A First Principles Simulation Framework for the Interactions between a Si(001) Surface and a Scanning Probe


By means of total energy calculations within the framework of the local density approximation (LDA), the interactions between a silicon Si(001) surface and a scanning probe are investigated. The tip of the probe, comprising 4 Si atoms scans along the dimer lines above an asymmetric p(2 × 1) surface, at a distance where the chemical interaction between tip-surface is dominant and responsible for image resolution. At that distance, the tip causes the dimer to toggle when it scans above the lower atom of a dimer. The toggled dimers create an alternating pattern, where the immediately adjacent neighbours of a toggled dimer remain unchanged. After the tip has fully scanned across the p(2 × 1) surface, causes the dimers to arrange in a p(2 × 2) reconstruction, reproducing the images obtained in scanning probe experiments. Our modelling methodology includes simulations that reveal the energy input required to overcome the barrier to the onset of dimer toggling. The results show that the energy input to overcome this barrier is lower for the p(2 × 1) surface than that for the p(2 × 2) or c(4 × 2) surfaces.

Share and Cite:

D. Ly and C. Makatsoris, "A First Principles Simulation Framework for the Interactions between a Si(001) Surface and a Scanning Probe," Journal of Surface Engineered Materials and Advanced Technology, Vol. 2 No. 3A, 2012, pp. 194-202. doi: 10.4236/jsemat.2012.223030.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] R. A. Wolkow, “Direct Observation of an Increase in Buckled Dimers on Si(001) at Low Temperature,” Physical Review Letters, Vol. 68, No. 17, 1992, pp. 2636-2639. doi:10.1103/PhysRevLett.68.2636
[2] H. Tochihara, T. Amakusa and M. Iwatsuki, “Low-Temperature Scanning-Tunneling-Microscopy Observations of the Si(001) Surface with a Low Surface-Defect Density,” Physical Review B, Vol. 50, No. 16, 1994, pp. 12262- 12265. doi:10.1103/PhysRevB.50.12262
[3] T. Mitsui and K. Takayanagi, “Extrinsic Structure Changes by STM at 65 K on Si(001),” Physical Review B, Vol. 62, No. 24, 2000, pp. R16251-R16254. doi:10.1103/PhysRevB.62.R16251
[4] K. Suzuki, M. Iwatsuki, S. Kitamura and C. B. Mooney, “Development of Low Temperature Ultrahigh Vacuum Atomic Force Micro-scope/Scanning Tunneling Micro-scope,” Japanese Journal of Applied Physics, Vol. 39, 2000, pp. 3750-3752. doi:10.1143/JJAP.39.3750
[5] T. Uozumi, Y. Tomiyoshi, N. Suehira, Y. Sugawara and S. Morita, “Observation of Si(100) Surface with Noncontact Atomic Force Microscope at 5 K,” Applied Surface Science, Vol. 188, No. 3-4, 2002, pp. 279-284. doi:10.1016/S0169-4332(01)00939-4
[6] R. J. Hamers, R. M. Tromp and J. E. Demuth, “Scanning Tunneling Microscopy of Si(001),” Physical Review B, Vol. 34, No. 8, 1986, pp. 5343-5357. doi:10.1103/PhysRevB.34.5343
[7] K. Yokoyama, T. Ochi, A. Yoshimoto, Y. Sugawara and S. Morita, “Atomic Resolution Imaging on Si(100)2 × 1 and Si(100)2 × 1:H Surfaces with Noncontact Atomic Force Microscopy,” Japanese Journal of Applied Physics, Vol. 39, 2000, pp. L113-L115. doi:10.1143/JJAP.39.L113
[8] T. Tabata, T. Aruga and Y. Murata, “Order-Disorder Transition on Si(001): c(4 × 2) to (2 × 1),” Surface Science, Vol. 179, No. 1, 1987, pp. L63-L70. doi:10.1016/0039-6028(87)90114-2
[9] Y. Kondo, T. Amakusa, M. Iwatsuki and H. Tokumoto, “Phase Transition of the Si(001) Surface Below 100 K,” Surface Science, Vol. 453, No. 1-3, 2000, pp. L318-L322. doi:10.1016/S0039-6028(00)00391-5
[10] K. Sagisaka, D. Fujita and G. Kido, “Phase Manipulation between c(4 × 2) and p(2 × 2) on the Si(100) Surface at 4.2 K,” Physical Review Letters, Vol. 91, No. 14, 2003, pp. 146103-146106. doi:10.1103/PhysRevLett.91.146103
[11] M. Ono, A. Kamoshida, N. Matsuura, E. Ishikawa, T. Egu-chi and Y. Ha-segawa, “Dimer Buckling of the Si(001)2 × 1 Surface Below 10 K Observed by Low-Temperature Scanning Tunneling Microscopy,” Physical Review B, Vol. 67, No. 20, 2003, pp. 201306-201309. doi:10.1103/PhysRevB.67.201306
[12] S. Yoshida, T. Kimura, O. Takeuchi, K. Hata, H. Oigawa, T. Nagamura, H. Sakama and H. Shigekawa, “Probe Effect in Scanning Tunneling Microscopy on Si(001) Low- Temperature Phases,” Physical Review B, Vol. 70, No. 23, 2004, pp. 235411-235421. doi:10.1103/PhysRevB.70.235411
[13] K. Cho and J. D. Joannopoulos, “Flipping Silicon Dimers on Si(100) Using Scanning Tip Microscopy: A Theoretical Investigation,” Physical Review B, Vol. 53, No. 8, 1996, pp. 4553-4556. doi:10.1103/PhysRevB.53.4553
[14] Y. J. Li, H. Nomura, N. Ozaki, Y. Naitoh, M. Kageshima, Y. Sugawara C. Hobbs and L. Kantorovich, “Origin of p(2 × 1) Phase on Si(001) by Noncon-tact Atomic Force Microscopy at 5 K,” Physical Review Letters, Vol. 96, No. 10, 2006, pp. 106104-106107. doi:10.1103/PhysRevLett.96.106104
[15] L. Kantorovich and C. Hobbs, “Probing the Si(001) Surface with a Si Tip: An ab Initio Study,” Physical Review B, Vol. 73, No. 24, 2006, pp. 245420-245431. doi:10.1103/PhysRevB.73.245420
[16] R. Perez, I. Stich, M. C. Payne and K. Terakura, “Surface-Tip Interactions in Noncontact Atomic-Force Microscopy on Reactive Surfaces: Si(111),” Physical Review B, Vol. 58, No. 16, 1998, pp. 10835-10849. doi:10.1103/PhysRevB.58.10835
[17] D. Q. Ly, L. Paramonov and C. Makatsoris, “First Principles Studies of an Si Tip on an Si(100)2 × 1 Reconstructed Surface,” Journal of Physics: Condensed Matter, Vol. 21, No. 18, 2009, pp. 185006-185013. doi:10.1088/0953-8984/21/18/185006
[18] K. Seino, W. G. Schmidt and F. Bechstedt, “Energetics of Si(001) Surfaces Exposed to Electric Fields and Charge Injection,” Physical Review Letters, Vol. 93, No. 3, 2004, pp. 036101-036104. doi:10.1103/PhysRevLett.93.036101
[19] Y. Sugimoto, M. Abe, S. Hirayama, N. Oyabu, C. Custance and S. Morita, “Atom Inlays Performed at Room Temperature Using Atomic Force Microscopy,” Nature, Vol. 4, No. 2, 2005, pp. 156-159. doi:10.1038/nmat1297
[20] Y. Sugimoto, P. Lou, M. Abe, P. Jelinek, R. Perez, S. Morita and O. Custance, “Chemical Identification of Individual Surface Atoms by Atomic Force Microscopy,” Nature, Vol. 446, No. 7131, 2007, pp. 64-67. doi:10.1038/nature05530
[21] Y. Sugimoto, P. Pou, O. Custance, P. Jelinek, M. Abe, R. Perez and S. Morita, “Complex Patterning by Vertical Interchange Atom Manipulation Using Atomic Force Microscopy,” Science, Vol. 322, No. 5900, 2008, pp. 413- 417. doi:10.1126/science.1160601
[22] M. C. Payne, M. P. Teter, D. C. Allan, T. A. Arias and J. D. Joannopoulos, “Iterative Minimization Techniques for ab Initio Total-Energy Calculations: Molecular Dynamics and Conjugate Gradients,” Physical Review Letters, Vol. 64, No. 4, 1992, pp. 1045-1097. doi:10.1103/RevModPhys.64.1045
[23] S. J. Clark, M. D. Segall, C. J. Pickard, P. J. Hasnip, M. J. Probert, K. Refson and M. C Payne, “First Principles Methods Using CASTEP,” Zeitschrift fur Kristallographie, Vol. 220, No. 5-6, 2005, pp. 567-570. doi:10.1524/zkri.220.5.567.65075
[24] J. P. Perdew and A. Zunger, “Self-Interaction Correction to Density-Functional Approximations for Many-Electron Systems,” Physical Review B, Vol. 23, No. 10, 1981, pp. 5048-5079. doi:10.1103/PhysRevB.23.5048
[25] J. P. Perdew, K. Burke and M. Ernzerhof, “Generalized Gradient Approximation Made Simple,” Physical Review Letters, Vol. 77, No. 18, 1996, pp. 3865-3868. doi:10.1103/PhysRevLett.77.3865
[26] A. Sweetman, S. Jarvis, R. Danza, J. Bamidele, S. Gan- gopadhyay, G. A. Shaw, L. Kantorovich and P. Poriaty, “Toggling Bistable Atoms via Mechanical Switching of Bond Angle,” Physical Review Letters, Vol. 106, No. 13, 2011, pp. 136101-136104. doi:10.1103/PhysRevLett.106.136101
[27] T. Shirasawa, S. Mizuno and H. Tochihara, “Structural Analysis of the c(4 × 2) Reconstruction in Si(001) and Ge(001) Surfaces by Low-Energy Electron Diffraction,” Surface Science, Vol. 600, No. 4, 2006, pp. 815-819. doi:10.1016/j.susc.2005.11.031
[28] H. Over, J. Wasserfall, W. Ranke, C. Ambiatello, R. Sawitzki, D. Wolf and W. Moritz, “Surface Atomic Ge-ometry of Si(001)-(2 × 1): A Low-Energy Electron-Diffraction Structure Analysis,” Physical Review B, Vol. 55, No. 7, 1997, pp. 4731-4736. doi:10.1103/PhysRevB.55.4731
[29] N. Oyabu, O. Custance, I. Yi, Y. Sugawara and S. Morita, “Mechanical Vertical Manipulation of Selected Single Atoms by Soft Nanoindentation Using Near Contact Atomic Force Microscopy,” Physical Review Letters, Vol. 90, No. 17, 2003, pp. 176102-176105. doi:10.1103/PhysRevLett.90.176102
[30] N. Oyabu, Y. Sugimoto, M. Abe, O. Custance and S. Morita, “Lateral Manipulation of Single Atoms At Semi-conductor Surfaces Using Atomic Force Microscopy,” Nanotechnology, Vol. 16, No. 3, 2005, pp. S112-S117. doi:10.1088/0957-4484/16/3/021
[31] N. Oyabu, P. Pou, Y. Sugimoto, P. Jelinek, M. Abe, S. Morita, R. Perez and O. Custance, “Single Atomic Con- tact Adhesion and Dissipation in Dynamic Force Microscopy,” Physical Review Letters, Vol. 96, No. 10, 2006, pp. 106101-106104. doi:10.1103/PhysRevLett.96.106101
[32] R. C. Merkle and R. A. Freitas, “Theoretical Analysis of a Carbon-Carbon Dimer Placement Tool for Diamond Mechanosynthesis,” Journal of Nanoscience and Nanotechnology, Vol. 3, No. 4, 2003, pp. 319-324. doi:10.1166/jnn.2003.203

Copyright © 2022 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.