Nano Research

, Volume 11, Issue 12, pp 6217–6226 | Cite as

E-beam manipulation of Si atoms on graphene edges with an aberration-corrected scanning transmission electron microscope

  • Ondrej DyckEmail author
  • Songkil Kim
  • Sergei V. Kalinin
  • Stephen Jesse
Research Article


The burgeoning field of atomic-level material control holds great promise for future breakthroughs in quantum and memristive device manufacture and fundamental studies of atomic-scale chemistry. Realization of atom-by-atom control of matter represents a complex and ongoing challenge. Here, we explore the feasibility of controllable motion of dopant Si atoms at the edges of graphene via the sub-atomically focused electron beam in a scanning transmission electron microscope. We demonstrate that the graphene edges can be cleaned of Si atoms and then subsequently replenished from nearby source material. It is also shown how Si edge atoms may be “pushed” from the edge of a small hole into the bulk of the graphene lattice and from the bulk of the lattice back to the edge. This is accomplished through sputtering of the edge of the graphene lattice to bury or uncover Si dopant atoms. Finally, we demonstrate e-beam mediated hole healing and incorporation of dopant atoms. These experiments form an initial step toward general atomic-scale material control.


atomic manipulation graphene scanning transmission electron microscopy edge passivation silicon dopant electron beam dynamics 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.



We would like to thank Dr. Ivan Vlassiouk for provision of the graphene samples and Dr. Francois Amet for assisting with the argon-oxygen cleaning procedure. Research is supported by Oak Ridge National Laboratory’s Center for Nanophase Materials Sciences (CNMS), which is sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy (S. V. K.), and by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the U.S. Department of Energy (O. D, S. K., and S. J.).

Supplementary material

12274_2018_2141_MOESM1_ESM.avi (37.8 mb)
Supplementary material, approximately 37.7 MB.
12274_2018_2141_MOESM2_ESM.pdf (717 kb)
E-beam manipulation of Si atoms on graphene edges with an aberration-corrected scanning transmission electron microscope


  1. [1]
    Eigler, D. M.; Schweizer, E. K. Positioning single atoms with a scanning tunnelling microscope. Nature 1990, 344, 524–526.CrossRefGoogle Scholar
  2. [2]
    Crommie, M. F.; Lutz, C. P.; Eigler, D. M. Confinement of electrons to quantum corrals on a metal surface. Science 1993, 262, 218–220.CrossRefGoogle Scholar
  3. [3]
    Crommie, M. F.; Lutz, C. P.; Eigler, D. M. Imaging standing waves in a two-dimensional electron gas. Nature 1993, 363, 524–527.CrossRefGoogle Scholar
  4. [4]
    Heinrich, A. J.; Lutz, C. P.; Gupta, J. A.; Eigler, D. M. Molecule cascades. Science 2002, 298, 1381–1387.CrossRefGoogle Scholar
  5. [5]
    Eigler, D. M.; Lutz, C. P.; Rudge, W. E. An atomic switch realized with the scanning tunnelling microscope. Nature 1991, 352, 600–603.CrossRefGoogle Scholar
  6. [6]
    Pennycook, S. J.; Nellist, P. D. Scanning Transmission Electron Microscopy: Imaging and Analysis; Springer: New York, 2011.CrossRefGoogle Scholar
  7. [7]
    Pennycook, S. J. The impact of STEM aberration correction on materials science. Ultramicroscopy 2017, 180, 22–33.CrossRefGoogle Scholar
  8. [8]
    Krivanek, O. L.; Lovejoy, T. C.; Murfitt, M. F.; Skone, G.; Batson, P. E.; Dellby, N. Towards sub-10 meV energy resolution STEM-EELS. J. Phys.: Conf. Ser. 2014, 522, 012023.Google Scholar
  9. [9]
    Egerton, R. F.; Li, P.; Malac, M. Radiation damage in the TEM and SEM. Micron 2004, 35, 399–409.CrossRefGoogle Scholar
  10. [10]
    Jiang, N. Electron beam damage in oxides: A review. Rep. Prog. Phys. 2016, 79, 016501.CrossRefGoogle Scholar
  11. [11]
    Zan, R.; Ramasse, Q. M.; Bangert, U.; Novoselov, K. S. Graphene reknits its holes. Nano Lett. 2012, 12, 3936–3940.CrossRefGoogle Scholar
  12. [12]
    van Dorp, W. F.; Zhang, X.; Feringa, B. L.; Wagner, J. B.; Hansen, T. W.; De Hosson, J. T. M. Nanometer-scale lithography on microscopically clean graphene. Nanotechnology 2011, 22, 505303.CrossRefGoogle Scholar
  13. [13]
    Ramasse, Q. M.; Zan, R.; Bangert, U.; Boukhvalov, D. W.; Son, Y.-W.; Novoselov, K. S. Direct experimental evidence of metal-mediated etching of suspended graphene. ACS Nano 2012, 6, 4063–4071.CrossRefGoogle Scholar
  14. [14]
    Xu, S. Y.; Tian, M. L.; Wang, J. G.; Xu, J.; Redwing, J. M.; Chan, M. H. W. Nanometer-scale modification and welding of silicon and metallic nanowires with a high-intensity electron beam. Small 2005, 1, 1221–1229.CrossRefGoogle Scholar
  15. [15]
    Jesse, S.; He, Q.; Lupini, A. R.; Leonard, D. N.; Oxley, M. P.; Ovchinnikov, O.; Unocic, R. R.; Tselev, A.; Fuentes- Cabrera, M.; Sumpter, B. G. et al. Atomic-level sculpting of crystalline oxides: Toward bulk nanofabrication with single atomic plane precision. Small 2015, 11, 5895–5900.CrossRefGoogle Scholar
  16. [16]
    Krasheninnikov, A. V.; Banhart, F. Engineering of nanostructured carbon materials with electron or ion beams. Nat. Mater. 2007, 6, 723–733.CrossRefGoogle Scholar
  17. [17]
    Krasheninnikov, A. V.; Nordlund, K. Ion and electron irradiation-induced effects in nanostructured materials. J. Appl. Phys. 2010, 107, 071301.CrossRefGoogle Scholar
  18. [18]
    Kim, M. J.; McNally, B.; Murata, K.; Meller, A. Characteristics of solid-state nanometre pores fabricated using a transmission electron microscope. Nanotechnology 2007, 18, 205302.CrossRefGoogle Scholar
  19. [19]
    El-Barbary, A. A.; Telling, R. H.; Ewels, C. P.; Heggie, M. I.; Briddon, P. R. Structure and energetics of the vacancy in graphite. Phys. Rev. B 2003, 68, 144107.CrossRefGoogle Scholar
  20. [20]
    Meyer, J. C.; Kisielowski, C.; Erni, R.; Rossell, M. D.; Crommie, M. F.; Zettl, A. Direct imaging of lattice atoms and topological defects in graphene membranes. Nano Lett. 2008, 8, 3582–3586.CrossRefGoogle Scholar
  21. [21]
    Robertson, A. W.; Lee, G.-D.; He, K.; Fan, Y.; Allen, C. S.; Lee, S.; Kim, H.; Yoon, E.; Zheng, H. M.; Kirkland, A. I. et al. Partial dislocations in graphene and their atomic level migration dynamics. Nano Lett. 2015, 15, 5950–5955.CrossRefGoogle Scholar
  22. [22]
    Robertson, A. W.; Lee, G.-D.; He, K.; Yoon, E.; Kirkland, A. I.; Warner, J. H. Stability and dynamics of the tetravacancy in graphene. Nano Lett. 2014, 14, 1634–1642.CrossRefGoogle Scholar
  23. [23]
    Robertson, A. W.; Lee, G.-D.; He, K.; Yoon, E.; Kirkland, A. I.; Warner, J. H. The role of the bridging atom in stabilizing odd numbered graphene vacancies. Nano Lett. 2014, 14, 3972–3980.CrossRefGoogle Scholar
  24. [24]
    Robertson, A. W.; Montanari, B.; He, K.; Kim, J.; Allen, C. S.; Wu, Y. A.; Olivier, J.; Neethling, J.; Harrison, N.; Kirkland, A. I. et al. Dynamics of single Fe atoms in graphene vacancies. Nano Lett. 2013, 13, 1468–1475.CrossRefGoogle Scholar
  25. [25]
    Susi, T.; Kotakoski, J.; Kepaptsoglou, D.; Mangler, C.; Lovejoy, T. C.; Krivanek, O. L.; Zan, R.; Bangert, U.; Ayala, P.; Meyer, J. C. et al. Silicon-carbon bond inversions driven by 60-keV electrons in graphene. Phys. Rev. Lett. 2014, 113, 115501.CrossRefGoogle Scholar
  26. [26]
    Shinada, T.; Koyama, H.; Hinoshita, C.; Imamura, K.; Ohdomari, I. Improvement of focused ion-beam optics in single-ion implantation for higher aiming precision of one-by-one doping of impurity atoms into nano-scale semiconductor devices. Jpn. J. Appl. Phys. 2002, 41, L287.CrossRefGoogle Scholar
  27. [27]
    Ishikawa, R.; Lupini, A. R.; Findlay, S. D.; Taniguchi, T.; Pennycook, S. J. Three-dimensional location of a single dopant with atomic precision by aberration-corrected scanning transmission electron microscopy. Nano Lett. 2014, 14, 1903–1908.CrossRefGoogle Scholar
  28. [28]
    Sharma, R. An environmental transmission electron microscope for in situ synthesis and characterization of nanomaterials. J. Mater. Res. 2005, 20, 1695–1707.CrossRefGoogle Scholar
  29. [29]
    Evans, J. E.; Jungjohann, K. L.; Browning, N. D.; Arslan, I. Controlled growth of nanoparticles from solution with in situ liquid transmission electron microscopy. Nano Lett. 2011, 11, 2809–2813.CrossRefGoogle Scholar
  30. [30]
    Jesse, S.; Borisevich, A. Y.; Fowlkes, J. D.; Lupini, A. R.; Rack, P. D.; Unocic, R. R.; Sumpter, B. G.; Kalinin, S. V.; Belianinov, A.; Ovchinnikova, O. S. Directing matter: Toward atomic-scale 3D nanofabrication. ACS Nano 2016, 10, 5600–5618.CrossRefGoogle Scholar
  31. [31]
    Susi, T.; Kepaptsoglou, D.; Lin, Y.-C.; Ramasse, Q. M.; Meyer, J. C.; Suenaga, K.; Kotakoski, J. Towards atomically precise manipulation of 2D nanostructures in the electron microscope. 2D Mater. 2017, 4, 042004.CrossRefGoogle Scholar
  32. [32]
    Dyck, O.; Kim, S.; Kalinin, S. V.; Jesse, S. Mitigating e-beam-induced hydrocarbon deposition on graphene for atomic-scale scanning transmission electron microscopy studies. J. Vac. Sci. Technol. B 2018, 36, 011801.CrossRefGoogle Scholar
  33. [33]
    Garcia, A. G. F.; Neumann, M.; Amet, F.; Williams, J. R.; Watanabe, K.; Taniguchi, T.; Goldhaber-Gordon, D. Effective cleaning of hexagonal boron nitride for graphene devices. Nano Lett. 2012, 12, 4449–4454.CrossRefGoogle Scholar
  34. [34]
    Dyck, O.; Kim, S.; Kalinin, S. V.; Jesse, S. Placing single atoms in graphene with a scanning transmission electron microscope. Appl. Phys. Lett. 2017, 111, 113104.CrossRefGoogle Scholar
  35. [35]
    Susi, T.; Meyer, J. C.; Kotakoski, J. Manipulating lowdimensional materials down to the level of single atoms with electron irradiation. Ultramicroscopy 2017, 180, 163–172.CrossRefGoogle Scholar
  36. [36]
    Kotakoski, J.; Santos-Cottin, D.; Krasheninnikov, A. V. Stability of graphene edges under electron beam: Equilibrium energetics versus dynamic effects. ACS Nano 2012, 6, 671–676.CrossRefGoogle Scholar
  37. [37]
    Meyer, J. C.; Eder, F.; Kurasch, S.; Skakalova, V.; Kotakoski, J.; Park, H. J.; Roth, S.; Chuvilin, A.; Eyhusen, S.; Benner, G. et al. Accurate measurement of electron beam induced displacement cross sections for single-layer graphene. Phys. Rev. Lett. 2012, 108, 196102.CrossRefGoogle Scholar
  38. [38]
    Susi, T.; Hofer, C.; Argentero, G.; Leuthner, G. T.; Pennycook, T. J.; Mangler, C.; Meyer, J. C.; Kotakoski, J. Isotope analysis in the transmission electron microscope. Nat. Commun. 2016, 7, 13040.CrossRefGoogle Scholar
  39. [39]
    Song, B.; Schneider, G. F.; Xu, Q.; Pandraud, G.; Dekker, C.; Zandbergen, H. Atomic-scale electron-beam sculpting of near-defect-free graphene nanostructures. Nano Lett. 2011, 11, 2247–2250.CrossRefGoogle Scholar
  40. [40]
    Ma, Y. C. Simulation of interstitial diffusion in graphite. Phys. Rev. B 2007, 76, 075419.CrossRefGoogle Scholar
  41. [41]
    Dyck, O.; Kim, S.; Jimenez-Izal, E.; Alexandrova, A. N.; Kalinin, S. V.; Jesse, S. Assembling di- and multiatomic Si clusters in graphene via electron beam manipulation. 2017, arXiv:1710.09416. e-Print archive. (accessed Apr 19, 2018).Google Scholar

Copyright information

© Tsinghua University Press and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Ondrej Dyck
    • 1
    • 2
    Email author
  • Songkil Kim
    • 3
  • Sergei V. Kalinin
    • 1
    • 2
  • Stephen Jesse
    • 1
    • 2
  1. 1.Center for Nanophase Materials ScienceOak Ridge National LaboratoryOak RidgeUSA
  2. 2.Institute for Functional Imaging of MaterialsOak Ridge National LaboratoryOak RidgeUSA
  3. 3.School of Mechanical EngineeringPusan National UniversityBusanRepublic of Korea

Personalised recommendations