{
  "abstract": "Resolving the formation and dissociation mechanisms of hydrate requires identifying not only hydrate-like water, but also the specific cage topologies by which disordered liquid water reorganizes into, or escapes from, crystalline hydrate networks. Here we introduce HyTopo, a cage-topology-centered analysis framework that combines a hydrate order parameter, hierarchical ring and cage recognition, and cage-transition network analysis. Based on local orientational correlations, HyTopo classifies water molecules into liquid-like, precursor-like, hydrate-like, and ice-like environments, and uses this information to guide efficient topological searches for crystalline hydrate cages and defective intermediates. Applications to methane hydrate growth, homogeneous nucleation, and depressurization-induced dissociation reveal that hydrate evolution is governed by heterogeneous and pathway-dependent cage dynamics. During hydrate growth, EA-WPU suppresses the overall proliferation of cage-like structures while altering the balance between defective cages and crystalline sI cages. During nucleation, incomplete cage motifs dominate the early pathway and provide a structural reservoir from which a small fraction of stable 512 and 51262 cages. Hydrate dissociation proceeds through interfacial collapse, bulk decomposition, and dissolved-gas exsolution, with cage lifetimes and transition pathways strongly dependent on cage topology. These results show that HyTopo provides a physically interpretable and topology-resolved route to connect local water ordering, cage formation, structural defects, and hydrate phase transitions in complex molecular simulations.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2609.37036",
  "author_total": 9,
  "authors": [
    {
      "name": "Zherui Chen"
    },
    {
      "name": "Shuquan Huang"
    },
    {
      "name": "Ke Xu"
    },
    {
      "name": "Zhanbo Li"
    },
    {
      "name": "Xinyu Song"
    },
    {
      "name": "Haijun Wang"
    },
    {
      "name": "Dingyuan Tang"
    },
    {
      "name": "Qingxia Liu"
    },
    {
      "name": "Yajun Deng"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/22ftde71mznnc.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2609.37036",
  "fulltext_url": null,
  "id": "22ftde71mznnc",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2609.37036",
  "language": null,
  "licence": "LicenseRef-arXiv-nonexclusive-1.0",
  "licence_label": "arXiv licence",
  "licence_source": "article",
  "licence_url": "http://arxiv.org/licenses/nonexclusive-distrib/1.0/",
  "metadata_licence": "CC0-1.0",
  "native_subjects": [
    [
      "arxiv",
      "cond-mat.mtrl-sci"
    ],
    [
      "openalex",
      "2304|Methane Hydrates and Related Phenomena"
    ]
  ],
  "openalex": "W7214998227",
  "pdf_url": "https://arxiv.org/pdf/2609.37036",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-29",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/22ftde71mznnc.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:25:31Z",
      "native_id": "2609.37036",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2609.37036"
    }
  ],
  "subjects": [
    {
      "field": "physics",
      "origin": "arxiv:cond-mat.mtrl-sci",
      "subfield": "condensed-matter"
    }
  ],
  "title": "HyTopo A High-Performance Hierarchical Algorithm for Mapping the Structural Evolution and Transition Networks of Gas Hydrates",
  "title_text": "HyTopo A High-Performance Hierarchical Algorithm for Mapping the Structural Evolution and Transition Networks of Gas Hydrates",
  "type": "preprint",
  "updated_at": "2026-10-30T12:25:31Z",
  "url": "https://research.draconitic.com/paper/22ftde71mznnc",
  "venue": "arXiv",
  "versions": []
}