Atomic electron tomography in three and four dimensions

Zhou, Jihan; Yang, Yongsoo; Ercius, Peter; Miao, Jianwei

doi:10.1557/mrs.2020.88

Title: Atomic electron tomography in three and four dimensions

Abstract

Atomic electron tomography (AET) has become a powerful tool for atomic-scale structural characterization in three and four dimensions. It provides the ability to correlate structures and properties of materials at the single-atom level. With recent advances in data acquisition methods, iterative three-dimensional (3D) reconstruction algorithms, and post-processing methods, AET can now determine 3D atomic coordinates and chemical species with sub-Angstrom precision, and reveal their atomic-scale time evolution during dynamical processes. In this work, we review the recent experimental and algorithmic developments of AET and highlight several groundbreaking experiments, which include pinpointing the 3D atom positions and chemical order/disorder in technologically relevant materials and capturing how atoms rearrange during early nucleation at four-dimensional atomic resolution.

Authors:

Zhou, Jihan ^[1]; Yang, Yongsoo ^[2]; Ercius, Peter ^[3]; Miao, Jianwei ^[1]

Univ. of California, Los Angeles, CA (United States)
Korea Advanced Inst. Science and Technology (KAIST), Daejeon (Korea, Republic of)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Publication Date:: Thu Apr 09 00:00:00 EDT 2020

Research Org.:: Univ. of California, Los Angeles, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Materials Sciences & Engineering Division; USDOE Office of Science (SC), Basic Energy Sciences (BES), Scientific User Facilities Division; National Science Foundation (NSF); US Army Research Office (ARO); National Research Foundation of Korea (NRF)

OSTI Identifier:: 1657165

Alternate Identifier(s):: OSTI ID: 1616980

Grant/Contract Number:: AC02-05CH11231; DMR-1548924; SC0010378; 18057522; DMR-1437263; 2019R1F1A1058236

Resource Type:: Accepted Manuscript

Journal Name:: MRS Bulletin

Additional Journal Information:: Journal Volume: 45; Journal Issue: 4; Journal ID: ISSN 0883-7694

Publisher:: Materials Research Society

Country of Publication:: United States

Language:: English

Subject:: 30 DIRECT ENERGY CONVERSION; atomic electron tomography (AET); tranmission electron microscopy (TEM); scanning transmission electron microscopy (STEM); 4D atomic resolution

Citation Formats


                    Zhou, Jihan, Yang, Yongsoo, Ercius, Peter, and Miao, Jianwei. Atomic electron tomography in three and four dimensions.  United States: N. p., 2020. 
Web.  doi:10.1557/mrs.2020.88.

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                    Zhou, Jihan, Yang, Yongsoo, Ercius, Peter, & Miao, Jianwei. Atomic electron tomography in three and four dimensions.  United States.  https://doi.org/10.1557/mrs.2020.88

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                    Zhou, Jihan, Yang, Yongsoo, Ercius, Peter, and Miao, Jianwei. Thu .  
"Atomic electron tomography in three and four dimensions".  United States.  https://doi.org/10.1557/mrs.2020.88.  https://www.osti.gov/servlets/purl/1657165.

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@article{osti_1657165,

  title        = {Atomic electron tomography in three and four dimensions},

  author       = {Zhou, Jihan and Yang, Yongsoo and Ercius, Peter and Miao, Jianwei},

  abstractNote = {Atomic electron tomography (AET) has become a powerful tool for atomic-scale structural characterization in three and four dimensions. It provides the ability to correlate structures and properties of materials at the single-atom level. With recent advances in data acquisition methods, iterative three-dimensional (3D) reconstruction algorithms, and post-processing methods, AET can now determine 3D atomic coordinates and chemical species with sub-Angstrom precision, and reveal their atomic-scale time evolution during dynamical processes. In this work, we review the recent experimental and algorithmic developments of AET and highlight several groundbreaking experiments, which include pinpointing the 3D atom positions and chemical order/disorder in technologically relevant materials and capturing how atoms rearrange during early nucleation at four-dimensional atomic resolution.},

  doi          = {10.1557/mrs.2020.88},

  journal      = {MRS Bulletin},

  number       = 4,

  volume       = 45,

  place        = {United States},

  year         = {Thu Apr 09 00:00:00 EDT 2020},

  month        = {Thu Apr 09 00:00:00 EDT 2020}

}

Copy to clipboard

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Atomic electron tomography: 3D structures without crystals

Journal Article Miao, J. ; Ercius, P. ; Billinge, S. J. L. - Science

Crystallography has been fundamental to the development of many fields of science over the last century. However, much of our modern science and technology relies on materials with defects and disorders, and their three-dimensional (3D) atomic structures are not accessible to crystallography. One method capable of addressing this major challenge is atomic electron tomography. By combining advanced electron microscopes and detectors with powerful data analysis and tomographic reconstruction algorithms, it is now possible to determine the 3D atomic structure of crystal defects such as grain boundaries, stacking faults, dislocations, and point defects, as well as to precisely localize the 3Dmore »« less
Cited by 149
https://doi.org/10.1126/science.aaf2157
Correlating the three-dimensional atomic defects and electronic properties of two-dimensional transition metal dichalcogenides

Journal Article Tian, Xuezeng ; Kim, Dennis S. ; Yang, Shize ; ... - Nature Materials

The electronic, optical and chemical properties of two-dimensional transition metal dichalcogenides strongly depend on their three-dimensional atomic structure and crystal defects. Using Re-doped MoS₂ as a model system, here we present scanning atomic electron tomography as a method to determine three-dimensional atomic positions as well as positions of crystal defects such as dopants, vacancies and ripples with a precision down to 4 pm. We further measure the three-dimensional bond distortion and local strain tensor induced by single dopants. By directly offering these experimental three-dimensional atomic coordinates to density functional theory, we obtain more accurate electronic band structures than derived frommore »« less
Cited by 79
https://doi.org/10.1038/s41563-020-0636-5

Full Text Available
Deciphering chemical order/disorder and material properties at the single-atom level

Journal Article Yang, Yongsoo ; Chen, Chien-Chun ; Scott, M. C. ; ... - Nature (London)

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling ‘real’ materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily onmore »« less
Cited by 175
https://doi.org/10.1038/nature21042

Full Text Available
Observing crystal nucleation in four dimensions using atomic electron tomography

Journal Article Zhou, Jihan ; Yang, Yongsoo ; Yang, Yao ; ... - Nature (London)

Nucleation plays a critical role in many physical and biological phenomena that range from crystallization, melting and evaporation to the formation of clouds and the initiation of neurodegenerative diseases. However, nucleation is a challenging process to study in experiments, especially in the early stage when several atoms or molecules start to form a new phase from a parent phase. A number of experimental and computational methods have been used to investigate nucleation processes, but experimental determination of the three-dimensional atomic structure and the dynamics of early stage nuclei has been unachievable. Here we use atomic electron tomography to study earlymore »« less
Cited by 198
https://doi.org/10.1038/s41586-019-1317-x

Full Text Available

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Title: Atomic electron tomography in three and four dimensions

Abstract

Citation Formats

Three-dimensional coordinates of individual atoms in materials revealed by electron tomography journal, September 2015

Correcting nonlinear drift distortion of scanning probe and scanning transmission electron microscopies from image pairs with orthogonal scan directions journal, March 2016

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging journal, September 2017

Observing crystal nucleation in four dimensions using atomic electron tomography journal, June 2019

Electron tomography at 2.4-ångström resolution journal, March 2012

Coherent X-ray diffraction imaging of strain at the nanoscale journal, April 2009

Three-dimensional imaging of nanovoids in copper interconnects using incoherent bright field tomography journal, June 2006

Extending the methodology of X-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens journal, July 1999

Electron tomography and holography in materials science journal, April 2009

High-Resolution Scanning Transmission Electron Tomography and Elemental Analysis of Zeptogram Quantities of Heterogeneous Catalyst journal, April 2004

Atom probe tomography journal, March 2007

‘Big Bang’ tomography as a new route to atomic-resolution electron tomography journal, June 2012

Beyond crystallography: Diffractive imaging using coherent x-ray light sources journal, April 2015

Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research journal, June 2015

Electron Microscopy of Unstained Biological Material: The Polytropic Montage journal, March 1968

Reconstruction of Three Dimensional Structures from Electron Micrographs journal, January 1968

Image Denoising by Sparse 3-D Transform-Domain Collaborative Filtering journal, August 2007

Fast Fourier method for the accurate rotation of sampled images journal, June 1997

Atomic-scale determination of surface facets in gold nanorods journal, October 2012

Battery materials for ultrafast charging and discharging journal, March 2009

Atomically thin two-dimensional organic-inorganic hybrid perovskites journal, September 2015

High tensile ductility in a nanostructured metal journal, October 2002

Electron microscopy image enhanced journal, April 1998

Electron Tomography in the (S)TEM: From Nanoscale Morphological Analysis to 3D Atomic Imaging journal, August 2012

Visualizing Gas Molecules Interacting with Supported Nanoparticulate Catalysts at Reaction Conditions journal, January 2012

Deciphering chemical order/disorder and material properties at the single-atom level journal, February 2017

On the topological, morphological, and microstructural characterization of nanoporous metals journal, January 2018

Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution journal, March 2013

Advances in cryo-electron tomography and subtomogram averaging and classification journal, October 2019

Quantitative Three-Dimensional Reconstruction of Catalyst Particles for Bamboo-like Carbon Nanotubes journal, December 2007

Nanoporous Metals for Catalytic and Optical Applications journal, August 2009

Three-Dimensional Imaging of Individual Dopant Atoms in SrTiO 3 journal, December 2013

Three-dimensional imaging of pore structures inside low-κ dielectrics journal, May 2010

Atomic electron tomography: 3D structures without crystals journal, September 2016

Atomic-Resolution Imaging with a Sub-50-pm Electron Probe journal, March 2009

Electron ptychographic microscopy for three-dimensional imaging journal, July 2017

Single-Particle Cryo-EM at Crystallographic Resolution journal, April 2015

The development of cryo-EM into a mainstream structural biology technique journal, December 2015

A fracture-resistant high-entropy alloy for cryogenic applications journal, September 2014

An Atom-Probe Tomography Primer journal, October 2009

Gold Nanoparticles for Nucleic Acid Delivery journal, June 2014

A marker-free alignment method for electron tomography journal, June 1995

2D materials for quantum information science journal, August 2019

Low-temperature hydrogen production from water and methanol using Pt/α-MoC catalysts journal, March 2017

Improved Oxygen Reduction Activity on Pt3Ni(111) via Increased Surface Site Availability journal, January 2007

Quantitative characterization of high temperature oxidation using electron tomography and energy-dispersive X-ray spectroscopy journal, July 2018

Electron microscopy of gold nanoparticles at atomic resolution journal, August 2014

Embedded Nanostructures Revealed in Three Dimensions journal, September 2005

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

Topological nanomaterials journal, June 2019

Cryo-STEM mapping of solid–liquid interfaces and dendrites in lithium-metal batteries journal, August 2018

A multiple scattering algorithm for three dimensional phase contrast atomic electron tomography journal, January 2020

Algebraic Reconstruction Techniques (ART) for three-dimensional electron microscopy and X-ray photography journal, December 1970

Real-Time Imaging of Pt3Fe Nanorod Growth in Solution journal, May 2012

Hierarchical 3D electrodes for electrochemical energy storage journal, December 2018

Real-space charge-density imaging with sub-ångström resolution by four-dimensional electron microscopy journal, October 2019

Atomic-Scale Chemical Imaging of Composition and Bonding by Aberration-Corrected Microscopy journal, February 2008

Nanotomography in the chemical, biological and materials sciences journal, January 2007

3D structure of individual nanocrystals in solution by electron microscopy journal, July 2015

Coaxial silicon nanowires as solar cells and nanoelectronic power sources journal, October 2007

Simultaneous atomic-resolution electron ptychography and Z-contrast imaging of light and heavy elements in complex nanostructures journal, August 2016

High-performance transition metal-doped Pt3Ni octahedra for oxygen reduction reaction journal, June 2015

SEMICONDUCTOR NANOWIRES AND NANOTUBES journal, August 2004

3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography journal, September 2003

Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry journal, February 2016

XEDS STEM tomography for 3D chemical characterization of nanoscale particles journal, August 2013

Radiation damage in the TEM and SEM journal, August 2004

Observation of three-dimensional elemental distributions of a Si device using a 360°-tilt FIB and the cold field-emission STEM system journal, November 2008

Nanostructured materials for advanced energy conversion and storage devices journal, May 2005

Formation of bimetallic clusters in superfluid helium nanodroplets analysed by atomic resolution electron tomography journal, October 2015

Quantum spin Hall effect in two-dimensional transition metal dichalcogenides journal, November 2014

Three-Dimensional Electron Microscopy of Macromolecular Assemblies book, January 2006

Multimodal x-ray and electron microscopy of the Allende meteorite journal, September 2019

Electron ptychography of 2D materials to deep sub-ångström resolution journal, July 2018

Nanostructures in Biodiagnostics journal, April 2005

Colloidal nanoparticles as advanced biological sensors journal, October 2014

Pd-Pt Bimetallic Nanodendrites with High Activity for Oxygen Reduction journal, May 2009

Three-dimensional coordinates of individual atoms in materials revealed by electron tomography
journal, September 2015

Correcting nonlinear drift distortion of scanning probe and scanning transmission electron microscopies from image pairs with orthogonal scan directions
journal, March 2016

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging
journal, September 2017

Observing crystal nucleation in four dimensions using atomic electron tomography
journal, June 2019

Electron tomography at 2.4-ångström resolution
journal, March 2012

Coherent X-ray diffraction imaging of strain at the nanoscale
journal, April 2009

Three-dimensional imaging of nanovoids in copper interconnects using incoherent bright field tomography
journal, June 2006

Extending the methodology of X-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens
journal, July 1999

Electron tomography and holography in materials science
journal, April 2009

High-Resolution Scanning Transmission Electron Tomography and Elemental Analysis of Zeptogram Quantities of Heterogeneous Catalyst
journal, April 2004

Atom probe tomography
journal, March 2007

‘Big Bang’ tomography as a new route to atomic-resolution electron tomography
journal, June 2012

Beyond crystallography: Diffractive imaging using coherent x-ray light sources
journal, April 2015

Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research
journal, June 2015

Electron Microscopy of Unstained Biological Material: The Polytropic Montage
journal, March 1968

Reconstruction of Three Dimensional Structures from Electron Micrographs
journal, January 1968

Image Denoising by Sparse 3-D Transform-Domain Collaborative Filtering
journal, August 2007

Fast Fourier method for the accurate rotation of sampled images
journal, June 1997

Atomic-scale determination of surface facets in gold nanorods
journal, October 2012

Battery materials for ultrafast charging and discharging
journal, March 2009

Atomically thin two-dimensional organic-inorganic hybrid perovskites
journal, September 2015

High tensile ductility in a nanostructured metal
journal, October 2002

Electron microscopy image enhanced
journal, April 1998

Electron Tomography in the (S)TEM: From Nanoscale Morphological Analysis to 3D Atomic Imaging
journal, August 2012

Visualizing Gas Molecules Interacting with Supported Nanoparticulate Catalysts at Reaction Conditions
journal, January 2012

Deciphering chemical order/disorder and material properties at the single-atom level
journal, February 2017

On the topological, morphological, and microstructural characterization of nanoporous metals
journal, January 2018

Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution
journal, March 2013

Advances in cryo-electron tomography and subtomogram averaging and classification
journal, October 2019

Quantitative Three-Dimensional Reconstruction of Catalyst Particles for Bamboo-like Carbon Nanotubes
journal, December 2007

Nanoporous Metals for Catalytic and Optical Applications
journal, August 2009

Three-Dimensional Imaging of Individual Dopant Atoms in ${SrTiO}_{3}$
journal, December 2013

Three-dimensional imaging of pore structures inside low-κ dielectrics
journal, May 2010

Atomic electron tomography: 3D structures without crystals
journal, September 2016

Atomic-Resolution Imaging with a Sub-50-pm Electron Probe
journal, March 2009

Electron ptychographic microscopy for three-dimensional imaging
journal, July 2017

Single-Particle Cryo-EM at Crystallographic Resolution
journal, April 2015

The development of cryo-EM into a mainstream structural biology technique
journal, December 2015

A fracture-resistant high-entropy alloy for cryogenic applications
journal, September 2014

An Atom-Probe Tomography Primer
journal, October 2009

Gold Nanoparticles for Nucleic Acid Delivery
journal, June 2014

A marker-free alignment method for electron tomography
journal, June 1995

2D materials for quantum information science
journal, August 2019

Low-temperature hydrogen production from water and methanol using Pt/α-MoC catalysts
journal, March 2017

Improved Oxygen Reduction Activity on Pt₃Ni(111) via Increased Surface Site Availability
journal, January 2007

Quantitative characterization of high temperature oxidation using electron tomography and energy-dispersive X-ray spectroscopy
journal, July 2018

Electron microscopy of gold nanoparticles at atomic resolution
journal, August 2014

Embedded Nanostructures Revealed in Three Dimensions
journal, September 2005

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

Topological nanomaterials
journal, June 2019

Cryo-STEM mapping of solid–liquid interfaces and dendrites in lithium-metal batteries
journal, August 2018

A multiple scattering algorithm for three dimensional phase contrast atomic electron tomography
journal, January 2020

Algebraic Reconstruction Techniques (ART) for three-dimensional electron microscopy and X-ray photography
journal, December 1970

Real-Time Imaging of Pt3Fe Nanorod Growth in Solution
journal, May 2012

Hierarchical 3D electrodes for electrochemical energy storage
journal, December 2018

Real-space charge-density imaging with sub-ångström resolution by four-dimensional electron microscopy
journal, October 2019

Atomic-Scale Chemical Imaging of Composition and Bonding by Aberration-Corrected Microscopy
journal, February 2008

Nanotomography in the chemical, biological and materials sciences
journal, January 2007

3D structure of individual nanocrystals in solution by electron microscopy
journal, July 2015

Coaxial silicon nanowires as solar cells and nanoelectronic power sources
journal, October 2007

Simultaneous atomic-resolution electron ptychography and Z-contrast imaging of light and heavy elements in complex nanostructures
journal, August 2016

High-performance transition metal-doped Pt3Ni octahedra for oxygen reduction reaction
journal, June 2015

SEMICONDUCTOR NANOWIRES AND NANOTUBES
journal, August 2004

3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography
journal, September 2003

Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry
journal, February 2016

XEDS STEM tomography for 3D chemical characterization of nanoscale particles
journal, August 2013

Radiation damage in the TEM and SEM
journal, August 2004

Observation of three-dimensional elemental distributions of a Si device using a 360°-tilt FIB and the cold field-emission STEM system
journal, November 2008

Nanostructured materials for advanced energy conversion and storage devices
journal, May 2005

Formation of bimetallic clusters in superfluid helium nanodroplets analysed by atomic resolution electron tomography
journal, October 2015

Quantum spin Hall effect in two-dimensional transition metal dichalcogenides
journal, November 2014

Three-Dimensional Electron Microscopy of Macromolecular Assemblies
book, January 2006

Multimodal x-ray and electron microscopy of the Allende meteorite
journal, September 2019

Electron ptychography of 2D materials to deep sub-ångström resolution
journal, July 2018

Nanostructures in Biodiagnostics
journal, April 2005

Colloidal nanoparticles as advanced biological sensors
journal, October 2014

Pd-Pt Bimetallic Nanodendrites with High Activity for Oxygen Reduction
journal, May 2009

Atomic structure of sensitive battery materials and interfaces revealed by cryo–electron microscopy
journal, October 2017

Simultaneous Algebraic Reconstruction Technique (SART): A Superior Implementation of the Art Algorithm
journal, January 1984

Three-dimensional atomic-scale structure of size-selected gold nanoclusters
journal, December 2007