1
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Zeng M, Wang W, Yin Y, Zheng C. A simple coordinate transformation method for quickly locating the features of interest in TEM samples. Microscopy (Oxf) 2024; 73:381-387. [PMID: 38421047 DOI: 10.1093/jmicro/dfae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/16/2024] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
We developed a simple coordinate transformation method for quickly locating features of interest (FOIs) of samples in transmission electron microscope (TEM). The method is well suited for conducting sample searches in aberration-corrected scanning/transmission electron microscopes (S/TEM), where the survey can be very time-consuming because of the limited field of view imposed by the highly excited objective lens after fine-tuning the aberration correctors. For implementation, a digital image of the sample and the TEM holder was captured using a simple stereo-optical microscope. Naturally presented geometric patterns on the holder were referenced to construct a projective transformation between the electron and optical coordinate systems. The test results demonstrated that the method was accurate and required no electron microscope or specimen holder modifications. Additionally, it eliminated the need to mount the sample onto specific patterned TEM grids or deposit markers, resulting in universal applications for most TEM samples, holders and electron microscopes for fast FOI identification. Furthermore, we implemented the method into a Gatan script for graphical-user-interface-based step-by-step instructions. Through online communication, the script enabled real-time navigation and tracking of the motion of samples in TEM on enlarged optical images with a panoramic view.
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Affiliation(s)
- Mingzhi Zeng
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Songhu Rd 2005, Yangpu District, Shanghai 200438, China
| | - Wenzhao Wang
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Songhu Rd 2005, Yangpu District, Shanghai 200438, China
| | - Yang Yin
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Songhu Rd 2005, Yangpu District, Shanghai 200438, China
| | - Changlin Zheng
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Songhu Rd 2005, Yangpu District, Shanghai 200438, China
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2
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Ishida Y. Atomic-Scale Imaging of Clay Mineral Nanosheets and Their Supramolecular Complexes through Electron Microscopy: A Supramolecular Chemist's Perspective. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:6065-6076. [PMID: 38484331 DOI: 10.1021/acs.langmuir.3c03779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Recent advancements in electron microscopy techniques have revolutionized the ability to directly visualize and understand the intricate world of supramolecular chemistry. This paper provides a concise overview of a study delving into the atomic-scale imaging of monolayer clay mineral nanosheets and their associated supramolecular complexes. The imaging is conducted by harnessing the power of aberration-corrected scanning transmission electron microscopy (STEM). Clay mineral nanosheets, with their anionic charge and ultrathin thickness (of 1 nm), serve as a stable Coulombic host material for cationic guest molecules through electrostatic interactions, facilitating exceptional stability and control during observation. By incorporation of heavy-metal atom markers coordinated within the target molecules, high-angle annular dark field STEM enables a clear visualization of these supramolecular complexes. This approach helps to overcome the limitations of graphene-based systems and expands the possibilities of atomic-scale imaging of nonperiodic molecular assemblies formed by weak supramolecular interactions. The fusion of electron microscopy techniques with the principles of supramolecular and material chemistry offers exciting opportunities for studying the structure, behavior, and properties of complex supramolecular systems. It sheds light on the intricate molecular architectures and design principles governing these systems. This study showcases the immense potential of electron microscopy in supramolecular chemistry and invites researchers from various disciplines to explore the transformative possibilities of atomic-scale imaging in the field.
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Affiliation(s)
- Yohei Ishida
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Fukuoka 816-8580 Japan
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3
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Lin A, Sheng P, Ning S, Zhang F. Rotational position error correction in ptychography. APPLIED OPTICS 2024; 63:804-809. [PMID: 38294394 DOI: 10.1364/ao.510143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024]
Abstract
Accurate determination of scan positions is essential for achieving high-quality reconstructions in ptychographic imaging. This study presents and demonstrates a method for determining the rotation angle of the scan pattern relative to the detector pixel array using diffraction data. The method is based on the Fourier-Mellin transform and cross-correlation calculation. It can correct rotation errors up to 60 deg. High-quality reconstructions were obtained for visible light and electron microscopy datasets, and intricate structures of samples can be revealed. We believe that this refinement method for rotary position errors can be valuable for improving the performance of ptychographic four-dimensional scanning transmission electron microscopy.
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4
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Mares-Briones F, Higareda A, Lopez-Miranda JL, Mendoza-Cruz R, Esparza R. Bimetallic AgPt Nanoalloys as an Electrocatalyst for Ethanol Oxidation Reaction: Synthesis, Structural Analysis, and Electro-Catalytic Activity. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1396. [PMID: 37110981 PMCID: PMC10145194 DOI: 10.3390/nano13081396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 06/19/2023]
Abstract
In the present work, the chemical synthesis of AgPt nanoalloys is reported by the polyol method using polyvinylpyrrolidone (PVP) as a surfactant and a heterogeneous nucleation approach. Nanoparticles with different atomic compositions of the Ag and Pt elements (1:1 and 1:3) were synthesized by adjusting the molar ratios of the precursors. The physicochemical and microstructural characterization was initially performed using the UV-Vis technique to determine the presence of nanoparticles in suspension. Then, the morphology, size, and atomic structure were determined using XRD, SEM, and HAADF-STEM techniques, confirming the formation of a well-defined crystalline structure and homogeneous nanoalloy with an average particle size of less than 10 nm. Finally, the cyclic voltammetry technique evaluated the electrochemical activity of bimetallic AgPt nanoparticles supported on Vulcan XC-72 carbon for the ethanol oxidation reaction in an alkaline medium. Chronoamperometry and accelerated electrochemical degradation tests were performed to determine their stability and long-term durability. The synthesized AgPt (1:3)/C electrocatalyst presented significative catalytic activity and superior durability due to the introduction of Ag that weakens the chemisorption of the carbonaceous species. Thus, it could be an attractive candidate for cost-effective ethanol oxidation compared to commercial Pt/C.
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Affiliation(s)
- Fabian Mares-Briones
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, Santiago de Querétaro 76230, Qro., Mexico; (F.M.-B.); (J.L.L.-M.)
| | - América Higareda
- Unidad de Energía Renovable, Centro de Investigación Científica de Yucatán A.C., Carretera Sierra Papacal-Chuburná Puerto, Km 5, Sierra Papacal, Mérida 97302, Yuc., Mexico;
| | - Jose Luis Lopez-Miranda
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, Santiago de Querétaro 76230, Qro., Mexico; (F.M.-B.); (J.L.L.-M.)
| | - Rubén Mendoza-Cruz
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Circuito de la Investigación Científica, C.U., Ciudad de México 04510, CDMX, Mexico;
| | - Rodrigo Esparza
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, Santiago de Querétaro 76230, Qro., Mexico; (F.M.-B.); (J.L.L.-M.)
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5
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Bertoni G, Rotunno E, Marsmans D, Tiemeijer P, Tavabi AH, Dunin-Borkowski RE, Grillo V. Near-real-time diagnosis of electron optical phase aberrations in scanning transmission electron microscopy using an artificial neural network. Ultramicroscopy 2023; 245:113663. [PMID: 36566529 DOI: 10.1016/j.ultramic.2022.113663] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/17/2022] [Accepted: 12/17/2022] [Indexed: 12/23/2022]
Abstract
The key to optimizing spatial resolution in a state-of-the-art scanning transmission electron microscope is the ability to measure and correct for electron optical aberrations of the probe-forming lenses precisely. Several diagnostic methods for aberration measurement and correction have been proposed, albeit often at the cost of relatively long acquisition times. Here, we illustrate how artificial intelligence can be used to provide near-real-time diagnosis of aberrations from individual Ronchigrams. The demonstrated speed of aberration measurement is important because microscope conditions can change rapidly. It is also important for the operation of MEMS-based hardware correction elements, which have less intrinsic stability than conventional electromagnetic lenses.
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Affiliation(s)
- Giovanni Bertoni
- Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Via G. Campi 213/A, 41125 Modena, Italy.
| | - Enzo Rotunno
- Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Via G. Campi 213/A, 41125 Modena, Italy.
| | - Daan Marsmans
- Thermo Fisher Scientific, PO Box 80066, 5600 KA Eindhoven, the Netherlands
| | - Peter Tiemeijer
- Thermo Fisher Scientific, PO Box 80066, 5600 KA Eindhoven, the Netherlands
| | - Amir H Tavabi
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rafal E Dunin-Borkowski
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Vincenzo Grillo
- Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Via G. Campi 213/A, 41125 Modena, Italy
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6
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Roccapriore KM, Kalinin SV, Ziatdinov M. Physics Discovery in Nanoplasmonic Systems via Autonomous Experiments in Scanning Transmission Electron Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203422. [PMID: 36344455 PMCID: PMC9798976 DOI: 10.1002/advs.202203422] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Physics-driven discovery in an autonomous experiment has emerged as a dream application of machine learning in physical sciences. Here, this work develops and experimentally implements a deep kernel learning (DKL) workflow combining the correlative prediction of the target functional response and its uncertainty from the structure, and physics-based selection of acquisition function, which autonomously guides the navigation of the image space. Compared to classical Bayesian optimization (BO) methods, this approach allows to capture the complex spatial features present in the images of realistic materials, and dynamically learn structure-property relationships. In combination with the flexible scalarizer function that allows to ascribe the degree of physical interest to predicted spectra, this enables physical discovery in automated experiment. Here, this approach is illustrated for nanoplasmonic studies of nanoparticles and experimentally implemented in a truly autonomous fashion for bulk- and edge plasmon discovery in MnPS3 , a lesser-known beam-sensitive layered 2D material. This approach is universal, can be directly used as-is with any specimen, and is expected to be applicable to any probe-based microscopic techniques including other STEM modalities, scanning probe microscopies, chemical, and optical imaging.
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Affiliation(s)
- Kevin M. Roccapriore
- Center for Nanophase Materials SciencesOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Sergei V. Kalinin
- Center for Nanophase Materials SciencesOak Ridge National LaboratoryOak RidgeTN37831USA
- Department of Materials Science and EngineeringUniversity of TennesseeKnoxvilleTN37916USA
| | - Maxim Ziatdinov
- Center for Nanophase Materials SciencesOak Ridge National LaboratoryOak RidgeTN37831USA
- Computational Sciences and Engineering DivisionOak Ridge National LaboratoryOak RidgeTN37831USA
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7
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Ugartemendia A, Garcia Lekue A, Jimenez Izal E. Tailoring magnetism in silicon-doped zigzag graphene edges. Sci Rep 2022; 12:13032. [PMID: 35906454 PMCID: PMC9338279 DOI: 10.1038/s41598-022-16902-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
Recently, the edges of single-layer graphene have been experimentally doped with silicon atoms by means of scanning transmission electron microscopy. In this work, density functional theory is applied to model and characterize a wide range of experimentally inspired silicon doped zigzag-type graphene edges. The thermodynamic stability is assessed and the electronic and magnetic properties of the most relevant edge configurations are unveiled. Importantly, we show that silicon doping of graphene edges can induce a reversion of the spin orientation on the adjacent carbon atoms, leading to novel magnetic properties with possible applications in the field of spintronics.
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Affiliation(s)
- Andoni Ugartemendia
- Polimero eta Material Aurreratuak Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), M. de Lardizabal Pasealekua 3, Donostia, Euskadi, Spain.,Donostia International Physics Center (DIPC), M. de Lardizabal Pasealekua 3, Donostia, Euskadi, Spain
| | - Aran Garcia Lekue
- Donostia International Physics Center (DIPC), M. de Lardizabal Pasealekua 3, Donostia, Euskadi, Spain. .,IKERBASQUE, Basque Foundation for Science, Bilbao, Euskadi, Spain.
| | - Elisa Jimenez Izal
- Polimero eta Material Aurreratuak Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), M. de Lardizabal Pasealekua 3, Donostia, Euskadi, Spain. .,Donostia International Physics Center (DIPC), M. de Lardizabal Pasealekua 3, Donostia, Euskadi, Spain. .,IKERBASQUE, Basque Foundation for Science, Bilbao, Euskadi, Spain.
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8
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Dynamic hetero-metallic bondings visualized by sequential atom imaging. Nat Commun 2022; 13:2968. [PMID: 35624108 PMCID: PMC9142510 DOI: 10.1038/s41467-022-30533-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/28/2022] [Indexed: 11/16/2022] Open
Abstract
Traditionally, chemistry has been developed to obtain thermodynamically stable and isolable compounds such as molecules and solids by chemical reactions. However, recent developments in computational chemistry have placed increased importance on studying the dynamic assembly and disassembly of atoms and molecules formed in situ. This study directly visualizes the formation and dissociation dynamics of labile dimers and trimers at atomic resolution with elemental identification. The video recordings of many homo- and hetero-metallic dimers are carried out by combining scanning transmission electron microscopy (STEM) with elemental identification based on the Z-contrast principle. Even short-lived molecules with low probability of existence such as AuAg, AgCu, and AuAgCu are directly visualized as a result of identifying moving atoms at low electron doses. The dynamic assembly and disassembly of atoms and molecules is challenging to characterize in real time, with atomic resolution and elemental identification. Here, the authors report direct observation of more than twenty homo and hetero-metallic compounds, including labile Ag-Cu dimers and Au-Ag-Cu trimers.
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9
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Auad Y, Walls M, Blazit JD, Stéphan O, Tizei LH, Kociak M, De la Peña F, Tencé M. Event-based hyperspectral EELS: Towards nanosecond temporal resolution. Ultramicroscopy 2022; 239:113539. [DOI: 10.1016/j.ultramic.2022.113539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 11/16/2022]
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10
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Ning S, Xu W, Ma Y, Loh L, Pennycook TJ, Zhou W, Zhang F, Bosman M, Pennycook SJ, He Q, Loh ND. Accurate and Robust Calibration of the Uniform Affine Transformation Between Scan-Camera Coordinates for Atom-Resolved In-Focus 4D-STEM Datasets. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-11. [PMID: 35260221 DOI: 10.1017/s1431927622000320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Accurate geometrical calibration between the scan coordinates and the camera coordinates is critical in four-dimensional scanning transmission electron microscopy (4D-STEM) for both quantitative imaging and ptychographic reconstructions. For atomic-resolved, in-focus 4D-STEM datasets, we propose a hybrid method incorporating two sub-routines, namely a J-matrix method and a Fourier method, which can calibrate the uniform affine transformation between the scan-camera coordinates using raw data, without a priori knowledge of the crystal structure of the specimen. The hybrid method is found robust against scan distortions and residual probe aberrations. It is also effective even when defects are present in the specimen, or the specimen becomes relatively thick. We will demonstrate that a successful geometrical calibration with the hybrid method will lead to a more reliable recovery of both the specimen and the electron probe in a ptychographic reconstruction. We will also show that, although the elimination of local scan position errors still requires an iterative approach, the rate of convergence can be improved, and the residual errors can be further reduced if the hybrid method can be firstly applied for initial calibration. The code is made available as a simple-to-use tool to correct affine transformations of the scan-camera coordinates in 4D-STEM experiments.
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Affiliation(s)
- Shoucong Ning
- Department of Materials Science and Engineering, National University of Singapore, Singapore117575, Singapore
- Center for Bio-Imaging Sciences, National University of Singapore, Singapore117557, Singapore
| | - Wenhui Xu
- Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen518055, China
- Harbin Institute of Technology, Harbin150001, China
| | - Yinhang Ma
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing100049, China
| | - Leyi Loh
- Department of Materials Science and Engineering, National University of Singapore, Singapore117575, Singapore
| | | | - Wu Zhou
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing100049, China
| | - Fucai Zhang
- Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen518055, China
| | - Michel Bosman
- Department of Materials Science and Engineering, National University of Singapore, Singapore117575, Singapore
| | - Stephen J Pennycook
- School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing100049, China
| | - Qian He
- Department of Materials Science and Engineering, National University of Singapore, Singapore117575, Singapore
| | - N Duane Loh
- Center for Bio-Imaging Sciences, National University of Singapore, Singapore117557, Singapore
- Department of Physics, National University of Singapore, Singapore117551, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore117557, Singapore
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11
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Nicholls D, Wells J, Stevens A, Zheng Y, Castagna J, Browning ND. Sub-Sampled Imaging for STEM: Maximising Image Speed, Resolution and Precision Through Reconstruction Parameter Refinement. Ultramicroscopy 2022; 233:113451. [PMID: 34915288 DOI: 10.1016/j.ultramic.2021.113451] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 11/19/2022]
Abstract
Sub-sampling during image acquisition in scanning transmission electron microscopy (STEM) has been shown to provide a means to increase the overall speed of acquisition while at the same time providing an efficient means to control the dose, dose rate and dose overlap delivered to the sample. In this paper, we discuss specifically the parameters used to reconstruct sub-sampled images and highlight their effect on inpainting using the beta-process factor analysis (BPFA) methodology. The selection of the main control parameters can have a significant effect on the resolution, precision and sensitivity of the final inpainted images, and here we demonstrate a method by which these parameters can be optimised for any image in STEM. As part of this work, we also provide a link to open source code and a tutorial on its use, whereby these parameters can be tested for any datasets. When coupled with the hardware necessary to rapidly sub-sample images in STEM, this approach can have significant implications for imaging beam sensitive materials and dynamic processes.
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Affiliation(s)
- Daniel Nicholls
- Department of Mechanical, Materials and Aerospace Engineering, University of Liverpool, Liverpool, L69 3GH, United Kingdom.
| | - Jack Wells
- Distributed Algorithms Centre for Doctoral Training, University of Liverpool, Liverpool, L69 3GH, United Kingdom
| | | | - Yalin Zheng
- Department of Eye and Vision Science, University of Liverpool, Liverpool, L7 8TX, United Kingdom
| | - Jony Castagna
- UKRI-STFC Hartree Centre, Daresbury Laboratory, Warrington, WA4 4AD, United Kingdom
| | - Nigel D Browning
- Department of Mechanical, Materials and Aerospace Engineering, University of Liverpool, Liverpool, L69 3GH, United Kingdom; Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA; Sivananthan Laboratories, 590 Territorial Drive, Bolingbrook, IL 60440. USA; The Faraday Institution, Quad One, Harwell Science and Innovation Campus, Didcot OX11 0RA, United Kingdom
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12
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Ziatdinov MA, Ghosh A, Kalinin SV. Physics makes the difference: Bayesian optimization and active learning via augmented Gaussian process. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1088/2632-2153/ac4baa] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Abstract
Both experimental and computational methods for the exploration of structure, functionality, and properties of materials often necessitate the search across broad parameter spaces to discover optimal experimental conditions and regions of interest in the image space or parameter space of computational models. The direct grid search of the parameter space tends to be extremely time-consuming, leading to the development of strategies balancing exploration of unknown parameter spaces and exploitation towards required performance metrics. However, classical Bayesian optimization (BO) strategies based on the Gaussian process (GP) do not readily allow for the incorporation of the known physical behaviors or past knowledge. Here we explore a hybrid optimization/exploration algorithm created by augmenting the standard GP with a structured probabilistic model of the expected system’s behavior. This approach balances the flexibility of the non-parametric GP approach with a rigid structure of physical knowledge encoded into the parametric model. The fully Bayesian treatment of the latter allows additional control over the optimization via the selection of priors for the model parameters. The method is demonstrated for a noisy version of a standard univariate test function used to evaluate optimization algorithms and further extended to physical lattice models. This methodology is expected to be universally suitable for injecting prior knowledge in the form of physical models and past data in the BO framework.
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13
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Zhang J, Wu TS, Thang HV, Tseng KY, Hao X, Xu B, Chen HYT, Peng YK. Cluster Nanozymes with Optimized Reactivity and Utilization of Active Sites for Effective Peroxidase (and Oxidase) Mimicking. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104844. [PMID: 34825478 DOI: 10.1002/smll.202104844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/26/2021] [Indexed: 06/13/2023]
Abstract
Single-atom catalysts have attracted attention in the past decade since they maximize the utilization of active sites and facilitate the understanding of product distribution in some catalytic reactions. Recently, this idea has been extended to single-atom nanozymes (SAzymes) for the mimicking of natural enzymes such as horseradish peroxidase (HRP) often used in bioanalytical applications. Herein, it is demonstrated that those SAzymes without constructing the reaction pocket of HRP still undergo the OH radical-mediated pathway like most of the reported nanozymes. Their positively charged single-atom centers resulting from support electronegative oxygen/nitrogen hinder the reductive conversion of H2 O2 to OH radicals and hence display low activity per site. In contrast, it is found that this step can be facilitated over their metallic counterparts on cluster nanozymes with much higher site activity and atom efficiency (cf. SAzymes with 100% atom utilization). Besides the mimicking of HRP in glucose detection, cluster nanozymes are also demonstrated as a better oxidase mimetic for glutathione detection.
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Affiliation(s)
- Jieru Zhang
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Tai-Sing Wu
- National Synchrotron Radiation Research Centre, Hsinchu, 30076, Taiwan
| | - Ho Viet Thang
- The University of Da-Nang, University of Science and Technology, Da-Nang, 550000, Vietnam
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Kai-Yu Tseng
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Xiaodong Hao
- Materials Institute of Atomic and Molecular Science, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Bingshe Xu
- Materials Institute of Atomic and Molecular Science, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Hsin-Yi Tiffany Chen
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Yung-Kang Peng
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China
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14
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Zhang Y, Qu W, Peng G, Zhang C, Liu Z, Liu J, Li S, Wu H, Meng L, Gao L. Seeing Structural Mechanisms of Optimized Piezoelectric and Thermoelectric Bulk Materials through Structural Defect Engineering. MATERIALS 2022; 15:ma15020487. [PMID: 35057205 PMCID: PMC8780573 DOI: 10.3390/ma15020487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 02/04/2023]
Abstract
Aberration-corrected scanning transmission electron microscopy (AC-STEM) has evolved into the most powerful characterization and manufacturing platform for all materials, especially functional materials with complex structural characteristics that respond dynamically to external fields. It has become possible to directly observe and tune all kinds of defects, including those at the crucial atomic scale. In-depth understanding and technically tailoring structural defects will be of great significance for revealing the structure-performance relation of existing high-property materials, as well as for foreseeing paths to the design of high-performance materials. Insights would be gained from piezoelectrics and thermoelectrics, two representative functional materials. A general strategy is highlighted for optimizing these functional materials’ properties, namely defect engineering at the atomic scale.
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Affiliation(s)
- Yang Zhang
- Instrumental Analysis Center of Xi’an Jiaotong University, Xi’an Jiaotong University, Xi’an 710049, China; (L.M.); (L.G.)
- Correspondence:
| | - Wanbo Qu
- State Key Laboratory for Mechanical Behavior of Materials, Xi’an Jiaotong University, Xi’an 710049, China; (W.Q.); (G.P.); (C.Z.); (Z.L.); (J.L.); (S.L.); (H.W.)
| | - Guyang Peng
- State Key Laboratory for Mechanical Behavior of Materials, Xi’an Jiaotong University, Xi’an 710049, China; (W.Q.); (G.P.); (C.Z.); (Z.L.); (J.L.); (S.L.); (H.W.)
| | - Chenglong Zhang
- State Key Laboratory for Mechanical Behavior of Materials, Xi’an Jiaotong University, Xi’an 710049, China; (W.Q.); (G.P.); (C.Z.); (Z.L.); (J.L.); (S.L.); (H.W.)
| | - Ziyu Liu
- State Key Laboratory for Mechanical Behavior of Materials, Xi’an Jiaotong University, Xi’an 710049, China; (W.Q.); (G.P.); (C.Z.); (Z.L.); (J.L.); (S.L.); (H.W.)
| | - Juncheng Liu
- State Key Laboratory for Mechanical Behavior of Materials, Xi’an Jiaotong University, Xi’an 710049, China; (W.Q.); (G.P.); (C.Z.); (Z.L.); (J.L.); (S.L.); (H.W.)
| | - Shurong Li
- State Key Laboratory for Mechanical Behavior of Materials, Xi’an Jiaotong University, Xi’an 710049, China; (W.Q.); (G.P.); (C.Z.); (Z.L.); (J.L.); (S.L.); (H.W.)
| | - Haijun Wu
- State Key Laboratory for Mechanical Behavior of Materials, Xi’an Jiaotong University, Xi’an 710049, China; (W.Q.); (G.P.); (C.Z.); (Z.L.); (J.L.); (S.L.); (H.W.)
| | - Lingjie Meng
- Instrumental Analysis Center of Xi’an Jiaotong University, Xi’an Jiaotong University, Xi’an 710049, China; (L.M.); (L.G.)
| | - Lumei Gao
- Instrumental Analysis Center of Xi’an Jiaotong University, Xi’an Jiaotong University, Xi’an 710049, China; (L.M.); (L.G.)
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15
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Enhanced Mechanical Properties in 6082 Aluminum Alloy Processed by Cyclic Deformation. METALS 2021. [DOI: 10.3390/met11111735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Aging heat treatment is the most commonly used strengthening method for Al–Mg–Si alloys since high-density precipitates will be formed to hinder the movement of dislocations. In the current work, room temperature cyclic deformation was attempted to strengthen the alloy. We compared tensile test results of aged samples and cyclically deformed samples. It was found that cyclically deformed samples can achieve similar strength and approximately twice the uniform elongation as the peak aged samples. The high density of dislocations and nanoclusters observed in the cyclically deformed samples is thought to be the main reason for strengthening. Different cyclic deformation conditions have been tried and their effects were discussed.
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16
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Liu JJ. Advances and Applications of Atomic-Resolution Scanning Transmission Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 27:1-53. [PMID: 34414878 DOI: 10.1017/s1431927621012125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Although scanning transmission electron microscopy (STEM) images of individual heavy atoms were reported 50 years ago, the applications of atomic-resolution STEM imaging became wide spread only after the practical realization of aberration correctors on field-emission STEM/TEM instruments to form sub-Ångstrom electron probes. The innovative designs and advances of electron optical systems, the fundamental understanding of electron–specimen interaction processes, and the advances in detector technology all played a major role in achieving the goal of atomic-resolution STEM imaging of practical materials. It is clear that tremendous advances in computer technology and electronics, image acquisition and processing algorithms, image simulations, and precision machining synergistically made atomic-resolution STEM imaging routinely accessible. It is anticipated that further hardware/software development is needed to achieve three-dimensional atomic-resolution STEM imaging with single-atom chemical sensitivity, even for electron-beam-sensitive materials. Artificial intelligence, machine learning, and big-data science are expected to significantly enhance the impact of STEM and associated techniques on many research fields such as materials science and engineering, quantum and nanoscale science, physics and chemistry, and biology and medicine. This review focuses on advances of STEM imaging from the invention of the field-emission electron gun to the realization of aberration-corrected and monochromated atomic-resolution STEM and its broad applications.
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Affiliation(s)
- Jingyue Jimmy Liu
- Department of Physics, Arizona State University, Tempe, AZ85287, USA
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17
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Dyck O, Swett JL, Lupini AR, Mol JA, Jesse S. Imaging Secondary Electron Emission from a Single Atomic Layer. SMALL METHODS 2021; 5:e2000950. [PMID: 34927845 DOI: 10.1002/smtd.202000950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/17/2020] [Indexed: 06/14/2023]
Abstract
Graphene-based devices hold promise for a wide range of technological applications. Yet characterizing the structure and the electrical properties of a material that is only one atomic layer thick still poses technical challenges. Recent investigations indicate that secondary-electron electron-beam-induced current (SE-EBIC) imaging can reveal subtle details regarding electrical conductivity and electron transport with high spatial resolution. Here, it is shown that the SEEBIC imaging mode can be used to detect suspended single layers of graphene and distinguish between different numbers of layers. Pristine and contaminated areas of graphene are also compared to show that pristine graphene exhibits a substantially lower SE yield than contaminated regions. This SEEBIC imaging mode may provide valuable information for the engineering of surface coatings where SE yield is a priority.
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Affiliation(s)
- Ondrej Dyck
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Jacob L Swett
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Andrew R Lupini
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Jan A Mol
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
- School of Physics and Astronomy, Queen Mary University of London, London, E1 4NS, UK
| | - Stephen Jesse
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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18
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Abstract
Abstract
Deep learning is transforming most areas of science and technology, including electron microscopy. This review paper offers a practical perspective aimed at developers with limited familiarity. For context, we review popular applications of deep learning in electron microscopy. Following, we discuss hardware and software needed to get started with deep learning and interface with electron microscopes. We then review neural network components, popular architectures, and their optimization. Finally, we discuss future directions of deep learning in electron microscopy.
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19
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Zhao X, Loh KP, Pennycook SJ. Electron beam triggered single-atom dynamics in two-dimensional materials. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:063001. [PMID: 33007771 DOI: 10.1088/1361-648x/abbdb9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Controlling atomic structure and dynamics with single-atom precision is the ultimate goal in nanoscience and nanotechnology. Despite great successes being achieved by scanning tunneling microscopy (STM) over the past a few decades, fundamental limitations, such as ultralow temperature, and low throughput, significantly hinder the fabrication of a large array of atomically defined structures by STM. The advent of aberration correction in scanning transmission electron microscopy (STEM) revolutionized the field of nanomaterials characterization pushing the detection limit down to single-atom sensitivity. The sub-angstrom focused electron beam (e-beam) of STEM is capable of interacting with an individual atom, thereby it is the ideal platform to direct and control matter at the level of a single atom or a small cluster. In this article, we discuss the transfer of energy and momentum from the incident e-beam to atoms and their subsequent potential dynamics under different e-beam conditions in 2D materials, particularly transition metal dichalcogenides (TMDs). Next, we systematically discuss the e-beam triggered structural evolutions of atomic defects, line defects, grain boundaries, and stacking faults in a few representative 2D materials. Their formation mechanisms, kinetic paths, and practical applications are comprehensively discussed. We show that desired structural evolution or atom-by-atom assembly can be precisely manipulated by e-beam irradiation which could introduce intriguing functionalities to 2D materials. In particular, we highlight the recent progress on controlling single Si atom migration in real-time on monolayer graphene along an extended path with high throughput in automated STEM. These results unprecedentedly demonstrate that single-atom dynamics can be realized by an atomically focused e-beam. With the burgeoning of artificial intelligence and big data, we can expect that fully automated microscopes with real-time data analysis and feedback could readily design and fabricate large scale nanostructures with unique functionalities in the near future.
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Affiliation(s)
- Xiaoxu Zhao
- Department of Materials Science and Engineering, National University of Singapore, 9 Engineering Drive 1, 117575, Singapore
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Kian Ping Loh
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Stephen J Pennycook
- Department of Materials Science and Engineering, National University of Singapore, 9 Engineering Drive 1, 117575, Singapore
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20
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Wang W, Cai W. Dynamic observation and motion tracking of individual gold atoms with HAADF-STEM imaging. RSC Adv 2021; 11:11057-11061. [PMID: 35423611 PMCID: PMC8695860 DOI: 10.1039/d0ra09799c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/10/2021] [Indexed: 11/21/2022] Open
Abstract
The tracked trajectories give direct visualization of individual atoms' movements, and the number of tracked atoms in each frame is quantified.
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Affiliation(s)
- Wei Wang
- School of Instrumentation and Optoelectronic Engineering
- Beihang University
- Beijing
- China
| | - Wei Cai
- Key Laboratory of Micro-nano Measurement-manipulation and Physics (Ministry of Education)
- School of Physics
- Beihang University
- Beijing
- China
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21
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Zhang X, Zhang X, Yuan B, Liang C, Yu Y. Atomic-scale study of nanocatalysts by aberration-corrected electron microscopy. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:413004. [PMID: 32666936 DOI: 10.1088/1361-648x/ab977c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Aberration-corrected electron microscopy (AC-EM) including transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) has become one of the most powerful technologies in the studies of nanocatalysts. With the current spatial resolution of sub-0.5 Å and energy resolution of 10 meV, AC-EM can quantificationally articulate the connection between catalytic properties and atomic configurations of nanocatalysts. However, the restricted irradiation sensitive characteristics of specimens pose an obstacle to solve their intrinsic structure. Low-dose imaging should be applied to overcome this problem. In addition, the choice of appropriate imaging method is also crucial to tackle specific structural problems of nanocatalysts. On the basis of careful management of electron dose and selection of suitable imaging method,in situgas and liquid S/TEM are able to reveal the structure evolution of nanocatalysts in real-time. Further combination with residual gas analysis would deepen the understanding of the catalytic reaction.
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Affiliation(s)
- Xun Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - Xiuli Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - Biao Yuan
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - Chao Liang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - Yi Yu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
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22
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Ede JM, Beanland R. Improving electron micrograph signal-to-noise with an atrous convolutional encoder-decoder. Ultramicroscopy 2019; 202:18-25. [PMID: 30928639 DOI: 10.1016/j.ultramic.2019.03.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/19/2019] [Accepted: 03/25/2019] [Indexed: 11/20/2022]
Abstract
We present an atrous convolutional encoder-decoder trained to denoise electron micrographs. It consists of a modified Xception backbone, atrous convoltional spatial pyramid pooling module and a multi-stage decoder. Our neural network was trained end-to-end using 512 × 512 micrographs created from a large dataset of high-dose ( > 2500 counts per pixel) micrographs with added Poisson noise to emulate low-dose ( ≪ 300 counts per pixel) data. It was then fine-tuned for high dose data (200-2500 counts per pixel). Its performance is benchmarked against bilateral, Gaussian, median, total variation, wavelet, and Wiener restoration methods with their default parameters. Our network outperforms their best mean squared error and structural similarity index performances by 24.6% and 9.6% for low doses and by 43.7% and 5.5% for high doses. In both cases, our network's mean squared error has the lowest variance. Source code and links to our high-quality dataset and pre-trained models are available at https://github.com/Jeffrey-Ede/Electron-Micrograph-Denoiser.
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Affiliation(s)
- Jeffrey M Ede
- Department of Physics, University of Warwick, Coventry, England CV4 7AL, United Kingdom.
| | - Richard Beanland
- Department of Physics, University of Warwick, Coventry, England CV4 7AL, United Kingdom.
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23
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Baletto F. Structural properties of sub-nanometer metallic clusters. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:113001. [PMID: 30562724 DOI: 10.1088/1361-648x/aaf989] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
At the nanoscale, the investigation of structural features becomes fundamental as we can establish relationships between cluster geometries and their physicochemical properties. The peculiarity lies in the variety of shapes often unusual and far from any geometrical and crystallographic intuition clusters can assume. In this respect, we should treat and consider nanoparticles as a new form of matter. Nanoparticle structures depend on their size, chemical composition, ordering, as well as external conditions e.g. synthesis method, pressure, temperature, support. On top of that, at finite temperatures nanoparticles can fluctuate among different structures, opening new and exciting horizons for the design of optimal nanoparticles for advanced applications. This article aims to overview geometrical features of transition metal clusters and of their various rearrangements.
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Affiliation(s)
- Francesca Baletto
- Physics Department, King's College London, WC2R 2LS, London, United Kingdom
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24
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Yang J, Koo J, Kim S, Jeon S, Choi BK, Kwon S, Kim J, Kim BH, Lee WC, Lee WB, Lee H, Hyeon T, Ercius P, Park J. Amorphous-Phase-Mediated Crystallization of Ni Nanocrystals Revealed by High-Resolution Liquid-Phase Electron Microscopy. J Am Chem Soc 2019; 141:763-768. [DOI: 10.1021/jacs.8b11972] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jiwoong Yang
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | - Jahyun Koo
- Department of Physics, Konkuk University, Seoul 05029, Republic of Korea
| | - Seulwoo Kim
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | - Sungho Jeon
- Department of Mechanical Engineering, Hanyang University, Ansan, Gyeonggido 15588, Republic of Korea
| | - Back Kyu Choi
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | - Sangwoo Kwon
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | - Joodeok Kim
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung Hyo Kim
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | - Won Chul Lee
- Department of Mechanical Engineering, Hanyang University, Ansan, Gyeonggido 15588, Republic of Korea
| | - Won Bo Lee
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | - Hoonkyung Lee
- Department of Physics, Konkuk University, Seoul 05029, Republic of Korea
| | - Taeghwan Hyeon
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | | | - Jungwon Park
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
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25
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Li X, Dyck O, Kalinin SV, Jesse S. Compressed Sensing of Scanning Transmission Electron Microscopy (STEM) With Nonrectangular Scans. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2018; 24:623-633. [PMID: 30588912 DOI: 10.1017/s143192761801543x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Scanning transmission electron microscopy (STEM) has become the main stay for materials characterization on atomic level, with applications ranging from visualization of localized and extended defects to mapping order parameter fields. In recent years, attention has focused on the potential of STEM to explore beam induced chemical processes and especially manipulating atomic motion, enabling atom-by-atom fabrication. These applications, as well as traditional imaging of beam sensitive materials, necessitate increasing the dynamic range of STEM in imaging and manipulation modes, and increasing the absolute scanning speed which can be achieved by combining sparse sensing methods with nonrectangular scanning trajectories. Here we have developed a general method for real-time reconstruction of sparsely sampled images from high-speed, noninvasive and diverse scanning pathways, including spiral scan and Lissajous scan. This approach is demonstrated on both the synthetic data and experimental STEM data on the beam sensitive material graphene. This work opens the door for comprehensive investigation and optimal design of dose efficient scanning strategies and real-time adaptive inference and control of e-beam induced atomic fabrication.
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Affiliation(s)
- Xin Li
- 1Center for Nanophase Materials Sciences,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA
| | - Ondrej Dyck
- 1Center for Nanophase Materials Sciences,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA
| | - Sergei V Kalinin
- 1Center for Nanophase Materials Sciences,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA
| | - Stephen Jesse
- 1Center for Nanophase Materials Sciences,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA
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26
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Wu H, Zhao X, Guan C, Zhao LD, Wu J, Song D, Li C, Wang J, Loh KP, Venkatesan TV, Pennycook SJ. The Atomic Circus: Small Electron Beams Spotlight Advanced Materials Down to the Atomic Scale. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1802402. [PMID: 30306651 DOI: 10.1002/adma.201802402] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 08/06/2018] [Indexed: 06/08/2023]
Abstract
Defects in crystalline materials have a tremendous impact on their functional behavior. Controlling and tuning of these imperfections can lead to marked improvements in their physical, electrical, magnetic, and optical properties. Thanks to the development of aberration-corrected (scanning) transmission electron microscopy (STEM/TEM), direct visualization of defects at multiple length scales has now become possible, including those critically important defects at the atomic scale. Thorough understanding of the nature and dynamics of these defects is the key to unraveling the fundamental origins of structure-property relationships. Such insight can therefore allow the creation of new materials with desired properties through appropriate defect engineering. Herein, several examples of new insights obtained from representative functional materials are shown, including piezoelectrics/ferroelectrics, oxide interfaces, thermoelectrics, electrocatalysts, and 2D materials.
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Affiliation(s)
- Haijun Wu
- Department of Materials Science and Engineering, National University of Singapore (NUS), Singapore, 117574, Singapore
| | - Xiaoxu Zhao
- Department of Materials Science and Engineering, National University of Singapore (NUS), Singapore, 117574, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 13 Centre for Life Sciences, #05-01, 28 Medical Drive, Singapore, 117456, Singapore
| | - Cao Guan
- Department of Materials Science and Engineering, National University of Singapore (NUS), Singapore, 117574, Singapore
| | - Li-Dong Zhao
- School of Materials Science and Engineering, Beihang University, Beijing, 100191, China
| | - Jiagang Wu
- Department of Materials Science, Sichuan University, Chengdu, 610064, China
| | - Dongsheng Song
- NUSNNI-NanoCore, National University of Singapore, Singapore, 117411, Singapore
| | - Changjian Li
- Department of Materials Science and Engineering, National University of Singapore (NUS), Singapore, 117574, Singapore
| | - John Wang
- Department of Materials Science and Engineering, National University of Singapore (NUS), Singapore, 117574, Singapore
| | - Kian Ping Loh
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
- Centre for Advanced 2D Materials (CA2DM), National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore
| | - Thirumalai V Venkatesan
- Department of Materials Science and Engineering, National University of Singapore (NUS), Singapore, 117574, Singapore
- NUSNNI-NanoCore, National University of Singapore, Singapore, 117411, Singapore
| | - Stephen J Pennycook
- Department of Materials Science and Engineering, National University of Singapore (NUS), Singapore, 117574, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 13 Centre for Life Sciences, #05-01, 28 Medical Drive, Singapore, 117456, Singapore
- Centre for Advanced 2D Materials (CA2DM), National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore
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27
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Wu H, Zhao X, Song D, Tian F, Wang J, Loh KP, Pennycook SJ. Progress and prospects of aberration-corrected STEM for functional materials. Ultramicroscopy 2018; 194:182-192. [DOI: 10.1016/j.ultramic.2018.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/14/2018] [Accepted: 08/07/2018] [Indexed: 11/16/2022]
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28
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Spherical aberration correction in a scanning transmission electron microscope using a sculpted thin film. Ultramicroscopy 2018; 189:46-53. [DOI: 10.1016/j.ultramic.2018.03.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/18/2018] [Accepted: 03/24/2018] [Indexed: 11/19/2022]
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29
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Yang Z, Zhang L, Chisholm MF, Zhou X, Ye H, Pennycook SJ. Precipitation of binary quasicrystals along dislocations. Nat Commun 2018; 9:809. [PMID: 29476133 PMCID: PMC5824953 DOI: 10.1038/s41467-018-03250-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/31/2018] [Indexed: 11/08/2022] Open
Abstract
Dislocations in crystals naturally break the symmetry of the bulk, introducing local atomic configurations with symmetries such as fivefold rings. But dislocations do not usually nucleate aperiodic structure along their length. Here we demonstrate the formation of extended binary quasicrystalline precipitates with Penrose-like random-tiling structures, beginning with chemical ordering within the pentagonal structure at cores of prismatic dislocations in Mg-Zn alloys. Atomic resolution observations indicate that icosahedral chains centered along [0001] pillars of Zn interstitial atoms are formed templated by the fivefold rings at dislocation cores. They subsequently form columns of rhombic and elongated hexagonal tiles parallel to the dislocation lines. Quasicrystalline precipitates are formed by random tiling of these rhombic and hexagonal tiles. Such precipitation may impact dislocation glide and alloy strength.
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Affiliation(s)
- Zhiqing Yang
- Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, School of Materials Science and Engineering, University of Science and Technology of China, Shenyang, 110016, China.
- Division of Materials Science and Technology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Lifeng Zhang
- Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, School of Materials Science and Engineering, University of Science and Technology of China, Shenyang, 110016, China
| | - Matthew F Chisholm
- Division of Materials Science and Technology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Xinzhe Zhou
- Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, School of Materials Science and Engineering, University of Science and Technology of China, Shenyang, 110016, China
| | - Hengqiang Ye
- Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, School of Materials Science and Engineering, University of Science and Technology of China, Shenyang, 110016, China
| | - Stephen J Pennycook
- Department of Materials Science and Engineering, National University of Singapore, Singapore, 117576, Singapore.
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30
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Pryor A, Ophus C, Miao J. A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy. ACTA ACUST UNITED AC 2017; 3:15. [PMID: 29104852 PMCID: PMC5656717 DOI: 10.1186/s40679-017-0048-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/13/2017] [Indexed: 11/25/2022]
Abstract
Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. Here, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditional multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.
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Affiliation(s)
- Alan Pryor
- Department of Physics and Astronomy and California NanoSystems Institute, University of California at Los Angeles, Los Angeles, CA 90095 USA
| | - Colin Ophus
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Jianwei Miao
- Department of Physics and Astronomy and California NanoSystems Institute, University of California at Los Angeles, Los Angeles, CA 90095 USA
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