{
  "abstract": "Quantitative identification of molecular products and reaction pathways from scanning tunneling microscopy images is difficult when labeled images are unavailable for a new chemical system. We develop a simulation-assisted framework for zero-shot analysis that requires only precursor information for a new target system, with no experimental images or annotations from that system used during model training. The framework couples two functional components: NanoSim generates physics-grounded synthetic images from predicted reaction products and sampled surface scenes, while NanoAnalysis translates molecular detections into product populations, spatial arrangements, and mechanistic interpretations. Applied to a representative on-surface reaction, the detector achieves a micro-averaged F1 score of 0.92 on experimental images. Analysis of the detected molecules reveals annealing-dependent population changes and reaction-site preferences consistent with experimental observations. Beyond this capability, its modular organization allows heterogeneous data from other systems to be used to improve each component independently, providing a scalable route for continued generalization.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2610.40666",
  "author_total": 5,
  "authors": [
    {
      "name": "Yuanqin He"
    },
    {
      "name": "Zhiyu Wang"
    },
    {
      "name": "Yang Bao"
    },
    {
      "name": "Tao Lin"
    },
    {
      "name": "Hai Bi"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/b5cdnhpber38c.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2610.40666",
  "fulltext_url": null,
  "id": "b5cdnhpber38c",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2610.40666",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "http://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": "CC0-1.0",
  "native_subjects": [
    [
      "arxiv",
      "cond-mat.mtrl-sci"
    ],
    [
      "arxiv",
      "q-bio.QM"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://arxiv.org/pdf/2610.40666",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-10",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/b5cdnhpber38c.ris",
  "sources": [
    {
      "first_seen": "2026-11-02T12:21:15Z",
      "native_id": "2610.40666",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2610.40666"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "arxiv:q-bio.QM",
      "subfield": "bioinformatics"
    },
    {
      "field": "physics",
      "origin": "arxiv:cond-mat.mtrl-sci",
      "subfield": "condensed-matter"
    }
  ],
  "title": "Physics-Grounded Simulation Enables Zero-Shot Molecular and Reaction Analysis in Scanning Tunneling Microscopy",
  "title_text": "Physics-Grounded Simulation Enables Zero-Shot Molecular and Reaction Analysis in Scanning Tunneling Microscopy",
  "type": "preprint",
  "updated_at": "2026-11-03T12:20:38Z",
  "url": "https://research.draconitic.com/paper/b5cdnhpber38c",
  "venue": "arXiv",
  "versions": []
}