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Author |
De wael, A.; De Backer, A.; Van Aert, S. |
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Title |
Hidden Markov model for atom-counting from sequential ADF STEM images: Methodology, possibilities and limitations |
Type |
A1 Journal article |
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Year |
2020 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
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Volume |
219 |
Issue |
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Pages |
113131 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract  |
We present a quantitative method which allows us to reliably measure dynamic changes in the atomic structure of monatomic crystalline nanomaterials from a time series of atomic resolution annular dark field scanning transmission electron microscopy images. The approach is based on the so-called hidden Markov model and estimates the number of atoms in each atomic column of the nanomaterial in each frame of the time series. We discuss the origin of the improved performance for time series atom-counting as compared to the current state-of-the-art atom-counting procedures, and show that the so-called transition probabilities that describe the probability for an atomic column to lose or gain one or more atoms from frame to frame are particularly important. Using these transition probabilities, we show that the method can also be used to estimate the probability and cross section related to structural changes. Furthermore, we explore the possibilities for applying the method to time series recorded under variable environmental conditions. The method is shown to be promising for a reliable quantitative analysis of dynamic processes such as surface diffusion, adatom dynamics, beam effects, or in situ experiments. |
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Wos |
000594770500003 |
Publication Date |
2020-10-03 |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0304-3991 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.2 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N and EOS 30489208. |
Approved |
Most recent IF: 2.2; 2020 IF: 2.843 |
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Call Number |
EMAT @ emat @c:irua:172449 |
Serial |
6417 |
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Author |
Peters, J.L.; van den Bos, K.H.W.; Van Aert, S.; Goris, B.; Bals, S.; Vanmaekelbergh, D. |
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Title |
Ligand-Induced Shape Transformation of PbSe Nanocrystals |
Type |
A1 Journal article |
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Year |
2017 |
Publication |
Chemistry of materials |
Abbreviated Journal |
Chem Mater |
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Volume |
29 |
Issue |
29 |
Pages |
4122-4128 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
We present a study of the relation between the surface chemistry and nanocrystal shape of PbSe nanocrystals with a variable Pb-to-Se stoichiometry and density of oleate ligands. The oleate ligand density and binding configuration are monitored by nuclear magnetic resonance and Fourier transform infrared absorbance spectroscopy, allowing us to quantify the number of surface-attached ligands per NC and the nature of the surface−Pb−oleate configuration. The three-dimensional shape of the PbSe nanocrystals is obtained from high-angle annular dark field scanning transmission electron microscopy combined with an atom counting method. We show that the enhanced oleate capping results in a stabilization and extension of the {111} facets, and a crystal shape transformation from a truncated nanocube to a truncated octahedron. |
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Wos |
000401221700034 |
Publication Date |
2017-05-09 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0897-4756 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
9.466 |
Times cited |
45 |
Open Access |
OpenAccess |
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Notes |
D.V. acknowledges the European Research Council, ERC advanced grant, Project 692691-First Step, for financial support. We also acknowledge the Dutch FOM programme “Designing Dirac carriers in honeycomb semiconductor superlattices” (FOM Program 152) for financial support. The authors gratefully acknowledge funding from the Research Foundation Flanders (G.036915, G.037413, and funding of a Ph.D. research grant to K.H.W.v.d.B. and a postdoctoral grant to B.G.). S.B. acknowledges the European Research Council, ERC Grant 335078-Colouratom. (ROMEO:white; preprint:; postprint:restricted 12 months embargo; pdfversion:cannot); ECAS_Sara |
Approved |
Most recent IF: 9.466 |
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Call Number |
EMAT @ emat @ c:irua:143750 c:irua:142983UA @ admin @ c:irua:143750 |
Serial |
4571 |
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Author |
De wael, A.; De Backer, A.; Jones, L.; Varambhia, A.; Nellist, P.D.; Van Aert, S. |
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Title |
Measuring Dynamic Structural Changes of Nanoparticles at the Atomic Scale Using Scanning Transmission Electron Microscopy |
Type |
A1 Journal article |
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Year |
2020 |
Publication |
Physical Review Letters |
Abbreviated Journal |
Phys Rev Lett |
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Volume |
124 |
Issue |
10 |
Pages |
106105 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
We propose a new method to measure atomic scale dynamics of nanoparticles from experimental high-resolution annular dark field scanning transmission electron microscopy images. By using the so-called hidden Markov model, which explicitly models the possibility of structural changes, the number of atoms in each atomic column can be quantified over time. This newly proposed method outperforms the current atom-counting procedure and enables the determination of the probabilities and cross sections for surface diffusion. This method is therefore of great importance for revealing and quantifying the atomic structure when it evolves over time via adatom dynamics, surface diffusion, beam effects, or during in situ experiments. |
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Wos |
000519718100015 |
Publication Date |
2020-03-13 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0031-9007 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
8.6 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N and EOS 30489208. L.J. acknowledges the SFI AMBER Centre for support. A.V. and P.D.N. acknowledge the UK Engineering and Physical Sciences Council (EPSRC) for support (EP/K040375/1 and 1772738). A.V. also acknowledges Johnson-Matthey for support. We would like to thank Brian Theobald and Jonathan Sharman from JMTC Sonning for provision of the Pt sample. |
Approved |
Most recent IF: 8.6; 2020 IF: 8.462 |
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Call Number |
EMAT @ emat @c:irua:167148 |
Serial |
6347 |
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Author |
Croitoru, M.D.; van Dyck, D.; Van Aert, S.; Bals, S.; Verbeeck, J. |
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Title |
An efficient way of including thermal diffuse scattering in simulation of scanning transmission electron microscopic images |
Type |
A1 Journal article |
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Year |
2006 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
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Volume |
106 |
Issue |
10 |
Pages |
933-940 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Condensed Matter Theory (CMT); Vision lab |
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Abstract |
We propose an improved image simulation procedure for atomic-resolution annular dark-field scanning transmission electron microscopy (STEM) based on the multislice formulation, which takes thermal diffuse scattering fully into account. The improvement with regard to the classical frozen phonon approach is realized by separating the lattice configuration statistics from the dynamical scattering so as to avoid repetitive calculations. As an example, the influence of phonon scattering on the image contrast is calculated and investigated. STEM image simulation of crystals can be applied with reasonable computing times to problems involving a large number of atoms and thick or large supercells. |
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Place of Publication |
Amsterdam |
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Wos |
000240397200006 |
Publication Date |
2006-05-10 |
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Abbreviated Series Title |
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Series Volume |
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Edition |
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ISSN |
0304-3991; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.843 |
Times cited |
18 |
Open Access |
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Notes |
Fwo; Fwo-V |
Approved |
Most recent IF: 2.843; 2006 IF: 1.706 |
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Call Number |
UA @ lucian @ c:irua:87604UA @ admin @ c:irua:87604 |
Serial |
876 |
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Author |
Van Aert, S.; de Backer, A.; Martinez, G.T.; Goris, B.; Bals, S.; Van Tendeloo, G.; Rosenauer, A. |
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Title |
Procedure to count atoms with trustworthy single-atom sensitivity |
Type |
A1 Journal article |
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Year |
2013 |
Publication |
Physical review : B : condensed matter and materials physics |
Abbreviated Journal |
Phys Rev B |
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Volume |
87 |
Issue |
6 |
Pages |
064107-6 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
We report a method to reliably count the number of atoms from high-angle annular dark field scanning transmission electron microscopy images. A model-based analysis of the experimental images is used to measure scattering cross sections at the atomic level. The high sensitivity of these measurements in combination with a thorough statistical analysis enables us to count atoms with single-atom sensitivity. The validity of the results is confirmed by means of detailed image simulations. We will show that the method can be applied to nanocrystals of arbitrary shape, size, and atom type without the need for a priori knowledge about the atomic structure. |
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Wos |
000315144700006 |
Publication Date |
2013-02-20 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1098-0121;1550-235X; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.836 |
Times cited |
106 |
Open Access |
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Notes |
FWO; 262348 ESMI; 312483 ESTEEM2;246791 COUNTATOMS; Hercules 3; esteem2_jra2 |
Approved |
Most recent IF: 3.836; 2013 IF: 3.664 |
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Call Number |
UA @ lucian @ c:irua:105674 |
Serial |
2718 |
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Author |
Robert, Hl.; Lobato, I.; Lyu, Fj.; Chen, Q.; Van Aert, S.; Van Dyck, D.; Müller-Caspary, K. |
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Title |
Dynamical diffraction of high-energy electrons investigated by focal series momentum-resolved scanning transmission electron microscopy at atomic resolution |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
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Volume |
233 |
Issue |
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Pages |
113425 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
We report a study of scattering dynamics in crystals employing momentum-resolved scanning transmission
electron microscopy under varying illumination conditions. As we perform successive changes of the probe
focus, multiple real-space signals are obtained in dependence of the shape of the incident electron wave.
With support from extensive simulations, each signal is shown to be characterised by an optimum focus for
which the contrast is maximum and which differs among different signals. For instance, a systematic focus
mismatch is found between images formed by high-angle scattering, being sensitive to thickness and chemical
composition, and the first moment in diffraction space, being sensitive to electric fields. It follows that a single
recording at one specific probe focus is usually insufficient to characterise materials comprehensively. Most
importantly, we demonstrate in experiment and simulation that the second moment ( |
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Wos |
000734396800009 |
Publication Date |
2021-11-13 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0304-3991 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.2 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
We thank Dr. Florian Winkler for valuable discussions and experimental work at the early stages of this study. This work was supported by the Initiative and Network Fund of the Helmholtz Association (Germany) under contracts VH-NG-1317 and ZT-I-0025. This project furthermore received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 770887). |
Approved |
Most recent IF: 2.2 |
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Call Number |
EMAT @ emat @c:irua:184833 |
Serial |
6898 |
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Author |
Gonnissen, J.; de Backer, A.; den Dekker, A.J.; Martinez, G.T.; Rosenauer, A.; Sijbers, J.; Van Aert, S. |
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Title |
Optimal experimental design for the detection of light atoms from high-resolution scanning transmission electron microscopy images |
Type |
A1 Journal article |
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Year |
2014 |
Publication |
Applied physics letters |
Abbreviated Journal |
Appl Phys Lett |
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Volume |
105 |
Issue |
6 |
Pages |
063116 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
We report an innovative method to explore the optimal experimental settings to detect light atoms from scanning transmission electron microscopy (STEM) images. Since light elements play a key role in many technologically important materials, such as lithium-battery devices or hydrogen storage applications, much effort has been made to optimize the STEM technique in order to detect light elements. Therefore, classical performance criteria, such as contrast or signal-to-noise ratio, are often discussed hereby aiming at improvements of the direct visual interpretability. However, when images are interpreted quantitatively, one needs an alternative criterion, which we derive based on statistical detection theory. Using realistic simulations of technologically important materials, we demonstrate the benefits of the proposed method and compare the results with existing approaches. |
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Publisher |
American Institute of Physics |
Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
000341188700073 |
Publication Date |
2014-08-14 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0003-6951;1077-3118; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.411 |
Times cited |
12 |
Open Access |
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Notes |
FWO (G.0393.11; G.0064.10; and G.0374.13); European Union Seventh Framework Programme [FP7/2007-2013] under Grant Agreement No. 312483 (ESTEEM2); esteem2_jra2 |
Approved |
Most recent IF: 3.411; 2014 IF: 3.302 |
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Call Number |
UA @ lucian @ c:irua:118333 |
Serial |
2482 |
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Author |
Müller-Caspary, K.; Grieb, T.; Müßener, J.; Gauquelin, N.; Hille, P.; Schörmann, J.; Verbeeck, J.; Van Aert, S.; Eickhoff, M.; Rosenauer, A. |
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Title |
Electrical Polarization in AlN/GaN Nanodisks Measured by Momentum-Resolved 4D Scanning Transmission Electron Microscopy |
Type |
A1 Journal article |
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Year |
2019 |
Publication |
Physical review letters |
Abbreviated Journal |
Phys Rev Lett |
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Volume |
122 |
Issue |
10 |
Pages |
106102 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
We report the mapping of polarization-induced internal electric fields in AlN/GaN nanowire heterostructures at unit cell resolution as a key for the correlation of optical and structural phenomena in semiconductor optoelectronics. Momentum-resolved aberration-corrected scanning transmission electron microscopy is employed as a new imaging mode that simultaneously provides four-dimensional data in real and reciprocal space. We demonstrate how internal mesoscale and atomic electric fields can be separated in an experiment, which is verified by comprehensive dynamical simulations of multiple electron scattering. A mean difference of 5.3 +- 1.5 MV/cm is found for the polarization-induced electric fields in AlN and GaN, being in accordance with dedicated simulations and photoluminescence measurements in previous publications. |
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Wos |
000461067700007 |
Publication Date |
2019-03-11 |
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Series Editor |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0031-9007 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
8.462 |
Times cited |
26 |
Open Access |
OpenAccess |
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Notes |
The authors gratefully acknowledge the help of Natalie Claes for analyzing the EDX data. K. M.-C. acknowledges funding from the Initiative and Network Fund of the Helmholtz Association within the Helmholtz Young Investigator Group moreSTEM under Contract No. VHNG- 1317 at Forschungszentrum Jülich in Germany. The direct electron detector (Medipix3, Quantum Detectors) was funded by the Hercules fund from the Flemish Government. N. G. and J. V. acknowledge funding from the Geconcentreerde Onderzoekacties project Solarpaint of the University of Antwerp. T. G. and A. R. acknowledge support from the Deutsche Forschungsgemeinschaft (Germany) under Contract No. RO2057/8-3. This work also received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Contract No. 770887). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project funding (G.0368.15N).; Helmholtz Association, VH-NG-1317 ; Forschungszentrum Jülich; Flemish Government; Universiteit Antwerpen; Deutsche Forschungsgemeinschaft, RO2057/8-3 ; H2020 European Research Council, 770887 ; Fonds Wetenschappelijk Onderzoek, G.0368.15N ; |
Approved |
Most recent IF: 8.462 |
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Call Number |
UA @ lucian @UA @ admin @ c:irua:158120 |
Serial |
5157 |
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