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Title: Atomic Mechanisms for the Si Atom Dynamics in Graphene: Chemical Transformations at the Edge and in the Bulk

Abstract

The dynamic behavior of e-beam irradiated Si atoms in the bulk and at the edges of single-layer graphene is examined using scanning transmission electron microscopy (STEM). A deep learning network is used to convert experimental STEM movies into coordinates of individual Si and carbon atoms. A Gaussian mixture model is further used to establish the elementary atomic configurations of the Si atoms, defining the bonding geometries and chemical species and accounting for the discrete rotational symmetry of the host lattice. The frequencies and Markov transition probabilities between these states are determined. This analysis enables insight into the defect populations and chemical transformation networks from the atomically resolved STEM data. Here, a clear tendency is observed for the formation of a 1D Si crystal along zigzag direction of graphene edges and for the Si impurity coupling to topological defects in bulk graphene.

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [2]; ORCiD logo [2]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science (CNMS), and Computational Sciences and Engineering Division
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science (CNMS)
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)
OSTI Identifier:
1607241
Alternate Identifier(s):
OSTI ID: 1575294
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Advanced Functional Materials
Additional Journal Information:
Journal Volume: 29; Journal Issue: 52; Journal ID: ISSN 1616-301X
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; atom dynamics; electron microscopy; graphene; machine learning

Citation Formats

Ziatdinov, Maxim, Dyck, Ondrej, Jesse, Stephen, and Kalinin, Sergei V. Atomic Mechanisms for the Si Atom Dynamics in Graphene: Chemical Transformations at the Edge and in the Bulk. United States: N. p., 2019. Web. https://doi.org/10.1002/adfm.201904480.
Ziatdinov, Maxim, Dyck, Ondrej, Jesse, Stephen, & Kalinin, Sergei V. Atomic Mechanisms for the Si Atom Dynamics in Graphene: Chemical Transformations at the Edge and in the Bulk. United States. https://doi.org/10.1002/adfm.201904480
Ziatdinov, Maxim, Dyck, Ondrej, Jesse, Stephen, and Kalinin, Sergei V. Fri . "Atomic Mechanisms for the Si Atom Dynamics in Graphene: Chemical Transformations at the Edge and in the Bulk". United States. https://doi.org/10.1002/adfm.201904480. https://www.osti.gov/servlets/purl/1607241.
@article{osti_1607241,
title = {Atomic Mechanisms for the Si Atom Dynamics in Graphene: Chemical Transformations at the Edge and in the Bulk},
author = {Ziatdinov, Maxim and Dyck, Ondrej and Jesse, Stephen and Kalinin, Sergei V.},
abstractNote = {The dynamic behavior of e-beam irradiated Si atoms in the bulk and at the edges of single-layer graphene is examined using scanning transmission electron microscopy (STEM). A deep learning network is used to convert experimental STEM movies into coordinates of individual Si and carbon atoms. A Gaussian mixture model is further used to establish the elementary atomic configurations of the Si atoms, defining the bonding geometries and chemical species and accounting for the discrete rotational symmetry of the host lattice. The frequencies and Markov transition probabilities between these states are determined. This analysis enables insight into the defect populations and chemical transformation networks from the atomically resolved STEM data. Here, a clear tendency is observed for the formation of a 1D Si crystal along zigzag direction of graphene edges and for the Si impurity coupling to topological defects in bulk graphene.},
doi = {10.1002/adfm.201904480},
journal = {Advanced Functional Materials},
number = 52,
volume = 29,
place = {United States},
year = {2019},
month = {11}
}

Works referenced in this record:

Atomic-Level Sculpting of Crystalline Oxides: Toward Bulk Nanofabrication with Single Atomic Plane Precision
journal, October 2015


The impact of STEM aberration correction on materials science
journal, September 2017


U-Net: Convolutional Networks for Biomedical Image Segmentation
book, November 2015

  • Ronneberger, Olaf; Fischer, Philipp; Brox, Thomas
  • Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015: 18th International Conference, Munich, Germany, October 5-9, 2015, Proceedings, Part III
  • DOI: 10.1007/978-3-319-24574-4_28

Building Structures Atom by Atom via Electron Beam Manipulation
journal, August 2018


Direct atomic fabrication and dopant positioning in Si using electron beams with active real-time image-based feedback
journal, April 2018


Interference Effects in the Electron Microscopy of Thin Crystal Foils
journal, September 1956


An atomic switch realized with the scanning tunnelling microscope
journal, August 1991

  • Eigler, D. M.; Lutz, C. P.; Rudge, W. E.
  • Nature, Vol. 352, Issue 6336
  • DOI: 10.1038/352600a0

Directed Atom-by-Atom Assembly of Dopants in Silicon
journal, May 2018


Phase-Field Models for Microstructure Evolution
journal, August 2002


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
  • DOI: 10.1002/adts.201800037

E-beam manipulation of Si atoms on graphene edges with an aberration-corrected scanning transmission electron microscope
journal, July 2018


Computation of ring statistics for network models of solids
journal, September 1991


Direct Observation of Atomic Dynamics and Silicon Doping at a Topological Defect in Graphene
journal, June 2014

  • Yang, Zhiqing; Yin, Lichang; Lee, Jaekwang
  • Angewandte Chemie International Edition, Vol. 53, Issue 34
  • DOI: 10.1002/anie.201403382

Manipulating low-dimensional materials down to the level of single atoms with electron irradiation
journal, September 2017


Building and exploring libraries of atomic defects in graphene: Scanning transmission electron and scanning tunneling microscopy study
journal, September 2019


Radiation damage in the TEM and SEM
journal, August 2004


Direct Determination of the Chemical Bonding of Individual Impurities in Graphene
journal, November 2012


Image Quality Assessment: From Error Visibility to Structural Similarity
journal, April 2004

  • Wang, Z.; Bovik, A. C.; Sheikh, H. R.
  • IEEE Transactions on Image Processing, Vol. 13, Issue 4
  • DOI: 10.1109/TIP.2003.819861

Towards atomically precise manipulation of 2D nanostructures in the electron microscope
journal, September 2017


Electron-Beam Manipulation of Silicon Dopants in Graphene
journal, June 2018


Kinetics of Phase Change. II Transformation‐Time Relations for Random Distribution of Nuclei
journal, February 1940

  • Avrami, Melvin
  • The Journal of Chemical Physics, Vol. 8, Issue 2
  • DOI: 10.1063/1.1750631

Granulation, Phase Change, and Microstructure Kinetics of Phase Change. III
journal, February 1941

  • Avrami, Melvin
  • The Journal of Chemical Physics, Vol. 9, Issue 2, p. 177-184
  • DOI: 10.1063/1.1750872

In Situ Observation of Oxygen Vacancy Dynamics and Ordering in the Epitaxial LaCoO 3 System
journal, June 2017


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
  • DOI: 10.1557/mrs.2017.184

Single-atom dynamics in scanning transmission electron microscopy
journal, September 2017

  • Mishra, Rohan; Ishikawa, Ryo; Lupini, Andrew R.
  • MRS Bulletin, Vol. 42, Issue 09
  • DOI: 10.1557/mrs.2017.187

Kinetics of Phase Change. I General Theory
journal, December 1939

  • Avrami, Melvin
  • The Journal of Chemical Physics, Vol. 7, Issue 12, p. 1103-1112
  • DOI: 10.1063/1.1750380

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
  • DOI: 10.1557/mrs.2017.183

Imaging active topological defects in carbon nanotubes
journal, May 2007

  • Suenaga, Kazu; Wakabayashi, Hideaki; Koshino, Masanori
  • Nature Nanotechnology, Vol. 2, Issue 6
  • DOI: 10.1038/nnano.2007.141

Beam-Induced Damage to Thin Specimens in an Intense Electron Probe
journal, December 2005

  • Egerton, Raymond F.; Wang, Feng; Crozier, Peter A.
  • Microscopy and Microanalysis, Vol. 12, Issue 01
  • DOI: 10.1017/S1431927606060065

Imaging atomic-level random walk of a point defect in graphene
journal, May 2014

  • Kotakoski, Jani; Mangler, Clemens; Meyer, Jannik C.
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms4991

Positioning single atoms with a scanning tunnelling microscope
journal, April 1990

  • Eigler, D. M.; Schweizer, E. K.
  • Nature, Vol. 344, Issue 6266
  • DOI: 10.1038/344524a0

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
  • DOI: 10.1021/nl304187e

Direct Imaging of Lattice Atoms and Topological Defects in Graphene Membranes
journal, November 2008

  • Meyer, Jannik C.; Kisielowski, C.; Erni, R.
  • Nano Letters, Vol. 8, Issue 11
  • DOI: 10.1021/nl801386m

Building Structures Atom by Atom via Electron Beam Manipulation
journal, February 2019