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https://w3id.org/np/RAtHF0KE4BIXq7ygIRs84cl72YMgSnibqs-bMtX1r2ybs

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Content

@prefix this: <https://w3id.org/np/RAtHF0KE4BIXq7ygIRs84cl72YMgSnibqs-bMtX1r2ybs> .
@prefix sub: <https://w3id.org/np/RAtHF0KE4BIXq7ygIRs84cl72YMgSnibqs-bMtX1r2ybs/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix dc: <http://purl.org/dc/terms/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

sub:Head {
  this: a np:Nanopublication;
    np:hasAssertion sub:assertion;
    np:hasProvenance sub:provenance;
    np:hasPublicationInfo sub:pubinfo .
}

sub:assertion {
  <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>
    a prov:SoftwareAgent;
    <http://www.w3.org/2000/01/rdf-schema#label> "delphisci dataset-resolvability assessor (Gemini 4 Argon)";
    prov:actedOnBehalfOf <https://orcid.org/0009-0007-4948-9192>;
    <https://w3id.org/delphi/ontology/usesModel> <https://w3id.org/delphi/resource/model/gemini-4-argon-medium> .
  
  <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini>
    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
    dc:description "In the paper's coarse-grained bead model, the piecewise-linear springs prior to rupture are conservative by construction, meaning unloading is trivially reversible and does not actually test hydrogen-bond reformation. Evaluating the claim across its stated biological scope therefore depends on all-atom cyclic MD simulations of alpha-helices in explicit water and published cyclic AFM or macrorheology studies on intermediate filament networks and keratin fibers. Those resources exist in the literature and standard MD packages can test single-helix refolding at 300 K, but network-level experimental cyclic recovery data are scattered and confounded by inter-filament sliding.";
    dc:subject <https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0>;
    <http://www.w3.org/2000/01/rdf-schema#comment> "Proposed test with existing data: Subject alpha-helical filaments and intermediate-filament networks to cyclic loading-unloading protocols up to the unfolding plateau (prior to covalent bond rupture) at 300 K in all-atom MD or experimental rheology/AFM, measuring hysteresis loop recovery, alpha-helical hydrogen-bond reformation fraction, and residual strain after relaxation. The claim is confirmed if hydrogen bonds and initial stiffness recover on physiological timescales whenever peak stress remains below the covalent rupture regime, and refuted if irreversible plastic sliding or misfolded aggregation persists upon unloading.";
    <http://www.w3.org/2000/01/rdf-schema#label> "Gemini 4 Argon on buehler-2009-helical-networks-11: partially-resolvable, resolvability 0.57";
    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
    <https://w3id.org/delphi/ontology/assessmentType> "dataset-resolvability/0.2.0";
    <https://w3id.org/delphi/ontology/evidenceAgainst> "In real intermediate filament networks under physiological conditions, inter-filament sliding and beta-sheet aggregation can introduce irreversible residual strain before any covalent bonds break.",
      "The paper's own coarse-grained LAMMPS potential is purely hyperelastic (conservative) prior to bond rupture, so it cannot test dissipative hysteresis or thermally activated H-bond refolding kinetics.";
    <https://w3id.org/delphi/ontology/hasConfidence> "0.8"^^xsd:double;
    <https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/buehler-2009-helical-networks-11--gemini--dataset-1>,
      <https://w3id.org/delphi/resource/evidence/buehler-2009-helical-networks-11--gemini--dataset-2>;
    <https://w3id.org/delphi/ontology/hasScore> "0.573"^^xsd:double;
    <https://w3id.org/delphi/ontology/hasVerdict> "partially-resolvable" .
  
  <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini--analysis-feasibility>
    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
    dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini>;
    dc:subject <https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-analysis-feasibility>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Analysis feasibility of buehler-2009-helical-networks-11 by Gemini 4 Argon: 0.65";
    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
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  <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini--data-adequacy>
    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
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    <http://www.w3.org/2000/01/rdf-schema#label> "Data adequacy of buehler-2009-helical-networks-11 by Gemini 4 Argon: 0.45";
    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
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    <https://w3id.org/delphi/ontology/hasScore> "0.45"^^xsd:double .
  
  <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini--data-existence>
    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
    dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini>;
    dc:subject <https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-data-existence>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Data existence of buehler-2009-helical-networks-11 by Gemini 4 Argon: 0.5";
    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
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    <https://w3id.org/delphi/ontology/hasScore> "0.5"^^xsd:double .
  
  <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini--discriminating-power>
    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
    dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini>;
    dc:subject <https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-discriminating-power>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Discriminating power of buehler-2009-helical-networks-11 by Gemini 4 Argon: 0.6";
    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
    <https://w3id.org/delphi/ontology/assessmentType> "dataset-resolvability/0.2.0/discriminating-power";
    <https://w3id.org/delphi/ontology/hasScore> "0.6"^^xsd:double .
  
  <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini--operationalizability>
    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
    dc:isPartOf <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini>;
    dc:subject <https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-operationalizability>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Operationalizability of buehler-2009-helical-networks-11 by Gemini 4 Argon: 0.7";
    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
    <https://w3id.org/delphi/ontology/assessmentType> "dataset-resolvability/0.2.0/operationalizability";
    <https://w3id.org/delphi/ontology/hasScore> "0.7"^^xsd:double .
  
  <https://w3id.org/delphi/resource/claim/buehler-2009-helical-networks-11> <https://w3id.org/delphi/ontology/hasAssessment>
      <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini>,
      <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini--analysis-feasibility>,
      <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini--data-adequacy>,
      <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini--data-existence>,
      <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini--discriminating-power>,
      <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini--operationalizability> .
  
  <https://w3id.org/delphi/resource/evidence/buehler-2009-helical-networks-11--gemini--dataset-1>
    a <https://w3id.org/delphi/ontology/EvidenceItem>;
    dc:description "Experimental structures of alpha-helical intermediate filament segments (such as vimentin and lamin) for cyclic all-atom loading-unloading MD";
    <http://www.w3.org/2000/01/rdf-schema#label> "Candidate dataset: RCSB Protein Data Bank";
    prov:wasDerivedFrom <https://www.rcsb.org/> .
  
  <https://w3id.org/delphi/resource/evidence/buehler-2009-helical-networks-11--gemini--dataset-2>
    a <https://w3id.org/delphi/ontology/EvidenceItem>;
    dc:description "Open-source all-atom MD suite capable of simulating cyclic stretching and hydrogen-bond refolding of alpha-helices in explicit solvent at 300 K";
    <http://www.w3.org/2000/01/rdf-schema#label> "Candidate dataset: GROMACS Molecular Dynamics Package";
    prov:wasDerivedFrom <https://www.gromacs.org/> .
  
  <https://w3id.org/delphi/resource/model/gemini-4-argon-medium> a <https://w3id.org/delphi/ontology/LanguageModel>;
    dc:identifier "gemini-4-argon-medium";
    <http://www.w3.org/2000/01/rdf-schema#label> "Gemini 4 Argon" .
}

sub:provenance {
  sub:assertion prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
    prov:wasDerivedFrom <https://github.com/fractastical/delphisci/blob/67fe5b156cfeca15a2ded33e0face4177d03101c/claim-sources/buehler-protein-materials/assessment/raw/gemini/batch-3.json>,
      <https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0>;
    prov:wasGeneratedBy sub:assessment .
  
  sub:assessment a prov:Activity;
    prov:qualifiedAssociation sub:assessmentPlan;
    prov:wasAssociatedWith <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium> .
  
  sub:assessmentPlan prov:hadPlan <https://github.com/fractastical/delphisci/blob/67fe5b156cfeca15a2ded33e0face4177d03101c/claim-sources/buehler-protein-materials/README.md> .
}

sub:pubinfo {
  <https://w3id.org/delphi/resource/domain/buehler-protein-materials> <http://www.w3.org/2000/01/rdf-schema#label>
      "buehler-protein-materials" .
  
  this: dc:created "2026-11-08T04:48:50.317Z"^^xsd:dateTime;
    dc:creator <https://orcid.org/0009-0007-4948-9192>;
    dc:license <https://creativecommons.org/licenses/by/4.0/>;
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    npx:introduces <https://w3id.org/delphi/resource/assessment/buehler-2009-helical-networks-11--gemini>;
    <http://www.w3.org/2000/01/rdf-schema#label> "Gemini 4 Argon on buehler-2009-helical-networks-11: partially-resolvable, resolvability 0.57";
    <https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/buehler-protein-materials> .
  
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