{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2018:G62FHK5P5BM6QTPDYYCYIGPVAG","short_pith_number":"pith:G62FHK5P","canonical_record":{"source":{"id":"1801.02362","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.CE","submitted_at":"2018-01-08T09:55:08Z","cross_cats_sorted":["cs.DC","cs.NA"],"title_canon_sha256":"08f1b9f63d80bb7fc5d987abcec6cd6bc0f46648f413442e073fb4b5772ef892","abstract_canon_sha256":"0635b72779d4393ae5651a1972ac61226b91e6b56dbf2852811e3c12a25996b1"},"schema_version":"1.0"},"canonical_sha256":"37b453abafe859e84de3c6058419f501a907e4606f97cb022899e8b7f2346109","source":{"kind":"arxiv","id":"1801.02362","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1801.02362","created_at":"2026-05-18T00:26:31Z"},{"alias_kind":"arxiv_version","alias_value":"1801.02362v1","created_at":"2026-05-18T00:26:31Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1801.02362","created_at":"2026-05-18T00:26:31Z"},{"alias_kind":"pith_short_12","alias_value":"G62FHK5P5BM6","created_at":"2026-05-18T12:32:25Z"},{"alias_kind":"pith_short_16","alias_value":"G62FHK5P5BM6QTPD","created_at":"2026-05-18T12:32:25Z"},{"alias_kind":"pith_short_8","alias_value":"G62FHK5P","created_at":"2026-05-18T12:32:25Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2018:G62FHK5P5BM6QTPDYYCYIGPVAG","target":"record","payload":{"canonical_record":{"source":{"id":"1801.02362","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.CE","submitted_at":"2018-01-08T09:55:08Z","cross_cats_sorted":["cs.DC","cs.NA"],"title_canon_sha256":"08f1b9f63d80bb7fc5d987abcec6cd6bc0f46648f413442e073fb4b5772ef892","abstract_canon_sha256":"0635b72779d4393ae5651a1972ac61226b91e6b56dbf2852811e3c12a25996b1"},"schema_version":"1.0"},"canonical_sha256":"37b453abafe859e84de3c6058419f501a907e4606f97cb022899e8b7f2346109","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T00:26:31.883256Z","signature_b64":"omTkcSJGBdVASxDqEDQfPsjfNmSZD0XJzXuGth3xJjhP+XqXqjb3IgNO7QBy7is4+sAKdRo9nTc1aWX2tIz7Bg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"37b453abafe859e84de3c6058419f501a907e4606f97cb022899e8b7f2346109","last_reissued_at":"2026-05-18T00:26:31.882776Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T00:26:31.882776Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1801.02362","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":"2026-05-18T00:26:31Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"+JJiH7n+61a9cEE+XkK8tSYO+qlFIia4eKdd8xccjE90M0I09jwTRtLzyvvwToMrjJC7Fq0Vt8fme2X80MdpAw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-21T17:49:59.463154Z"},"content_sha256":"9480331f330655e3c93c7b24be8e73f6d2a5cb86ffdd50d0dfd901301fd2370b","schema_version":"1.0","event_id":"sha256:9480331f330655e3c93c7b24be8e73f6d2a5cb86ffdd50d0dfd901301fd2370b"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2018:G62FHK5P5BM6QTPDYYCYIGPVAG","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.DC","cs.NA"],"primary_cat":"cs.CE","authors_text":"Ale\\v{s} K\\v{r}enek, Jana Paz\\'urikov\\'a, Jaroslav O\\v{l}ha, Vojt\\v{e}ch Spiwok","submitted_at":"2018-01-08T09:55:08Z","abstract_excerpt":"Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to \"push the~simulation forward\". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing the~simulated process. However, the~evaluation of these variables can include numerous mean square distance calculations that introduce substantial computational demands, thus jeopardize the~benefit of the~approach. Recently, we proposed an~approximative method that significantly reduces the~number of these distance calculations. Here we evaluate the~perfor"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1801.02362","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":"2026-05-18T00:26:31Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"LEtQ7zDvRE5IZIIGH4QQG+3LRMsSA8Z2V8ChTbTkdG6yoItGXw9Om+sRidDiePnrmY9BZhLexoTQPrWFkXcjDQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-21T17:49:59.463614Z"},"content_sha256":"f85f53350d37bddbfabb8e0bec7913f42d4c2111888dfc5a1da0e11482b6b5d2","schema_version":"1.0","event_id":"sha256:f85f53350d37bddbfabb8e0bec7913f42d4c2111888dfc5a1da0e11482b6b5d2"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/G62FHK5P5BM6QTPDYYCYIGPVAG/bundle.json","state_url":"https://pith.science/pith/G62FHK5P5BM6QTPDYYCYIGPVAG/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/G62FHK5P5BM6QTPDYYCYIGPVAG/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":"2026-08-21T17:49:59Z","links":{"resolver":"https://pith.science/pith/G62FHK5P5BM6QTPDYYCYIGPVAG","bundle":"https://pith.science/pith/G62FHK5P5BM6QTPDYYCYIGPVAG/bundle.json","state":"https://pith.science/pith/G62FHK5P5BM6QTPDYYCYIGPVAG/state.json","well_known_bundle":"https://pith.science/.well-known/pith/G62FHK5P5BM6QTPDYYCYIGPVAG/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2018:G62FHK5P5BM6QTPDYYCYIGPVAG","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":"0635b72779d4393ae5651a1972ac61226b91e6b56dbf2852811e3c12a25996b1","cross_cats_sorted":["cs.DC","cs.NA"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.CE","submitted_at":"2018-01-08T09:55:08Z","title_canon_sha256":"08f1b9f63d80bb7fc5d987abcec6cd6bc0f46648f413442e073fb4b5772ef892"},"schema_version":"1.0","source":{"id":"1801.02362","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1801.02362","created_at":"2026-05-18T00:26:31Z"},{"alias_kind":"arxiv_version","alias_value":"1801.02362v1","created_at":"2026-05-18T00:26:31Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1801.02362","created_at":"2026-05-18T00:26:31Z"},{"alias_kind":"pith_short_12","alias_value":"G62FHK5P5BM6","created_at":"2026-05-18T12:32:25Z"},{"alias_kind":"pith_short_16","alias_value":"G62FHK5P5BM6QTPD","created_at":"2026-05-18T12:32:25Z"},{"alias_kind":"pith_short_8","alias_value":"G62FHK5P","created_at":"2026-05-18T12:32:25Z"}],"graph_snapshots":[{"event_id":"sha256:f85f53350d37bddbfabb8e0bec7913f42d4c2111888dfc5a1da0e11482b6b5d2","target":"graph","created_at":"2026-05-18T00:26:31Z","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":"Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to \"push the~simulation forward\". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing the~simulated process. However, the~evaluation of these variables can include numerous mean square distance calculations that introduce substantial computational demands, thus jeopardize the~benefit of the~approach. Recently, we proposed an~approximative method that significantly reduces the~number of these distance calculations. Here we evaluate the~perfor","authors_text":"Ale\\v{s} K\\v{r}enek, Jana Paz\\'urikov\\'a, Jaroslav O\\v{l}ha, Vojt\\v{e}ch Spiwok","cross_cats":["cs.DC","cs.NA"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.CE","submitted_at":"2018-01-08T09:55:08Z","title":"Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1801.02362","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":"sha256:9480331f330655e3c93c7b24be8e73f6d2a5cb86ffdd50d0dfd901301fd2370b","target":"record","created_at":"2026-05-18T00:26:31Z","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":"0635b72779d4393ae5651a1972ac61226b91e6b56dbf2852811e3c12a25996b1","cross_cats_sorted":["cs.DC","cs.NA"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.CE","submitted_at":"2018-01-08T09:55:08Z","title_canon_sha256":"08f1b9f63d80bb7fc5d987abcec6cd6bc0f46648f413442e073fb4b5772ef892"},"schema_version":"1.0","source":{"id":"1801.02362","kind":"arxiv","version":1}},"canonical_sha256":"37b453abafe859e84de3c6058419f501a907e4606f97cb022899e8b7f2346109","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"37b453abafe859e84de3c6058419f501a907e4606f97cb022899e8b7f2346109","first_computed_at":"2026-05-18T00:26:31.882776Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T00:26:31.882776Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"omTkcSJGBdVASxDqEDQfPsjfNmSZD0XJzXuGth3xJjhP+XqXqjb3IgNO7QBy7is4+sAKdRo9nTc1aWX2tIz7Bg==","signature_status":"signed_v1","signed_at":"2026-05-18T00:26:31.883256Z","signed_message":"canonical_sha256_bytes"},"source_id":"1801.02362","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:9480331f330655e3c93c7b24be8e73f6d2a5cb86ffdd50d0dfd901301fd2370b","sha256:f85f53350d37bddbfabb8e0bec7913f42d4c2111888dfc5a1da0e11482b6b5d2"],"state_sha256":"9656458893edb7d3ac2903543eea49fe25a718929ff6a7c4741446c96abf47ba"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"vIekbalaIM6ctbfaSrDxgjIq2AD5Ue8HaBB1+uXfezVENDOB5XeAIn4zWYNExo2mLdSsRHp5Howed4RekJd0Dw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-21T17:49:59.467053Z","bundle_sha256":"02847d05c6312b213d911d1edcdf05a3e8d6d126304ff9b98edc16229b3e3720"}}