{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2026:DS2PIBAYSNQ7RI227R4ZDFDQTW","short_pith_number":"pith:DS2PIBAY","canonical_record":{"source":{"id":"2604.01940","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.soft","submitted_at":"2026-04-02T11:58:55Z","cross_cats_sorted":["physics.bio-ph","physics.chem-ph"],"title_canon_sha256":"79aa29e823ff08afb06bf0e4c8102b19e4724380358b37c75476a6bd12ec6904","abstract_canon_sha256":"1e125429816c8a5585e7580a39e924ab4c21585e8042a25fb9c0fbda7f17c747"},"schema_version":"1.0"},"canonical_sha256":"1cb4f404189361f8a35afc799194709da89b033eb1fe067fd53cbf2444a92140","source":{"kind":"arxiv","id":"2604.01940","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2604.01940","created_at":"2026-07-01T01:17:49Z"},{"alias_kind":"arxiv_version","alias_value":"2604.01940v2","created_at":"2026-07-01T01:17:49Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2604.01940","created_at":"2026-07-01T01:17:49Z"},{"alias_kind":"pith_short_12","alias_value":"DS2PIBAYSNQ7","created_at":"2026-07-01T01:17:49Z"},{"alias_kind":"pith_short_16","alias_value":"DS2PIBAYSNQ7RI22","created_at":"2026-07-01T01:17:49Z"},{"alias_kind":"pith_short_8","alias_value":"DS2PIBAY","created_at":"2026-07-01T01:17:49Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2026:DS2PIBAYSNQ7RI227R4ZDFDQTW","target":"record","payload":{"canonical_record":{"source":{"id":"2604.01940","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.soft","submitted_at":"2026-04-02T11:58:55Z","cross_cats_sorted":["physics.bio-ph","physics.chem-ph"],"title_canon_sha256":"79aa29e823ff08afb06bf0e4c8102b19e4724380358b37c75476a6bd12ec6904","abstract_canon_sha256":"1e125429816c8a5585e7580a39e924ab4c21585e8042a25fb9c0fbda7f17c747"},"schema_version":"1.0"},"canonical_sha256":"1cb4f404189361f8a35afc799194709da89b033eb1fe067fd53cbf2444a92140","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-01T01:17:49.942468Z","signature_b64":"3Dm0L0T6H+KLOa//5FX1Z+MJR0l5Rg4EZRtVJ3r7LdtEBvYgYULmGaMcYfjsx4yq5A3F5hK681DAkAF0M8iOBw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"1cb4f404189361f8a35afc799194709da89b033eb1fe067fd53cbf2444a92140","last_reissued_at":"2026-07-01T01:17:49.941955Z","signature_status":"signed_v1","first_computed_at":"2026-07-01T01:17:49.941955Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2604.01940","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":"2026-07-01T01:17:49Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"mrSmZaFuocaNxezaOpYKUuY3Xuf17xlFDhXAJ6U1j2G0c18Ghv95sKgefxZV7awLLatLNS5NOcNLzMF5T/+ACg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-21T07:43:38.831079Z"},"content_sha256":"f82410d086e84a1eb890568aa2fe8c7e79860fd6dd376b428aff2d2523d692e5","schema_version":"1.0","event_id":"sha256:f82410d086e84a1eb890568aa2fe8c7e79860fd6dd376b428aff2d2523d692e5"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2026:DS2PIBAYSNQ7RI227R4ZDFDQTW","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"A Residence-Time Approach for Determining Position-Dependent Diffusivities from Biased Molecular Simulations","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":"Michael von Domaros, Praveen Ranganath Prabhakar, Rinto Thomas","submitted_at":"2026-04-02T11:58:55Z","abstract_excerpt":"Position-dependent diffusivities are central parameters in reduced stochastic descriptions of molecular transport in heterogeneous environments, but their reliable estimation from molecular dynamics simulations remains challenging. We present a residence-time approach (RTA) that extracts local diffusivities from first-exit statistics measured in biased simulations after compensation of the mean free-energy gradient. We apply the method to oxygen diffusion across a hexadecane/water slab, water permeation across a POPC lipid bilayer, and transport of water and volatile organic compounds through "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2604.01940","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/2604.01940/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":"2026-07-01T01:17:49Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"k2PtdCzfKfb3/6YurZgjCGpHuOQ1snRD8/xuoAn/98mZL8lZUR/3UAdzWi08+mGGlhMGawir4huyIszlBu1uAA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-21T07:43:38.831452Z"},"content_sha256":"754e0fa49e397d6a16951a1b811bb7f77fb2ecbe7d8a3a36feb144cc934c895f","schema_version":"1.0","event_id":"sha256:754e0fa49e397d6a16951a1b811bb7f77fb2ecbe7d8a3a36feb144cc934c895f"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/DS2PIBAYSNQ7RI227R4ZDFDQTW/bundle.json","state_url":"https://pith.science/pith/DS2PIBAYSNQ7RI227R4ZDFDQTW/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/DS2PIBAYSNQ7RI227R4ZDFDQTW/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":"2026-08-21T07:43:38Z","links":{"resolver":"https://pith.science/pith/DS2PIBAYSNQ7RI227R4ZDFDQTW","bundle":"https://pith.science/pith/DS2PIBAYSNQ7RI227R4ZDFDQTW/bundle.json","state":"https://pith.science/pith/DS2PIBAYSNQ7RI227R4ZDFDQTW/state.json","well_known_bundle":"https://pith.science/.well-known/pith/DS2PIBAYSNQ7RI227R4ZDFDQTW/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2026:DS2PIBAYSNQ7RI227R4ZDFDQTW","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":"1e125429816c8a5585e7580a39e924ab4c21585e8042a25fb9c0fbda7f17c747","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":"2026-04-02T11:58:55Z","title_canon_sha256":"79aa29e823ff08afb06bf0e4c8102b19e4724380358b37c75476a6bd12ec6904"},"schema_version":"1.0","source":{"id":"2604.01940","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2604.01940","created_at":"2026-07-01T01:17:49Z"},{"alias_kind":"arxiv_version","alias_value":"2604.01940v2","created_at":"2026-07-01T01:17:49Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2604.01940","created_at":"2026-07-01T01:17:49Z"},{"alias_kind":"pith_short_12","alias_value":"DS2PIBAYSNQ7","created_at":"2026-07-01T01:17:49Z"},{"alias_kind":"pith_short_16","alias_value":"DS2PIBAYSNQ7RI22","created_at":"2026-07-01T01:17:49Z"},{"alias_kind":"pith_short_8","alias_value":"DS2PIBAY","created_at":"2026-07-01T01:17:49Z"}],"graph_snapshots":[{"event_id":"sha256:754e0fa49e397d6a16951a1b811bb7f77fb2ecbe7d8a3a36feb144cc934c895f","target":"graph","created_at":"2026-07-01T01:17:49Z","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/2604.01940/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Position-dependent diffusivities are central parameters in reduced stochastic descriptions of molecular transport in heterogeneous environments, but their reliable estimation from molecular dynamics simulations remains challenging. We present a residence-time approach (RTA) that extracts local diffusivities from first-exit statistics measured in biased simulations after compensation of the mean free-energy gradient. We apply the method to oxygen diffusion across a hexadecane/water slab, water permeation across a POPC lipid bilayer, and transport of water and volatile organic compounds through ","authors_text":"Michael von Domaros, Praveen Ranganath Prabhakar, Rinto Thomas","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":"2026-04-02T11:58:55Z","title":"A Residence-Time Approach for Determining Position-Dependent Diffusivities from Biased Molecular Simulations"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2604.01940","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:f82410d086e84a1eb890568aa2fe8c7e79860fd6dd376b428aff2d2523d692e5","target":"record","created_at":"2026-07-01T01:17:49Z","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":"1e125429816c8a5585e7580a39e924ab4c21585e8042a25fb9c0fbda7f17c747","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":"2026-04-02T11:58:55Z","title_canon_sha256":"79aa29e823ff08afb06bf0e4c8102b19e4724380358b37c75476a6bd12ec6904"},"schema_version":"1.0","source":{"id":"2604.01940","kind":"arxiv","version":2}},"canonical_sha256":"1cb4f404189361f8a35afc799194709da89b033eb1fe067fd53cbf2444a92140","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"1cb4f404189361f8a35afc799194709da89b033eb1fe067fd53cbf2444a92140","first_computed_at":"2026-07-01T01:17:49.941955Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-01T01:17:49.941955Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"3Dm0L0T6H+KLOa//5FX1Z+MJR0l5Rg4EZRtVJ3r7LdtEBvYgYULmGaMcYfjsx4yq5A3F5hK681DAkAF0M8iOBw==","signature_status":"signed_v1","signed_at":"2026-07-01T01:17:49.942468Z","signed_message":"canonical_sha256_bytes"},"source_id":"2604.01940","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:f82410d086e84a1eb890568aa2fe8c7e79860fd6dd376b428aff2d2523d692e5","sha256:754e0fa49e397d6a16951a1b811bb7f77fb2ecbe7d8a3a36feb144cc934c895f"],"state_sha256":"83cdd51ca9e828b1a961fe9f307488d2c9f70bf9a12730b8050291d54efe8259"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"oQHJwvRWVZQJ3NkseR3rAv5fCbWH7v1j85vuokaeBDgJGP6H62ZVxW9olVRs+ZRxSag4fa4q62lIrdS1mEfsBQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-21T07:43:38.834769Z","bundle_sha256":"1266f8cdb6b6dad36f20af20466c40e87852fda26c0a2f79066abd4f25033069"}}