{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2017:KV37ZI2EWQY62RAMCGPUMJQNGG","short_pith_number":"pith:KV37ZI2E","canonical_record":{"source":{"id":"1708.02194","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2017-08-07T16:41:20Z","cross_cats_sorted":["q-bio.BM"],"title_canon_sha256":"b8dc92c4f4b6658ee479d328f0f35a2acab77829f42ecb26a4e4d267f3623266","abstract_canon_sha256":"d6e6c02bff19337dfb083693bdfe60a6940490a7a82c72b8506b47b257c73569"},"schema_version":"1.0"},"canonical_sha256":"5577fca344b431ed440c119f46260d31b763bd397fa055cafbff1d41040c3d3a","source":{"kind":"arxiv","id":"1708.02194","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1708.02194","created_at":"2026-05-18T00:38:31Z"},{"alias_kind":"arxiv_version","alias_value":"1708.02194v1","created_at":"2026-05-18T00:38:31Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1708.02194","created_at":"2026-05-18T00:38:31Z"},{"alias_kind":"pith_short_12","alias_value":"KV37ZI2EWQY6","created_at":"2026-05-18T12:31:28Z"},{"alias_kind":"pith_short_16","alias_value":"KV37ZI2EWQY62RAM","created_at":"2026-05-18T12:31:28Z"},{"alias_kind":"pith_short_8","alias_value":"KV37ZI2E","created_at":"2026-05-18T12:31:28Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2017:KV37ZI2EWQY62RAMCGPUMJQNGG","target":"record","payload":{"canonical_record":{"source":{"id":"1708.02194","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2017-08-07T16:41:20Z","cross_cats_sorted":["q-bio.BM"],"title_canon_sha256":"b8dc92c4f4b6658ee479d328f0f35a2acab77829f42ecb26a4e4d267f3623266","abstract_canon_sha256":"d6e6c02bff19337dfb083693bdfe60a6940490a7a82c72b8506b47b257c73569"},"schema_version":"1.0"},"canonical_sha256":"5577fca344b431ed440c119f46260d31b763bd397fa055cafbff1d41040c3d3a","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T00:38:31.808658Z","signature_b64":"Lm70RAKxZ+tdSk25lIu4A1M68Wr6ZLe4OEe0emNdkYqfTLiAMmp9OPdhp9kQ1UYojsKL6IECLDuc6/gKULBKAQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"5577fca344b431ed440c119f46260d31b763bd397fa055cafbff1d41040c3d3a","last_reissued_at":"2026-05-18T00:38:31.808226Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T00:38:31.808226Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1708.02194","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":"2026-05-18T00:38:31Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"fMPpBpE3tDElGhQZ5W3W/CyQif59mv93LLm6nyWyofKZoYpb4mx9EQIhmUy0b25q4lm6/sWo8TgtfEgaZoF9CA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-07-03T16:01:20.109100Z"},"content_sha256":"58106b42e374e9551fae8952eaab2133418833758928e58b351dc8a863072a63","schema_version":"1.0","event_id":"sha256:58106b42e374e9551fae8952eaab2133418833758928e58b351dc8a863072a63"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2017:KV37ZI2EWQY62RAMCGPUMJQNGG","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Modeling Bacterial DNA: Simulation of Self-avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.BM"],"primary_cat":"physics.bio-ph","authors_text":"Ivan Junier, Thibaut Lepage","submitted_at":"2017-08-07T16:41:20Z","abstract_excerpt":"Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation bubbles and other alternative structures. Various polymer models have been developed to capture these properties, with Monte-Carlo (MC) approaches dedicated to the inference of thermodynamic properties. In this chapter, we explain how to perform such Monte-Carlo simulations, following two objectives. On one hand, we present the self-avoiding supercoiled Worm-Li"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1708.02194","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":"2026-05-18T00:38:31Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"Ij0NE0AVWKRZWTveyn0tVlXEagOP6IwEeKy94IUWwqerxmNqPFIW/Zq4dEBXF3pX7wJSFad7pjFJnPWbXI1tAQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-07-03T16:01:20.109465Z"},"content_sha256":"feff9c492e6051478fcb52703c2338e3c0d24e84ad5b04850afa92dbfc47c871","schema_version":"1.0","event_id":"sha256:feff9c492e6051478fcb52703c2338e3c0d24e84ad5b04850afa92dbfc47c871"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/KV37ZI2EWQY62RAMCGPUMJQNGG/bundle.json","state_url":"https://pith.science/pith/KV37ZI2EWQY62RAMCGPUMJQNGG/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/KV37ZI2EWQY62RAMCGPUMJQNGG/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":"2026-07-03T16:01:20Z","links":{"resolver":"https://pith.science/pith/KV37ZI2EWQY62RAMCGPUMJQNGG","bundle":"https://pith.science/pith/KV37ZI2EWQY62RAMCGPUMJQNGG/bundle.json","state":"https://pith.science/pith/KV37ZI2EWQY62RAMCGPUMJQNGG/state.json","well_known_bundle":"https://pith.science/.well-known/pith/KV37ZI2EWQY62RAMCGPUMJQNGG/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2017:KV37ZI2EWQY62RAMCGPUMJQNGG","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":"d6e6c02bff19337dfb083693bdfe60a6940490a7a82c72b8506b47b257c73569","cross_cats_sorted":["q-bio.BM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2017-08-07T16:41:20Z","title_canon_sha256":"b8dc92c4f4b6658ee479d328f0f35a2acab77829f42ecb26a4e4d267f3623266"},"schema_version":"1.0","source":{"id":"1708.02194","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1708.02194","created_at":"2026-05-18T00:38:31Z"},{"alias_kind":"arxiv_version","alias_value":"1708.02194v1","created_at":"2026-05-18T00:38:31Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1708.02194","created_at":"2026-05-18T00:38:31Z"},{"alias_kind":"pith_short_12","alias_value":"KV37ZI2EWQY6","created_at":"2026-05-18T12:31:28Z"},{"alias_kind":"pith_short_16","alias_value":"KV37ZI2EWQY62RAM","created_at":"2026-05-18T12:31:28Z"},{"alias_kind":"pith_short_8","alias_value":"KV37ZI2E","created_at":"2026-05-18T12:31:28Z"}],"graph_snapshots":[{"event_id":"sha256:feff9c492e6051478fcb52703c2338e3c0d24e84ad5b04850afa92dbfc47c871","target":"graph","created_at":"2026-05-18T00:38:31Z","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":"Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation bubbles and other alternative structures. Various polymer models have been developed to capture these properties, with Monte-Carlo (MC) approaches dedicated to the inference of thermodynamic properties. In this chapter, we explain how to perform such Monte-Carlo simulations, following two objectives. On one hand, we present the self-avoiding supercoiled Worm-Li","authors_text":"Ivan Junier, Thibaut Lepage","cross_cats":["q-bio.BM"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2017-08-07T16:41:20Z","title":"Modeling Bacterial DNA: Simulation of Self-avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1708.02194","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":"sha256:58106b42e374e9551fae8952eaab2133418833758928e58b351dc8a863072a63","target":"record","created_at":"2026-05-18T00:38:31Z","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":"d6e6c02bff19337dfb083693bdfe60a6940490a7a82c72b8506b47b257c73569","cross_cats_sorted":["q-bio.BM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2017-08-07T16:41:20Z","title_canon_sha256":"b8dc92c4f4b6658ee479d328f0f35a2acab77829f42ecb26a4e4d267f3623266"},"schema_version":"1.0","source":{"id":"1708.02194","kind":"arxiv","version":1}},"canonical_sha256":"5577fca344b431ed440c119f46260d31b763bd397fa055cafbff1d41040c3d3a","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"5577fca344b431ed440c119f46260d31b763bd397fa055cafbff1d41040c3d3a","first_computed_at":"2026-05-18T00:38:31.808226Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T00:38:31.808226Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"Lm70RAKxZ+tdSk25lIu4A1M68Wr6ZLe4OEe0emNdkYqfTLiAMmp9OPdhp9kQ1UYojsKL6IECLDuc6/gKULBKAQ==","signature_status":"signed_v1","signed_at":"2026-05-18T00:38:31.808658Z","signed_message":"canonical_sha256_bytes"},"source_id":"1708.02194","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:58106b42e374e9551fae8952eaab2133418833758928e58b351dc8a863072a63","sha256:feff9c492e6051478fcb52703c2338e3c0d24e84ad5b04850afa92dbfc47c871"],"state_sha256":"74904bc727aadbaedc71029be99a29cd8f97332f41cef13dada09f6a6ce1ae83"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"CcEBYKF0LvdKBlWzUsxrv82p2lq1MdYdLKtuL3wtOM0vQ0aFqQrxZqY57JhV4vRfKSApoVIeI09nBX/hVC5TCw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-07-03T16:01:20.111425Z","bundle_sha256":"5244063e19fbba3b57488d9d2fa4f85ab815ccd425dc7b7ef575cc27d7320c0d"}}