Atomic Observation on Diamond (001) Surfaces with Near-Contact Atomic Force Microscopy
masahiro.fukuda / C001_dimer_chain_AFM
Overview
Density-functional-theory calculations revealed that the formation of tilted Si–C bonds between scanning Si probes and diamond (001) surfaces, coupled with the reordering of surface C–C dimers, are critical factors for achieving atomic resolution. The mechanism of high-resolution AFM imaging was elucidated by force spectroscopy combined with first-principles calculations. This database provides the input files and the results of the DFT calculations by OpenMX.
- URL
- https://isspns-gitlab.issp.u-tokyo.ac.jp/masahiro.fukuda/C001_dimer_chain_AFM
- DOI
- 10.1021/acs.nanolett.4c05395
- Citations
- 9 (OpenAlex, as of 2026-10-05)
- Authors
- Runnan Zhang, Yuuki Yasui, Masahiro Fukuda, Taisuke Ozaki, Masahiko Ogura, Toshiharu Makino, Daisuke Takeuchi, Yoshiaki Sugimoto
- License
- CC BY 4.0
- Keywords
- diamond (001) surfaceatomic resolution imagingC–Si bond formationdiamond growthsurface defectsadsorbed moleculesartificial nanostructures (keywords of the paper, from OpenAlex)
- Category
- Electronic structure (solid state physics)
- References
- Nano Letters 2025 25 (3), 1101-1107
- Related software
- OpenMX (Links to: PASUMS software catalog)
- Contact
- masahiro.fukuda__at__issp.u-tokyo.ac.jp (Please replace __at__ with @.)
Paper and citation
If you use this data, please cite the following paper.
Runnan Zhang et al., "Atomic Observation on Diamond (001) Surfaces with Near-Contact Atomic Force Microscopy", Nano Letters 25(3), 1101–1107 (2025). https://doi.org/10.1021/acs.nanolett.4c05395
Show BibTeX
@article{Zhang_2025, title={Atomic Observation on Diamond (001) Surfaces with Near-Contact Atomic Force Microscopy}, volume={25}, ISSN={1530-6992}, url={http://dx.doi.org/10.1021/acs.nanolett.4c05395}, DOI={10.1021/acs.nanolett.4c05395}, number={3}, journal={Nano Letters}, publisher={American Chemical Society (ACS)}, author={Zhang, Runnan and Yasui, Yuuki and Fukuda, Masahiro and Ozaki, Taisuke and Ogura, Masahiko and Makino, Toshiharu and Takeuchi, Daisuke and Sugimoto, Yoshiaki}, year={2025}, month=Jan, pages={1101–1107} }Bibliographic details and the open-access link are from OpenAlex; the BibTeX is from doi.org (as registered by the publisher).
README
Atomic Observation on Diamond (001) Surfaces with Near-Contact Atomic Force Microscopy
About
Density-functional-theory calculations revealed that the formation of tilted Si-C bonds between scanning Si probes and diamond (001) surfaces, coupled with the reordering of surface C-C dimers, are critical factors for achieving atomic resolution. The mechanism of high-resolution AFM imaging was elucidated by force spectroscopy combined with first-principles calculations. This database provides the input files and the results of the DFT calculations by OpenMX.
License, Copyright of the database
- CC BY 4.0
We hope that you cite the reference when you publish the results using our data:
Nano Letters 2025 25 (3), 1101-1107
Usage
Install Database
Using git
git clone https://isspns-gitlab.issp.u-tokyo.ac.jp/masahiro.fukuda/C001_dimer_chain_AFM.gitOn browser Click the download button of this project.
Data info
- This database includes input files and results of AFM simulation by DFT.
data/calc/C001- Carbon dimer chains on the C(001) diamond surface.
data/calc/HC001- Hydrogenated carbon dimer chains on the C(001) diamond surface.
data/calc/C001_vacancy_for_FigS1- Carbon dimer chains on the C(001) diamond surface with vacancy shown in Fig.S1.
data/calc/Si001_vacancy_for_FigS1- Carbon dimer chains on the Si(001) diamond surface with vacancy shown in Fig.S1.
data/Data_of_Fig3- Raw data for ploting Fig.3 in the paper.
data/Data_of_Fig4- Raw data for ploting Fig.4 in the paper.
- This database includes input files and results of AFM simulation by DFT.
Contact
Masahiro FUKUDA (ISSP, Univ. of Tokyo)
masahiro.fukuda__at__issp.u-tokyo.ac.jp
please replace __at__ by @.
Source: https://isspns-gitlab.issp.u-tokyo.ac.jp/masahiro.fukuda/C001_dimer_chain_AFM README