{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2017:JNVXRDVSDITTAE6Z6IQNC3LPOV","short_pith_number":"pith:JNVXRDVS","schema_version":"1.0","canonical_sha256":"4b6b788eb21a273013d9f220d16d6f75663e52873eb137d4904bbf4166eb1bcb","source":{"kind":"arxiv","id":"1701.05770","version":2},"attestation_state":"computed","paper":{"title":"Origin of spatial organization of DNA-polymer in bacterial chromosomes","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cond-mat.stat-mech","physics.bio-ph"],"primary_cat":"cond-mat.soft","authors_text":"Apratim Chatterji, Farhat Habib, G.P. Manjunath, Tejal Agarwal","submitted_at":"2017-01-20T11:50:36Z","abstract_excerpt":"In-vivo DNA organization at large length scales ($\\sim 100nm$) is highly debated and polymer models have proved useful to understand the principle of DNA-organization. Here, we show that $<2$% cross-links at specific points in a ring polymer can lead to a distinct spatial organization of the polymer. The specific pairs of cross-linked monomers were extracted from contact maps of bacterial DNA. We are able to predict the structure of 2 DNAs using Monte Carlo simulations of the bead-spring polymer with cross-links at these special positions. Simulations with cross-links at random positions along"},"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":"1701.05770","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.soft","submitted_at":"2017-01-20T11:50:36Z","cross_cats_sorted":["cond-mat.stat-mech","physics.bio-ph"],"title_canon_sha256":"73ea72bac25220823b91777efb34c2c790c8685bd460222107121baa8ec1d1c3","abstract_canon_sha256":"619bead6087f9e1f07151c7e50b8b89773957bbfb30886a48bbe07364fa7920d"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T00:19:35.962597Z","signature_b64":"xKE9v2wf1sFBreYYrvCuObv29i9hEc708wKiww5vPyo8UJ0sAlwm9tvrjb6rweT/lrdHywlydejivADuAUt9Cg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"4b6b788eb21a273013d9f220d16d6f75663e52873eb137d4904bbf4166eb1bcb","last_reissued_at":"2026-05-18T00:19:35.961938Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T00:19:35.961938Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"Origin of spatial organization of DNA-polymer in bacterial chromosomes","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cond-mat.stat-mech","physics.bio-ph"],"primary_cat":"cond-mat.soft","authors_text":"Apratim Chatterji, Farhat Habib, G.P. Manjunath, Tejal Agarwal","submitted_at":"2017-01-20T11:50:36Z","abstract_excerpt":"In-vivo DNA organization at large length scales ($\\sim 100nm$) is highly debated and polymer models have proved useful to understand the principle of DNA-organization. Here, we show that $<2$% cross-links at specific points in a ring polymer can lead to a distinct spatial organization of the polymer. The specific pairs of cross-linked monomers were extracted from contact maps of bacterial DNA. We are able to predict the structure of 2 DNAs using Monte Carlo simulations of the bead-spring polymer with cross-links at these special positions. Simulations with cross-links at random positions along"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1701.05770","kind":"arxiv","version":2},"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":"1701.05770","created_at":"2026-05-18T00:19:35.962040+00:00"},{"alias_kind":"arxiv_version","alias_value":"1701.05770v2","created_at":"2026-05-18T00:19:35.962040+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1701.05770","created_at":"2026-05-18T00:19:35.962040+00:00"},{"alias_kind":"pith_short_12","alias_value":"JNVXRDVSDITT","created_at":"2026-05-18T12:31:24.725408+00:00"},{"alias_kind":"pith_short_16","alias_value":"JNVXRDVSDITTAE6Z","created_at":"2026-05-18T12:31:24.725408+00:00"},{"alias_kind":"pith_short_8","alias_value":"JNVXRDVS","created_at":"2026-05-18T12:31:24.725408+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/JNVXRDVSDITTAE6Z6IQNC3LPOV","json":"https://pith.science/pith/JNVXRDVSDITTAE6Z6IQNC3LPOV.json","graph_json":"https://pith.science/api/pith-number/JNVXRDVSDITTAE6Z6IQNC3LPOV/graph.json","events_json":"https://pith.science/api/pith-number/JNVXRDVSDITTAE6Z6IQNC3LPOV/events.json","paper":"https://pith.science/paper/JNVXRDVS"},"agent_actions":{"view_html":"https://pith.science/pith/JNVXRDVSDITTAE6Z6IQNC3LPOV","download_json":"https://pith.science/pith/JNVXRDVSDITTAE6Z6IQNC3LPOV.json","view_paper":"https://pith.science/paper/JNVXRDVS","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=1701.05770&json=true","fetch_graph":"https://pith.science/api/pith-number/JNVXRDVSDITTAE6Z6IQNC3LPOV/graph.json","fetch_events":"https://pith.science/api/pith-number/JNVXRDVSDITTAE6Z6IQNC3LPOV/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/JNVXRDVSDITTAE6Z6IQNC3LPOV/action/timestamp_anchor","attest_storage":"https://pith.science/pith/JNVXRDVSDITTAE6Z6IQNC3LPOV/action/storage_attestation","attest_author":"https://pith.science/pith/JNVXRDVSDITTAE6Z6IQNC3LPOV/action/author_attestation","sign_citation":"https://pith.science/pith/JNVXRDVSDITTAE6Z6IQNC3LPOV/action/citation_signature","submit_replication":"https://pith.science/pith/JNVXRDVSDITTAE6Z6IQNC3LPOV/action/replication_record"}},"created_at":"2026-05-18T00:19:35.962040+00:00","updated_at":"2026-05-18T00:19:35.962040+00:00"}