Lawrence Berkeley National Laboratory

Advances in electron microscopy have enabled visualizations of the three-dimensional (3D) atom arrangements in nano-scale objects. The observations are, however, prone to electron-beam-induced object alterations, so tracking of single atoms in space and time becomes key to unravel inherent structures and properties. Here, we introduce an analytical approach to quantitatively account for atom dynamics in 3D atomic-resolution imaging. The approach is showcased for a Co-Mo-S nanocrystal by analysis of time-resolved in-line holograms achieving ~1.5 Å resolution in 3D. The analysis reveals a decay of phase image contrast towards the nanocrystal edges and meta-stable edge motifs with crystallographic dependence. These findings are explained by beam-stimulated vibrations that exceed Debye-Waller factors and cause chemical transformations at catalytically relevant edges. This ability to simultaneously probe atom vibrations and displacements enables a recovery of the pristine Co-Mo-S structure and establishes, in turn, a foundation to understand heterogeneous chemical functionality of nanostructures, surfaces and molecules.