{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2009:TAGGPIARF4GNT7ZFRYL75RH4A7","short_pith_number":"pith:TAGGPIAR","canonical_record":{"source":{"id":"0911.3661","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2009-11-18T21:16:52Z","cross_cats_sorted":[],"title_canon_sha256":"3f9174ddb73e313f2a80148afbbaad1a9e132dde4e35fa84fc688385e10aeedf","abstract_canon_sha256":"3ca15a23b380eeff861b93c33cb9b82a6efd1d9d4397cb935fcfd3aa40ae009d"},"schema_version":"1.0"},"canonical_sha256":"980c67a0112f0cd9ff258e17fec4fc07ef350bb28d8d4f1efcd01dbe0735af29","source":{"kind":"arxiv","id":"0911.3661","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"0911.3661","created_at":"2026-05-18T02:10:46Z"},{"alias_kind":"arxiv_version","alias_value":"0911.3661v1","created_at":"2026-05-18T02:10:46Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.0911.3661","created_at":"2026-05-18T02:10:46Z"},{"alias_kind":"pith_short_12","alias_value":"TAGGPIARF4GN","created_at":"2026-05-18T12:26:01Z"},{"alias_kind":"pith_short_16","alias_value":"TAGGPIARF4GNT7ZF","created_at":"2026-05-18T12:26:01Z"},{"alias_kind":"pith_short_8","alias_value":"TAGGPIAR","created_at":"2026-05-18T12:26:01Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2009:TAGGPIARF4GNT7ZFRYL75RH4A7","target":"record","payload":{"canonical_record":{"source":{"id":"0911.3661","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2009-11-18T21:16:52Z","cross_cats_sorted":[],"title_canon_sha256":"3f9174ddb73e313f2a80148afbbaad1a9e132dde4e35fa84fc688385e10aeedf","abstract_canon_sha256":"3ca15a23b380eeff861b93c33cb9b82a6efd1d9d4397cb935fcfd3aa40ae009d"},"schema_version":"1.0"},"canonical_sha256":"980c67a0112f0cd9ff258e17fec4fc07ef350bb28d8d4f1efcd01dbe0735af29","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T02:10:46.190101Z","signature_b64":"hXb6OOk4s0ZFbWhqem/pRTx3kbGnJaMT0o01xV7M0Kh1yhboeQS4OHvFuk+F3CPvVqtvA1FkLYyn0GCruZXRBw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"980c67a0112f0cd9ff258e17fec4fc07ef350bb28d8d4f1efcd01dbe0735af29","last_reissued_at":"2026-05-18T02:10:46.189391Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T02:10:46.189391Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"0911.3661","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":"2026-05-18T02:10:46Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"zEwyRZTN69aFIBuJFs7p87/MpDJP0318n9nSM0/1FxK3QzssJj5PicyASaKm23INfjma24LOnd6mSNd+G2m/AQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-23T02:15:58.523929Z"},"content_sha256":"5cd13dfd09f19e4323b89b6dfc53b2e611f2bb64143fa96ab933dc288068b1ec","schema_version":"1.0","event_id":"sha256:5cd13dfd09f19e4323b89b6dfc53b2e611f2bb64143fa96ab933dc288068b1ec"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2009:TAGGPIARF4GNT7ZFRYL75RH4A7","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"A Generalized Theory of DNA Looping and Cyclization","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.BM","authors_text":"Alexei V. Tkachenko, David P. Wilson, Jens-Christian Meiners","submitted_at":"2009-11-18T21:16:52Z","abstract_excerpt":"We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise boundary conditions on DNA, which necessitates a treatment beyond the Shimada-Yamakawa model for ring cyclization. Our model allows for DNA to be treated as a heteropolymer with sequence-dependent intrinsic curvature and stiffness. In this framework, we independently compute enthlapic and entropic contributions to the $J$ factor and show that even at small length"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"0911.3661","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":"2026-05-18T02:10:46Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"s352i9ibnNFD+n4hCoeuzmdMircFt8pKsyREROT+KJOW6zmIVCHsVEvDn5E6K22oDezlTmgQDj2dNgc1bhC6Cw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-23T02:15:58.524275Z"},"content_sha256":"57526e139600527a5826dd5467ad4d1ab953c36749bc879149b28cf21ddd11ef","schema_version":"1.0","event_id":"sha256:57526e139600527a5826dd5467ad4d1ab953c36749bc879149b28cf21ddd11ef"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/TAGGPIARF4GNT7ZFRYL75RH4A7/bundle.json","state_url":"https://pith.science/pith/TAGGPIARF4GNT7ZFRYL75RH4A7/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/TAGGPIARF4GNT7ZFRYL75RH4A7/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":"2026-06-23T02:15:58Z","links":{"resolver":"https://pith.science/pith/TAGGPIARF4GNT7ZFRYL75RH4A7","bundle":"https://pith.science/pith/TAGGPIARF4GNT7ZFRYL75RH4A7/bundle.json","state":"https://pith.science/pith/TAGGPIARF4GNT7ZFRYL75RH4A7/state.json","well_known_bundle":"https://pith.science/.well-known/pith/TAGGPIARF4GNT7ZFRYL75RH4A7/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2009:TAGGPIARF4GNT7ZFRYL75RH4A7","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":"3ca15a23b380eeff861b93c33cb9b82a6efd1d9d4397cb935fcfd3aa40ae009d","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2009-11-18T21:16:52Z","title_canon_sha256":"3f9174ddb73e313f2a80148afbbaad1a9e132dde4e35fa84fc688385e10aeedf"},"schema_version":"1.0","source":{"id":"0911.3661","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"0911.3661","created_at":"2026-05-18T02:10:46Z"},{"alias_kind":"arxiv_version","alias_value":"0911.3661v1","created_at":"2026-05-18T02:10:46Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.0911.3661","created_at":"2026-05-18T02:10:46Z"},{"alias_kind":"pith_short_12","alias_value":"TAGGPIARF4GN","created_at":"2026-05-18T12:26:01Z"},{"alias_kind":"pith_short_16","alias_value":"TAGGPIARF4GNT7ZF","created_at":"2026-05-18T12:26:01Z"},{"alias_kind":"pith_short_8","alias_value":"TAGGPIAR","created_at":"2026-05-18T12:26:01Z"}],"graph_snapshots":[{"event_id":"sha256:57526e139600527a5826dd5467ad4d1ab953c36749bc879149b28cf21ddd11ef","target":"graph","created_at":"2026-05-18T02:10:46Z","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":"We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise boundary conditions on DNA, which necessitates a treatment beyond the Shimada-Yamakawa model for ring cyclization. Our model allows for DNA to be treated as a heteropolymer with sequence-dependent intrinsic curvature and stiffness. In this framework, we independently compute enthlapic and entropic contributions to the $J$ factor and show that even at small length","authors_text":"Alexei V. Tkachenko, David P. Wilson, Jens-Christian Meiners","cross_cats":[],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2009-11-18T21:16:52Z","title":"A Generalized Theory of DNA Looping and Cyclization"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"0911.3661","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":"sha256:5cd13dfd09f19e4323b89b6dfc53b2e611f2bb64143fa96ab933dc288068b1ec","target":"record","created_at":"2026-05-18T02:10:46Z","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":"3ca15a23b380eeff861b93c33cb9b82a6efd1d9d4397cb935fcfd3aa40ae009d","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2009-11-18T21:16:52Z","title_canon_sha256":"3f9174ddb73e313f2a80148afbbaad1a9e132dde4e35fa84fc688385e10aeedf"},"schema_version":"1.0","source":{"id":"0911.3661","kind":"arxiv","version":1}},"canonical_sha256":"980c67a0112f0cd9ff258e17fec4fc07ef350bb28d8d4f1efcd01dbe0735af29","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"980c67a0112f0cd9ff258e17fec4fc07ef350bb28d8d4f1efcd01dbe0735af29","first_computed_at":"2026-05-18T02:10:46.189391Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T02:10:46.189391Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"hXb6OOk4s0ZFbWhqem/pRTx3kbGnJaMT0o01xV7M0Kh1yhboeQS4OHvFuk+F3CPvVqtvA1FkLYyn0GCruZXRBw==","signature_status":"signed_v1","signed_at":"2026-05-18T02:10:46.190101Z","signed_message":"canonical_sha256_bytes"},"source_id":"0911.3661","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:5cd13dfd09f19e4323b89b6dfc53b2e611f2bb64143fa96ab933dc288068b1ec","sha256:57526e139600527a5826dd5467ad4d1ab953c36749bc879149b28cf21ddd11ef"],"state_sha256":"4483d6b54d9293743259d37aecbd4827ced2626a9fa389c4d9d8ca5cad988a9d"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"1QA8Epl/1XpiNmm05/NXI3qVZEgei/B53aqeQfrEHWpviDepY19GPxVMIoX91oBo0C4QGZBeEKxELVEsDMOxAw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-06-23T02:15:58.526250Z","bundle_sha256":"44809beb17ec94b760e6edca7ba0c73124b9084e86aa04fa782f674a1c387289"}}