Building and exploring libraries of atomic defects in graphene: Scanning transmission electron and scanning tunneling microscopy study
Abstract
The presence and configurations of defects are primary components determining materials functionality. Their population and distribution are often nonergodic and dependent on synthesis history, and therefore rarely amenable to direct theoretical prediction. Here, dynamic electron beam–induced transformations in Si deposited on a graphene monolayer are used to create libraries of possible Si and carbon vacancy defects. Deep learning networks are developed for automated image analysis and recognition of the defects, creating a library of (meta) stable defect configurations. Density functional theory is used to estimate atomically resolved scanning tunneling microscopy (STM) signatures of the classified defects from the created library, allowing identification of several defect types across imaging platforms. This approach allows automatic creation of defect libraries in solids, exploring the metastable configurations always present in real materials, and correlative studies with other atomically resolved techniques, providing comprehensive insight into defect functionalities.
- Authors:
-
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division
- OSTI Identifier:
- 1607267
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Science Advances
- Additional Journal Information:
- Journal Volume: 5; Journal Issue: 9; Journal ID: ISSN 2375-2548
- Publisher:
- AAAS
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 36 MATERIALS SCIENCE
Citation Formats
Ziatdinov, Maxim, Dyck, Ondrej, Li, Xin, Sumpter, Bobby G., Jesse, Stephen, Vasudevan, Rama K., and Kalinin, Sergei V. Building and exploring libraries of atomic defects in graphene: Scanning transmission electron and scanning tunneling microscopy study. United States: N. p., 2019.
Web. doi:10.1126/sciadv.aaw8989.
Ziatdinov, Maxim, Dyck, Ondrej, Li, Xin, Sumpter, Bobby G., Jesse, Stephen, Vasudevan, Rama K., & Kalinin, Sergei V. Building and exploring libraries of atomic defects in graphene: Scanning transmission electron and scanning tunneling microscopy study. United States. https://doi.org/10.1126/sciadv.aaw8989
Ziatdinov, Maxim, Dyck, Ondrej, Li, Xin, Sumpter, Bobby G., Jesse, Stephen, Vasudevan, Rama K., and Kalinin, Sergei V. Fri .
"Building and exploring libraries of atomic defects in graphene: Scanning transmission electron and scanning tunneling microscopy study". United States. https://doi.org/10.1126/sciadv.aaw8989. https://www.osti.gov/servlets/purl/1607267.
@article{osti_1607267,
title = {Building and exploring libraries of atomic defects in graphene: Scanning transmission electron and scanning tunneling microscopy study},
author = {Ziatdinov, Maxim and Dyck, Ondrej and Li, Xin and Sumpter, Bobby G. and Jesse, Stephen and Vasudevan, Rama K. and Kalinin, Sergei V.},
abstractNote = {The presence and configurations of defects are primary components determining materials functionality. Their population and distribution are often nonergodic and dependent on synthesis history, and therefore rarely amenable to direct theoretical prediction. Here, dynamic electron beam–induced transformations in Si deposited on a graphene monolayer are used to create libraries of possible Si and carbon vacancy defects. Deep learning networks are developed for automated image analysis and recognition of the defects, creating a library of (meta) stable defect configurations. Density functional theory is used to estimate atomically resolved scanning tunneling microscopy (STM) signatures of the classified defects from the created library, allowing identification of several defect types across imaging platforms. This approach allows automatic creation of defect libraries in solids, exploring the metastable configurations always present in real materials, and correlative studies with other atomically resolved techniques, providing comprehensive insight into defect functionalities.},
doi = {10.1126/sciadv.aaw8989},
journal = {Science Advances},
number = 9,
volume = 5,
place = {United States},
year = {2019},
month = {9}
}
Web of Science
Works referenced in this record:
Atom-by-atom structural and chemical analysis by annular dark-field electron microscopy
journal, March 2010
- Krivanek, Ondrej L.; Chisholm, Matthew F.; Nicolosi, Valeria
- Nature, Vol. 464, Issue 7288
Analysis of graphene nanoribbons as a channel material for field-effect transistors
journal, April 2006
- Obradovic, B.; Kotlyar, R.; Heinz, F.
- Applied Physics Letters, Vol. 88, Issue 14
Placing single atoms in graphene with a scanning transmission electron microscope
journal, September 2017
- Dyck, Ondrej; Kim, Songkil; Kalinin, Sergei V.
- Applied Physics Letters, Vol. 111, Issue 11
Materials Data Infrastructure: A Case Study of the Citrination Platform to Examine Data Import, Storage, and Access
journal, June 2016
- O’Mara, Jordan; Meredig, Bryce; Michel, Kyle
- JOM, Vol. 68, Issue 8
Spin qubits in graphene quantum dots
journal, February 2007
- Trauzettel, Björn; Bulaev, Denis V.; Loss, Daniel
- Nature Physics, Vol. 3, Issue 3
Image registration of low signal-to-noise cryo-STEM data
journal, August 2018
- Savitzky, Benjamin H.; El Baggari, Ismail; Clement, Colin B.
- Ultramicroscopy, Vol. 191
Theory and Application for the Scanning Tunneling Microscope
journal, June 1983
- Tersoff, J.; Hamann, D. R.
- Physical Review Letters, Vol. 50, Issue 25
Graphene Reknits Its Holes
journal, July 2012
- Zan, Recep; Ramasse, Quentin M.; Bangert, Ursel
- Nano Letters, Vol. 12, Issue 8
Focal Loss for Dense Object Detection
conference, October 2017
- Lin, Tsung-Yi; Goyal, Priya; Girshick, Ross
- 2017 IEEE International Conference on Computer Vision (ICCV)
Deep Learning of Atomically Resolved Scanning Transmission Electron Microscopy Images: Chemical Identification and Tracking Local Transformations
journal, October 2016
- Ziatdinov, Maxim; Dyck, Ondrej; Maksov, Artem
- ACS Nano, Vol. 11, Issue 12
Van der Waals density functionals applied to solids
journal, May 2011
- Klimeš, Jiří; Bowler, David R.; Michaelides, Angelos
- Physical Review B, Vol. 83, Issue 19
A Deep Learning Approach to Identify Local Structures in Atomic-Resolution Transmission Electron Microscopy Images
journal, July 2018
- Madsen, Jacob; Liu, Pei; Kling, Jens
- Advanced Theory and Simulations, Vol. 1, Issue 8
Norm-conserving and ultrasoft pseudopotentials for first-row and transition elements
journal, October 1994
- Kresse, G.; Hafner, J.
- Journal of Physics: Condensed Matter, Vol. 6, Issue 40
Deep learning analysis of defect and phase evolution during electron beam-induced transformations in WS2
journal, February 2019
- Maksov, Artem; Dyck, Ondrej; Wang, Kai
- npj Computational Materials, Vol. 5, Issue 1
From ultrasoft pseudopotentials to the projector augmented-wave method
journal, January 1999
- Kresse, G.; Joubert, D.
- Physical Review B, Vol. 59, Issue 3, p. 1758-1775
Learning surface molecular structures via machine vision
journal, August 2017
- Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.
- npj Computational Materials, Vol. 3, Issue 1
Picometre-precision analysis of scanning transmission electron microscopy images of platinum nanocatalysts
journal, June 2014
- Yankovich, Andrew B.; Berkels, Benjamin; Dahmen, W.
- Nature Communications, Vol. 5, Issue 1
Manipulating low-dimensional materials down to the level of single atoms with electron irradiation
journal, September 2017
- Susi, Toma; Meyer, Jannik C.; Kotakoski, Jani
- Ultramicroscopy, Vol. 180
The Atomic Circus: Small Electron Beams Spotlight Advanced Materials Down to the Atomic Scale
journal, October 2018
- Wu, Haijun; Zhao, Xiaoxu; Guan, Cao
- Advanced Materials, Vol. 30, Issue 47
Transition-Metal-Atom-Embedded Graphane and Its Spintronic Device Applications
journal, October 2011
- Da, Haixia; Feng, Yuan Ping; Liang, Gengchaiu
- The Journal of Physical Chemistry C, Vol. 115, Issue 46
SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation
journal, December 2017
- Badrinarayanan, Vijay; Kendall, Alex; Cipolla, Roberto
- IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 39, Issue 12
Theory of the scanning tunneling microscope
journal, January 1985
- Tersoff, J.; Hamann, D. R.
- Physical Review B, Vol. 31, Issue 2
Carrier-induced antiferromagnet of graphene islands embedded in hexagonal boron nitride
journal, August 2011
- Ramasubramaniam, Ashwin; Naveh, Doron
- Physical Review B, Vol. 84, Issue 7
Z-shaped graphene nanoribbon quantum dot device
journal, July 2007
- Wang, Z. F.; Shi, Q. W.; Li, Qunxiang
- Applied Physics Letters, Vol. 91, Issue 5
Effective Cleaning of Hexagonal Boron Nitride for Graphene Devices
journal, January 2012
- Garcia, Andrei G. F.; Neumann, Michael; Amet, François
- Nano Letters, Vol. 12, Issue 9
Mitigating e-beam-induced hydrocarbon deposition on graphene for atomic-scale scanning transmission electron microscopy studies
journal, January 2018
- Dyck, Ondrej; Kim, Songkil; Kalinin, Sergei V.
- Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena, Vol. 36, Issue 1
Electron-Beam Manipulation of Silicon Dopants in Graphene
journal, June 2018
- Tripathi, Mukesh; Mittelberger, Andreas; Pike, Nicholas A.
- Nano Letters, Vol. 18, Issue 8
Ballistic Transport in Graphene Nanostrips in the Presence of Disorder: Importance of Edge Effects
journal, January 2007
- Areshkin, Denis A.; Gunlycke, Daniel; White, Carter T.
- Nano Letters, Vol. 7, Issue 1
Performance Projections for Ballistic Graphene Nanoribbon Field-Effect Transistors
journal, April 2007
- Liang, Gengchiau; Neophytou, Neophytos; Nikonov, Dmitri E.
- IEEE Transactions on Electron Devices, Vol. 54, Issue 4
Fulfilling the promise of the materials genome initiative with high-throughput experimental methodologies
journal, March 2017
- Green, M. L.; Choi, C. L.; Hattrick-Simpers, J. R.
- Applied Physics Reviews, Vol. 4, Issue 1
Soft self-consistent pseudopotentials in a generalized eigenvalue formalism
journal, April 1990
- Vanderbilt, David
- Physical Review B, Vol. 41, Issue 11, p. 7892-7895
Engineering and modifying two-dimensional materials by electron beams
journal, September 2017
- Zhao, Xiaoxu; Kotakoski, Jani; Meyer, Jannik C.
- MRS Bulletin, Vol. 42, Issue 09
Stone-Wales-type transformations in carbon nanostructures driven by electron irradiation
journal, June 2011
- Kotakoski, J.; Meyer, J. C.; Kurasch, S.
- Physical Review B, Vol. 83, Issue 24
Addressing the isomer cataloguing problem for nanopores in two-dimensional materials
journal, January 2019
- Govind Rajan, Ananth; Silmore, Kevin S.; Swett, Jacob
- Nature Materials, Vol. 18, Issue 2
Atom-by-atom fabrication by electron beam via induced phase transformations
journal, September 2017
- Jiang, Nan; Zarkadoula, Eva; Narang, Prineha
- MRS Bulletin, Vol. 42, Issue 09
Quantum dots and spin qubits in graphene
journal, July 2010
- Recher, Patrik; Trauzettel, Björn
- Nanotechnology, Vol. 21, Issue 30
High performance current and spin diode of atomic carbon chain between transversely symmetric ribbon electrodes
journal, August 2014
- Dong, Yao-Jun; Wang, Xue-Feng; Yang, Shuo-Wang
- Scientific Reports, Vol. 4, Issue 1
Machine-learning-assisted materials discovery using failed experiments
journal, May 2016
- Raccuglia, Paul; Elbert, Katherine C.; Adler, Philip D. F.
- Nature, Vol. 533, Issue 7601
Direct Sub-Angstrom Imaging of a Crystal Lattice
journal, September 2004
- Nellist, P. D.
- Science, Vol. 305, Issue 5691
The Materials Data Facility: Data Services to Advance Materials Science Research
journal, July 2016
- Blaiszik, B.; Chard, K.; Pruyne, J.
- JOM, Vol. 68, Issue 8
Graphene quantum dots embedded in hexagonal boron nitride sheets
journal, January 2011
- Li, Junwen; Shenoy, Vivek B.
- Applied Physics Letters, Vol. 98, Issue 1
Role of materials data science and informatics in accelerated materials innovation
journal, August 2016
- Kalidindi, Surya R.; Brough, David B.; Li, Shengyen
- MRS Bulletin, Vol. 41, Issue 08
Probing the Bonding and Electronic Structure of Single Atom Dopants in Graphene with Electron Energy Loss Spectroscopy
journal, January 2013
- Ramasse, Quentin M.; Seabourne, Che R.; Kepaptsoglou, Despoina-Maria
- Nano Letters, Vol. 13, Issue 10
Large scale atmospheric pressure chemical vapor deposition of graphene
journal, April 2013
- Vlassiouk, Ivan; Fulvio, Pasquale; Meyer, Harry
- Carbon, Vol. 54
Correlating Josephson supercurrents and Shiba states in quantum spins unconventionally coupled to superconductors
journal, February 2021
- Küster, Felix; Montero, Ana M.; Guimarães, Filipe S. M.
- Nature Communications, Vol. 12, Issue 1
Reducing Dzyaloshinskii-Moriya interaction and field-free spin-orbit torque switching in synthetic antiferromagnets
journal, May 2021
- Chen, Ruyi; Cui, Qirui; Liao, Liyang
- Nature Communications, Vol. 12, Issue 1
Focal Loss for Dense Object Detection
journal, February 2020
- Lin, Tsung-Yi; Goyal, Priya; Girshick, Ross
- IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 42, Issue 2
SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation.
text, January 2017
- Badrinarayanan, Vijay; Kendall, Alex; Cipolla, Roberto
- Apollo - University of Cambridge Repository
Quantum dots and spin qubits in graphene
text, January 2010
- Recher, Patrik; Trauzettel, Bjoern
- arXiv
Graphene quantum dots embedded in hexagonal boron nitride sheets
text, January 2010
- Li, Junwen; Shenoy, Vivek B.
- arXiv
Van der Waals density functionals applied to solids
text, January 2011
- Klimeš, Jiří; Bowler, David R.; Michaelides, Angelos
- arXiv
High performance current and spin diode of atomic carbon chain between transversely symmetric ribbon electrodes
text, January 2014
- Dong, Y. J.; Wang, X. F.; Yang, S. W.
- arXiv
SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation
preprint, January 2015
- Badrinarayanan, Vijay; Kendall, Alex; Cipolla, Roberto
- arXiv
Deep Learning of Atomically Resolved Scanning Transmission Electron Microscopy Images: Chemical Identification and Tracking Local Transformations
text, January 2018
- Ziatdinov, Maxim; Dyck, Ondrej; Maksov, Artem
- arXiv
Deep Learning Analysis of Defect and Phase Evolution During Electron Beam Induced Transformations in WS2
text, January 2018
- Maksov, Artem; Dyck, Ondrej; Wang, Kai
- arXiv
Si-Vacancy complexes in Graphene
dataset, January 2018
- Ziatdinov, Maxim; Dyck, Ondrej; Kalinin, Sergei
- Citrine Informatics
Works referencing / citing this record:
Atomic Mechanisms for the Si Atom Dynamics in Graphene: Chemical Transformations at the Edge and in the Bulk
journal, November 2019
- Ziatdinov, Maxim; Dyck, Ondrej; Jesse, Stephen
- Advanced Functional Materials, Vol. 29, Issue 52
Atomic mechanisms for the Si atom dynamics in graphene: chemical transformations at the edge and in the bulk
text, January 2019
- Ziatdinov, Maxim; Dyck, Ondrej; Jesse, Stephen
- arXiv