Skip to main content
SpringerLink
Log in

Gate-modulated graphene quantum point contact device for DNA sensing

  • Published:
Journal of Computational Electronics Aims and scope Submit manuscript

Abstract

In this paper, we present a computational model to describe the electrical response of a constricted graphene nanoribbon (GNR) to biomolecules translocating through a nanopore. For this purpose, we use a self-consistent 3D Poisson equation solver coupled with an accurate three-orbital tight-binding model to assess the ability for a gate electrode to modulate both the carrier concentration as well as the conductance in the GNR. We also investigate the role of electrolytic screening on the sensitivity of the conductance to external charges and find that the gate electrode can either suppress or enhance the screening of biomolecular charges in the nanopore depending on the value of its potential. Translocating a double-stranded DNA molecule along the pore axis imparted a large change in the conductance at particular gate voltages, suggesting that such a device can be used to sense translocating biomolecules and can be actively tuned to maximize its sensitivity.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Avdoshenko, S.M., Nozaki, D., Gomes da Rocha, C., González, J.W., Lee, M.H., Gutierrez, R., Cuniberti, G.: Dynamic and electronic transport properties of dna translocation through graphene nanopores. Nano Lett. 3(5), 1969–1976 (2013)

    Article  Google Scholar 

  2. Baskin, A., Král, P.: Electronic structures of porous nanocarbons. Scientific reports 1 (2011).

  3. Boykin, T.B., Luisier, M., Klimeck, G., Jiang, X., Kharche, N., Zhou, Y., Nayak, S.K.: Accurate six-band nearest-neighbor tight-binding model for the \(\pi \)-bands of bulk graphene and graphene nanoribbons. J. Appl. Phys. 109(10), 104304 (2011)

    Article  Google Scholar 

  4. Branton, D., Deamer, D.W., Marziali, A., Bayley, H., Benner, S.A., Butler, T., Di Ventra, M., Garaj, S., Hibbs, A., Huang, X., et al.: The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26(10), 1146–1153 (2008)

    Article  Google Scholar 

  5. Brey, L., Fertig, H.: Electronic states of graphene nanoribbons studied with the dirac equation. Phys. Rev. B 73(23), 235411 (2006)

    Article  Google Scholar 

  6. Cervantes-Sodi, F., Csanyi, G., Piscanec, S., Ferrari, A.: Edge-functionalized and substitutionally doped graphene nanoribbons: electronic and spin properties. Phys. Rev. B 77(16), 165427 (2008)

    Article  Google Scholar 

  7. Datta, S.: Electronic Transport in Mesoscopic Systems. Cambridge University Press, Cambridge (1997)

    Google Scholar 

  8. Ezawa, M.: Peculiar width dependence of the electronic properties of carbon nanoribbons. Phys. Rev. B 73(4), 045432 (2006)

    Article  Google Scholar 

  9. Garaj, S., Hubbard, W., Reina, A., Kong, J., Branton, D., Golovchenko, J.: Graphene as a subnanometre trans-electrode membrane. Nature 467(7312), 190–193 (2010)

    Article  Google Scholar 

  10. Garaj, S., Liu, S., Golovchenko, J.A., Branton, D.: Molecule-hugging graphene nanopores. Proc. Natl. Acad. Sci. 110(30), 12192–12196 (2013)

    Article  Google Scholar 

  11. Girdhar, A., Sathe, C., Schulten, K., Leburton, J.P.: Graphene quantum point contact transistor for dna sensing. Proc. Natl. Acad. Sci. 110(42), 16748–16753 (2013)

    Article  Google Scholar 

  12. Gracheva, M.E., Aksimentiev, A., Leburton, J.P.: Electrical signatures of single-stranded dna with single base mutations in a nanopore capacitor. Nanotechnology 17(13), 3160 (2006)

    Article  Google Scholar 

  13. Gracheva, M.E., Xiong, A., Aksimentiev, A., Schulten, K., Timp, G., Leburton, J.P.: Simulation of the electric response of dna translocation through a semiconductor nanopore-capacitor. Nanotechnology 17(3), 622 (2006)

    Article  Google Scholar 

  14. Han, M.Y., Özyilmaz, B., Zhang, Y., Kim, P.: Energy band-gap engineering of graphene nanoribbons. Phys. Rev. Lett. 98(20), 206805 (2007)

    Article  Google Scholar 

  15. Ho, C., Qiao, R., Heng, J.B., Chatterjee, A., Timp, R.J., Aluru, N.R., Timp, G.: Electrolytic transport through a synthetic nanometer-diameter pore. Proc. Natl. Acad. Sci. USA 102(30), 10445–10450 (2005)

    Article  Google Scholar 

  16. Ivanov, A.P., Instuli, E., McGilvery, C.M., Baldwin, G., McComb, D.W., Albrecht, T., Edel, J.B.: DNA tunneling detector embedded in a nanopore. Nano Lett. 11(1), 279–285 (2010)

    Article  Google Scholar 

  17. Konschuh, S., Gmitra, M., Fabian, J.: Tight-binding theory of the spin-orbit coupling in graphene. Phys. Rev. B 82(24), 245412 (2010).

  18. Lagerqvist, J., Zwolak, M., Di Ventra, M.: Fast dna sequencing via transverse electronic transport. Nano Lett. 6(4), 779–782 (2006)

    Article  Google Scholar 

  19. Merchant, C.A., Healy, K., Wanunu, M., Ray, V., Peterman, N., Bartel, J., Fischbein, M.D., Venta, K., Luo, Z., Johnson, A.C., et al.: Dna translocation through graphene nanopores. Nano Lett. 10(8), 2915–2921 (2010)

    Article  Google Scholar 

  20. Meric, I., Han, M.Y., Young, A.F., Ozyilmaz, B., Kim, P., Shepard, K.L.: Current saturation in zero-bandgap, top-gated graphene field-effect transistors. Nature Nanotechnol. 3(11), 654–659 (2008)

    Article  Google Scholar 

  21. Nelson, T., Zhang, B., Prezhdo, O.V.: Detection of nucleic acids with graphene nanopores: ab initio characterization of a novel sequencing device. Nano Lett. 10(9), 3237–3242 (2010)

    Article  Google Scholar 

  22. Neto, A.C., Guinea, F., Peres, N., Novoselov, K.S., Geim, A.K.: The electronic properties of graphene. Rev. Modern Phys. 81(1), 109 (2009)

    Article  Google Scholar 

  23. Nikolaev, A., Gracheva, M.E.: Simulation of ionic current through the nanopore in a double-layered semiconductor membrane. Nanotechnology 22(16), 165202 (2011)

    Article  Google Scholar 

  24. Ntalikwa, J.W.: Determination of surface charge density of \(\alpha \)-alumina by acid-base titration. Bull. Chem. Soc. Ethiopia 21(1), 117–128 (2007)

    Article  Google Scholar 

  25. Postma, H.W.C.: Rapid sequencing of individual dna molecules in graphene nanogaps. Nano Lett. 10(2), 420–425 (2010)

    Article  Google Scholar 

  26. Ritter, K.A., Lyding, J.W.: The influence of edge structure on the electronic properties of graphene quantum dots and nanoribbons. Nat. Mater. 8(3), 235–242 (2009)

    Article  Google Scholar 

  27. Saha, K.K., Drndić, M., Nikolic, B.K.: Dna base-specific modulation of microampere transverse edge currents through a metallic graphene nanoribbon with a nanopore. Nano Lett. 12(1), 50–55 (2011)

    Article  Google Scholar 

  28. Sathe, C., Zou, X., Leburton, J.P., Schulten, K.: Computational investigation of dna detection using graphene nanopores. ACS Nano 5(11), 8842–8851 (2011)

    Article  Google Scholar 

  29. Schadt, E.E., Turner, S., Kasarskis, A.: A window into third-generation sequencing. Hum. Mol. Genet. 19(R2), R227–R240 (2010)

    Article  Google Scholar 

  30. Schneider, G.F., Kowalczyk, S.W., Calado, V.E., Pandraud, G., Zandbergen, H.W., Vandersypen, L.M., Dekker, C.: Dna translocation through graphene nanopores. Nano Lett. 10(8), 3163–3167 (2010)

  31. Sint, K., Wang, B., Král, P.: Selective ion passage through functionalized graphene nanopores. J. Am. Chem. Soc. 130(49), 16448–16449 (2008)

    Article  Google Scholar 

  32. Storm, A., Chen, J., Ling, X., Zandbergen, H., Dekker, C.: Fabrication of solid-state nanopores with single-nanometre precision. Nat. Mater. 2(8), 537–540 (2003)

    Article  Google Scholar 

  33. Sverjensky, D.A.: Prediction of surface charge on oxides in salt solutions. Geochimica et Cosmochimica Acta 69(2), 225–257 (2005)

    Article  Google Scholar 

  34. Wells, D.B., Belkin, M., Comer, J., Aksimentiev, A.: Assessing graphene nanopores for sequencing dna. Nano Lett. 12(8), 4117–4123 (2012)

    Article  Google Scholar 

  35. Xie, P., Xiong, Q., Fang, Y., Qing, Q., Lieber, C.M.: Local electrical potential detection of dna by nanowire-nanopore sensors. Nat. Nanotechnol. 7(2), 119–125 (2012)

    Article  Google Scholar 

Download references

Acknowledgments

A.G. and J.-P.L. thank Oxford Nanopore Technology for their support. A.G. and C.S. would like to thank the Beckman Institute for their support through the Beckman Graduate Fellowship, as well as the Taub Campus Cluster for computational resources. This work was supported by National Institutes of Health (NIH) grant 9P41GM104601 and by the National Science Foundation (NSF) grant HPY0822613. This work used computer time on Stampede at the Texas Advanced Computing Center (TACC), provided by grant MCA93S028 from the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant number OCI-1053575

Author information

Authors and Affiliations

  1. Beckman Institute for Advanced Science and Technology, 405 N Mathews Ave, Urbana, IL, 61801, USA

    Anuj Girdhar, Chaitanya Sathe, Klaus Schulten & Jean-Pierre Leburton

Authors
  1. Anuj Girdhar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chaitanya Sathe
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Klaus Schulten
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jean-Pierre Leburton
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jean-Pierre Leburton.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Girdhar, A., Sathe, C., Schulten, K. et al. Gate-modulated graphene quantum point contact device for DNA sensing. J Comput Electron 13, 839–846 (2014). https://doi.org/10.1007/s10825-014-0596-6

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10825-014-0596-6

Keywords

Search

Navigation