{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2015:SBURQZBPKWLRH7SEJR32YYO6HE","short_pith_number":"pith:SBURQZBP","schema_version":"1.0","canonical_sha256":"906918642f559713fe444c77ac61de390f90c8054b36c1a8bcefa0921557fcbc","source":{"kind":"arxiv","id":"1504.00821","version":3},"attestation_state":"computed","paper":{"title":"Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cond-mat.soft","physics.bio-ph"],"primary_cat":"q-bio.BM","authors_text":"Ard A. Louis, Benedict E. K. Snodin, Eyal Nir, Ferdinando Randisi, Flavio Romano, John S. Schreck, Jonathan P. K. Doye, Majid Mosayebi, Petr Sulc, Roman Tsukanov, Thomas E. Ouldridge","submitted_at":"2015-04-03T11:46:00Z","abstract_excerpt":"We introduce an extended version of oxDNA, a coarse-grained model of DNA designed to capture the thermodynamic, structural and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves, and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures such as DNA origami which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na$^+$]=0.5M), so that it can be used fo"},"verification_status":{"content_addressed":true,"pith_receipt":true,"author_attested":false,"weak_author_claims":0,"strong_author_claims":0,"externally_anchored":false,"storage_verified":false,"citation_signatures":0,"replication_records":0,"graph_snapshot":true,"references_resolved":false,"formal_links_present":false},"canonical_record":{"source":{"id":"1504.00821","kind":"arxiv","version":3},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2015-04-03T11:46:00Z","cross_cats_sorted":["cond-mat.soft","physics.bio-ph"],"title_canon_sha256":"262e0521798affef1dfd987310d74169d1d4f26bb3e94caa01af8edd184c0dae","abstract_canon_sha256":"2a38aa1cb025c05de0e602f6f025c841380cbc2da86328908cef1e685576057f"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T01:38:53.701204Z","signature_b64":"xcrEvDxY56m/xLTZljzQEZjHfSnjSLZkwoTrrav45QJP3lxtqt+ZjJ+OSFHbejNh7vtnrY5uUIryDWbUYZS1Bg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"906918642f559713fe444c77ac61de390f90c8054b36c1a8bcefa0921557fcbc","last_reissued_at":"2026-05-18T01:38:53.700412Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T01:38:53.700412Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cond-mat.soft","physics.bio-ph"],"primary_cat":"q-bio.BM","authors_text":"Ard A. Louis, Benedict E. K. Snodin, Eyal Nir, Ferdinando Randisi, Flavio Romano, John S. Schreck, Jonathan P. K. Doye, Majid Mosayebi, Petr Sulc, Roman Tsukanov, Thomas E. Ouldridge","submitted_at":"2015-04-03T11:46:00Z","abstract_excerpt":"We introduce an extended version of oxDNA, a coarse-grained model of DNA designed to capture the thermodynamic, structural and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves, and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures such as DNA origami which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na$^+$]=0.5M), so that it can be used fo"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1504.00821","kind":"arxiv","version":3},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"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"},"aliases":[{"alias_kind":"arxiv","alias_value":"1504.00821","created_at":"2026-05-18T01:38:53.700555+00:00"},{"alias_kind":"arxiv_version","alias_value":"1504.00821v3","created_at":"2026-05-18T01:38:53.700555+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1504.00821","created_at":"2026-05-18T01:38:53.700555+00:00"},{"alias_kind":"pith_short_12","alias_value":"SBURQZBPKWLR","created_at":"2026-05-18T12:29:39.896362+00:00"},{"alias_kind":"pith_short_16","alias_value":"SBURQZBPKWLRH7SE","created_at":"2026-05-18T12:29:39.896362+00:00"},{"alias_kind":"pith_short_8","alias_value":"SBURQZBP","created_at":"2026-05-18T12:29:39.896362+00:00"}],"events":[],"event_summary":{},"paper_claims":[],"inbound_citations":{"count":0,"internal_anchor_count":0,"sample":[]},"formal_canon":{"evidence_count":0,"sample":[],"anchors":[]},"links":{"html":"https://pith.science/pith/SBURQZBPKWLRH7SEJR32YYO6HE","json":"https://pith.science/pith/SBURQZBPKWLRH7SEJR32YYO6HE.json","graph_json":"https://pith.science/api/pith-number/SBURQZBPKWLRH7SEJR32YYO6HE/graph.json","events_json":"https://pith.science/api/pith-number/SBURQZBPKWLRH7SEJR32YYO6HE/events.json","paper":"https://pith.science/paper/SBURQZBP"},"agent_actions":{"view_html":"https://pith.science/pith/SBURQZBPKWLRH7SEJR32YYO6HE","download_json":"https://pith.science/pith/SBURQZBPKWLRH7SEJR32YYO6HE.json","view_paper":"https://pith.science/paper/SBURQZBP","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=1504.00821&json=true","fetch_graph":"https://pith.science/api/pith-number/SBURQZBPKWLRH7SEJR32YYO6HE/graph.json","fetch_events":"https://pith.science/api/pith-number/SBURQZBPKWLRH7SEJR32YYO6HE/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/SBURQZBPKWLRH7SEJR32YYO6HE/action/timestamp_anchor","attest_storage":"https://pith.science/pith/SBURQZBPKWLRH7SEJR32YYO6HE/action/storage_attestation","attest_author":"https://pith.science/pith/SBURQZBPKWLRH7SEJR32YYO6HE/action/author_attestation","sign_citation":"https://pith.science/pith/SBURQZBPKWLRH7SEJR32YYO6HE/action/citation_signature","submit_replication":"https://pith.science/pith/SBURQZBPKWLRH7SEJR32YYO6HE/action/replication_record"}},"created_at":"2026-05-18T01:38:53.700555+00:00","updated_at":"2026-05-18T01:38:53.700555+00:00"}