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Lindner J, Ross U, Meyer T, Boureau V, Seibt M, Jooss C. Reconstruction of Angstrom resolution exit-waves by the application of drift-corrected phase-shifting off-axis electron holography. Ultramicroscopy 2023; 256:113880. [PMID: 37952372 DOI: 10.1016/j.ultramic.2023.113880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/05/2023] [Accepted: 10/21/2023] [Indexed: 11/14/2023]
Abstract
Phase-shifting electron holography is an excellent method to reveal electron wave phase information with very high phase sensitivity over a large range of spatial frequencies. It circumvents the limiting trade-off between fringe spacing and visibility of standard off-axis holography. Previous implementations have been limited by the independent drift of biprism and sample. We demonstrate here an advanced drift correction scheme for the hologram series that exploits the presence of an interface of the TEM specimen to the vacuum area in the hologram. It allows to obtain reliable phase information up to 2π/452 at the 1 Å information limit of the Titan 80-300 kV environmental transmission electron microscope used, by applying a moderate voltage of 250 V to a single biprism for a fringe spacing of 1 Å. The obtained phase and amplitude information is validated at a thin Pt sample by use of multislice image simulation with the frozen lattice approximation and shows excellent agreement. The presented method is applicable in any TEM equipped with at least one electron biprism and thus enables achieving high resolution off-axis holography in various instruments including those for in-situ applications. A software implementation for the acquisition, calibration and reconstruction is provided.
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Affiliation(s)
- J Lindner
- Institute of Materials Physics, University of Goettingen, Friedrich-Hund-Platz 1, 37077, Goettingen, Germany
| | - U Ross
- 4th Institute of Physics - Solids and Nanostructures, University of Goettingen, Friedrich-Hund-Platz 1, 37077, Goettingen, Germany
| | - T Meyer
- Institute of Materials Physics, University of Goettingen, Friedrich-Hund-Platz 1, 37077, Goettingen, Germany
| | - V Boureau
- Interdisciplinary Center for Electron Microscopy, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - M Seibt
- 4th Institute of Physics - Solids and Nanostructures, University of Goettingen, Friedrich-Hund-Platz 1, 37077, Goettingen, Germany
| | - Ch Jooss
- Institute of Materials Physics, University of Goettingen, Friedrich-Hund-Platz 1, 37077, Goettingen, Germany; International Center for Advanced Studies of Energy Conversion (ICASEC), University of Goettingen, D-37077, Goettingen, Germany.
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2
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Botifoll M, Pinto-Huguet I, Arbiol J. Machine learning in electron microscopy for advanced nanocharacterization: current developments, available tools and future outlook. NANOSCALE HORIZONS 2022; 7:1427-1477. [PMID: 36239693 DOI: 10.1039/d2nh00377e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the last few years, electron microscopy has experienced a new methodological paradigm aimed to fix the bottlenecks and overcome the challenges of its analytical workflow. Machine learning and artificial intelligence are answering this call providing powerful resources towards automation, exploration, and development. In this review, we evaluate the state-of-the-art of machine learning applied to electron microscopy (and obliquely, to materials and nano-sciences). We start from the traditional imaging techniques to reach the newest higher-dimensionality ones, also covering the recent advances in spectroscopy and tomography. Additionally, the present review provides a practical guide for microscopists, and in general for material scientists, but not necessarily advanced machine learning practitioners, to straightforwardly apply the offered set of tools to their own research. To conclude, we explore the state-of-the-art of other disciplines with a broader experience in applying artificial intelligence methods to their research (e.g., high-energy physics, astronomy, Earth sciences, and even robotics, videogames, or marketing and finances), in order to narrow down the incoming future of electron microscopy, its challenges and outlook.
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Affiliation(s)
- Marc Botifoll
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain.
| | - Ivan Pinto-Huguet
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain.
| | - Jordi Arbiol
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain.
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
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3
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Wang L, Zhang Y, Zeng Z, Zhou H, He J, Liu P, Chen M, Han J, Srolovitz DJ, Teng J, Guo Y, Yang G, Kong D, Ma E, Hu Y, Yin B, Huang X, Zhang Z, Zhu T, Han X. Tracking the sliding of grain boundaries at the atomic scale. Science 2022; 375:1261-1265. [PMID: 35298254 DOI: 10.1126/science.abm2612] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Grain boundaries (GBs) play an important role in the mechanical behavior of polycrystalline materials. Despite decades of investigation, the atomic-scale dynamic processes of GB deformation remain elusive, particularly for the GBs in polycrystals, which are commonly of the asymmetric and general type. We conducted an in situ atomic-resolution study to reveal how sliding-dominant deformation is accomplished at general tilt GBs in platinum bicrystals. We observed either direct atomic-scale sliding along the GB or sliding with atom transfer across the boundary plane. The latter sliding process was mediated by movements of disconnections that enabled the transport of GB atoms, leading to a previously unrecognized mode of coupled GB sliding and atomic plane transfer. These results enable an atomic-scale understanding of how general GBs slide in polycrystalline materials.
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Affiliation(s)
- Lihua Wang
- Institute of Microstructure and Property of Advanced Materials, Beijing Key Lab of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124, China
| | - Yin Zhang
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Zhi Zeng
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hao Zhou
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jian He
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634 USA
| | - Pan Liu
- Shanghai Key Laboratory of Advanced High-Temperature Materials and Precision Forming, State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Mingwei Chen
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jian Han
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - David J Srolovitz
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong SAR, China.,International Digital Economy Academy (IDEA), Shenzhen, China
| | - Jiao Teng
- Department of Material Physics and Chemistry, University of Science and Technology Beijing, Beijing 100083, China
| | - Yizhong Guo
- Institute of Microstructure and Property of Advanced Materials, Beijing Key Lab of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124, China
| | - Guo Yang
- Institute of Microstructure and Property of Advanced Materials, Beijing Key Lab of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124, China
| | - Deli Kong
- Institute of Microstructure and Property of Advanced Materials, Beijing Key Lab of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124, China
| | - En Ma
- Center for Alloy Innovation and Design (CAID), State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yongli Hu
- Beijing Institute of Artificial Intelligence, Faculty of Information Technology, Beijing Key Laboratory of Multimedia and Intelligent Software Technology, Beijing University of Technology, Beijing 100124, China
| | - Baocai Yin
- Beijing Institute of Artificial Intelligence, Faculty of Information Technology, Beijing Key Laboratory of Multimedia and Intelligent Software Technology, Beijing University of Technology, Beijing 100124, China
| | - XiaoXu Huang
- College of Materials Science and Engineering, Chongqing University, Chongqing 40044, China
| | - Ze Zhang
- Institute of Microstructure and Property of Advanced Materials, Beijing Key Lab of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124, China.,Department of Materials Science, Zhejiang University, Hangzhou 310008, China
| | - Ting Zhu
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Xiaodong Han
- Institute of Microstructure and Property of Advanced Materials, Beijing Key Lab of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124, China
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Direct estimation and correction of residual aberrations in the reconstructed exit-wavefunction of a crystalline specimen. Micron 2022; 157:103247. [DOI: 10.1016/j.micron.2022.103247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 11/18/2022]
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5
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Prismatic 2.0 - Simulation software for scanning and high resolution transmission electron microscopy (STEM and HRTEM). Micron 2021; 151:103141. [PMID: 34560356 DOI: 10.1016/j.micron.2021.103141] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/20/2021] [Accepted: 08/22/2021] [Indexed: 11/22/2022]
Abstract
Scanning transmission electron microscopy (STEM), where a converged electron probe is scanned over a sample's surface and an imaging, diffraction, or spectroscopic signal is measured as a function of probe position, is an extremely powerful tool for materials characterization. The widespread adoption of hardware aberration correction, direct electron detectors, and computational imaging methods have made STEM one of the most important tools for atomic-resolution materials science. Many of these imaging methods rely on accurate imaging and diffraction simulations in order to interpret experimental results. However, STEM simulations have traditionally required large calculation times, as modeling the electron scattering requires a separate simulation for each of the typically millions of probe positions. We have created the Prismatic simulation code for fast simulation of STEM experiments with support for multi-CPU and multi-GPU (graphics processing unit) systems, using both the conventional multislice and our recently-introduced PRISM method. In this paper, we introduce Prismatic version 2.0, which adds many new algorithmic improvements, an updated graphical user interface (GUI), post-processing of simulation data, and additional operating modes such as plane-wave TEM. We review various aspects of the simulation methods and codes in detail and provide various simulation examples. Prismatic 2.0 is freely available both as an open-source package that can be run using a C++ or Python command line interface, or GUI, as well within a Docker container environment.
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Sadre R, Ophus C, Butko A, Weber GH. Deep Learning Segmentation of Complex Features in Atomic-Resolution Phase-Contrast Transmission Electron Microscopy Images. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 27:804-814. [PMID: 34353384 DOI: 10.1017/s1431927621000167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Phase-contrast transmission electron microscopy (TEM) is a powerful tool for imaging the local atomic structure of materials. TEM has been used heavily in studies of defect structures of two-dimensional materials such as monolayer graphene due to its high dose efficiency. However, phase-contrast imaging can produce complex nonlinear contrast, even for weakly scattering samples. It is, therefore, difficult to develop fully automated analysis routines for phase-contrast TEM studies using conventional image processing tools. For automated analysis of large sample regions of graphene, one of the key problems is segmentation between the structure of interest and unwanted structures such as surface contaminant layers. In this study, we compare the performance of a conventional Bragg filtering method with a deep learning routine based on the U-Net architecture. We show that the deep learning method is more general, simpler to apply in practice, and produces more accurate and robust results than the conventional algorithm. We provide easily adaptable source code for all results in this paper and discuss potential applications for deep learning in fully automated TEM image analysis.
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Affiliation(s)
- Robbie Sadre
- Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA94720, USA
| | - Colin Ophus
- NCEM, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA94720, USA
| | - Anastasiia Butko
- Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA94720, USA
| | - Gunther H Weber
- Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA94720, USA
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Lopatin S, Aljarb A, Roddatis V, Meyer T, Wan Y, Fu JH, Hedhili M, Han Y, Li LJ, Tung V. Aberration-corrected STEM imaging of 2D materials: Artifacts and practical applications of threefold astigmatism. SCIENCE ADVANCES 2020; 6:6/37/eabb8431. [PMID: 32917685 DOI: 10.1126/sciadv.abb8431] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
High-resolution scanning transmission electron microscopy (HR-STEM) with spherical aberration correction enables researchers to peer into two-dimensional (2D) materials and correlate the material properties with those of single atoms. The maximum intensity of corrected electron beam is confined in the area having sub-angstrom size. Meanwhile, the residual threefold astigmatism of the electron probe implies a triangular shape distribution of the intensity, whereas its tails overlap and thus interact with several atomic species simultaneously. The result is the resonant modulation of contrast that interferes the determination of phase transition of 2D materials. Here, we theoretically reveal and experimentally determine the origin of resonant modulation of contrast and its unintended impact on violating the power-law dependence of contrast on coordination modes between transition metal and chalcogenide atoms. The finding illuminates the correlation between atomic contrast, spatially inequivalent chalcogenide orientation, and residual threefold astigmatism on determining the atomic structure of emerging 2D materials.
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Affiliation(s)
- Sergei Lopatin
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal 23955-6900, Saudi Arabia.
| | - Areej Aljarb
- Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), KAUST Solar Center, Thuwal 23955-6900, Saudi Arabia
- Department of Physics, King Abdulaziz University, Jeddah 23955-6900, Saudi Arabia
| | - Vladimir Roddatis
- Institute of Materials Physics, University of Goettingen, Goettingen, Germany
| | - Tobias Meyer
- 4th Institute of Physics - Solids and Nanostructures, University of Goettingen, Goettingen, Germany
| | - Yi Wan
- Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Jui-Han Fu
- Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), KAUST Solar Center, Thuwal 23955-6900, Saudi Arabia
| | - Mohamed Hedhili
- Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Yimo Han
- Department of Molecular Biology, Princeton University, NJ 08544-1044, USA
| | - Lain-Jong Li
- Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Vincent Tung
- Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
- Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), KAUST Solar Center, Thuwal 23955-6900, Saudi Arabia
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8
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Levin BD, Lawrence EL, Crozier PA. Tracking the picoscale spatial motion of atomic columns during dynamic structural change. Ultramicroscopy 2020; 213:112978. [PMID: 32278963 DOI: 10.1016/j.ultramic.2020.112978] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 03/03/2020] [Accepted: 03/15/2020] [Indexed: 10/24/2022]
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9
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Winkler F, Barthel J, Dunin-Borkowski RE, Müller-Caspary K. Direct measurement of electrostatic potentials at the atomic scale: A conceptual comparison between electron holography and scanning transmission electron microscopy. Ultramicroscopy 2020; 210:112926. [PMID: 31955112 DOI: 10.1016/j.ultramic.2019.112926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/18/2019] [Accepted: 12/28/2019] [Indexed: 10/25/2022]
Abstract
Off-axis electron holography and first moment STEM are sensitive to electromagnetic potentials or fields, respectively. In this work, we investigate in what sense the results obtained from both techniques are equivalent and work out the major differences. The analysis is focused on electrostatic (Coulomb) potentials at atomic spatial resolution. It is shown that the probe-forming/objective aperture strongly affects the reconstructed electrostatic potentials and that, as a result of the different illumination setups, dynamical diffraction effects show a specific response with increasing specimen thickness. It is shown that thermal diffuse scattering is negligible for a wide range of specimen thicknesses, when evaluating the first moment of diffraction patterns.
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10
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A multiple scattering algorithm for three dimensional phase contrast atomic electron tomography. Ultramicroscopy 2020; 208:112860. [DOI: 10.1016/j.ultramic.2019.112860] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 09/27/2019] [Accepted: 10/15/2019] [Indexed: 11/17/2022]
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11
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Winkler F, Barthel J, Tavabi AH, Borghardt S, Kardynal BE, Dunin-Borkowski RE. Absolute Scale Quantitative Off-Axis Electron Holography at Atomic Resolution. PHYSICAL REVIEW LETTERS 2018; 120:156101. [PMID: 29756849 DOI: 10.1103/physrevlett.120.156101] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Indexed: 06/08/2023]
Abstract
An absolute scale match between experiment and simulation in atomic-resolution off-axis electron holography is demonstrated, with unknown experimental parameters determined directly from the recorded electron wave function using an automated numerical algorithm. We show that the local thickness and tilt of a pristine thin WSe_{2} flake can be measured uniquely, whereas some electron optical aberrations cannot be determined unambiguously for a periodic object. The ability to determine local specimen and imaging parameters directly from electron wave functions is of great importance for quantitative studies of electrostatic potentials in nanoscale materials, in particular when performing in situ experiments and considering that aberrations change over time.
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Affiliation(s)
- Florian Winkler
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C), Forschungszentrum Jülich, 52425 Jülich, Germany
- Peter Grünberg Institute 5 (PGI-5), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Juri Barthel
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C), Forschungszentrum Jülich, 52425 Jülich, Germany
- Gemeinschaftslabor für Elektronenmikroskopie (GFE), RWTH Aachen University, 52074 Aachen, Germany
| | - Amir H Tavabi
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C), Forschungszentrum Jülich, 52425 Jülich, Germany
- Peter Grünberg Institute 5 (PGI-5), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Sven Borghardt
- Peter Grünberg Institute 9 (PGI-9), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Beata E Kardynal
- Peter Grünberg Institute 9 (PGI-9), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rafal E Dunin-Borkowski
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C), Forschungszentrum Jülich, 52425 Jülich, Germany
- Peter Grünberg Institute 5 (PGI-5), Forschungszentrum Jülich, 52425 Jülich, Germany
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