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DOE OSTI · 3013078

Physics-informed machine learning analysis for nanoscale grain mapping by synchrotron Laue microdiffraction

Chan, Ka Hung [Hong Kong University of Science and Technology (HKUST) (Hong Kong); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)] (ORCID:0000000337025124)·Huang, Xinyue [Hong Kong University of Science and Technology (HKUST) (Hong Kong)]·Tamura, Nobumichi [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)] (ORCID:0000000236982611)·Chen, Xian [Hong Kong University of Science and Technology (HKUST) (Hong Kong)] (ORCID:0000000201144642)
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Abstract

Understanding the grain morphology, orientation distribution and crystal structure of nanocrystals is essential for optimizing the mechanical and physical properties of functional materials. Synchrotron X-ray Laue microdiffraction is a powerful technique for characterizing crystal structures and orientation mapping using focused X-rays. However, when the grain sizes are smaller than the beam size, mixed peaks in the Laue pattern from neighboring grains limit the resolution of grain morphology mapping. We propose a physics-informed machine learning (PIML) approach that combines a convolutional neural network feature extractor with a physics-informed filtering algorithm to overcome the spatial resolution limits of X-rays, achieving nanoscale resolution for grain mapping. Our PIML method successfully resolves the grain size, orientation distribution and morphology of Au nanocrystals through synchrotron microdiffraction scans, showing good agreement with electron backscatter diffraction results. This PIML-assisted synchrotron microdiffraction analysis can be generalized to other diffraction-based probes, enabling the characterization of nanosized structures with micrometre-sized probes.

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X-ray crystallographygrain mappingnanocrystalsphysics-informed machine learningsynchrotron Laue microdiffraction

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Chan, Ka Hung [Hong Kong University of Science and Technology (HKUST) (Hong Kong); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)] (ORCID:0000000337025124), Huang, Xinyue [Hong Kong University of Science and Technology (HKUST) (Hong Kong)], Tamura, Nobumichi [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)] (ORCID:0000000236982611), Chen, Xian [Hong Kong University of Science and Technology (HKUST) (Hong Kong)] (ORCID:0000000201144642). 2025-10-18. Physics-informed machine learning analysis for nanoscale grain mapping by synchrotron Laue microdiffraction. https://doi.org/10.1107/s160057672500826x

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DOE OSTI2025

Neutron diffraction reveals protonation states in pyridoxal‐5′‐phosphate‐free and glycine external aldimine‐bound serine hydroxymethyltransferase

Serine hydroxymethyltransferase (SHMT) is a critical enzyme in the one-carbon (1C) metabolism pathway catalyzing the reversible conversion of L-Ser into Gly and concurrent transfer of 1C unit to tetrahydrofolate (THF) to give 5,10-methylene-THF (5,10-MTHF), which is used in the downstream syntheses of biomolecules critical for cell proliferation. The cellular 1C metabolism is hijacked by many cancer types to support cancer cell proliferation, making SHMT a promising target for the design and development of novel small-molecule antimetabolite chemotherapies. To advance structure-assisted drug design, knowledge of SHMT catalysis is crucial, but can only be fully realized when the atomic details of each reaction step governed by the acid–base catalysis are elucidated by visualizing active site hydrogen atoms. Here, we used room-temperature neutron crystallography to directly determine protonation states in Thermus thermophilus SHMT (TthSHMT), capturing protomer A in the apo form lacking the coenzyme pyridoxal 5′-phosphate (PLP), and protomer B as a ternary complex with PLP–Gly-external aldimine and (6S)-5-methyltetrahydrofolate (5MTHF). We observed protonation of the Schiff base nitrogen in PLP–Gly and neutrality of the catalytic Lys226 side chain in the ternary complex, whereas Lys226 is protonated and positively charged in the apo-active site. Furthermore, we obtained an X-ray structure of TthSHMT in complex with the substrate THF, which binds identically as 5MTHF at the peripheral binding site. In conclusion, the unique structural and functional information provided by neutron crystallography, in combination with X-ray structures, can be employed in the rational design of SHMT inhibitors.

X-ray crystallography↗