{"paper":{"title":"A Topology-Preserving Python Framework for Reliable Initialization of Star and Cyclic Polymer Architectures in Molecular Dynamics (LAMMPS) Simulations","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cond-mat.mtrl-sci"],"primary_cat":"cond-mat.soft","authors_text":"Akpevweoghene Ogheneowho Ugono, Nkosinathi Dlamini, Oluwatumininu Emmanuel Ayo-Ojo","submitted_at":"2026-06-19T20:09:25Z","abstract_excerpt":"Accurate initialization of polymer architectures remains a critical yet underappreciated determinant of reliability in molecular dynamics simulations of soft matter systems. Errors in coordinate generation and connectivity assignment frequently introduce artificial stresses, topological inconsistencies, and numerical instabilities that propagate throughout simulation trajectories. Here, we present a topology-preserving Python framework for generating star and cyclic polymer architectures with deterministic bond connectivity, exact ring closure, excluded volume enforcement, and spatial-hashing-"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.21719","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2606.21719/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}