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First-principles vs. semi-empirical modeling of global and local electronic transport properties of graphene nanopore-based sensors for DNA sequencing
Mesoscale and Nanoscale Physics · Submitted 19 Aug 2014
abstract compiled · 2026-09-23 · no language-model review
The authors' main claim The large discrepancy we find between the results obtained from NEGF+DFT vs. those obtained from NEGF+SCC-DFTB or NEGF+SC-EH approaches could be of great importance when selecting proper computational algorithms for {\em in silico} design of optimal nanoelectronic sensors for rapid DNA sequencing.
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Using first-principles quantum transport simulations, based on the nonequilibrium Green function formalism combined with density functional theory (NEGF+DFT), we examine changes in the total and local electronic currents within the plane of graphene nanoribbon with zigzag edges (ZGNR) hosting a nanopore which are induced by inserting a DNA nucleobase into the pore. We find a sizable change of the zero-bias conductance of two-terminal ZGNR + nanopore device after the nucleobase is placed into the most probable position (according to molecular dynamics trajectories) inside the nanopore of a small diameter \mbox{$D=1.2$ nm}. Although such effect decreases as the nanopore size is increased to \mbox{$D=1.7$ nm}, the contrast between currents in ZGNR + nanopore and ZGNR + nanopore + nucleobase systems can be enhanced by applying a small bias voltage $V_b \lesssim 0.1$ V. This is explained microscopically as being due to DNA nucleobase-induced modification of spatial profile of local current density around the edges of ZGNR. We repeat the same analysis using NEGF combined with self-consistent charge density functional tight-binding (NEGF+SCC-DFTB) or self-consistent extended H\"{u}ckel (NEGF+SC-EH) semi-empirical methodologies. The large discrepancy we find between the results obtained from NEGF+DFT vs. those obtained from NEGF+SCC-DFTB or NEGF+SC-EH approaches could be of great importance when selecting proper computational algorithms for {\em in silico} design of optimal nanoelectronic sensors for rapid DNA sequencing.
background contribution method result interpretation main claim
| # | sentence | role | the authors' own work | states the main conclusion | strength |
|---|---|---|---|---|---|
| s0 | Using first-principles quantum transport simulations, based on the nonequilibrium Green function formalism combined with density functional theory (NEGF+DFT), we examine changes in the total and local electronic currents within the plane of graphene nanoribbon with zigzag edges (ZGNR) hosting a nanopore which are induced by inserting a DNA nucleobase into the pore. | contribution 0.57 | 0.95 | 0.05 | asserted 0.94 |
| s1 | We find a sizable change of the zero-bias conductance of two-terminal ZGNR + nanopore device after the nucleobase is placed into the most probable position (according to molecular dynamics trajectories) inside the nanopore of a small diameter \mbox{$D=1.2$ nm}. | result 1.00 | 0.97 | 0.19 | asserted 1.00 |
| s2 | Although such effect decreases as the nanopore size is increased to \mbox{$D=1.7$ nm}, the contrast between currents in ZGNR + nanopore and ZGNR + nanopore + nucleobase systems can be enhanced by applying a small bias voltage $V_b \lesssim 0.1$ V. | result 1.00 | 0.94 | 0.12 | asserted 0.97 |
| s3 | This is explained microscopically as being due to DNA nucleobase-induced modification of spatial profile of local current density around the edges of ZGNR. | interpretation 1.00 | 0.85 | 0.11 | asserted 0.99 |
| s4 | We repeat the same analysis using NEGF combined with self-consistent charge density functional tight-binding (NEGF+SCC-DFTB) or self-consistent extended H\"{u}ckel (NEGF+SC-EH) semi-empirical methodologies. | method 0.93 | 0.94 | 0.04 | asserted 0.92 |
| s5 | The large discrepancy we find between the results obtained from NEGF+DFT vs. those obtained from NEGF+SCC-DFTB or NEGF+SC-EH approaches could be of great importance when selecting proper computational algorithms for {\em in silico} design of optimal nanoelectronic sensors for rapid DNA sequencing. | interpretation 0.97 | 0.92 | 0.78 | hedged possibility 0.99 |
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Original abstract
Using first-principles quantum transport simulations, based on the nonequilibrium Green function formalism combined with density functional theory (NEGF+DFT), we examine changes in the total and local electronic currents within the plane of graphene nanoribbon with zigzag edges (ZGNR) hosting a nanopore which are induced by inserting a DNA nucleobase into the pore. We find a sizable change of the zero-bias conductance of two-terminal ZGNR + nanopore device after the nucleobase is placed into the most probable position (according to molecular dynamics trajectories) inside the nanopore of a small diameter \mbox{$D=1.2$ nm}. Although such effect decreases as the nanopore size is increased to \mbox{$D=1.7$ nm}, the contrast between currents in ZGNR + nanopore and ZGNR + nanopore + nucleobase systems can be enhanced by applying a small bias voltage $V_b \lesssim 0.1$ V. This is explained microscopically as being due to DNA nucleobase-induced modification of spatial profile of local current density around the edges of ZGNR. We repeat the same analysis using NEGF combined with self-consistent charge density functional tight-binding (NEGF+SCC-DFTB) or self-consistent extended H\"{u}ckel (NEGF+SC-EH) semi-empirical methodologies. The large discrepancy we find between the results obtained from NEGF+DFT vs. those obtained from NEGF+SCC-DFTB or NEGF+SC-EH approaches could be of great importance when selecting proper computational algorithms for {\em in silico} design of optimal nanoelectronic sensors for rapid DNA sequencing.
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