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Updated: Oct 2, 2025

Optimizing the Growth of Endothiapepsin Crystals for Serial Crystallography Experiments
Published on: February 4, 2021
Unsupervised topological learning approach of crystal nucleation
Sébastien Becker1,2, Emilie Devijver2, Rémi Molinier3
1Université Grenoble Alpes, CNRS, Grenoble INP, SIMaP, 38000, Grenoble, France.
This study unveils crystal nucleation mechanisms using unsupervised learning and topological descriptors. It reveals simultaneous translational and orientational ordering during homogeneous nucleation in metals, challenging classical nucleation theory.
Area of Science:
- Materials Science
- Computational Physics
- Chemistry
Background:
- Crystal nucleation is vital but its atomic-level mechanisms remain unclear.
- Experimental observation of nucleation's sub-picosecond and nanometer scales is challenging.
- Classical Nucleation Theory has limitations in explaining complex nucleation pathways.
Purpose of the Study:
- To reveal the detailed structural features of crystal nucleation without prior assumptions.
- To investigate the interplay of ordering phenomena during homogeneous nucleation.
- To explore element-specific nucleation pathways beyond Classical Nucleation Theory.
Main Methods:
- An unsupervised learning approach utilizing topological descriptors from persistent homology.
- Simulations applied to monatomic metals to observe nucleation phenomena.
- Analysis of structural features at nanometer length and sub-picosecond time scales.
Main Results:
- Identified simultaneous translational and orientational ordering during homogeneous nucleation.
- Demonstrated that ordering occurs in regions with low five-fold symmetry due to strong bonding.
- Revealed element-specific nucleation pathways that differ from Classical Nucleation Theory predictions.
Conclusions:
- Unsupervised learning with topological descriptors effectively reveals nucleation mechanisms.
- Homogeneous nucleation in metals involves simultaneous ordering driven by bonding.
- Nucleation pathways are element-dependent and more complex than previously hypothesized.
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