{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2022:5N4NKAOKZJWJEQJ6C2POCK4C2M","short_pith_number":"pith:5N4NKAOK","canonical_record":{"source":{"id":"2207.02149","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2022-06-27T14:01:06Z","cross_cats_sorted":["cs.LG","physics.chem-ph"],"title_canon_sha256":"53783cd2b5ffd7206004d0a54c3797471abebfd71783f4db7bd3a210b5ba73ae","abstract_canon_sha256":"fb7498249d7d5291fcb9db53b46ab7d9c3ae95d87b52360e04ca929277f41989"},"schema_version":"1.0"},"canonical_sha256":"eb78d501caca6c92413e169ee12b82d31527e7e9b72efc5ddec99f7ca6016544","source":{"kind":"arxiv","id":"2207.02149","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2207.02149","created_at":"2026-07-05T06:31:29Z"},{"alias_kind":"arxiv_version","alias_value":"2207.02149v2","created_at":"2026-07-05T06:31:29Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2207.02149","created_at":"2026-07-05T06:31:29Z"},{"alias_kind":"pith_short_12","alias_value":"5N4NKAOKZJWJ","created_at":"2026-07-05T06:31:29Z"},{"alias_kind":"pith_short_16","alias_value":"5N4NKAOKZJWJEQJ6","created_at":"2026-07-05T06:31:29Z"},{"alias_kind":"pith_short_8","alias_value":"5N4NKAOK","created_at":"2026-07-05T06:31:29Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2022:5N4NKAOKZJWJEQJ6C2POCK4C2M","target":"record","payload":{"canonical_record":{"source":{"id":"2207.02149","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2022-06-27T14:01:06Z","cross_cats_sorted":["cs.LG","physics.chem-ph"],"title_canon_sha256":"53783cd2b5ffd7206004d0a54c3797471abebfd71783f4db7bd3a210b5ba73ae","abstract_canon_sha256":"fb7498249d7d5291fcb9db53b46ab7d9c3ae95d87b52360e04ca929277f41989"},"schema_version":"1.0"},"canonical_sha256":"eb78d501caca6c92413e169ee12b82d31527e7e9b72efc5ddec99f7ca6016544","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T06:31:29.106142Z","signature_b64":"oijXKa4ANIoY2t7u9nsqwMD1tjum8UTicX7aAymJkwm+FQE7niWxPHaLTGaHyOsfzDuL147GKojR58zA3WSsDw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"eb78d501caca6c92413e169ee12b82d31527e7e9b72efc5ddec99f7ca6016544","last_reissued_at":"2026-07-05T06:31:29.105646Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T06:31:29.105646Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2207.02149","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":"2026-07-05T06:31:29Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"8W/lDg9bmuH9GW7hmgn88Dm8YhO3fkudRnOntrLoWosn8xk+g2U+ogu6gH/9CG1Y3+vNIcPxcchPeSj0xyGsAQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T17:54:20.774139Z"},"content_sha256":"101eb7c9a8122162b24c69ac8f1e247fe90dc9e9b3b2197a8ba8ae7c77c2fecf","schema_version":"1.0","event_id":"sha256:101eb7c9a8122162b24c69ac8f1e247fe90dc9e9b3b2197a8ba8ae7c77c2fecf"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2022:5N4NKAOKZJWJEQJ6C2POCK4C2M","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Stochastic Optimal Control for Collective Variable Free Sampling of Molecular Transition Paths","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.LG","physics.chem-ph"],"primary_cat":"q-bio.BM","authors_text":"Bernd Ensing, Ferry Hooft, Lars Holdijk, Max Welling, Priyank Jaini, Yuanqi Du","submitted_at":"2022-06-27T14:01:06Z","abstract_excerpt":"We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy barriers separating the states, these transition paths are unlikely to be sampled with standard Molecular Dynamics (MD) simulation. Traditional methods to augment MD with a bias potential to increase the probability of the transition rely on a dimensionality reduction step based on Collective Variables (CVs). Unfortunately, selecting appropriate CVs requires chemic"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2207.02149","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/2207.02149/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":"2026-07-05T06:31:29Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"wvRm87pS6ndMx0YX7ojG1h8WvepSTqx1yyiOt3r5CG8zRxddfPO0M6ExHkicCEahQWVSrxhdJ/oCuksHiK63AA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T17:54:20.774844Z"},"content_sha256":"95b0a6d921ffc159ef79809f3f6d37c12aa916eb2a5234550ff04492628cf8ba","schema_version":"1.0","event_id":"sha256:95b0a6d921ffc159ef79809f3f6d37c12aa916eb2a5234550ff04492628cf8ba"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/5N4NKAOKZJWJEQJ6C2POCK4C2M/bundle.json","state_url":"https://pith.science/pith/5N4NKAOKZJWJEQJ6C2POCK4C2M/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/5N4NKAOKZJWJEQJ6C2POCK4C2M/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":"2026-08-04T17:54:20Z","links":{"resolver":"https://pith.science/pith/5N4NKAOKZJWJEQJ6C2POCK4C2M","bundle":"https://pith.science/pith/5N4NKAOKZJWJEQJ6C2POCK4C2M/bundle.json","state":"https://pith.science/pith/5N4NKAOKZJWJEQJ6C2POCK4C2M/state.json","well_known_bundle":"https://pith.science/.well-known/pith/5N4NKAOKZJWJEQJ6C2POCK4C2M/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2022:5N4NKAOKZJWJEQJ6C2POCK4C2M","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":"fb7498249d7d5291fcb9db53b46ab7d9c3ae95d87b52360e04ca929277f41989","cross_cats_sorted":["cs.LG","physics.chem-ph"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2022-06-27T14:01:06Z","title_canon_sha256":"53783cd2b5ffd7206004d0a54c3797471abebfd71783f4db7bd3a210b5ba73ae"},"schema_version":"1.0","source":{"id":"2207.02149","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2207.02149","created_at":"2026-07-05T06:31:29Z"},{"alias_kind":"arxiv_version","alias_value":"2207.02149v2","created_at":"2026-07-05T06:31:29Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2207.02149","created_at":"2026-07-05T06:31:29Z"},{"alias_kind":"pith_short_12","alias_value":"5N4NKAOKZJWJ","created_at":"2026-07-05T06:31:29Z"},{"alias_kind":"pith_short_16","alias_value":"5N4NKAOKZJWJEQJ6","created_at":"2026-07-05T06:31:29Z"},{"alias_kind":"pith_short_8","alias_value":"5N4NKAOK","created_at":"2026-07-05T06:31:29Z"}],"graph_snapshots":[{"event_id":"sha256:95b0a6d921ffc159ef79809f3f6d37c12aa916eb2a5234550ff04492628cf8ba","target":"graph","created_at":"2026-07-05T06:31:29Z","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/2207.02149/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy barriers separating the states, these transition paths are unlikely to be sampled with standard Molecular Dynamics (MD) simulation. Traditional methods to augment MD with a bias potential to increase the probability of the transition rely on a dimensionality reduction step based on Collective Variables (CVs). Unfortunately, selecting appropriate CVs requires chemic","authors_text":"Bernd Ensing, Ferry Hooft, Lars Holdijk, Max Welling, Priyank Jaini, Yuanqi Du","cross_cats":["cs.LG","physics.chem-ph"],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2022-06-27T14:01:06Z","title":"Stochastic Optimal Control for Collective Variable Free Sampling of Molecular Transition Paths"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2207.02149","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":"sha256:101eb7c9a8122162b24c69ac8f1e247fe90dc9e9b3b2197a8ba8ae7c77c2fecf","target":"record","created_at":"2026-07-05T06:31:29Z","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":"fb7498249d7d5291fcb9db53b46ab7d9c3ae95d87b52360e04ca929277f41989","cross_cats_sorted":["cs.LG","physics.chem-ph"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2022-06-27T14:01:06Z","title_canon_sha256":"53783cd2b5ffd7206004d0a54c3797471abebfd71783f4db7bd3a210b5ba73ae"},"schema_version":"1.0","source":{"id":"2207.02149","kind":"arxiv","version":2}},"canonical_sha256":"eb78d501caca6c92413e169ee12b82d31527e7e9b72efc5ddec99f7ca6016544","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"eb78d501caca6c92413e169ee12b82d31527e7e9b72efc5ddec99f7ca6016544","first_computed_at":"2026-07-05T06:31:29.105646Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T06:31:29.105646Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"oijXKa4ANIoY2t7u9nsqwMD1tjum8UTicX7aAymJkwm+FQE7niWxPHaLTGaHyOsfzDuL147GKojR58zA3WSsDw==","signature_status":"signed_v1","signed_at":"2026-07-05T06:31:29.106142Z","signed_message":"canonical_sha256_bytes"},"source_id":"2207.02149","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:101eb7c9a8122162b24c69ac8f1e247fe90dc9e9b3b2197a8ba8ae7c77c2fecf","sha256:95b0a6d921ffc159ef79809f3f6d37c12aa916eb2a5234550ff04492628cf8ba"],"state_sha256":"a3beb3a52f0fa52e7a7b52085d5d412ce4c864c529ca05c63ea1a8fe547cf3f3"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"hCDc5e2//UjHwbH6TLdN618qdzz7B5R7h3FriHAhEMtVqHQLDjrRy0FiTTgGg0abEMNUBtW4KAnMoplI4jg4Dg==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-04T17:54:20.779454Z","bundle_sha256":"78f49f4bd38e96b4a692bc99abb22c13e41667f7fed25d82e29b8f80e19b222a"}}