Applied Nanoscience

, Volume 9, Issue 7, pp 1459–1468 | Cite as

AFM induced diffusion of large scale mobile HOPG defects

  • Mümin Mehmet KoçEmail author
  • Georgios E. Ragkousis
Original Article


Defects on crystal and/or thin film surfaces play an important role in their physical and chemical properties. Diffusion or motion of such structures results in microstructural dynamic changes. The diffusion of single atom/point defects were previously reported, due to the difficulty of observation, the motion of large-scale defects (the defect consist of multiple missing atoms) using combination of consecutive images has not been possible since today. For the first time, the diffusion of three mobile large-scale highly oriented pyrolytic graphite monolayer defect domains is reported using non-contact atomic force microscopy in ultra-high vacuum conditions. It was suspected that the diffusion of the defects was triggered by the rastering motion of the tip of atomic force microscope. It was evidenced that the diffusion of large defects is shown to be size-dependent, with smaller defects moving with higher speeds than larger defects. The diffusion results fit well with the models previously reported for the diffusion of particles for varying sizes and indicates that the diffusion of defects and particles show similar behaviours.


Defect diffusion Atomic force microscopy HOPG Monolayer defects 



Part of this project was funded by Kirklareli University Scientific Research Office with project number of KLUBAP115. Finally, we are also thankful Dr Klaus von Haeften and Prof Chris Bins for allowing us to use their microscope facility at University of Leicester.

Supplementary material

Supplementary material 1 (WMV 7600 KB)


  1. Ala-Nissila T, Ferrando R, Ying SC (2002) Collective and single particle diffusion on surfaces. Adv Phys 51(3):949–1078. CrossRefGoogle Scholar
  2. Amara H et al (2007) Scanning tunneling microscopy fingerprints of point defects in graphene: a theoretical prediction. Phys Rev B 76(11):115423. CrossRefGoogle Scholar
  3. Babenko B, Yang M-H, Belongie S (2011) Robust object tracking with online multiple instance learning. IEEE Trans Pattern Anal Mach Intell 33(8):1619–1632. CrossRefGoogle Scholar
  4. Bassett DW, Parsley MJ (1970) Field ion microscope studies of transition metal adatom diffusion on (110), (211) and (321) tungsten surfaces. J Phys D Appl Phys 3(5):309. CrossRefGoogle Scholar
  5. Bikondoa O et al (2006) Direct visualization of defect-mediated dissociation of water on TiO2(110). Nat Mater 5(3):189–192. CrossRefGoogle Scholar
  6. Björkman T et al (2013) Defects in bilayer silica and graphene: common trends in diverse hexagonal two-dimensional systems. Sci Rep 3:3482. Accessed 22 May 2018
  7. Bradski G (2007) Tools, A K.-D. D. journal of software and 2000, undefined (no date) ‘OpenCV’, Accessed 22 May 2018
  8. Campanera JM et al (2007) Density functional calculations on the intricacies of Moiré patterns on graphite. Phys Rev B 75(23):235449. CrossRefGoogle Scholar
  9. Chang H, Bard AJ (1991) Observation and characterization by scanning tunneling microscopy of structures generated by cleaving highly oriented pyrolytic graphite. Langmuir 7(6):1143–1153. CrossRefGoogle Scholar
  10. Compton R et al (2008) Design, fabrication, characterisation and application of nanoelectrode arrays.pdf. Chem Phys Lett 1–6(459):1–17. Accessed 22 May 2018CrossRefGoogle Scholar
  11. Das D et al (2013) Li diffusion through doped and defected graphene. Phys Chem Chem Phys 15(36):15128. CrossRefGoogle Scholar
  12. Eyre BL (1973) Transmission electron microscope studies of point defect clusters in fcc and bcc metals. J Phys F Met Phys 3(2):422–470. CrossRefGoogle Scholar
  13. Gan Y, Sun L, Banhart F (2008) One- and two-dimensional diffusion of metal atoms in graphene. Small 4(5):587–591. CrossRefGoogle Scholar
  14. Gao J et al (2013) Structures, mobilities, electronic and magnetic properties of point defects in silicene. Nanoscale 5(20):9785. CrossRefGoogle Scholar
  15. Guo L et al (2018) Direct formation of wafer-scale single-layer graphene films on the rough surface substrate by PECVD. Carbon 129:456–461. CrossRefGoogle Scholar
  16. Hashimoto A et al (2004) Direct evidence for atomic defects in graphene layers. Nature 430(7002):870–873. CrossRefGoogle Scholar
  17. Herrero CP, Ramírez R (2009) Vibrational properties and diffusion of hydrogen on graphene. Phys Rev B 79(11):115429. CrossRefGoogle Scholar
  18. Horcas I et al (2007) WSXM: a software for scanning probe microscopy and a tool for nanotechnology. Rev Sci Instrum Am Inst Phys 78(1):013705. CrossRefGoogle Scholar
  19. Hövel H et al (1997) Crystalline structure and orientation of gold clusters grown in preformed nanometer-sized pits. Appl Surf Sci 2(115):124–127. Accessed 23 May 2018CrossRefGoogle Scholar
  20. Hwang IS, Theiss SK, Golovchenko JA (1994) Mobile point-defects and atomic basis for structural transformations of a crystal-surface. Science 265(5171):490–496CrossRefGoogle Scholar
  21. Iovino G et al (2013) Effects of pressure, temperature, and particles size on O2 diffusion dynamics in silica nanoparticles. J Phys Chem C 117:18. CrossRefGoogle Scholar
  22. Jacobsen J, Jacobsen KW, Sethna JP (1997) Rate theory for correlated processes: double jumps in adatom diffusion. Phys Rev Lett 79(15):2843–2846. CrossRefGoogle Scholar
  23. Jensen P (1999) Growth of nanostructures by cluster deposition: experiments and simple models. Rev Mod Phys 71(5):1695–1735. CrossRefGoogle Scholar
  24. José-Yacamán M et al (2005) Surface diffusion and coalescence of mobile metal nanoparticles. J Phys Chem B 109(19):9703–9711. CrossRefGoogle Scholar
  25. Kellogg GL (1994) Field ion microscope studies of single-atom surface diffusion and cluster nucleation on metal surfaces. Surf Sci Rep 21(1–2):1–88. Accessed 22 May 2018CrossRefGoogle Scholar
  26. Kellogg GL, Feibelman PJ (1990) Surface self-diffusion on Pt(001) by an atomic exchange mechanism. Phys Rev Lett 64(26):3143–3146. CrossRefGoogle Scholar
  27. Koc M (2015) Non contact atomic force microscopy investigation of silicon nanoparticles deposited on HOPG. Accessed 22 May 2018
  28. Kotakoski J, Mangler C, Meyer JC (2014) Imaging atomic-level random walk of a point defect in graphene. Nat Commun. CrossRefGoogle Scholar
  29. Lo R-L et al (1998) Diffusion of single hydrogen atoms on Si(111)-(7 × 7) surfaces. Phys Rev Lett 80(25):5584–5587. CrossRefGoogle Scholar
  30. Melmed AJ et al (1979) Evidence for reconstructed {001} tungsten obtained by field-ion microscopy. Phys Rev Lett 43(20):1521–1524. CrossRefGoogle Scholar
  31. Mitsui T et al (2005) Diffusion and pair interactions of CO molecules on Pd(111). Phys Rev Lett 94(3):036101. CrossRefGoogle Scholar
  32. Mo YW et al (1991) Activation energy for surface diffusion of Si on Si(001): a scanning-tunneling-microscopy study. Phys Rev Lett 66(15):1998–2001. CrossRefGoogle Scholar
  33. Newburgh R, Peidle J, Rueckner W (2006) Einstein, Perrin, and the reality of atoms: 1905 revisited. Am J Phys 74(6):478–481. CrossRefGoogle Scholar
  34. Özçelik VO, Gurel HH, Ciraci S (2013) Self-healing of vacancy defects in single-layer graphene and silicene. Phys Rev B 88(4):045440. CrossRefGoogle Scholar
  35. Özden S, Koc MM (2018) Spectroscopic and microscopic investigation of MBE-grown CdTe (211)B epitaxial thin films on GaAs (211)B substrates. Appl Nanosci 8(4):891–903. p.CrossRefGoogle Scholar
  36. Prévot G et al (2000) Non-isotropic surface diffusion of lead on Cu (110): a molecular dynamics study. Surf Sci 459(1–2):57–68. Accessed 22 May 2018CrossRefGoogle Scholar
  37. Rabe JP, Buchholz S (1991) Commensurability and mobility in two-dimensional molecular patterns on graphite. Science 253(5018):424–427. CrossRefGoogle Scholar
  38. Robach JS et al (2003) In-situ transmission electron microscopy observations and molecular dynamics simulations of dislocation-defect interactions in ion-irradiated copper. Philos Mag 83(8):955–967. CrossRefGoogle Scholar
  39. Rong ZY, Kuiper P (1993) Electronic effects in scanning tunneling microscopy: Moiré pattern on a graphite surface. Phys Rev B 48(23):17427–17431. CrossRefGoogle Scholar
  40. Rose F et al (2006) Adsorption and combing of DNA on HOPG surfaces of bulk crystals and nanosheets: application to the bridging of DNA between HOPG/Si heterostructures. Nanotechnology 17(13):3325–3332. CrossRefGoogle Scholar
  41. Schaub R et al (2003) Oxygen-mediated diffusion of oxygen vacancies on the TiO2(110) surface. Science 299(5605):377–379. CrossRefGoogle Scholar
  42. Schroeder W et al (2006) The visualization toolkit: an object-oriented approach to 3D graphics. KitwareGoogle Scholar
  43. Seidman DN (1973) The direct observation of point defects in irradiated or quenched metals by quantitative field ion microscopy. J Phys F Met Phys 3(2):393–421. CrossRefGoogle Scholar
  44. Stabel A et al (1998) Surface defects and homogeneous distribution of silver particles on HOPG. Langmuir 14(25):7324–7326. CrossRefGoogle Scholar
  45. Sun GF et al (2011) Si diffusion path for pit-free graphene growth on SiC(0001). Phys Rev B 84(19):195455. CrossRefGoogle Scholar
  46. Swartzentruber BS (1996) Direct measurement of surface diffusion using atom-tracking scanning tunneling microscopy. Phys Rev Lett 76(3):459–462. CrossRefGoogle Scholar
  47. Tan TY, Gösele U (1985) Point defects, diffusion processes, and swirl defect formation in silicon. Appl Phys A Solids Surf 37(1):1–17. CrossRefGoogle Scholar
  48. Trevethan T et al (2014) Vacancy diffusion and coalescence in graphene directed by defect strain fields. Nanoscale 6(5):2978–2986. CrossRefGoogle Scholar
  49. Tsetseris L, Pantelides ST (2009) Adatom complexes and self-healing mechanisms on graphene and single-wall carbon nanotubes. Carbon 47(3):901–908. CrossRefGoogle Scholar
  50. Vadukumpully S, Paul J, Valiyaveettil S (2009) Cationic surfactant mediated exfoliation of graphite into graphene flakes. Carbon 47(14):3288–3294. CrossRefGoogle Scholar
  51. Wang B et al (2017) In situ TEM study of interaction between dislocations and a single nanotwin under nanoindentation. ACS Appl Mater Interfaces Am Chem Soc 9(35):29451–29456. CrossRefGoogle Scholar
  52. Wang B et al (2018) New deformation-induced nanostructure in silicon. Nano Lett Am Chem Soc 18(7):4611–4617. CrossRefGoogle Scholar
  53. Yi M, Shen AZ (2015) A review on mechanical exfoliation for the scalable production of graphene. J Mater Chem A 3(22):11700–11715. Accessed 22 May 2018CrossRefGoogle Scholar
  54. Zhang Z, Guo D et al (2015) A novel approach of high speed scratching on silicon wafers at nanoscale depths of cut. Sci Rep Nat Publ Group 5(1):16395. CrossRefGoogle Scholar
  55. Zhang Z, Wang B et al (2015) Changes in surface layer of silicon wafers from diamond scratching. CIRP Ann 64(1):349–352. CrossRefGoogle Scholar
  56. Zhang Z, Wang B, Zhou P, Kang R et al (2016a) A novel approach of chemical mechanical polishing for cadmium zinc telluride wafers. Sci Rep Nat Publ Group 6(1):26891. CrossRefGoogle Scholar
  57. Zhang Z, Wang B, Zhou P, Guo D et al (2016b) A novel approach of chemical mechanical polishing using environment-friendly slurry for mercury cadmium telluride semiconductors. Sci Rep Nat Publ Group 6(1):22466. CrossRefGoogle Scholar
  58. Zhang Z, Huang S et al (2017) A novel approach of high-performance grinding using developed diamond wheels. Int J Adv Manuf Technol 91(9–12):3315–3326. CrossRefGoogle Scholar
  59. Zhang Z, Cui J et al (2017) A novel approach of mechanical chemical grinding. J Alloys Compd 726:514–524. CrossRefGoogle Scholar
  60. Zhang Z, Du Y et al (2017) Nanoscale wear layers on silicon wafers induced by mechanical chemical grinding. Tribol Lett 65(4):132. CrossRefGoogle Scholar
  61. Zhang Z et al (2018) A novel approach of chemical mechanical polishing for a titanium alloy using an environment-friendly slurry. Appl Surf Sci North Holland 427:409–415. CrossRefGoogle Scholar
  62. Zhang Z et al (2019) Environment friendly chemical mechanical polishing of copper. Appl Surf Sci North-Holland 467–468:5–11. CrossRefGoogle Scholar

Copyright information

© King Abdulaziz City for Science and Technology 2018

Authors and Affiliations

  1. 1.School of EngineeringUniversity of PortsmouthPortsmouthUK
  2. 2.Department of PhysicsKirklareli UniversityKirklareliTurkey

Personalised recommendations