IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-58160-3.html
   My bibliography  Save this article

Auto-resolving the atomic structure at van der Waals interfaces using a generative model

Author

Listed:
  • Wenqiang Huang

    (Peking University Shenzhen Graduate School
    National University of Defense Technology
    Central South University)

  • Yucheng Jin

    (Xiamen University
    Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM)
    Xiamen University)

  • Zhemin Li

    (National University of Defense Technology)

  • Lin Yao

    (DP Technology)

  • Yun Chen

    (National University of Defense Technology)

  • Zheng Luo

    (National University of Defense Technology)

  • Shen Zhou

    (National University of Defense Technology)

  • Jinguo Lin

    (Chinese Academy of Sciences)

  • Feng Liu

    (Chinese Academy of Sciences)

  • Zhifeng Gao

    (DP Technology)

  • Jun Cheng

    (Xiamen University
    Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM)
    Xiamen University)

  • Linfeng Zhang

    (DP Technology
    AI for Science Institute)

  • Fangping Ouyang

    (Central South University)

  • Jin Zhang

    (Peking University Shenzhen Graduate School)

  • Shanshan Wang

    (Peking University Shenzhen Graduate School
    National University of Defense Technology
    Peking University Shenzhen Graduate School)

Abstract

The high-resolution visualization of atomic structures is significant for understanding the relationship between the microscopic configurations and macroscopic properties of materials. However, a rapid, accurate, and robust approach to automatically resolve complex patterns in atomic-resolution microscopy remains difficult to implement. Here, we present a Trident strategy-enhanced disentangled representation learning method (a generative model), which utilizes a few unlabelled experimental images with abundant low-cost simulated images to generate a large corpus of annotated simulation data that closely resembles experimental results, producing a high-quality large-volume training dataset. A structural inference model is then trained via a residual neural network which can directly deduce the interlayer slip and rotation of diversified and complicated stacking patterns at van der Waals (vdW) interfaces with picometer-scale accuracy across various materials (e.g. MoS2, WS2, ReS2, ReSe2, and 1 T’-MoTe2) with different layer numbers (bilayer and trilayers), demonstrating robustness to defects, imaging quality, and surface contaminations. The framework can also identify pattern transition interfaces, quantify subtle motif variations, and discriminate moiré patterns that are difficult to distinguish in frequency domains. Finally, the high-throughput processing ability of our method provides insights into a vdW epitaxy mode where various thermodynamically favorable slip stackings can coexist.

Suggested Citation

  • Wenqiang Huang & Yucheng Jin & Zhemin Li & Lin Yao & Yun Chen & Zheng Luo & Shen Zhou & Jinguo Lin & Feng Liu & Zhifeng Gao & Jun Cheng & Linfeng Zhang & Fangping Ouyang & Jin Zhang & Shanshan Wang, 2025. "Auto-resolving the atomic structure at van der Waals interfaces using a generative model," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58160-3
    DOI: 10.1038/s41467-025-58160-3
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-58160-3
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-025-58160-3?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Alex Belianinov & Qian He & Mikhail Kravchenko & Stephen Jesse & Albina Borisevich & Sergei V. Kalinin, 2015. "Identification of phases, symmetries and defects through local crystallography," Nature Communications, Nature, vol. 6(1), pages 1-8, November.
    2. Haoxin Zhou & Tian Xie & Takashi Taniguchi & Kenji Watanabe & Andrea F. Young, 2021. "Superconductivity in rhombohedral trilayer graphene," Nature, Nature, vol. 598(7881), pages 434-438, October.
    3. Xiumei Zhang & Haiyan Nan & Shaoqing Xiao & Xi Wan & Xiaofeng Gu & Aijun Du & Zhenhua Ni & Kostya (Ken) Ostrikov, 2019. "Transition metal dichalcogenides bilayer single crystals by reverse-flow chemical vapor epitaxy," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    4. Sahar Pakdel & Asbjørn Rasmussen & Alireza Taghizadeh & Mads Kruse & Thomas Olsen & Kristian S. Thygesen, 2024. "High-throughput computational stacking reveals emergent properties in natural van der Waals bilayers," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    5. Angelo Ziletti & Devinder Kumar & Matthias Scheffler & Luca M. Ghiringhelli, 2018. "Insightful classification of crystal structures using deep learning," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    6. Yuan Cao & Valla Fatemi & Shiang Fang & Kenji Watanabe & Takashi Taniguchi & Efthimios Kaxiras & Pablo Jarillo-Herrero, 2018. "Unconventional superconductivity in magic-angle graphene superlattices," Nature, Nature, vol. 556(7699), pages 43-50, April.
    7. Andreas Leitherer & Angelo Ziletti & Luca M. Ghiringhelli, 2021. "Robust recognition and exploratory analysis of crystal structures via Bayesian deep learning," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Jing Ding & Hanxiao Xiang & Wenqiang Zhou & Naitian Liu & Qianmei Chen & Xinjie Fang & Kangyu Wang & Linfeng Wu & Kenji Watanabe & Takashi Taniguchi & Na Xin & Shuigang Xu, 2024. "Engineering band structures of two-dimensional materials with remote moiré ferroelectricity," Nature Communications, Nature, vol. 15(1), pages 1-8, December.
    2. Jonas B. Profe & Dante M. Kennes, 2022. "TU $$^2$$ 2 FRG: a scalable approach for truncated unity functional renormalization group in generic fermionic models," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 95(3), pages 1-13, March.
    3. Gal Shavit & Stevan Nadj-Perge & Gil Refael, 2025. "Ephemeral superconductivity atop the false vacuum," Nature Communications, Nature, vol. 16(1), pages 1-8, December.
    4. Sunghoon Kim & Juan Felipe Mendez-Valderrama & Xuepeng Wang & Debanjan Chowdhury, 2025. "Theory of correlated insulators and superconductor at ν = 1 in twisted WSe2," Nature Communications, Nature, vol. 16(1), pages 1-7, December.
    5. Dacen Waters & Ruiheng Su & Ellis Thompson & Anna Okounkova & Esmeralda Arreguin-Martinez & Minhao He & Katherine Hinds & Kenji Watanabe & Takashi Taniguchi & Xiaodong Xu & Ya-Hui Zhang & Joshua Folk , 2024. "Topological flat bands in a family of multilayer graphene moiré lattices," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    6. Xiaozhou Zan & Xiangdong Guo & Aolin Deng & Zhiheng Huang & Le Liu & Fanfan Wu & Yalong Yuan & Jiaojiao Zhao & Yalin Peng & Lu Li & Yangkun Zhang & Xiuzhen Li & Jundong Zhu & Jingwei Dong & Dongxia Sh, 2024. "Electron/infrared-phonon coupling in ABC trilayer graphene," Nature Communications, Nature, vol. 15(1), pages 1-6, December.
    7. Wenqiang Zhou & Jing Ding & Jiannan Hua & Le Zhang & Kenji Watanabe & Takashi Taniguchi & Wei Zhu & Shuigang Xu, 2024. "Layer-polarized ferromagnetism in rhombohedral multilayer graphene," Nature Communications, Nature, vol. 15(1), pages 1-8, December.
    8. Shubhayu Chatterjee & Taige Wang & Erez Berg & Michael P. Zaletel, 2022. "Inter-valley coherent order and isospin fluctuation mediated superconductivity in rhombohedral trilayer graphene," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    9. J. González & T. Stauber, 2023. "Ising superconductivity induced from spin-selective valley symmetry breaking in twisted trilayer graphene," Nature Communications, Nature, vol. 14(1), pages 1-7, December.
    10. Manzhang Xu & Hongjia Ji & Lu Zheng & Weiwei Li & Jing Wang & Hanxin Wang & Lei Luo & Qianbo Lu & Xuetao Gan & Zheng Liu & Xuewen Wang & Wei Huang, 2024. "Reconfiguring nucleation for CVD growth of twisted bilayer MoS2 with a wide range of twist angles," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    11. Dohun Kim & Seyoung Jin & Takashi Taniguchi & Kenji Watanabe & Jurgen H. Smet & Gil Young Cho & Youngwook Kim, 2025. "Observation of 1/3 fractional quantum Hall physics in balanced large angle twisted bilayer graphene," Nature Communications, Nature, vol. 16(1), pages 1-6, December.
    12. Sami Dzsaber & Diego A. Zocco & Alix McCollam & Franziska Weickert & Ross McDonald & Mathieu Taupin & Gaku Eguchi & Xinlin Yan & Andrey Prokofiev & Lucas M. K. Tang & Bryan Vlaar & Laurel E. Winter & , 2022. "Control of electronic topology in a strongly correlated electron system," Nature Communications, Nature, vol. 13(1), pages 1-7, December.
    13. Sahar Pakdel & Asbjørn Rasmussen & Alireza Taghizadeh & Mads Kruse & Thomas Olsen & Kristian S. Thygesen, 2024. "High-throughput computational stacking reveals emergent properties in natural van der Waals bilayers," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    14. Keshav Singh & Aaron Chew & Jonah Herzog-Arbeitman & B. Andrei Bernevig & Oskar Vafek, 2024. "Topological heavy fermions in magnetic field," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    15. Anushree Datta & M. J. Calderón & A. Camjayi & E. Bascones, 2023. "Heavy quasiparticles and cascades without symmetry breaking in twisted bilayer graphene," Nature Communications, Nature, vol. 14(1), pages 1-8, December.
    16. Suk Hyun Sung & Yin Min Goh & Hyobin Yoo & Rebecca Engelke & Hongchao Xie & Kuan Zhang & Zidong Li & Andrew Ye & Parag B. Deotare & Ellad B. Tadmor & Andrew J. Mannix & Jiwoong Park & Liuyan Zhao & Ph, 2022. "Torsional periodic lattice distortions and diffraction of twisted 2D materials," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    17. Robin Huber & Max-Niklas Steffen & Martin Drienovsky & Andreas Sandner & Kenji Watanabe & Takashi Taniguchi & Daniela Pfannkuche & Dieter Weiss & Jonathan Eroms, 2022. "Band conductivity oscillations in a gate-tunable graphene superlattice," Nature Communications, Nature, vol. 13(1), pages 1-7, December.
    18. Shouheng Chen & Zihan Liang & Jinshui Miao & Xiang-Long Yu & Shuo Wang & Yule Zhang & Han Wang & Yun Wang & Chun Cheng & Gen Long & Taihong Wang & Lin Wang & Han Zhang & Xiaolong Chen, 2024. "Infrared optoelectronics in twisted black phosphorus," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    19. Max Heyl & Kyosuke Adachi & Yuki M. Itahashi & Yuji Nakagawa & Yuichi Kasahara & Emil J. W. List-Kratochvil & Yusuke Kato & Yoshihiro Iwasa, 2022. "Vortex dynamics in the two-dimensional BCS-BEC crossover," Nature Communications, Nature, vol. 13(1), pages 1-7, December.
    20. Sunny Gupta & Henry Yu & Boris I. Yakobson, 2022. "Designing 1D correlated-electron states by non-Euclidean topography of 2D monolayers," Nature Communications, Nature, vol. 13(1), pages 1-6, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58160-3. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.