Skip to main content
SpringerLink
Log in

Drilling accurate nanopores for biosensors by energetic multi-wall carbon nanotubes: a molecular dynamics investigation

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

Drilling precise nanopores in thin layers is in rapid demand for biosensing applications. We demonstrate that an energetic multi-wall carbon nanotube (MWCNT) can be a good candidate to fabricate nanopores on graphene from molecular dynamics simulations with a bond-order potential. High-quality nanopores with expected size and smooth margins could be created by an incident nanotube at chosen size and energy. Besides, a nanotube is in advantage of absorbing and translocating many biological macromolecules due to its strong adsorption capacity. It implies a feasible way to drill nanopores and carry big molecules through the fabricated nanopores in one step for fast biosensing applications.

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

Data availability

All data are available on reasonable request to the corresponding author.

References

  1. Venkatesan B, Bashir R (2011) Nanopore sensors for nucleic acid analysis. Nat Nanotech 6:615–624. https://doi.org/10.1038/nnano.2011.129

    Article  CAS  Google Scholar 

  2. Fried JP, Swett JL, Nadappuram BP, et al. (2021) In situ solid-state nanopore fabrication. Chem Soc Rev 10:1039. https://doi.org/10.1039/D0CS00924E

    Google Scholar 

  3. Bell N, Keyser U (2016) Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores. Nat Nanotech 11:645–651. https://doi.org/10.1038/nnano.2016.50

    Article  CAS  Google Scholar 

  4. Kasianowicz JJ, Brandin E, Branton D, Deamer DW (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA 93:13770

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Dekker C (2007) Solid-state nanopores. Nat Nanotech 2:209–215. https://doi.org/10.1038/nnano.2007.27

    Article  CAS  Google Scholar 

  6. Plesa C, Kowalczyk SW, Zinsmeester R, Grosberg AY, Rabin Y, Dekker C (2013) Fast translocation of proteins through solid state nanopores. Nano Lett 13:658–63. https://doi.org/10.1021/nl3042678

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Squires A, Atas E, Meller A (2015) Nanopore sensing of individual transcription factors bound to DNA. Sci Rep 5:11643. https://doi.org/10.1038/srep11643

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Singer A, Wanunu M, Morrison W, et al. (2010) Nanopore based sequence specific detection of duplex DNA for genomic profiling. Nano Lett 10:738–742. https://doi.org/10.1021/nl100058y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Heerema SJ, Vicarelli L, Pud S, Schouten RN, Zandbergen HW, Dekker C (2018) Probing DNA translocations with inplane current signals in a graphene nanoribbon with a nanopore. ACS Nano 12:2623–2633. https://doi.org/10.1021/acsnano.7b08635

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Danda G, Masih Das P, Chou YC, Mlack JT, Parkin WM, Naylor CH, Fujisawa K, Zhang T, Fulton LB, Terrones M, Johnson AT, Drndic M (2017) Monolayer WS2 nanopores for DNA translocation with light-adjustable sizes. ACS Nano 11:1937–1945. https://doi.org/10.1021/acsnano.6b08028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Liu K, Feng J, Kis A, Radenovic A (2014) Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation. ACS Nano 8:2504–2511. https://doi.org/10.1021/nn406102h

    Article  CAS  PubMed  Google Scholar 

  12. Schneider GF, Kowalczyk SW, Calado VE, et al. (2010) DNA translocation through graphene nanopores. Nano Lett 10:3163–3167. https://doi.org/10.1021/nl102069z

    Article  CAS  PubMed  Google Scholar 

  13. Wang R, Gilboa T, Song J, et al. (2018) Single-molecule discrimination of labeled DNAs and polypeptides using photoluminescent-free TiO2 nanopores. ACS Nano 12:11648–11656. https://doi.org/10.1021/acsnano.8b07055

    Article  CAS  PubMed  Google Scholar 

  14. Xia D, Huynh C, McVey S, Kobler A, Stern L, Yuan Z, Ling XS (2018) Rapid fabrication of solid-state nanopores with high reproducibility over a large area using a helium ion microscope. Nanoscale 10:5198. https://doi.org/10.1039/C7NR08406D

    Article  CAS  PubMed  Google Scholar 

  15. Kim MJ, Wanunu M, Bell DC, Meller A (2006) Rapid fabrication of uniformly sized nanopores and nanopore arrays for parallel DNA analysis. Adv Mater 18:3149–3153

    Article  CAS  Google Scholar 

  16. Novoselov KS, Geim AK, Morozov SV, Jiang D, Zhang Y, Dubonos SV, Grigorieva IV, Firsov AA (2004) Electric field effect in atomically thin carbon films. Science 306:666–9. https://doi.org/10.1126/science.1102896

    Article  CAS  PubMed  Google Scholar 

  17. Herbig C, Michely T (2016) Graphene: the ultimately thin sputtering shield. 2D Mater 3:025032. https://doi.org/10.1088/2053-1583/3/2/025032

    Article  Google Scholar 

  18. Fischbein MD, Drndi M (2008) Electron beam nanosculpting of suspended graphene sheets. Appl Phys Lett 93:113107. https://doi.org/10.1063/1.2980518

    Article  Google Scholar 

  19. Storm AJ, Chen JH, Ling XS, et al. (2003) Fabrication of solid-state nanopores with single-nanometre precision. Nat Mater 2:537–540. https://doi.org/10.1038/nmat941

    Article  CAS  PubMed  Google Scholar 

  20. Watanabe K, Taniguchi T, Kanda H (2004) Direct-bandgap properties and evidence for ultraviolet lasing of hexagonal boron nitride single crystal. Nat Mater 3:404–409. https://doi.org/10.1038/nmat1134

    Article  CAS  PubMed  Google Scholar 

  21. Zvuloni E, Zrehen A, Gilboa T, Meller A (2021) Fast and deterministic fabrication of sub-5 nanometer solid-state pores by feedback-controlled laser processing. ACS Nano 10:1021. https://doi.org/10.1021/acsnano.1c03773

    Google Scholar 

  22. Gilboa T, Zvuloni E, Zrehen A, Squires AH, Meller A (2019) Automated, ultra-fast laser-drilling of nanometer scale pores and nanopore arrays in aqueous solutions. Adv Funct Mater 19:00642. https://doi.org/10.1002/adfm.201900642

    Google Scholar 

  23. Verschueren DV, Yang W, Dekker C (2018) Lithography-based fabrication of nanopore arrays in freestanding SiN and graphene membranes. Nanotechnology. 29:145302. https://doi.org/10.1088/1361-6528/aaabce

    Article  PubMed  PubMed Central  Google Scholar 

  24. Sawafta F, Clancy B, Carlsen AT, Huber M, Hall AR (2014) Solid-state nanopores and nanopore arrays optimized for optical detection. Nanoscale 6:6991. https://doi.org/10.1039/C4NR00305E

    Article  CAS  PubMed  Google Scholar 

  25. Zhao S, Xue J, Liang L, Wang Y, Yan JS (2012) Drilling nanopores in graphene with clusters: a molecular dynamics. J Phys Chem C 116:11776–11782. https://doi.org/10.1021/jp3023293

    Article  CAS  Google Scholar 

  26. Li W, Liang L, Zhao S, Zhang S, Xue J (2013) Fabrication of nanopores in a graphene sheet with heavy ions: a molecular dynamics study. J. Appl. Phys. 114:234304

    Article  Google Scholar 

  27. Lee JH, Loya PE, Lou J, Thomas EL (2014) Dynamic mechanical behavior of multilayer graphene via supersonic projectile penetration. Science 346:1092–1096. https://doi.org/10.1126/science.1258544

    Article  CAS  PubMed  Google Scholar 

  28. Berdiyorov GR, Mortazavi B, Ahzi S, Peeters FM, Khraisheh MK (2016) Effect of straining graphene on nanopore creation using Si cluster bombardment: a reactive atomistic investigation. J Appl Phys 120:225108. https://doi.org/10.1063/1.4971767

    Article  Google Scholar 

  29. Bai Z, Zhang L, Li H, Liu L (2016) Nanopore creation in graphene by ion beam irradiation: geometry, quality, and efficiency. In: Bai Z, Zhang L, Li H, Liu L (eds) Appl Mater Interfaces, vol 8, pp 24803–24809

  30. Verkhoturov SV, Czerwinski B, Verkhoturov DS, Geng S, Delcorte A, Schweikert EA (2017) Ejection-ionization of molecules from free standing graphene. J Chem Phys 146:084308. https://doi.org/10.1063/1.4976832

    Article  PubMed  Google Scholar 

  31. Geng S, Verkhoturov SV, Eller MJ, Della-Negra S, Schweikert EA (2017) The collision of a hypervelocity massive projectile with free-standing graphene: investigation of secondary ion emission and projectile fragmentation. J Chem Phys. 146:054305. https://doi.org/10.1063/1.4975171

    Article  PubMed  Google Scholar 

  32. Verkhoturov SV, Gounski M, Verkhoturov DS, Geng S, Postawa Z, Schweikert EA (2018) Trampoline ejection of organic molecules from graphene and graphite via keV cluster ions impacts. J Chem Phys 148:144309. https://doi.org/10.1063/1.5021352

    Article  PubMed  Google Scholar 

  33. Golunski M, Postawa Z (2018) Effect of kinetic energy and impact angle on carbon ejection from a free-standing graphene bombarded by kilo-electron-volt C60. J Vac Sci Technol B 36:03F112. https://doi.org/10.1116/1.5019732

    Article  Google Scholar 

  34. Abadi R, Shirazi A, Izadifar M, Sepahi M, Rabczuk T (2018) Fabrication of nanopores in polycrystalline boron-nitride nanosheet by using Si, SiC and diamond clusters bombardment. Comp Mater Sci 145:280–290

    Article  CAS  Google Scholar 

  35. Verkhoturov SV, Gounski M, Verkhoturov DS et al (2019) Hypervelocity cluster ion impacts on free standing graphene: experiment, theory, and applications. J Chem Phys 150:160901. https://doi.org/10.1063/1.5080606

    Article  PubMed  Google Scholar 

  36. Popok VN, Campbell EEB (2006) Beams of atomic cluster effect on impact with solids. Rev Adv Mater Sci 11:19–45

    CAS  Google Scholar 

  37. Plimpton S (1995) Fast parallel algorithms for short-range molecular dynamics. J Comput Phys 117:1–19. https://doi.org/10.1006/jcph.1995.1039

    Article  CAS  Google Scholar 

  38. Zhou XW, Ward DK, Foster ME (2015) An analytical bond-order potential for carbon. J Comput Chem 36:1719–1735. https://doi.org/10.1002/jcc.23949

    Article  CAS  PubMed  Google Scholar 

  39. Berendsen HJC, Postma JPM, Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684. https://doi.org/10.1063/1.448118

    Article  CAS  Google Scholar 

  40. Stukowski A (2010) Visualization and analysis of atomistic simulation data with OVITO the open visualization tool. Model Simul Mater Sci Eng 18:015012

    Article  Google Scholar 

  41. Zubieta-Lopez FA et al (2020) Li containing endohedral SWCNT: DFT study of the structural and electronic properties. Diamond Related Mater 110:108108. https://doi.org/10.1016/j.diamond.2020.108108

    Article  CAS  Google Scholar 

  42. Rodriguez-Juarez A, Chigo-Anota E, Hernandez-Cocoletzi H, Sanchez-Ramirez JF, Castro M (2017) Stability and electronic properties of armchair boron nitride/carbon nanotubes, fullerenes. Nanotubes and Carbon Nanostructures 25(12):716–725. https://doi.org/10.1080/1536383X.2017.1389905

    Article  Google Scholar 

  43. Garcia-Hernandez E, Chigo-Anota E (2021) Structural defects on (5,5) single-walled carbon nanotubes: impact on their electronic properties and chemical reactivity from a DFT perspective. Phys E 134:114874. https://doi.org/10.1016/j.physe.2021.114874

    Article  CAS  Google Scholar 

  44. Sozykin SA, Beskachko VP (2022) The structure and properties of a carbon nanotube (7, 7) with a vacancy defect. Lett Mater 12(1):32–36. https://doi.org/10.22226/2410-3535-2022-1-32-36

    Article  Google Scholar 

  45. Schneider CA, Rasband WS (2012) Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9(7):671–5. https://doi.org/10.1038/nmeth.2089

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Funding

This work was financially supported by the Hunan education department under Grant No. 19B386, and the key projects of Hunan education department (No. 20A344).

Author information

Authors and Affiliations

  1. Department of Physics, Hunan University of Arts and Science, Dongting Road 3150, Changde, 415000, Hunan, China

    Changsheng Li, Zilin Wang & Lei Ma

Authors
  1. Changsheng Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zilin Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lei Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

C.L.: conceptualization, simulation, validation, visualization, and writing of the manuscript. Z.W.: methodology, validation, and revising. L.M.: simulation, validation, and revising.

Corresponding author

Correspondence to Changsheng Li.

Ethics declarations

Conflict of interest

The authors declare no competing interests.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, C., Wang, Z. & Ma, L. Drilling accurate nanopores for biosensors by energetic multi-wall carbon nanotubes: a molecular dynamics investigation. J Mol Model 28, 304 (2022). https://doi.org/10.1007/s00894-022-05276-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-022-05276-8

Keywords

Search

Navigation