{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2013:BW7HMW6ENQW6Z3NIBL44CGAKZI","short_pith_number":"pith:BW7HMW6E","canonical_record":{"source":{"id":"1307.5565","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2013-07-21T20:12:24Z","cross_cats_sorted":["cond-mat.soft","physics.bio-ph","physics.chem-ph"],"title_canon_sha256":"1179a91e4da7be59578b9ddf7eea1e22760c9cd8a4b8226068a4f01cb694d4b5","abstract_canon_sha256":"83240e12d5c2b91b5a93e99877a5f1061d8fbbdb89b0e2d21ba21b2f4ad49a0c"},"schema_version":"1.0"},"canonical_sha256":"0dbe765bc46c2deceda80af9c1180aca28ffd229322e593c961e8c6b865fb05b","source":{"kind":"arxiv","id":"1307.5565","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1307.5565","created_at":"2026-05-18T03:17:55Z"},{"alias_kind":"arxiv_version","alias_value":"1307.5565v1","created_at":"2026-05-18T03:17:55Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1307.5565","created_at":"2026-05-18T03:17:55Z"},{"alias_kind":"pith_short_12","alias_value":"BW7HMW6ENQW6","created_at":"2026-05-18T12:27:40Z"},{"alias_kind":"pith_short_16","alias_value":"BW7HMW6ENQW6Z3NI","created_at":"2026-05-18T12:27:40Z"},{"alias_kind":"pith_short_8","alias_value":"BW7HMW6E","created_at":"2026-05-18T12:27:40Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2013:BW7HMW6ENQW6Z3NIBL44CGAKZI","target":"record","payload":{"canonical_record":{"source":{"id":"1307.5565","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2013-07-21T20:12:24Z","cross_cats_sorted":["cond-mat.soft","physics.bio-ph","physics.chem-ph"],"title_canon_sha256":"1179a91e4da7be59578b9ddf7eea1e22760c9cd8a4b8226068a4f01cb694d4b5","abstract_canon_sha256":"83240e12d5c2b91b5a93e99877a5f1061d8fbbdb89b0e2d21ba21b2f4ad49a0c"},"schema_version":"1.0"},"canonical_sha256":"0dbe765bc46c2deceda80af9c1180aca28ffd229322e593c961e8c6b865fb05b","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T03:17:55.332239Z","signature_b64":"Un5p2J73wjVE6TpIMfmDBSQfBBb0XrtZywpA09Oqnu/t1AFv8plVY6k5y0KRlyeb4vE2wr7V425GUjV5IJ7nBQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"0dbe765bc46c2deceda80af9c1180aca28ffd229322e593c961e8c6b865fb05b","last_reissued_at":"2026-05-18T03:17:55.331803Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T03:17:55.331803Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1307.5565","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":"2026-05-18T03:17:55Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"94y5316omjWisF4G6JyKzFs6XWWAd972HYSleukn8RgdgwmdHDxGvw7Ojaei+1Vj8gnGGQvbVbNl8lJjRc8JDg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-28T01:17:27.358806Z"},"content_sha256":"11ce8b1f7947cca0937d1bd2ebed86f23474cb887b989fb7710e81711ea01614","schema_version":"1.0","event_id":"sha256:11ce8b1f7947cca0937d1bd2ebed86f23474cb887b989fb7710e81711ea01614"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2013:BW7HMW6ENQW6Z3NIBL44CGAKZI","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"RNA/peptide binding driven by electrostatics -- Insight from bi-directional pulling simulations","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cond-mat.soft","physics.bio-ph","physics.chem-ph"],"primary_cat":"q-bio.BM","authors_text":"Gabriele Varani, Giovanni Bussi, Paolo Carloni, Trang N. Do","submitted_at":"2013-07-21T20:12:24Z","abstract_excerpt":"RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking methods are insufficient. We here present a computational method which allows studying the binding of RNA molecules and charged peptides with atomistic, explicit-solvent molecular dynamics. In our method, a suitable estimate of the electrostatic interaction is used as an order parameter (collective variable) which is then accelerated using bi-directional pulling"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1307.5565","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":"2026-05-18T03:17:55Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"P689xogVTYXHaoR9aX7mYbo8Qy65DiFLqbgnnRQjVO83CpqZUkELQSAN83SBrdW6ziqUKB8p12blyKbxdSdoBw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-28T01:17:27.359147Z"},"content_sha256":"0114160169e7f5d101a6e1af7351ba5b77d02f737d5e4f8602b179597f591851","schema_version":"1.0","event_id":"sha256:0114160169e7f5d101a6e1af7351ba5b77d02f737d5e4f8602b179597f591851"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/BW7HMW6ENQW6Z3NIBL44CGAKZI/bundle.json","state_url":"https://pith.science/pith/BW7HMW6ENQW6Z3NIBL44CGAKZI/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/BW7HMW6ENQW6Z3NIBL44CGAKZI/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":"2026-05-28T01:17:27Z","links":{"resolver":"https://pith.science/pith/BW7HMW6ENQW6Z3NIBL44CGAKZI","bundle":"https://pith.science/pith/BW7HMW6ENQW6Z3NIBL44CGAKZI/bundle.json","state":"https://pith.science/pith/BW7HMW6ENQW6Z3NIBL44CGAKZI/state.json","well_known_bundle":"https://pith.science/.well-known/pith/BW7HMW6ENQW6Z3NIBL44CGAKZI/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2013:BW7HMW6ENQW6Z3NIBL44CGAKZI","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":"83240e12d5c2b91b5a93e99877a5f1061d8fbbdb89b0e2d21ba21b2f4ad49a0c","cross_cats_sorted":["cond-mat.soft","physics.bio-ph","physics.chem-ph"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2013-07-21T20:12:24Z","title_canon_sha256":"1179a91e4da7be59578b9ddf7eea1e22760c9cd8a4b8226068a4f01cb694d4b5"},"schema_version":"1.0","source":{"id":"1307.5565","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1307.5565","created_at":"2026-05-18T03:17:55Z"},{"alias_kind":"arxiv_version","alias_value":"1307.5565v1","created_at":"2026-05-18T03:17:55Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1307.5565","created_at":"2026-05-18T03:17:55Z"},{"alias_kind":"pith_short_12","alias_value":"BW7HMW6ENQW6","created_at":"2026-05-18T12:27:40Z"},{"alias_kind":"pith_short_16","alias_value":"BW7HMW6ENQW6Z3NI","created_at":"2026-05-18T12:27:40Z"},{"alias_kind":"pith_short_8","alias_value":"BW7HMW6E","created_at":"2026-05-18T12:27:40Z"}],"graph_snapshots":[{"event_id":"sha256:0114160169e7f5d101a6e1af7351ba5b77d02f737d5e4f8602b179597f591851","target":"graph","created_at":"2026-05-18T03:17:55Z","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":"RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking methods are insufficient. We here present a computational method which allows studying the binding of RNA molecules and charged peptides with atomistic, explicit-solvent molecular dynamics. In our method, a suitable estimate of the electrostatic interaction is used as an order parameter (collective variable) which is then accelerated using bi-directional pulling","authors_text":"Gabriele Varani, Giovanni Bussi, Paolo Carloni, Trang N. Do","cross_cats":["cond-mat.soft","physics.bio-ph","physics.chem-ph"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2013-07-21T20:12:24Z","title":"RNA/peptide binding driven by electrostatics -- Insight from bi-directional pulling simulations"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1307.5565","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":"sha256:11ce8b1f7947cca0937d1bd2ebed86f23474cb887b989fb7710e81711ea01614","target":"record","created_at":"2026-05-18T03:17:55Z","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":"83240e12d5c2b91b5a93e99877a5f1061d8fbbdb89b0e2d21ba21b2f4ad49a0c","cross_cats_sorted":["cond-mat.soft","physics.bio-ph","physics.chem-ph"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2013-07-21T20:12:24Z","title_canon_sha256":"1179a91e4da7be59578b9ddf7eea1e22760c9cd8a4b8226068a4f01cb694d4b5"},"schema_version":"1.0","source":{"id":"1307.5565","kind":"arxiv","version":1}},"canonical_sha256":"0dbe765bc46c2deceda80af9c1180aca28ffd229322e593c961e8c6b865fb05b","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"0dbe765bc46c2deceda80af9c1180aca28ffd229322e593c961e8c6b865fb05b","first_computed_at":"2026-05-18T03:17:55.331803Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T03:17:55.331803Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"Un5p2J73wjVE6TpIMfmDBSQfBBb0XrtZywpA09Oqnu/t1AFv8plVY6k5y0KRlyeb4vE2wr7V425GUjV5IJ7nBQ==","signature_status":"signed_v1","signed_at":"2026-05-18T03:17:55.332239Z","signed_message":"canonical_sha256_bytes"},"source_id":"1307.5565","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:11ce8b1f7947cca0937d1bd2ebed86f23474cb887b989fb7710e81711ea01614","sha256:0114160169e7f5d101a6e1af7351ba5b77d02f737d5e4f8602b179597f591851"],"state_sha256":"4f61448de1fdb1fac31c8dd7c3ef629498e09a3ab4e182b6091963e9eee5af90"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"om9skVv55CosXLyjQKEhTGcZLhcR3gWm0RGSM0srS6Q78GPQAi8CyZxziGRD23L1U30WLE9MrMGPktWa3wsxCA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-28T01:17:27.361214Z","bundle_sha256":"e90b027d5b0c8e45241fd159f5f7f8e81b4065214df99f2382f66807a5fa1d89"}}