@prefix this: <https://w3id.org/np/RAY4fvLI_KykOpC9UK6kL1ennMG-yRYSRBep2AnOr6eAU> .
@prefix sub: <https://w3id.org/np/RAY4fvLI_KykOpC9UK6kL1ennMG-yRYSRBep2AnOr6eAU/> .
@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#> .

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    np:hasProvenance sub:provenance;
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sub:assertion {
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    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
    dc:description "Testing this simulation claim directly requires first generating or obtaining the replica-exchange MD structures of MaSp1/MaSp2 assemblies and then running steered shear simulations to measure how deformation partitions between the beta-sheet nanocrystals and the glycine-rich semi-amorphous phase. Because neither the starting REMD coordinates nor the shearing scripts are publicly archived and only the abstract is vendored, a team must reconstruct the full two-stage simulation pipeline. Moreover, the qualitative phrasing ('is controlled by') limits discriminating power against alternative two-phase polymer network models.";
    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 assembled MaSp1 and MaSp2 two-phase structures (containing both poly-Ala beta-sheet crystalline domains and Gly-rich semi-amorphous domains) to steered MD shear loading, tracking domain-specific strain partitioning, hydrogen-bond rupture counts, and stress-strain response as a function of beta-sheet fraction and H-bond density. Confirmation requires that initial extensibility and hidden-length unfolding localize in the H-bonded 3_1-helical/turn amorphous regions while ultimate stiffness and yield strength scale with the beta-sheet crystalline H-bond network.";
    <http://www.w3.org/2000/01/rdf-schema#label> "Gemini 4 Argon on buehler-2010-silk-assemblies-02: partially-resolvable, resolvability 0.54";
    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> "The starting atomic structures come from the paper's unarchived replica-exchange MD runs, so testing requires regenerating the folded assemblies before shearing them.",
      "The statement that nanoscale behaviour 'is controlled by' secondary structure and H-bonding is qualitative, making it hard to define a sharp refutation criterion once basic two-phase behaviour is observed.";
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    a <https://w3id.org/delphi/ontology/LLMClaimAssessment>;
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  <https://w3id.org/delphi/resource/assessment/buehler-2010-silk-assemblies-02--gemini--data-existence>
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    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-2010-silk-assemblies-02--gemini--operationalizability>
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    prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium>;
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  <https://w3id.org/delphi/resource/evidence/buehler-2010-silk-assemblies-02--gemini--dataset-1>
    a <https://w3id.org/delphi/ontology/EvidenceItem>;
    dc:description "Sequences of Nephila clavipes MaSp1 and MaSp2 repeats needed to build the crystalline-amorphous silk assemblies";
    <http://www.w3.org/2000/01/rdf-schema#label> "Candidate dataset: UniProt Knowledgebase";
    prov:wasDerivedFrom <https://www.uniprot.org/> .
  
  <https://w3id.org/delphi/resource/evidence/buehler-2010-silk-assemblies-02--gemini--dataset-2>
    a <https://w3id.org/delphi/ontology/EvidenceItem>;
    dc:description "Open-source molecular dynamics suite for running replica-exchange assembly followed by steered mechanical shearing simulations";
    <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" .
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sub:provenance {
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  sub:assessmentPlan prov:hadPlan <https://github.com/fractastical/delphisci/blob/67fe5b156cfeca15a2ded33e0face4177d03101c/claim-sources/buehler-protein-materials/README.md> .
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      "buehler-protein-materials" .
  
  this: dc:created "2026-11-08T04:48:50.317Z"^^xsd:dateTime;
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