Yongsoo Yang

1. Atomic Electron Tomography (AET)

Atoms are the basic building blocks forming all the matters on Earth and all physical properties of materials are fully governed by how individual atoms are arranged in each material. Conventionally, x-ray crystallography has provided the averaged atomic structure by assuming that all the atoms are perfectly ordered within a crystal. However, perfect crystals are rare in nature. Most real materials contain disordered region such as defects, grain boundaries, stacking faults, and dislocations, and they strongly influence material properties and performance in modern science and technology. These defects and noncrystalline systems cannot be measured by crystallography, requiring new approaches to determine the true 3D atomic arrangement of real materials.

Here, I introduce atomic electron tomography (AET), which allows to measure 3D positions and atomic species of individual atoms with defects without assuming crystallinity or using averaging. To address this important problem, I co- developed a tomographic reconstruction algorithm called GENeralized Fourier Iterative REconstruction (GENFIRE), which gives more accurate and faithful 3D reconstructions compared to pre-existing methods. I implemented a self-consistent angle refinement method, which significantly improves the GENFIRE reconstruction, producing atomic resolution 3D reconstructions where individual atoms are clearly distinguishable. I also developed an unbiased atom tracing and classification method, which allowed to determine the species and 3D positions of individual atoms with high accuracy.

Based on these achievements on AET combined with the state-of-the-art electron microscope technology, we successfully measured the true 3D atomic structure of an Iron-Platinum (FePt) nanoparticle in 22 picometer (1 picometer is a trillionths of a meter) accuracy without crystallinity assumption. Rich structural variety and chemical order/disorder within the particle, including grain boundaries, anti-phase boundaries, anti-site defects and swap defects, were observed. This level of complexity have never been probed with conventional crystallography techniques. Moreover, we further demonstrated that the true atomic structure indeed provides important physical properties, such as magnetic moments or magnetocrystalline anisotropy, via quantum mechanical calculations.

AET allows to measure 3D positions and atomic species of individual atoms with defects without assuming crystallinity or using averaging. The ability to determine the 3D structure of crystal defects and noncrystalline systems at atomic resolution will transform our understanding of materials properties and functionality at the most fundamental level. Further developments of AET would allow atomic-level 3D localization and identification of complex systems (including dopants, interstitials, light elements, and vacancies), surfaces and interfaces, amorphous materials. Ultimately, dynamics of individual atoms and defects in materials can be fully revealed by monitoring the motion and interaction of individual atoms in complex systems during phase transitions or under external mechanical stress.

Video 1: Complex FePt nanoparticle grain structure fully revealed by AET.

Video 2: FePt nanoparticle 3D reconstruction orthoslice video. This clearly demonstrates the intensity contrast between Fe (weak) and Pt (strong) atoms, showing the complex grain structure of the nanoparticle.
Full-screen view recommended for this video.

A YouTube Clip made by Nature Materials:
Three-dimensional coordinates of individual atoms in materials revealed by electron tomography

Related Articles:

1. Y. Yang, C.-C. Chen, M. C. Scott, C. Ophus, R. Xu, A. Pryor Jr., L. Wu, F. Sun, W. Theis, J. Zhou, M. Eisenbach, P. R. C. Kent, R. F. Sabirianov, H. Zeng, P. Ercius, and J. Miao, "Deciphering chemical order/disorder and material properties at the single-atom level", Nature 542, 75-79 (2017). https://dx.doi.org/10.1038/nature21042

2. A. Pryor Jr.*, Y. Yang*, A. Rana, M. Gallagher-Jones, J. Zhou, Y. Lo, G. Melinte, W. Chiu, J. A. Rodriguez, J. Miao, "GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging", Sci. Rep. 7:10409 (2017). (* equal contribution) https://dx.doi.org/10.1038/s41598-017-09847-1

3. R. Xu, C.-C. Chen, L. Wu, M. C. Scott, W. Theis, C. Ophus, M. Bartels, Y. Yang, H. Ramezani-Dakhel, M. R. Sawaya, H. Heinz, L. D. Marks, P. Ercius, and J. Miao, "Three-dimensional coordinates of individual atoms in materials revealed by electron tomography", Nat. Mater. 14, 1099-1103 (2015). https://dx.doi.org/10.1038/NMAT4426

4. J. Miao, P. Ercius and S. J. L. Billinge, "Atomic electron tomography: 3D structures without crystals", Science 353, aaf2157 (2016). https://dx.doi.org/10.1038/10.1126/science.aaf2157

              Last updated: Jan 25, 2017