{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2025:S6GXUHIR662DFXREJBNMYTWBXY","short_pith_number":"pith:S6GXUHIR","canonical_record":{"source":{"id":"2504.13575","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"physics.comp-ph","submitted_at":"2025-04-18T09:19:09Z","cross_cats_sorted":[],"title_canon_sha256":"f9164589307b9e1959ff4b958863b989af71511f014ccca6b7cd0592d997ee69","abstract_canon_sha256":"dfac93d3b9a0b6ea9791b0fe43a8ef3e6365fd4422ab247de1fc82e183ba6a1a"},"schema_version":"1.0"},"canonical_sha256":"978d7a1d11f7b432de24485acc4ec1be3dfff28418ef0b23dd4a8476c8491473","source":{"kind":"arxiv","id":"2504.13575","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2504.13575","created_at":"2026-07-05T10:50:58Z"},{"alias_kind":"arxiv_version","alias_value":"2504.13575v1","created_at":"2026-07-05T10:50:58Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2504.13575","created_at":"2026-07-05T10:50:58Z"},{"alias_kind":"pith_short_12","alias_value":"S6GXUHIR662D","created_at":"2026-07-05T10:50:58Z"},{"alias_kind":"pith_short_16","alias_value":"S6GXUHIR662DFXRE","created_at":"2026-07-05T10:50:58Z"},{"alias_kind":"pith_short_8","alias_value":"S6GXUHIR","created_at":"2026-07-05T10:50:58Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2025:S6GXUHIR662DFXREJBNMYTWBXY","target":"record","payload":{"canonical_record":{"source":{"id":"2504.13575","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"physics.comp-ph","submitted_at":"2025-04-18T09:19:09Z","cross_cats_sorted":[],"title_canon_sha256":"f9164589307b9e1959ff4b958863b989af71511f014ccca6b7cd0592d997ee69","abstract_canon_sha256":"dfac93d3b9a0b6ea9791b0fe43a8ef3e6365fd4422ab247de1fc82e183ba6a1a"},"schema_version":"1.0"},"canonical_sha256":"978d7a1d11f7b432de24485acc4ec1be3dfff28418ef0b23dd4a8476c8491473","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T10:50:58.354932Z","signature_b64":"DprVMPEu8gL3EJabnVOQaBC5RgAZjRhlbDR9lEWIrxf+LP5DhIZRfl65/yTyknmtDLPpm8I15yd66p5Y1jYDDg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"978d7a1d11f7b432de24485acc4ec1be3dfff28418ef0b23dd4a8476c8491473","last_reissued_at":"2026-07-05T10:50:58.354459Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T10:50:58.354459Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2504.13575","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":"2026-07-05T10:50:58Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"G/RFpPTqyTeANN/Zfu1V6MMSDJXBUSWepRRMmHzmmMrwpoe0vegAkt8ZSVp623fu3fOOHpMU2PD9bLYyAw2NBw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-03T18:08:40.002766Z"},"content_sha256":"c1c1c6c1b6d64caa3ebb0010b3e1981277ba9d64fbe4625668b10f617e499813","schema_version":"1.0","event_id":"sha256:c1c1c6c1b6d64caa3ebb0010b3e1981277ba9d64fbe4625668b10f617e499813"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2025:S6GXUHIR662DFXREJBNMYTWBXY","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Autodifferentiable Geometric Restraints for Enhanced Sampling Simulations with Classical and Machine Learned Force Fields","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"physics.comp-ph","authors_text":"Cintia A. Menendez, Gustavo R. P\\'erez-Lemus, Juan J. de Pablo, Pablo F. Zubieta Rico, Yezhi Jin, Yinan Xu","submitted_at":"2025-04-18T09:19:09Z","abstract_excerpt":"The use of external restraints is ubiquitous in advanced molecular simulation techniques. In general, restraints serve to reduce the configurational space that is available for sampling, thereby reducing the computational demands associated with a given simulations. Examples include the use of positional restraints in docking simulations or positional restraints in studies of catalysis. Past work has sought to couple complex restraining potentials with enhanced sampling methods, including Metadynamics or Extended Adaptive Biasing Force approaches. Here, we introduce the use of more general geo"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2504.13575","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":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2504.13575/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":"2026-07-05T10:50:58Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"IbEGtbkpq6WTZrkWHXHHn6zTInpSUFOE4QSM1cAX8u4uLAfBo2yNz/insmErE7Ms3LgV2UNb+6P9MU5luUsJBw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-03T18:08:40.003920Z"},"content_sha256":"f6e1448b4d29904c3401c83f7e5b13a5d2c563ed9e175763de71ba60ca62f145","schema_version":"1.0","event_id":"sha256:f6e1448b4d29904c3401c83f7e5b13a5d2c563ed9e175763de71ba60ca62f145"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/S6GXUHIR662DFXREJBNMYTWBXY/bundle.json","state_url":"https://pith.science/pith/S6GXUHIR662DFXREJBNMYTWBXY/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/S6GXUHIR662DFXREJBNMYTWBXY/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":"2026-08-03T18:08:40Z","links":{"resolver":"https://pith.science/pith/S6GXUHIR662DFXREJBNMYTWBXY","bundle":"https://pith.science/pith/S6GXUHIR662DFXREJBNMYTWBXY/bundle.json","state":"https://pith.science/pith/S6GXUHIR662DFXREJBNMYTWBXY/state.json","well_known_bundle":"https://pith.science/.well-known/pith/S6GXUHIR662DFXREJBNMYTWBXY/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:S6GXUHIR662DFXREJBNMYTWBXY","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":"dfac93d3b9a0b6ea9791b0fe43a8ef3e6365fd4422ab247de1fc82e183ba6a1a","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"physics.comp-ph","submitted_at":"2025-04-18T09:19:09Z","title_canon_sha256":"f9164589307b9e1959ff4b958863b989af71511f014ccca6b7cd0592d997ee69"},"schema_version":"1.0","source":{"id":"2504.13575","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2504.13575","created_at":"2026-07-05T10:50:58Z"},{"alias_kind":"arxiv_version","alias_value":"2504.13575v1","created_at":"2026-07-05T10:50:58Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2504.13575","created_at":"2026-07-05T10:50:58Z"},{"alias_kind":"pith_short_12","alias_value":"S6GXUHIR662D","created_at":"2026-07-05T10:50:58Z"},{"alias_kind":"pith_short_16","alias_value":"S6GXUHIR662DFXRE","created_at":"2026-07-05T10:50:58Z"},{"alias_kind":"pith_short_8","alias_value":"S6GXUHIR","created_at":"2026-07-05T10:50:58Z"}],"graph_snapshots":[{"event_id":"sha256:f6e1448b4d29904c3401c83f7e5b13a5d2c563ed9e175763de71ba60ca62f145","target":"graph","created_at":"2026-07-05T10:50:58Z","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/2504.13575/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"The use of external restraints is ubiquitous in advanced molecular simulation techniques. In general, restraints serve to reduce the configurational space that is available for sampling, thereby reducing the computational demands associated with a given simulations. Examples include the use of positional restraints in docking simulations or positional restraints in studies of catalysis. Past work has sought to couple complex restraining potentials with enhanced sampling methods, including Metadynamics or Extended Adaptive Biasing Force approaches. Here, we introduce the use of more general geo","authors_text":"Cintia A. Menendez, Gustavo R. P\\'erez-Lemus, Juan J. de Pablo, Pablo F. Zubieta Rico, Yezhi Jin, Yinan Xu","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"physics.comp-ph","submitted_at":"2025-04-18T09:19:09Z","title":"Autodifferentiable Geometric Restraints for Enhanced Sampling Simulations with Classical and Machine Learned Force Fields"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2504.13575","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:c1c1c6c1b6d64caa3ebb0010b3e1981277ba9d64fbe4625668b10f617e499813","target":"record","created_at":"2026-07-05T10:50:58Z","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":"dfac93d3b9a0b6ea9791b0fe43a8ef3e6365fd4422ab247de1fc82e183ba6a1a","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"physics.comp-ph","submitted_at":"2025-04-18T09:19:09Z","title_canon_sha256":"f9164589307b9e1959ff4b958863b989af71511f014ccca6b7cd0592d997ee69"},"schema_version":"1.0","source":{"id":"2504.13575","kind":"arxiv","version":1}},"canonical_sha256":"978d7a1d11f7b432de24485acc4ec1be3dfff28418ef0b23dd4a8476c8491473","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"978d7a1d11f7b432de24485acc4ec1be3dfff28418ef0b23dd4a8476c8491473","first_computed_at":"2026-07-05T10:50:58.354459Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T10:50:58.354459Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"DprVMPEu8gL3EJabnVOQaBC5RgAZjRhlbDR9lEWIrxf+LP5DhIZRfl65/yTyknmtDLPpm8I15yd66p5Y1jYDDg==","signature_status":"signed_v1","signed_at":"2026-07-05T10:50:58.354932Z","signed_message":"canonical_sha256_bytes"},"source_id":"2504.13575","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:c1c1c6c1b6d64caa3ebb0010b3e1981277ba9d64fbe4625668b10f617e499813","sha256:f6e1448b4d29904c3401c83f7e5b13a5d2c563ed9e175763de71ba60ca62f145"],"state_sha256":"ad4f14c92687f40d7d83858abe1ba93aa62fd0d107e98b48c1ca70a31d2778cd"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"cc3eCc8WliNrrzY3Ax9THSgBkktAiYBkCU+1kUe+qFAJX3M+TA3vetXxeWZfCbDiXzU70nb0gVoYGyjcKj0QAw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-03T18:08:40.008659Z","bundle_sha256":"ec92ae70d22d49d8121e029c22bfe5e372c8a98eecfce703ac7e9769a7ca7e04"}}