Computational modeling of graphene nanopore for using in DNA sequencing devices

Rouzbeh Abadi, Mohammadreza Izadifar, Mohammad Sepahi, Naif Alajlan, Timon Rabczuk

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)


Graphene is a promising material for nanopore-sequencing DNA technology. In the current study, we have utilized molecular dynamic simulation in order to fabricate nanopores in the four divergent locations with different properties in a single-layer graphene nanosheet by using clusters bombardment. Ten different kinetic energies have been applied to three different diameters of SiC, Si and diamond clusters to fabricate nanopores. Image processing technology has also been applied to compute the exact area of regular and irregular drilled nanopores. The obtained results suggest that the desired size and qualities of nanopore can be achieved by controlling the type, diameter and the energy of the clusters. We have observed that the average area of nanopores increases by rising the kinetic energy in the most of cases. Moreover, the properties of the incident location can highly affect the area size and quality of the nanopores. The largest area size of the nanopores has been obtained when the incident location is placed in the center of the grains, while the smallest area of nanopores have been observed when the incident point is placed on the grain boundaries junction. Among all three types of clusters, the impact of the diamond cluster with diameter of 2 nm fabricates the most suitable nanopores. Therefore, we have used the diamond cluster to investigate the effect of straining the nanosheet on the topography of nanopores. We applied 3% and 5% of tensile and compressive strain to the graphene nanosheet. Under tensile strains we found that increasing the external tensile strain on the nanosheet fabricates larger nanopores with smoother edges. On the other hand, applying external compressive strains leads to nanopores with more irregular topography.

Original languageEnglish
Pages (from-to)403-416
Number of pages14
JournalPhysica E: Low-Dimensional Systems and Nanostructures
Publication statusPublished - 2018 Sept
Externally publishedYes


  • Bombardment
  • Cluster
  • Compressive
  • DNA sequencing
  • Diamond
  • Graphene
  • Nanopore
  • Nanosheet
  • Si
  • SiC
  • Tensile

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Atomic and Molecular Physics, and Optics
  • Condensed Matter Physics


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