{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2014:QZF4EFP3VUHDYBGMYBGZJRPXE3","short_pith_number":"pith:QZF4EFP3","canonical_record":{"source":{"id":"1401.0387","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/3.0/","primary_cat":"cond-mat.stat-mech","submitted_at":"2014-01-02T08:30:03Z","cross_cats_sorted":["physics.chem-ph","physics.comp-ph"],"title_canon_sha256":"ec9fd958b985fcbbda939bfb63dc2202c3fb2b896b038a2f57a15758bf877d82","abstract_canon_sha256":"da732f91553f905daf745a84955a5efb864ff26e37a9c2bf74e73368dbfd6147"},"schema_version":"1.0"},"canonical_sha256":"864bc215fbad0e3c04ccc04d94c5f726fa7db6d9f82b6bbc053cf1ba05ef1e91","source":{"kind":"arxiv","id":"1401.0387","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1401.0387","created_at":"2026-05-18T03:03:23Z"},{"alias_kind":"arxiv_version","alias_value":"1401.0387v1","created_at":"2026-05-18T03:03:23Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1401.0387","created_at":"2026-05-18T03:03:23Z"},{"alias_kind":"pith_short_12","alias_value":"QZF4EFP3VUHD","created_at":"2026-05-18T12:28:46Z"},{"alias_kind":"pith_short_16","alias_value":"QZF4EFP3VUHDYBGM","created_at":"2026-05-18T12:28:46Z"},{"alias_kind":"pith_short_8","alias_value":"QZF4EFP3","created_at":"2026-05-18T12:28:46Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2014:QZF4EFP3VUHDYBGMYBGZJRPXE3","target":"record","payload":{"canonical_record":{"source":{"id":"1401.0387","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/3.0/","primary_cat":"cond-mat.stat-mech","submitted_at":"2014-01-02T08:30:03Z","cross_cats_sorted":["physics.chem-ph","physics.comp-ph"],"title_canon_sha256":"ec9fd958b985fcbbda939bfb63dc2202c3fb2b896b038a2f57a15758bf877d82","abstract_canon_sha256":"da732f91553f905daf745a84955a5efb864ff26e37a9c2bf74e73368dbfd6147"},"schema_version":"1.0"},"canonical_sha256":"864bc215fbad0e3c04ccc04d94c5f726fa7db6d9f82b6bbc053cf1ba05ef1e91","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T03:03:23.339777Z","signature_b64":"EHzSlV4Bub3pFmp10P9Dkf96I2fT6Lkr3vC8GZAx6d22uB2APFYD0IbofgA57V4lkEhS5+MHYv1x60Qn2KjOBQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"864bc215fbad0e3c04ccc04d94c5f726fa7db6d9f82b6bbc053cf1ba05ef1e91","last_reissued_at":"2026-05-18T03:03:23.339109Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T03:03:23.339109Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1401.0387","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":"2026-05-18T03:03:23Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"Xttx2TqjNyv0Nm5ws5nhdtTe5vlj69TGXx/sImWWyisK42nUYEdS+2Tccz0PvbAQtiwObVFDwdXBUbHIfFhPAA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-07T19:17:12.417342Z"},"content_sha256":"d1841d746ef07d751d7604764e466693729a4a662d02a8547b24e288e0aaafe2","schema_version":"1.0","event_id":"sha256:d1841d746ef07d751d7604764e466693729a4a662d02a8547b24e288e0aaafe2"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2014:QZF4EFP3VUHDYBGMYBGZJRPXE3","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration","license":"http://creativecommons.org/licenses/by/3.0/","headline":"","cross_cats":["physics.chem-ph","physics.comp-ph"],"primary_cat":"cond-mat.stat-mech","authors_text":"Cameron Abrams, Giovanni Bussi","submitted_at":"2014-01-02T08:30:03Z","abstract_excerpt":"We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1401.0387","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":"2026-05-18T03:03:23Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"7iNi7QXwkF5U/KoulAxQFP4iBh7UO/0peuz+hX7L34R+Gz0nhofGXGQW8i54pUnvSzV2rMHDY9L1TbBm9X2yCQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-07T19:17:12.417982Z"},"content_sha256":"0d06f51ce1b4eb2cb3e9b0a9ba5395100394c19f4b09b701fc68ef449174c823","schema_version":"1.0","event_id":"sha256:0d06f51ce1b4eb2cb3e9b0a9ba5395100394c19f4b09b701fc68ef449174c823"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/QZF4EFP3VUHDYBGMYBGZJRPXE3/bundle.json","state_url":"https://pith.science/pith/QZF4EFP3VUHDYBGMYBGZJRPXE3/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/QZF4EFP3VUHDYBGMYBGZJRPXE3/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":"2026-06-07T19:17:12Z","links":{"resolver":"https://pith.science/pith/QZF4EFP3VUHDYBGMYBGZJRPXE3","bundle":"https://pith.science/pith/QZF4EFP3VUHDYBGMYBGZJRPXE3/bundle.json","state":"https://pith.science/pith/QZF4EFP3VUHDYBGMYBGZJRPXE3/state.json","well_known_bundle":"https://pith.science/.well-known/pith/QZF4EFP3VUHDYBGMYBGZJRPXE3/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2014:QZF4EFP3VUHDYBGMYBGZJRPXE3","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":"da732f91553f905daf745a84955a5efb864ff26e37a9c2bf74e73368dbfd6147","cross_cats_sorted":["physics.chem-ph","physics.comp-ph"],"license":"http://creativecommons.org/licenses/by/3.0/","primary_cat":"cond-mat.stat-mech","submitted_at":"2014-01-02T08:30:03Z","title_canon_sha256":"ec9fd958b985fcbbda939bfb63dc2202c3fb2b896b038a2f57a15758bf877d82"},"schema_version":"1.0","source":{"id":"1401.0387","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1401.0387","created_at":"2026-05-18T03:03:23Z"},{"alias_kind":"arxiv_version","alias_value":"1401.0387v1","created_at":"2026-05-18T03:03:23Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1401.0387","created_at":"2026-05-18T03:03:23Z"},{"alias_kind":"pith_short_12","alias_value":"QZF4EFP3VUHD","created_at":"2026-05-18T12:28:46Z"},{"alias_kind":"pith_short_16","alias_value":"QZF4EFP3VUHDYBGM","created_at":"2026-05-18T12:28:46Z"},{"alias_kind":"pith_short_8","alias_value":"QZF4EFP3","created_at":"2026-05-18T12:28:46Z"}],"graph_snapshots":[{"event_id":"sha256:0d06f51ce1b4eb2cb3e9b0a9ba5395100394c19f4b09b701fc68ef449174c823","target":"graph","created_at":"2026-05-18T03:03:23Z","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":"We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We","authors_text":"Cameron Abrams, Giovanni Bussi","cross_cats":["physics.chem-ph","physics.comp-ph"],"headline":"","license":"http://creativecommons.org/licenses/by/3.0/","primary_cat":"cond-mat.stat-mech","submitted_at":"2014-01-02T08:30:03Z","title":"Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1401.0387","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:d1841d746ef07d751d7604764e466693729a4a662d02a8547b24e288e0aaafe2","target":"record","created_at":"2026-05-18T03:03:23Z","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":"da732f91553f905daf745a84955a5efb864ff26e37a9c2bf74e73368dbfd6147","cross_cats_sorted":["physics.chem-ph","physics.comp-ph"],"license":"http://creativecommons.org/licenses/by/3.0/","primary_cat":"cond-mat.stat-mech","submitted_at":"2014-01-02T08:30:03Z","title_canon_sha256":"ec9fd958b985fcbbda939bfb63dc2202c3fb2b896b038a2f57a15758bf877d82"},"schema_version":"1.0","source":{"id":"1401.0387","kind":"arxiv","version":1}},"canonical_sha256":"864bc215fbad0e3c04ccc04d94c5f726fa7db6d9f82b6bbc053cf1ba05ef1e91","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"864bc215fbad0e3c04ccc04d94c5f726fa7db6d9f82b6bbc053cf1ba05ef1e91","first_computed_at":"2026-05-18T03:03:23.339109Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T03:03:23.339109Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"EHzSlV4Bub3pFmp10P9Dkf96I2fT6Lkr3vC8GZAx6d22uB2APFYD0IbofgA57V4lkEhS5+MHYv1x60Qn2KjOBQ==","signature_status":"signed_v1","signed_at":"2026-05-18T03:03:23.339777Z","signed_message":"canonical_sha256_bytes"},"source_id":"1401.0387","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:d1841d746ef07d751d7604764e466693729a4a662d02a8547b24e288e0aaafe2","sha256:0d06f51ce1b4eb2cb3e9b0a9ba5395100394c19f4b09b701fc68ef449174c823"],"state_sha256":"a76f2c9bb09d6981f0709810abb6c934706745e961e975854869e67dac2a81a2"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"n+KvYkybc78cG//tq4NB1Bfb2Dl5oUQf1naH2AKBhubX4Fdt79lgSJqAysO3t92+M2qaMAK3u8yn+hiQug1UBQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-06-07T19:17:12.421645Z","bundle_sha256":"7c84ab785d7ba0deb1794a25c334c0576ac24416fd78ae8fbd71144f589e5646"}}