{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2012:DVBUQYBE7Q3Z3L7EC4AQKGBHJQ","short_pith_number":"pith:DVBUQYBE","canonical_record":{"source":{"id":"1207.1075","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2012-07-04T18:41:27Z","cross_cats_sorted":["cond-mat.mtrl-sci","cond-mat.soft"],"title_canon_sha256":"05aca32e2708de81c5c067649429870104a1c59c8c5aae523195ad3a64bd7474","abstract_canon_sha256":"4188bfef5c4a2f86b825a6b84c55e32132f9a980a163b607b8bb53a034b078eb"},"schema_version":"1.0"},"canonical_sha256":"1d43486024fc379dafe417010518274c269abdad7f40a3ea9696492544f7afac","source":{"kind":"arxiv","id":"1207.1075","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1207.1075","created_at":"2026-05-18T03:51:47Z"},{"alias_kind":"arxiv_version","alias_value":"1207.1075v1","created_at":"2026-05-18T03:51:47Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1207.1075","created_at":"2026-05-18T03:51:47Z"},{"alias_kind":"pith_short_12","alias_value":"DVBUQYBE7Q3Z","created_at":"2026-05-18T12:27:04Z"},{"alias_kind":"pith_short_16","alias_value":"DVBUQYBE7Q3Z3L7E","created_at":"2026-05-18T12:27:04Z"},{"alias_kind":"pith_short_8","alias_value":"DVBUQYBE","created_at":"2026-05-18T12:27:04Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2012:DVBUQYBE7Q3Z3L7EC4AQKGBHJQ","target":"record","payload":{"canonical_record":{"source":{"id":"1207.1075","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2012-07-04T18:41:27Z","cross_cats_sorted":["cond-mat.mtrl-sci","cond-mat.soft"],"title_canon_sha256":"05aca32e2708de81c5c067649429870104a1c59c8c5aae523195ad3a64bd7474","abstract_canon_sha256":"4188bfef5c4a2f86b825a6b84c55e32132f9a980a163b607b8bb53a034b078eb"},"schema_version":"1.0"},"canonical_sha256":"1d43486024fc379dafe417010518274c269abdad7f40a3ea9696492544f7afac","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T03:51:47.591705Z","signature_b64":"c3CHUxGycuXuLcs3pthuv2ayZUgX5k0qJdurNrwwr+x5ugqnJUvDOsXLk9hjZVob3+cPNvyPDBhoA48ziGjiCA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"1d43486024fc379dafe417010518274c269abdad7f40a3ea9696492544f7afac","last_reissued_at":"2026-05-18T03:51:47.590850Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T03:51:47.590850Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1207.1075","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T03:51:47Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"u6Lq03u/LDaeTYU7zXG8b0mt1vAmTFV/vFjrzXX2EJDgJTOSsLbHNxiRW/bB3rd5MZuGa4zpELg9wlz9pTbSAQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-08T12:26:09.612864Z"},"content_sha256":"d3b785d5efa9499b60b0a96fd85d7c28e4df0efe17b5c8eedd28e47f4218d14a","schema_version":"1.0","event_id":"sha256:d3b785d5efa9499b60b0a96fd85d7c28e4df0efe17b5c8eedd28e47f4218d14a"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2012:DVBUQYBE7Q3Z3L7EC4AQKGBHJQ","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Molecular Biology at the Quantum Level: Can Modern Density Functional Theory Forge the Path?","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cond-mat.mtrl-sci","cond-mat.soft"],"primary_cat":"physics.bio-ph","authors_text":"Brian Kolb, T. Thonhauser","submitted_at":"2012-07-04T18:41:27Z","abstract_excerpt":"Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory---a framework that can treat thousands of atoms on firm theoretical "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1207.1075","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"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T03:51:47Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"+MZALUNNtj3xhoGU+UUD5V5zQqZVCoUVzjf0RDPIUoP5cPy5FAYKM2iXI5Ceshqrc3cLFyz7RATEtpL5nDIiBg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-08T12:26:09.613205Z"},"content_sha256":"8e389f5710f3927413ab94485eb0d50bd7cf1233fead2c39c4826bd398ff2e50","schema_version":"1.0","event_id":"sha256:8e389f5710f3927413ab94485eb0d50bd7cf1233fead2c39c4826bd398ff2e50"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/DVBUQYBE7Q3Z3L7EC4AQKGBHJQ/bundle.json","state_url":"https://pith.science/pith/DVBUQYBE7Q3Z3L7EC4AQKGBHJQ/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/DVBUQYBE7Q3Z3L7EC4AQKGBHJQ/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-06-08T12:26:09Z","links":{"resolver":"https://pith.science/pith/DVBUQYBE7Q3Z3L7EC4AQKGBHJQ","bundle":"https://pith.science/pith/DVBUQYBE7Q3Z3L7EC4AQKGBHJQ/bundle.json","state":"https://pith.science/pith/DVBUQYBE7Q3Z3L7EC4AQKGBHJQ/state.json","well_known_bundle":"https://pith.science/.well-known/pith/DVBUQYBE7Q3Z3L7EC4AQKGBHJQ/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2012:DVBUQYBE7Q3Z3L7EC4AQKGBHJQ","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"4188bfef5c4a2f86b825a6b84c55e32132f9a980a163b607b8bb53a034b078eb","cross_cats_sorted":["cond-mat.mtrl-sci","cond-mat.soft"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2012-07-04T18:41:27Z","title_canon_sha256":"05aca32e2708de81c5c067649429870104a1c59c8c5aae523195ad3a64bd7474"},"schema_version":"1.0","source":{"id":"1207.1075","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1207.1075","created_at":"2026-05-18T03:51:47Z"},{"alias_kind":"arxiv_version","alias_value":"1207.1075v1","created_at":"2026-05-18T03:51:47Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1207.1075","created_at":"2026-05-18T03:51:47Z"},{"alias_kind":"pith_short_12","alias_value":"DVBUQYBE7Q3Z","created_at":"2026-05-18T12:27:04Z"},{"alias_kind":"pith_short_16","alias_value":"DVBUQYBE7Q3Z3L7E","created_at":"2026-05-18T12:27:04Z"},{"alias_kind":"pith_short_8","alias_value":"DVBUQYBE","created_at":"2026-05-18T12:27:04Z"}],"graph_snapshots":[{"event_id":"sha256:8e389f5710f3927413ab94485eb0d50bd7cf1233fead2c39c4826bd398ff2e50","target":"graph","created_at":"2026-05-18T03:51:47Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"paper":{"abstract_excerpt":"Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory---a framework that can treat thousands of atoms on firm theoretical ","authors_text":"Brian Kolb, T. Thonhauser","cross_cats":["cond-mat.mtrl-sci","cond-mat.soft"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2012-07-04T18:41:27Z","title":"Molecular Biology at the Quantum Level: Can Modern Density Functional Theory Forge the Path?"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1207.1075","kind":"arxiv","version":1},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:d3b785d5efa9499b60b0a96fd85d7c28e4df0efe17b5c8eedd28e47f4218d14a","target":"record","created_at":"2026-05-18T03:51:47Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"4188bfef5c4a2f86b825a6b84c55e32132f9a980a163b607b8bb53a034b078eb","cross_cats_sorted":["cond-mat.mtrl-sci","cond-mat.soft"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2012-07-04T18:41:27Z","title_canon_sha256":"05aca32e2708de81c5c067649429870104a1c59c8c5aae523195ad3a64bd7474"},"schema_version":"1.0","source":{"id":"1207.1075","kind":"arxiv","version":1}},"canonical_sha256":"1d43486024fc379dafe417010518274c269abdad7f40a3ea9696492544f7afac","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"1d43486024fc379dafe417010518274c269abdad7f40a3ea9696492544f7afac","first_computed_at":"2026-05-18T03:51:47.590850Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T03:51:47.590850Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"c3CHUxGycuXuLcs3pthuv2ayZUgX5k0qJdurNrwwr+x5ugqnJUvDOsXLk9hjZVob3+cPNvyPDBhoA48ziGjiCA==","signature_status":"signed_v1","signed_at":"2026-05-18T03:51:47.591705Z","signed_message":"canonical_sha256_bytes"},"source_id":"1207.1075","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:d3b785d5efa9499b60b0a96fd85d7c28e4df0efe17b5c8eedd28e47f4218d14a","sha256:8e389f5710f3927413ab94485eb0d50bd7cf1233fead2c39c4826bd398ff2e50"],"state_sha256":"07c8dff20167b5d5b44e8610ed7eee4314c8e4aa0553f2e64672bf56cd559b73"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"5FTlwwxU5Ya+/NQNBDh8O8SKy9+QIBGMOXTUDbTADeHyy7nUjaZa/NSroA4jweOIPQdYswq6n82AWjG4h//iDw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-06-08T12:26:09.615139Z","bundle_sha256":"9e71fb13240f59e53918cb19e004f2a9dcebea60168e4137ffdaa10726e38af4"}}