@prefix this: . @prefix sub: . @prefix np: . @prefix rdf: . @prefix prov: . @prefix npx: . @prefix dc: . @prefix xsd: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { a prov:SoftwareAgent; "delphisci dataset-resolvability assessor (Gemini 4 Argon)"; prov:actedOnBehalfOf ; . a ; dc:description "Scoped explicitly to single tropocollagen molecules in molecular simulation, the three-regime deformation sequence (entropic coiling unbending, inter-chain H-bond stretching/breaking, and covalent backbone stretching to fracture) is straightforward to reproduce using collagen triple-helix PDB structures and open MD packages like LAMMPS or GROMACS. The low-force entropic-to-energetic transition is also corroborated by published optical-tweezers force-extension curves."; dc:subject ; "Proposed test with existing data: Run atomistic molecular dynamics tensile stretching of a tropocollagen triple-helix model structure from zero strain to fracture using a reactive or bond-stretching force field, plotting force vs. strain alongside average H-bond count and covalent backbone bond strain to verify the sequential entropic -> H-bond breaking -> covalent stretching -> fracture regimes."; "Gemini 4 Argon on buehler-2007-tropocollagen-entropic-01: resolvable-now, resolvability 0.82"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0"; "Full-length tropocollagen (~300 nm) is computationally expensive in explicit solvent, so simulations typically use shorter triple-helical segments (~10–30 nm) or implicit solvent.", "Simulating covalent bond fracture at the end of the deformation curve requires a reactive force field (such as ReaxFF) rather than a harmonic-bond biomolecular force field."; "0.85"^^xsd:double; , ; "0.82"^^xsd:double; "resolvable-now" . a ; dc:isPartOf ; dc:subject ; "Analysis feasibility of buehler-2007-tropocollagen-entropic-01 by Gemini 4 Argon: 0.8"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/analysis-feasibility"; "0.8"^^xsd:double . a ; dc:isPartOf ; dc:subject ; "Data adequacy of buehler-2007-tropocollagen-entropic-01 by Gemini 4 Argon: 0.75"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/data-adequacy"; "0.75"^^xsd:double . a ; dc:isPartOf ; dc:subject ; "Data existence of buehler-2007-tropocollagen-entropic-01 by Gemini 4 Argon: 0.8"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/data-existence"; "0.8"^^xsd:double . a ; dc:isPartOf ; dc:subject ; "Discriminating power of buehler-2007-tropocollagen-entropic-01 by Gemini 4 Argon: 0.85"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/discriminating-power"; "0.85"^^xsd:double . a ; dc:isPartOf ; dc:subject ; "Operationalizability of buehler-2007-tropocollagen-entropic-01 by Gemini 4 Argon: 0.9"; prov:wasAttributedTo ; "dataset-resolvability/0.2.0/operationalizability"; "0.9"^^xsd:double . , , , , , . a ; dc:description "Collagen-like triple-helix crystal structures (e.g., 1CAG, 1BKV, 3HQV) to initialize single-molecule tropocollagen stretching simulations"; "Candidate dataset: RCSB Protein Data Bank"; prov:wasDerivedFrom . a ; dc:description "Open-source molecular dynamics engine supporting CHARMM and reactive (ReaxFF) potentials required to simulate both H-bond uncoiling and covalent backbone fracture"; "Candidate dataset: LAMMPS Molecular Dynamics Simulator"; prov:wasDerivedFrom . a ; dc:identifier "gemini-4-argon-medium"; "Gemini 4 Argon" . } sub:provenance { sub:assertion prov:wasAttributedTo ; prov:wasDerivedFrom , ; prov:wasGeneratedBy sub:assessment . sub:assessment a prov:Activity; prov:qualifiedAssociation sub:assessmentPlan; prov:wasAssociatedWith . sub:assessmentPlan prov:hadPlan . } sub:pubinfo { "buehler-protein-materials" . this: dc:created "2026-11-08T04:48:50.317Z"^^xsd:dateTime; dc:creator ; dc:license ; npx:hasNanopubType ; npx:introduces ; "Gemini 4 Argon on buehler-2007-tropocollagen-entropic-01: resolvable-now, resolvability 0.82"; . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB"; npx:hasSignature "teUuW7EXVemm0N57Dehs8SgOX8GNZH3aLBn/JNQfw9y0B84Yq5nBnZ3X3efSAgCvsaOlsoTeezdYrQasDNLfyMhLQraUzCOxSt8BiCFu6VkVOYnfBhOxfI9dTpqn8QmbZBqKURHvAyIC4YiTza3qWjMNs/XOydlmJtrn3w/HQRoKibcASBSEutLRkde2XBnK8mxKSb5PvGcdZmAee3asOIyNt4euYKYjr1MDn9QtRVPmV5h4Zrv9uCQy+ITCD4UEtZBpRh5hEyc1wSI2pzCpxdOD0qp7DkBPu6lJhnsr4jcQI6qjafdsK4RWqAzyHFsG2ODw/wIktVr7LU/f6TKU8A=="; npx:hasSignatureTarget this:; npx:signedBy . }