REFERENCES

1. Klein, J.; Roccapriore, K. M.; Weile, M.; et al. Mesoscale atomic engineering in a crystal lattice. Nature 2026, 653, 715-22.

2. Wang, H.; Fan, P.; Chen, J.; et al. Construction of topological quantum magnets from atomic spins on surfaces. Nat. Nanotechnol. 2024, 19, 1782-8.

3. Sierda, E.; Huang, X.; Badrtdinov, D. I.; et al. Quantum simulator to emulate lower-dimensional molecular structure. Science 2023, 380, 1048-52.

4. Bluvstein, D.; Evered, S. J.; Geim, A. A.; et al. Logical quantum processor based on reconfigurable atom arrays. Nature 2023, 626, 58-65.

5. Esat, T.; Borodin, D.; Oh, J.; et al. A quantum sensor for atomic-scale electric and magnetic fields. Nat. Nanotechnol. 2024, 19, 1466-71.

6. Kalff, F. E.; Rebergen, M. P.; Fahrenfort, E.; et al. A kilobyte rewritable atomic memory. Nat. Nanotechnol. 2016, 11, 926-9.

7. González-Herrero, H.; Gómez-Rodríguez, J. M.; Mallet, P.; et al. Atomic-scale control of graphene magnetism by using hydrogen atoms. Science 2016, 352, 437-41.

8. Klein, J.; Lorke, M.; Florian, M.; et al. Site-selectively generated photon emitters in monolayer MoS2 via local helium ion irradiation. Nat. Commun. 2019, 10, 2755.

9. Dyck, O.; Ziatdinov, M.; Lingerfelt, D. B.; et al. Atom-by-atom fabrication with electron beams. Nat. Rev. Mater. 2019, 4, 497-507.

10. Susi, T.; Kotakoski, J.; Kepaptsoglou, D.; et al. Silicon-Carbon bond inversions driven by 60-keV electrons in graphene. Phys. Rev. Lett. 2014, 113, 115501.

11. Kalinin, S. V.; Borisevich, A.; Jesse, S. Fire up the atom forge. Nature 2016, 539, 485-7.

12. Lin, J.; Cretu, O.; Zhou, W.; et al. Flexible metallic nanowires with self-adaptive contacts to semiconducting transition-metal dichalcogenide monolayers. Nat. Nanotechnol. 2014, 9, 436-42.

13. Lin, Y.; Dumcenco, D. O.; Huang, Y.; Suenaga, K. Atomic mechanism of the semiconducting-to-metallic phase transition in single-layered MoS₂. Nat. Nanotechnol. 2014, 9, 391-6.

14. Yang, S.; Sun, W.; Zhang, Y.; et al. Direct cation exchange in monolayer MoS₂ via recombination-enhanced migration. Phys. Rev. Lett. 2019, 122, 106101.

15. Da, Y.; Luo, R.; Lei, B.; Ji, W.; Zhou, W. Controlled fabrication of freestanding monolayer SiC by electron irradiation. Chinese. Phys. B. 2024, 33, 086802.

16. Yin, K.; Zhang, Y.; Zhou, Y.; et al. Unsupported single-atom-thick copper oxide monolayers. 2D. Mater. 2016, 4, 011001.

17. Hudak, B. M.; Song, J.; Sims, H.; et al. Directed atom-by-atom assembly of dopants in silicon. ACS. Nano. 2018, 12, 5873-9.

18. Jesse, S.; Hudak, B. M.; Zarkadoula, E.; et al. Direct atomic fabrication and dopant positioning in Si using electron beams with active real-time image-based feedback. Nanotechnology 2018, 29, 255303.

19. Chen, C.; Wang, Z.; Lichtenberg, F.; Ikuhara, Y.; Bednorz, J. G. Patterning oxide nanopillars at the atomic scale by phase transformation. Nano. Lett. 2015, 15, 6469-74.

20. Jesse, S.; He, Q.; Lupini, A. R.; et al. Atomic-level sculpting of crystalline oxides: toward bulk nanofabrication with single atomic plane precision. Small 2015, 11, 5895-900.

21. Chen, I.; Aapro, M.; Kipnis, A.; Ilin, A.; Liljeroth, P.; Foster, A. S. Precise atom manipulation through deep reinforcement learning. Nat. Commun. 2022, 13, 7499.

22. Maclaren, I.; Macgregor, T. A.; Allen, C. S.; Kirkland, A. I. Detectors—The ongoing revolution in scanning transmission electron microscopy and why this important to material characterization. APL. Mater. 2020, 8, 110901.

23. Pate, C. M.; Hart, J. L.; Taheri, M. L. RapidEELS: machine learning for denoising and classification in rapid acquisition electron energy loss spectroscopy. Sci. Rep. 2021, 11, 19515.

24. Roccapriore, K. M.; Ross, F. M.; Klein, J. Quantitative electron beam-single atom interactions enabled by sub-20-pm precision targeting. Adv. Sci. 2025, 12, e02551.

25. Roccapriore, K. M.; Torsi, R.; Robinson, J.; Kalinin, S.; Ziatdinov, M. Dynamic STEM-EELS of atom and defect evolution during electron beam transformations. Microsc. Microanal. 2024, 30, ozae044.1007.

26. Boebinger, M. G.; Yilmaz, D. E.; Ghosh, A.; et al. Direct fabrication of atomically defined pores in MXenes using feedback-driven STEM. Small. Methods. 2024, 8, 2400203.

27. Yan, Z.; Handoko, A. D.; Wu, W.; et al. Atomic-engineered gradient tunable solid-state metamaterials. Proc. Natl. Acad. Sci. USA. 2024, 121, e2408974121.

28. Jamali, V.; Aghazadeh, A.; Kacher, J. Thinking microscopes: agentic AI and the future of electron microscopy. NPJ. Comput. Mater. 2026, 12, 149.