Observing crystal nucleation in 4D using atomic electron tomography

[The experimental data, image reconstruction and data analysis source codes for J. Zhou, Yo. Yang, Ya. Yang, D. S. Kim, A. Yuan, X. Tian, C. Ophus, F. Sun, A. K. Schmid, M. Nathanson, H. Heinz, Q. An, H. Zeng, P. Ercius and J. Miao, Observing crystal nucleation in 4D using atomic electron tomography, Nature 570, 500-503 (2019).]

Posted on June 26, 2019

Nucleation plays a critical role in many physical and biological phenomena that range from crystallization, melting and evaporation to the formation of clouds and the initiation of neurodegenerative diseases. However, nucleation is a challenging process to study in experiments, especially in the early stage when several atoms or molecules start to form a new phase from a parent phase. A number of experimental and computational methods have been used to investigate nucleation processes, but experimental determination of the three-dimensional atomic structure and the dynamics of early stage nuclei has been unachievable. Here we use atomic electron tomography to study early stage nucleation in four dimensions (4D: that is, including time) at atomic resolution. Using FePt nanoparticles as a model system, we find that early stage nuclei are irregularly shaped, each has a core of one to a few atoms with the maximum order parameter, and the order parameter gradient points from the core to the boundary of the nucleus. We capture the structure and dynamics of the same nuclei undergoing growth, fluctuation, dissolution, merging and/or division, which are regulated by the order parameter distribution and its gradient. These experimental observations are corroborated by molecular dynamics simulations of heterogeneous and homogeneous nucleation in liquid-solid phase transitions of Pt. Our experimental and molecular dynamics results differ from classical nucleation theory, indicating that a theory beyond this is needed to describe early stage nucleation at the atomic scale. Looking forward, we anticipate that the reported approach will open the door to the study of many fundamental problems in materials science, nanoscience, condensed matter physics and chemistry, such as phase transition, atomic diffusion, grain boundary dynamics, interface motion, defect dynamics and surface reconstruction with 4D atomic resolution.

To facilitate those who are interested in our work, we make the data, image reconstruction and data analysis source codes in Matlab freely available below.

1)         Raw Experimental projeciton for the 7 tilt series:

Particle 1		Particle 2			Particle 3
Measurement 1	Measurement 2	9 min	16 min	26 min	9 min	16 min

2)         Denoised and aligned experimental projections by applying the Block-Matching and 3D filtering
            3D filtering (BM3D) algorithm for the 7 tilt series:

Particle 1		Particle 2			Particle 3
Measurement 1	Measurement 2	9 min	16 min	26 min	9 min	16 min

3)          The 3D reconstruction of the 7 tilt series using the GENeralized Fourier Iterative Reconstruction
             (GENFIRE) algorithm.

Particle 1		Particle 2			Particle 3
Measurement 1	Measurement 2	9 min	16 min	26 min	9 min	16 min

4)         Download the source codeto trace atomic positions from the 3D reconstruction.

5)         Download the source code to refine the atomic models by atom flipping steps
            (termed procedure 2).

6)         Download the source code to calculate the short-range order parameters.

7)         Download the source code to identify common nuclei.

8)         The final 3D atomic models after refinement procedures are deposited in the Materials Data Bank
             (MDB). Here are the MDB IDs linked to the atomic models of each nanoparticle:

Particle 1		Particle 2			Particle 3
Measurement 1	Measurement 2	9 min	16 min	26 min	9 min	16 min
MDB ID FePt00002	MDB ID FePt00003	MDB ID FePt00004	MDB ID FePt00005	MDB ID FePt00006	MDB ID FePt00007	MDB ID FePt00008

If you use any of the above data and source codes in your publications and/or presentations, we request you cite our paper: J. Zhou, Y. Yang, Y. Yang, D. S. Kim, A. Yuan, X. Tian, C. Ophus, F. Sun, A. K. Schmid, M. Nathanson, H. Heinz, Q. An, H. Zeng, P. Ercius and Jianwei Miao, Observing crystal nucleation in 4D using atomic electron tomography, Nature 570, 500-503 (2019).

This document was prepared by J. Zhou, Y. Yang, Y. Yang, D. S. Kim, A. Yuan, X. Tian and J. Miao in the Department of Physics & Astronomy and California NanoSystems Institute, University of California, Los Angeles, California, 90095, USA. Email: miao@physics.ucla.edu.