{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:6D5LYGR4CJK7QHHB6MI5HK2NQZ","short_pith_number":"pith:6D5LYGR4","canonical_record":{"source":{"id":"2404.11363","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.soft","submitted_at":"2024-04-17T13:20:19Z","cross_cats_sorted":["physics.bio-ph","physics.chem-ph"],"title_canon_sha256":"aa3d900a0e9b58a6faedb045849d078ddc6ee5ea666bd8c1fa9a2be88416699b","abstract_canon_sha256":"2b012c2ee28f3d9ef1436a7e7c301cb0d8a740fdebb3a7ec9aff0344a301f078"},"schema_version":"1.0"},"canonical_sha256":"f0fabc1a3c1255f81ce1f311d3ab4d8654108fbf6056ed5ebd213efddbfa713d","source":{"kind":"arxiv","id":"2404.11363","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2404.11363","created_at":"2026-07-05T08:43:55Z"},{"alias_kind":"arxiv_version","alias_value":"2404.11363v2","created_at":"2026-07-05T08:43:55Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2404.11363","created_at":"2026-07-05T08:43:55Z"},{"alias_kind":"pith_short_12","alias_value":"6D5LYGR4CJK7","created_at":"2026-07-05T08:43:55Z"},{"alias_kind":"pith_short_16","alias_value":"6D5LYGR4CJK7QHHB","created_at":"2026-07-05T08:43:55Z"},{"alias_kind":"pith_short_8","alias_value":"6D5LYGR4","created_at":"2026-07-05T08:43:55Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:6D5LYGR4CJK7QHHB6MI5HK2NQZ","target":"record","payload":{"canonical_record":{"source":{"id":"2404.11363","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.soft","submitted_at":"2024-04-17T13:20:19Z","cross_cats_sorted":["physics.bio-ph","physics.chem-ph"],"title_canon_sha256":"aa3d900a0e9b58a6faedb045849d078ddc6ee5ea666bd8c1fa9a2be88416699b","abstract_canon_sha256":"2b012c2ee28f3d9ef1436a7e7c301cb0d8a740fdebb3a7ec9aff0344a301f078"},"schema_version":"1.0"},"canonical_sha256":"f0fabc1a3c1255f81ce1f311d3ab4d8654108fbf6056ed5ebd213efddbfa713d","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T08:43:55.207579Z","signature_b64":"9JbQbNnEdBNOa+HZC9EQd4nwn2gXpyoTdG69jX0FjVhw+pKaFFxKP0n+BwZQP+VKN4ES4FxYJs9eP7WmP/obDQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"f0fabc1a3c1255f81ce1f311d3ab4d8654108fbf6056ed5ebd213efddbfa713d","last_reissued_at":"2026-07-05T08:43:55.207123Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T08:43:55.207123Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2404.11363","source_version":2,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T08:43:55Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"FtKykQZK+aExJBy0bqDcaPUJGrzoVsyPj0uW8wygkrID4A149FBNuSmyc+wMQQjTzl9gs25feOWYSILSdEp9Dw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-21T19:03:47.139521Z"},"content_sha256":"a519aca2d519e682ce4e3ed2ead969309e53cdcfd910861e6032225d135e20df","schema_version":"1.0","event_id":"sha256:a519aca2d519e682ce4e3ed2ead969309e53cdcfd910861e6032225d135e20df"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:6D5LYGR4CJK7QHHB6MI5HK2NQZ","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["physics.bio-ph","physics.chem-ph"],"primary_cat":"cond-mat.soft","authors_text":"Hiroshi Umakoshi, Kento Kasahara, Nobuyuki Matubayasi, Nozomi Morishita Watanabe, Ren Masayama, Ryo Okabe, Yuya Matsubara","submitted_at":"2024-04-17T13:20:19Z","abstract_excerpt":"We propose a theoretical approach to estimate the permeability coefficient of substrates (permeants) for crossing membranes from donor (D) phase to acceptor (A) phase by means of molecular dynamics (MD) simulation. A fundamental aspect of our approach involves reformulating the returning probability (RP) theory, a rigorous bimolecular reaction theory, to describe permeation phenomena. This reformulation relies on the parallelism between permeation and bimolecular reaction processes. In the present method, the permeability coefficient is represented in terms of the thermodynamic and kinetic qua"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2404.11363","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":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2404.11363/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"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":"2026-07-05T08:43:55Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"P4sojt9rwb+d5GoEIk1EUZcgTf228SCC5k+KdWYw879Iu/gBndgiIXgCIm6IcbVnipxcElP1/auYVWFVBz4BAA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-21T19:03:47.140092Z"},"content_sha256":"137faa5ed275ffcf3242224e9c57c3de354ac6568b9f25e45cb7c6ab7ea11875","schema_version":"1.0","event_id":"sha256:137faa5ed275ffcf3242224e9c57c3de354ac6568b9f25e45cb7c6ab7ea11875"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/6D5LYGR4CJK7QHHB6MI5HK2NQZ/bundle.json","state_url":"https://pith.science/pith/6D5LYGR4CJK7QHHB6MI5HK2NQZ/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/6D5LYGR4CJK7QHHB6MI5HK2NQZ/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":"2026-08-21T19:03:47Z","links":{"resolver":"https://pith.science/pith/6D5LYGR4CJK7QHHB6MI5HK2NQZ","bundle":"https://pith.science/pith/6D5LYGR4CJK7QHHB6MI5HK2NQZ/bundle.json","state":"https://pith.science/pith/6D5LYGR4CJK7QHHB6MI5HK2NQZ/state.json","well_known_bundle":"https://pith.science/.well-known/pith/6D5LYGR4CJK7QHHB6MI5HK2NQZ/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:6D5LYGR4CJK7QHHB6MI5HK2NQZ","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":"2b012c2ee28f3d9ef1436a7e7c301cb0d8a740fdebb3a7ec9aff0344a301f078","cross_cats_sorted":["physics.bio-ph","physics.chem-ph"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.soft","submitted_at":"2024-04-17T13:20:19Z","title_canon_sha256":"aa3d900a0e9b58a6faedb045849d078ddc6ee5ea666bd8c1fa9a2be88416699b"},"schema_version":"1.0","source":{"id":"2404.11363","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2404.11363","created_at":"2026-07-05T08:43:55Z"},{"alias_kind":"arxiv_version","alias_value":"2404.11363v2","created_at":"2026-07-05T08:43:55Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2404.11363","created_at":"2026-07-05T08:43:55Z"},{"alias_kind":"pith_short_12","alias_value":"6D5LYGR4CJK7","created_at":"2026-07-05T08:43:55Z"},{"alias_kind":"pith_short_16","alias_value":"6D5LYGR4CJK7QHHB","created_at":"2026-07-05T08:43:55Z"},{"alias_kind":"pith_short_8","alias_value":"6D5LYGR4","created_at":"2026-07-05T08:43:55Z"}],"graph_snapshots":[{"event_id":"sha256:137faa5ed275ffcf3242224e9c57c3de354ac6568b9f25e45cb7c6ab7ea11875","target":"graph","created_at":"2026-07-05T08:43:55Z","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"},"integrity":{"available":true,"clean":true,"detectors_run":[],"endpoint":"/pith/2404.11363/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"We propose a theoretical approach to estimate the permeability coefficient of substrates (permeants) for crossing membranes from donor (D) phase to acceptor (A) phase by means of molecular dynamics (MD) simulation. A fundamental aspect of our approach involves reformulating the returning probability (RP) theory, a rigorous bimolecular reaction theory, to describe permeation phenomena. This reformulation relies on the parallelism between permeation and bimolecular reaction processes. In the present method, the permeability coefficient is represented in terms of the thermodynamic and kinetic qua","authors_text":"Hiroshi Umakoshi, Kento Kasahara, Nobuyuki Matubayasi, Nozomi Morishita Watanabe, Ren Masayama, Ryo Okabe, Yuya Matsubara","cross_cats":["physics.bio-ph","physics.chem-ph"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.soft","submitted_at":"2024-04-17T13:20:19Z","title":"A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2404.11363","kind":"arxiv","version":2},"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:a519aca2d519e682ce4e3ed2ead969309e53cdcfd910861e6032225d135e20df","target":"record","created_at":"2026-07-05T08:43:55Z","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":"2b012c2ee28f3d9ef1436a7e7c301cb0d8a740fdebb3a7ec9aff0344a301f078","cross_cats_sorted":["physics.bio-ph","physics.chem-ph"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.soft","submitted_at":"2024-04-17T13:20:19Z","title_canon_sha256":"aa3d900a0e9b58a6faedb045849d078ddc6ee5ea666bd8c1fa9a2be88416699b"},"schema_version":"1.0","source":{"id":"2404.11363","kind":"arxiv","version":2}},"canonical_sha256":"f0fabc1a3c1255f81ce1f311d3ab4d8654108fbf6056ed5ebd213efddbfa713d","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"f0fabc1a3c1255f81ce1f311d3ab4d8654108fbf6056ed5ebd213efddbfa713d","first_computed_at":"2026-07-05T08:43:55.207123Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T08:43:55.207123Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"9JbQbNnEdBNOa+HZC9EQd4nwn2gXpyoTdG69jX0FjVhw+pKaFFxKP0n+BwZQP+VKN4ES4FxYJs9eP7WmP/obDQ==","signature_status":"signed_v1","signed_at":"2026-07-05T08:43:55.207579Z","signed_message":"canonical_sha256_bytes"},"source_id":"2404.11363","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:a519aca2d519e682ce4e3ed2ead969309e53cdcfd910861e6032225d135e20df","sha256:137faa5ed275ffcf3242224e9c57c3de354ac6568b9f25e45cb7c6ab7ea11875"],"state_sha256":"69fff0c8a997e6f17aa8af41882e26f6196124a6acda6b3c23db5d141caefc2a"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"gjtn0amVGfIUEF+VTF/k15dA/IDhi7lxTa35WGkSCLAz7ZnFWNczUjBwp2flyHGVOfVpu3Ht+uxn+fTSbDnsAg==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-21T19:03:47.144427Z","bundle_sha256":"d24aa69ae23b7ec631d8c9a71ad7c20fc7baaa05372fb6924843d6a1b946585e"}}