Physics-Informed 3D Atomic Reconstruction and Dynamics of Free-Standing Graphene from Single Low-Dose TEM Images
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arXiv
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| Autores principales: | , , , , , , |
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| Formato: | Preprint |
| Publicado: |
2026
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| _version_ | 1866918435199385600 |
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| author | Zhang, Xiaojun Hung, Shih-Wei Wu, Yawei Chou, Jyh-Pin Kirkland, Angus I. Kilaas, Roar Chen, Fu-Rong |
| author_facet | Zhang, Xiaojun Hung, Shih-Wei Wu, Yawei Chou, Jyh-Pin Kirkland, Angus I. Kilaas, Roar Chen, Fu-Rong |
| contents | Resolving the three-dimensional (3D) atomic geometry of free-standing graphene in real time is essential for understanding how intrinsic rippling governs its electronic properties. However, the low electron doses required to mitigate radiation damage impose severe signal-to-noise constraints that limit conventional reconstruction methods. Here, we present a physics-informed computational framework that reconstructs 3D atomic coordinates of single-layer graphene from individual low-dose transmission electron microscopy (TEM) frames (8x10^3 e-/Ang^2, 1 ms temporal resolution). The approach combines simulated annealing optimisation with molecular dynamics regularisation, achieving sub-angstrom out-of-plane accuracy (sigma_z < 0.45 Ang), validated against ground-truth simulations. A Kullback-Leibler divergence-based calibration aligns the forward model with experimental image statistics, reducing systematic bias. Applied to high-speed time-series data, the framework enables simultaneous extraction of real-time ripple dynamics, strain tensors, surface curvature, bond-length distributions, and density functional theory (DFT)-derived electron localisation functions (ELF). We establish quantitative relationships linking local geometry, strain, and bond-length variations to electron localisation, demonstrating that sub-angstrom structural fluctuations drive spatially localised, millisecond-scale electronic modulation. A critical dose threshold is identified below which structural information becomes irrecoverable, providing practical guidance for experimental design. The framework is broadly applicable to beam-sensitive two-dimensional materials. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2604_07271 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | Physics-Informed 3D Atomic Reconstruction and Dynamics of Free-Standing Graphene from Single Low-Dose TEM Images Zhang, Xiaojun Hung, Shih-Wei Wu, Yawei Chou, Jyh-Pin Kirkland, Angus I. Kilaas, Roar Chen, Fu-Rong Materials Science Resolving the three-dimensional (3D) atomic geometry of free-standing graphene in real time is essential for understanding how intrinsic rippling governs its electronic properties. However, the low electron doses required to mitigate radiation damage impose severe signal-to-noise constraints that limit conventional reconstruction methods. Here, we present a physics-informed computational framework that reconstructs 3D atomic coordinates of single-layer graphene from individual low-dose transmission electron microscopy (TEM) frames (8x10^3 e-/Ang^2, 1 ms temporal resolution). The approach combines simulated annealing optimisation with molecular dynamics regularisation, achieving sub-angstrom out-of-plane accuracy (sigma_z < 0.45 Ang), validated against ground-truth simulations. A Kullback-Leibler divergence-based calibration aligns the forward model with experimental image statistics, reducing systematic bias. Applied to high-speed time-series data, the framework enables simultaneous extraction of real-time ripple dynamics, strain tensors, surface curvature, bond-length distributions, and density functional theory (DFT)-derived electron localisation functions (ELF). We establish quantitative relationships linking local geometry, strain, and bond-length variations to electron localisation, demonstrating that sub-angstrom structural fluctuations drive spatially localised, millisecond-scale electronic modulation. A critical dose threshold is identified below which structural information becomes irrecoverable, providing practical guidance for experimental design. The framework is broadly applicable to beam-sensitive two-dimensional materials. |
| title | Physics-Informed 3D Atomic Reconstruction and Dynamics of Free-Standing Graphene from Single Low-Dose TEM Images |
| topic | Materials Science |
| url | https://arxiv.org/abs/2604.07271 |