecule serving as a linker fragment, which is used in experiment to attach certain aptamers, and a defective zigzag graphene nanoribbons (ZGNRs). Density functional theory including dispersive interaction is employed to study the energetics of the linker absorption on the defective ZGNRs. Combining non-equilibrium Green's function and the Landauer formalism, the total current-bias voltage dependence through the device is evaluated. Modifying the distance between the linker molecule and the nanojunction plane reveals a quantitative change in the total current-bias voltage dependence, which correlates to the experimental measurements. In order to illuminate the geometric origin of these variation observed in the considered systems, the local currents through the device are investigated using the method originally introduced by Evers and co-workers. In our new implementation, the numerical efficiency is improved by applying sparse matrix storage and spectral filtering techniques, without compromising the resolution of the local currents. Local current density maps qualitatively demonstrate the local variation of the interference between the linker molecule and the nanojunction plane.

Understanding Charge Transport in Triarylmethyl-Based Spintronic Nanodevices

“…The Hamiltonian of the nanojunction is parametrized as described in previous work. − In a nutshell, a finite cluster is composed of the central region connected to a finite number of oxTAM units serving as leads. The last oxTAM unit on each side is saturated by hydrogen atoms along the polymer direction.…”

“…For more detail on the implementation and convergence behavior of the method, see refs and . In the present work, we also compute the associated velocity field from the knowledge of the spin density, ρ σ ( r ), as This yields further physical insight into the transport mechanism.…”

“…To reduce the computational demands on matrix elements storage and the evaluation process of the current density, eq 7 is simplified using numerical techniques introduced in previous work. 42 To exploit the strong localization of the atom-centered basis used to compute the matrix elements H M , S M , and G σ as , only elements of the matrix of atomic orbitals and their derivatives larger than a chosen threshold value are stored in compressed row storage. Further, we extract the relevant spectral information from G σ as by keeping the largest N red values obtained via singular value decomposition,…”

Edge Effect in Electronic and Transport Properties of 1D Fluorinated Graphene Materials

“…In our previous work, we have introduced two numerical techniques to evaluate Equation ( 6 ) with improved computational efficiency: a real-space filter using the compressed row storage (CRS) format [ 50 ], and a spectral filter based on single value decomposition (SVD). A detailed description can be found in the Method section in [ 51 ]. Here, we apply the CRS on the atomic orbitals-based matrix and their derivatives, and the SVD technique on the matrix containing the antisymmetric elements.…”

The Limits of Inelastic Tunneling Spectroscopy for Identifying Transport Pathways

“…While a number of theoretical approaches exist for extracting pathway information, ,,,,,− access by experimental methods is limited. An experimental technique which is able to provide pathway information is inelastic tunneling spectroscopy (IETS), ,− in which signatures of tunneling electrons exciting molecular vibrations are recorded.…”