journal article·2026-04-27Open access

Autonomous fabrication of tailored defect structures in 2D materials using machine learning-enabled scanning transmission electron microscopy

Zijie Wu, Kevin M. Roccapriore, Ayana Ghosh, Kai Xiao, Raymond R. Unocic, Stephen Jesse, Rama Vasudevan, Matthew G. Boebinger

npj Computational Materials· Volume 12· Issue 1

Abstract

Abstract Materials with tailored quantum properties can be engineered from atomic-scale assembly techniques, but existing methods often lack the agility and accuracy to precisely and intelligently control the manufacturing process. Here, we demonstrate a fully autonomous approach for fabricating atomic-level defects using electron beams in scanning transmission electron microscopy (STEM) that combines advanced machine learning and automated beam control. As a proof of concept, we achieved controlled fabrication of MoS-nanowire (MoS-NW) edge structures by iterative and targeted exposure of MoS 2 monolayer to a focused electron beam to selectively eject sulfur atoms, utilizing high-angle annular dark-field (HAADF) imaging for feedback-controlled monitoring of structural evolution of defects. A machine learning framework combining a random forest model and a convolutional neural network (CNN) was developed to decode the HAADF image and accurately identify atomic positions and species. This atomic-level information was then integrated into an autonomous decision-making platform, which applied predefined fabrication strategies to instruct beam control about atomic sites to be ejected. The selected sites were subsequently exposed to a localized electron beam using an FPGA-controlled scan routine with precise control over beam positioning and duration. While the MoS-NW edge structures produced exhibit promising mechanical and electronic properties 1–3 , the proposed methods to build the autonomous fabrication framework is material-agnostic and can be extended to other 2D materials for the creation of diverse defect structures and heterostructures beyond MoS 2 .
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Advanced Electron Microscopy Techniques and Applications · Machine Learning in Materials Science · Nanowire Synthesis and Applications

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

References (63)

Show source-provided references
1. Pan, H. & Zhang, Y.-W. Edge-dependent structural, electronic and magnetic properties of MoS2 nanoribbons. J. Mater. Chem. 22, 7280–7290 (2012).10.1039/c2jm15906f ↗
2. Davelou, D., Kopidakis, G., Kioseoglou, G. & Remediakis, I. N. MoS2 nanostructures: semiconductors with metallic edges. Solid State Commun. 192, 42–46 (2014).10.1016/j.ssc.2014.04.023 ↗
3. Tinoco, M., Maduro, L., Masaki, M., Okunishi, E. & Conesa-Boj, S. Strain-dependent edge structures in MoS2 layers. Nano Lett. 17, 7021–7026 (2017).10.1021/acs.nanolett.7b03627 ↗
4. Dyck, O. et al. Atom-by-atom fabrication with electron beams. Nat. Rev. Mater. 4, 497–507 (2019).10.1038/s41578-019-0118-z ↗
5. Mathew, P. T., Rodriguez, B. J. & Fang, F. Atomic and close-to-atomic scale manufacturing: a review on atomic layer removal methods using atomic force microscopy. Nanomanuf. Metrol. 3, 167–186 (2020).10.1007/s41871-020-00067-2 ↗
6. Gao, J., Luo, X., Fang, F. & Sun, J. Fundamentals of atomic and close-to-atomic scale manufacturing: a review. Int. J. Extrem. Manuf. 4, 012001 (2022).10.1088/2631-7990/ac3bb2 ↗
7. Chen, Y., Fang, F. & Zhang, N. Advance in additive manufacturing of 2D materials at the atomic and close-to-atomic scale. npj 2D Mater. Appl. 8, 17 (2024).10.1038/s41699-024-00456-x ↗
8. Yu, C.-J., von Kugelgen, S., Laorenza, D. W. & Freedman, D. E. A molecular approach to quantum sensing. ACS Cent. Sci. 7, 712–723 (2021).10.1021/acscentsci.0c00737 ↗
9. Esat, T. et al. A quantum sensor for atomic-scale electric and magnetic fields. Nat. Nanotechnol. 19, 1466–1471 (2024).10.1038/s41565-024-01724-z ↗
10. Vajner, D. A., Rickert, L., Gao, T., Kaymazlar, K. & Heindel, T. Quantum communication using semiconductor quantum dots. Adv. Quantum Technol. 5, 2100116 (2022).10.1002/qute.202100116 ↗
11. Specht, H. P. et al. A single-atom quantum memory. Nature 473, 190–193 (2011).10.1038/nature09997 ↗
12. Hudak, B. M. et al. Directed atom-by-atom assembly of dopants in silicon. ACS Nano 12, 5873–5879 (2018).10.1021/acsnano.8b02001 ↗
13. Jesse, S. et al. Direct atomic fabrication and dopant positioning in Si using electron beams with active real-time image-based feedback. Nanotechnology 29, 255303 (2018).10.1088/1361-6528/aabb79 ↗
14. Xu, Q. et al. Controllable atomic scale patterning of freestanding monolayer graphene at elevated temperature. ACS Nano 7, 1566–1572 (2013).10.1021/nn3053582 ↗
15. Clark, N., Lewis, E. A., Haigh, S. J. & Vijayaraghavan, A. Nanometre electron beam sculpting of suspended graphene and hexagonal boron nitride heterostructures. 2D Mater. 6, 025032 (2019).10.1088/2053-1583/ab09a0 ↗
16. Lin, J., Zhang, Y., Zhou, W. & Pantelides, S. T. Structural flexibility and alloying in ultrathin transition-metal chalcogenide nanowires. ACS Nano 10, 2782–2790 (2016).10.1021/acsnano.5b07888 ↗
17. Lin, J. et al. Flexible metallic nanowires with self-adaptive contacts to semiconducting transition-metal dichalcogenide monolayers. Nat. Nanotechnol. 9, 436–442 (2014).10.1038/nnano.2014.81 ↗
18. Zhao, X. et al. Engineering and modifying two-dimensional materials by electron beams. MRS Bull. 42, 667–676 (2017).10.1557/mrs.2017.184 ↗
19. Zhao, X. et al. Atom-by-atom fabrication of monolayer molybdenum membranes. Adv. Mater. 30, 1707281 (2018).10.1002/adma.201707281 ↗
20. Sang, X. et al. In situ edge engineering in two-dimensional transition metal dichalcogenides. Nat. Commun. 9, 2051 (2018).10.1038/s41467-018-04435-x ↗
21. Susi, T., Meyer, J. C. & Kotakoski, J. Manipulating low-dimensional materials down to the level of single atoms with electron irradiation. Ultramicroscopy 180, 163–172 (2017).10.1016/j.ultramic.2017.03.005 ↗
22. Tripathi, M. et al. Electron-beam manipulation of silicon dopants in graphene. Nano Lett. 18, 5319–5323 (2018).10.1021/acs.nanolett.8b02406 ↗
23. Mustonen, K. et al. Electron-beam manipulation of silicon impurities in single-walled carbon nanotubes. Adv. Funct. Mater. 29, 1901327 (2019).10.1002/adfm.201901327 ↗
24. Dyck, O. et al. Building structures atom by atom via electron beam manipulation. Small 14, 1801771 (2018).10.1002/smll.201801771 ↗
25. Dyck, O. et al. Electron-beam introduction of heteroatomic Pt–Si structures in graphene. Carbon 161, 750–757 (2020).10.1016/j.carbon.2020.01.042 ↗
26. Dyck, O. et al. Doping of Cr in graphene using electron beam manipulation for functional defect engineering. ACS Appl. Nano Mater. 3, 10855–10863 (2020).10.1021/acsanm.0c02118 ↗
27. Dyck, O. et al. Doping transition-metal atoms in graphene for atomic-scale tailoring of electronic, magnetic, and quantum topological properties. Carbon 173, 205–214 (2021).10.1016/j.carbon.2020.11.015 ↗
28. Schwarzer, M. et al. Learning and controlling silicon dopant transitions in graphene using scanning transmission electron microscopy. Adv. Mater. Interf. 12, 2400998 (2025).10.1002/admi.202400998 ↗
29. Sang, X. et al. Precision controlled atomic resolution scanning transmission electron microscopy using spiral scan pathways. Sci. Rep. 7, 43585 (2017).10.1038/srep43585 ↗
30. Sang, X. et al. Dynamic scan control in STEM: spiral scans. Adv. Struct. Chem. Imaging 2, 6 (2016).10.1186/s40679-016-0020-3 ↗
31. Jesse, S. et al. Atomic-level sculpting of crystalline oxides: toward bulk nanofabrication with single atomic plane precision. Small 11, 5895–5900 (2015).10.1002/smll.201502048 ↗
32. Boebinger, M. G. et al. The atomic drill bit: precision controlled atomic fabrication of 2D materials. Adv. Mater. 35, 2210116 (2023).10.1002/adma.202210116 ↗
33. Roccapriore, K. M. et al. Probing electron beam induced transformations on a single-defect level via automated scanning transmission electron microscopy. ACS Nano 16, 17116–17127 (2022).10.1021/acsnano.2c07451 ↗
34. Hu, G., Fung, V., Sang, X., Unocic, R. R. & Ganesh, P. Predicting synthesizable multi-functional edge reconstructions in two-dimensional transition metal dichalcogenides. npj Comput. Mater. 6, 44 (2020).10.1038/s41524-020-0327-4 ↗
35. Ghosh, A., Sumpter, B. G., Dyck, O., Kalinin, S. V. & Ziatdinov, M. Ensemble learning-iterative training machine learning for uncertainty quantification and automated experiment in atom-resolved microscopy. npj Comput. Mater. 7, 100 (2021).10.1038/s41524-021-00569-7 ↗
36. Roccapriore, K. M., Torsi, R., Robinson, J., Kalinin, S. & Ziatdinov, M. Dynamic STEM-EELS for single-atom and defect measurement during electron beam transformations. Sci. Adv. 10, eadn5899 (2024).10.1126/sciadv.adn5899 ↗
37. Boebinger, M. G. et al. Exploring electron-beam induced modifications of materials with machine-learning assisted high temporal resolution electron microscopy. npj Comput. Mater. 10, 260 (2024).10.1038/s41524-024-01448-7 ↗
38. Boebinger, M. G. et al. Atomic-scale fabrication of 1D-2D nano hetero-structures within 2D materials through automated tracking and electron beam control. Microsc. Microanal. 28, 2178–2180 (2022).10.1017/S143192762200842X ↗
39. Kalinin, S. V. et al. Machine learning in scanning transmission electron microscopy. Nat. Rev. Methods Prim. 2, 11 (2022).10.1038/s43586-022-00095-w ↗
40. Kalinin, S. V. et al. Machine learning for automated experimentation in scanning transmission electron microscopy. npj Comput. Mater. 9, 227 (2023).10.1038/s41524-023-01142-0 ↗
41. Ziatdinov, M. et al. Deep learning of atomically resolved scanning transmission electron microscopy images: chemical identification and tracking local transformations. ACS Nano 11, 12742–12752 (2017).10.1021/acsnano.7b07504 ↗
42. Abebe, W. et al. SAM-I-Am: Semantic boosting for zero-shot atomic-scale electron micrograph segmentation. Comput. Mater. Sci. 246, 113400 (2025).10.1016/j.commatsci.2024.113400 ↗
43. Akers, S. et al. Rapid and flexible segmentation of electron microscopy data using few-shot machine learning. npj Comput. Mater. 7, 187 (2021).10.1038/s41524-021-00652-z ↗
44. Prifti, E., Buban, J. P., Thind, A. S. & Klie, R. F. Variational Convolutional Autoencoders for Anomaly Detection in Scanning Transmission Electron Microscopy. Small 19, 2205977 (2023).10.1002/smll.202205977 ↗
45. Sadre, R., Ophus, C., Butko, A. & Weber, G. H. Deep learning segmentation of complex features in atomic-resolution phase-contrast transmission electron microscopy images. Microsc. Microanal. 27, 804–814 (2021).10.1017/S1431927621000167 ↗
46. Lee, K. et al. STEM image analysis based on deep learning: identification of vacancy defects and polymorphs of MoS2. Nano Lett. 22, 4677–4685 (2022).10.1021/acs.nanolett.2c00550 ↗
47. Ter-Petrosyan, A. H. et al. Unsupervised segmentation of irradiation-induced order-disorder phase transitions in electron microscopy. Proceedings of Thirty-Seventh Conference on Neural Information Processing Systems (NeurIPS). (2023).
48. Khan, A., Lee, C.-H., Huang, P. Y. & Clark, B. K. Leveraging generative adversarial networks to create realistic scanning transmission electron microscopy images. npj Comput. Mater. 9, 85 (2023).10.1038/s41524-023-01042-3 ↗
49. Huang, W. et al. Auto-resolving the atomic structure at van der Waals interfaces using a generative model. Nat. Commun. 16, 2927 (2025).10.1038/s41467-025-58160-3 ↗
50. Bao, Y., Lu, X., Xia, Y., Ye, Z. & Chen, H. STEMDiff: a wavelet-enhanced diffusion model for physics-informed STEM image generation. Adv. Sci. 12, e08266 (2025).10.1002/advs.202508266 ↗
51. Liu, Y. et al. AEcroscopy: a software–hardware framework empowering microscopy toward automated and autonomous experimentation. Small Methods 8, 2301740 (2024).10.1002/smtd.202301740 ↗
52. Komsa, H.-P., Kurasch, S., Lehtinen, O., Kaiser, U. & Krasheninnikov, A. V. From point to extended defects in two-dimensional MoS2: evolution of atomic structure under electron irradiation. Phys. Rev. B 88, 035301 (2013).10.1103/PhysRevB.88.035301 ↗
53. Wang, S., Lee, G.-D., Lee, S., Yoon, E. & Warner, J. H. Detailed atomic reconstruction of extended line defects in monolayer MoS2. ACS Nano 10, 5419–5430 (2016).10.1021/acsnano.6b01673 ↗
54. Kretschmer, S., Lehnert, T., Kaiser, U. & Krasheninnikov, A. V. Formation of defects in two-dimensional MoS2 in the transmission electron microscope at electron energies below the knock-on threshold: the role of electronic excitations. Nano Lett. 20, 2865–2870 (2020).10.1021/acs.nanolett.0c00670 ↗
55. Yoshimura, A. et al. Quantum theory of electronic excitation and sputtering by transmission electron microscopy. Nanoscale 15, 1053–1067 (2023).10.1039/D2NR01018F ↗
56. Ester, M., Kriegel, H.-P., Sander, J. & Xu, X. in Proc. Second International Conference on Knowledge Discovery and Data Mining 226–231 (AAAI Press, 1996).
57. Chen, I. J. et al. Precise atom manipulation through deep reinforcement learning. Nat. Commun. 13, 7499 (2022).10.1038/s41467-022-35149-w ↗
58. Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011).
59. Bartók, A. P., Kondor, R. & Csányi, G. On representing chemical environments. Phys. Rev. B 87, 184115 (2013).10.1103/PhysRevB.87.184115 ↗
60. Drautz, R. Atomic cluster expansion for accurate and transferable interatomic potentials. Phys. Rev. B 99, 014104 (2019).10.1103/PhysRevB.99.014104 ↗
61. Ronneberger, O., Fischer, P. & Brox, T. in Medical Image Computing and Computer-Assisted Intervention – MICCAI (eds Navab, N., Hornegger, J., Wells, W. M. & Frangi, A. F.) (Springer International Publishing, 2015).
62. Ziatdinov, M., Ghosh, A., Wong, C. Y. & Kalinin, S. V. AtomAI framework for deep learning analysis of image and spectroscopy data in electron and scanning probe microscopy. Nat. Mach. Intell. 4, 1101–1112 (2022).10.1038/s42256-022-00555-8 ↗
63. Paszke, A. et al. in Proc. 33rd International Conference on Neural Information Processing Systems Article 721 (Curran Associates Inc., 2019).