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arXiv · 2609.37036

HyTopo A High-Performance Hierarchical Algorithm for Mapping the Structural Evolution and Transition Networks of Gas Hydrates

Zherui Chen·Shuquan Huang·Ke Xu·Zhanbo Li·Xinyu Song·Haijun Wang·Dingyuan Tang·Qingxia Liu·Yajun Deng
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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.

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Zherui Chen, Shuquan Huang, Ke Xu, Zhanbo Li, Xinyu Song, Haijun Wang, Dingyuan Tang, Qingxia Liu, Yajun Deng. 2026-09-29. HyTopo A High-Performance Hierarchical Algorithm for Mapping the Structural Evolution and Transition Networks of Gas Hydrates. https://arxiv.org/abs/2609.37036

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