{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2013:IRPP3BOFHIF335VKSRKV4EIRRY","short_pith_number":"pith:IRPP3BOF","schema_version":"1.0","canonical_sha256":"445efd85c53a0bbdf6aa94555e11118e327eebb105e8dc3f794706bb8291ce43","source":{"kind":"arxiv","id":"1309.3544","version":1},"attestation_state":"computed","paper":{"title":"Long-Time Mean Square Displacements in Proteins","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"physics.bio-ph","authors_text":"Derya Vural, Henry R. Glyde, Jeremy C. Smith, Liang Hong","submitted_at":"2013-09-13T19:23:58Z","abstract_excerpt":"We propose a method for obtaining the intrinsic, long time mean square displacement (MSD) of atoms and molecules in proteins from finite time molecular dynamics (MD) simulations. Typical data from simulations are limited to times of 1 to 10 ns and over this time period the calculated MSD continues to increase without a clear limiting value. The proposed method consists of fitting a model to MD simulation-derived values of the incoherent intermediate neutron scattering function, $I_{inc}(Q,t)$, for finite times. The infinite time MSD, $<r^2>$, appears as a parameter in the model and is determin"},"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":"1309.3544","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2013-09-13T19:23:58Z","cross_cats_sorted":[],"title_canon_sha256":"c8970c2c5f74afc17fdccfbd0e833ab92771c79aa8389e1f27ef9d2751359b0b","abstract_canon_sha256":"edf52140bd436f88bce2d1936248bab5b590a69e5b23cb4dc237230cdacfd572"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T01:47:41.920243Z","signature_b64":"MeUHfgnumTVfPEaGQ8dfXyJPNyV4pdniGamsGYfRXytuR4rROEyVUc733BGpV6uDgxSTQRiExbxRiR4nmhMuDg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"445efd85c53a0bbdf6aa94555e11118e327eebb105e8dc3f794706bb8291ce43","last_reissued_at":"2026-05-18T01:47:41.919831Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T01:47:41.919831Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"Long-Time Mean Square Displacements in Proteins","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"physics.bio-ph","authors_text":"Derya Vural, Henry R. Glyde, Jeremy C. Smith, Liang Hong","submitted_at":"2013-09-13T19:23:58Z","abstract_excerpt":"We propose a method for obtaining the intrinsic, long time mean square displacement (MSD) of atoms and molecules in proteins from finite time molecular dynamics (MD) simulations. Typical data from simulations are limited to times of 1 to 10 ns and over this time period the calculated MSD continues to increase without a clear limiting value. The proposed method consists of fitting a model to MD simulation-derived values of the incoherent intermediate neutron scattering function, $I_{inc}(Q,t)$, for finite times. The infinite time MSD, $<r^2>$, appears as a parameter in the model and is determin"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1309.3544","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":""},"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":"1309.3544","created_at":"2026-05-18T01:47:41.919901+00:00"},{"alias_kind":"arxiv_version","alias_value":"1309.3544v1","created_at":"2026-05-18T01:47:41.919901+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1309.3544","created_at":"2026-05-18T01:47:41.919901+00:00"},{"alias_kind":"pith_short_12","alias_value":"IRPP3BOFHIF3","created_at":"2026-05-18T12:27:49.015174+00:00"},{"alias_kind":"pith_short_16","alias_value":"IRPP3BOFHIF335VK","created_at":"2026-05-18T12:27:49.015174+00:00"},{"alias_kind":"pith_short_8","alias_value":"IRPP3BOF","created_at":"2026-05-18T12:27:49.015174+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/IRPP3BOFHIF335VKSRKV4EIRRY","json":"https://pith.science/pith/IRPP3BOFHIF335VKSRKV4EIRRY.json","graph_json":"https://pith.science/api/pith-number/IRPP3BOFHIF335VKSRKV4EIRRY/graph.json","events_json":"https://pith.science/api/pith-number/IRPP3BOFHIF335VKSRKV4EIRRY/events.json","paper":"https://pith.science/paper/IRPP3BOF"},"agent_actions":{"view_html":"https://pith.science/pith/IRPP3BOFHIF335VKSRKV4EIRRY","download_json":"https://pith.science/pith/IRPP3BOFHIF335VKSRKV4EIRRY.json","view_paper":"https://pith.science/paper/IRPP3BOF","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=1309.3544&json=true","fetch_graph":"https://pith.science/api/pith-number/IRPP3BOFHIF335VKSRKV4EIRRY/graph.json","fetch_events":"https://pith.science/api/pith-number/IRPP3BOFHIF335VKSRKV4EIRRY/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/IRPP3BOFHIF335VKSRKV4EIRRY/action/timestamp_anchor","attest_storage":"https://pith.science/pith/IRPP3BOFHIF335VKSRKV4EIRRY/action/storage_attestation","attest_author":"https://pith.science/pith/IRPP3BOFHIF335VKSRKV4EIRRY/action/author_attestation","sign_citation":"https://pith.science/pith/IRPP3BOFHIF335VKSRKV4EIRRY/action/citation_signature","submit_replication":"https://pith.science/pith/IRPP3BOFHIF335VKSRKV4EIRRY/action/replication_record"}},"created_at":"2026-05-18T01:47:41.919901+00:00","updated_at":"2026-05-18T01:47:41.919901+00:00"}