{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2016:T3PHHPBRBLO2CQSNG74JFB4A45","short_pith_number":"pith:T3PHHPBR","canonical_record":{"source":{"id":"1605.07090","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.soft","submitted_at":"2016-05-23T16:49:33Z","cross_cats_sorted":["physics.chem-ph","q-bio.BM"],"title_canon_sha256":"0de39046f921230d523de1c3022031547ea39ec05e3cd266ce1354326bff6a02","abstract_canon_sha256":"0cd306ac8a98e70ef23084f580d9714ce5ade19d084691bf1885154c3f389335"},"schema_version":"1.0"},"canonical_sha256":"9ede73bc310adda1424d37f8928780e74e2a3c6a95ed58cdb92a242c352cddf2","source":{"kind":"arxiv","id":"1605.07090","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1605.07090","created_at":"2026-05-18T01:08:09Z"},{"alias_kind":"arxiv_version","alias_value":"1605.07090v1","created_at":"2026-05-18T01:08:09Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1605.07090","created_at":"2026-05-18T01:08:09Z"},{"alias_kind":"pith_short_12","alias_value":"T3PHHPBRBLO2","created_at":"2026-05-18T12:30:44Z"},{"alias_kind":"pith_short_16","alias_value":"T3PHHPBRBLO2CQSN","created_at":"2026-05-18T12:30:44Z"},{"alias_kind":"pith_short_8","alias_value":"T3PHHPBR","created_at":"2026-05-18T12:30:44Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2016:T3PHHPBRBLO2CQSNG74JFB4A45","target":"record","payload":{"canonical_record":{"source":{"id":"1605.07090","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.soft","submitted_at":"2016-05-23T16:49:33Z","cross_cats_sorted":["physics.chem-ph","q-bio.BM"],"title_canon_sha256":"0de39046f921230d523de1c3022031547ea39ec05e3cd266ce1354326bff6a02","abstract_canon_sha256":"0cd306ac8a98e70ef23084f580d9714ce5ade19d084691bf1885154c3f389335"},"schema_version":"1.0"},"canonical_sha256":"9ede73bc310adda1424d37f8928780e74e2a3c6a95ed58cdb92a242c352cddf2","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T01:08:09.249231Z","signature_b64":"1s3wtHmh2Ph9epARBJNDtoNpabhnVhOSWBWWbadSIrTCHCrG/p8Bkh0TMpL/L02vCWsREZHPEILbY1wow5yOBA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"9ede73bc310adda1424d37f8928780e74e2a3c6a95ed58cdb92a242c352cddf2","last_reissued_at":"2026-05-18T01:08:09.248869Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T01:08:09.248869Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1605.07090","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":"2026-05-18T01:08:09Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"Lqdj598twRGFgrenXaL6/fNSEiQ3Gullj3bBnXyGfjtGY3vdEvHqTIx7I4OQREognX6xBOsqJpU2rPh5GWdOCw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-28T19:52:40.655614Z"},"content_sha256":"638cec9d3638929aef0bfe6d4ae325d5e9a95c55287783ce325e795583e619a1","schema_version":"1.0","event_id":"sha256:638cec9d3638929aef0bfe6d4ae325d5e9a95c55287783ce325e795583e619a1"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2016:T3PHHPBRBLO2CQSNG74JFB4A45","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"How wet should be the reaction coordinate for ligand unbinding?","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["physics.chem-ph","q-bio.BM"],"primary_cat":"cond-mat.soft","authors_text":"B. J. Berne, Pratyush Tiwary","submitted_at":"2016-05-23T16:49:33Z","abstract_excerpt":"We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) (Tiwary and Berne, Proc. Natl. Acad. Sci 2016, 113, 2839 (2016)), to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Usin"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1605.07090","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":"2026-05-18T01:08:09Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"O5QA9A7gMJBA/Vh41ND8aaK95gm5XnIGUpWB8lGOtc3tv6A9KGHLxVZyAxithbHBuCQeF0jtYfWYMXHDmqAHBA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-28T19:52:40.656342Z"},"content_sha256":"845822ffc0b0ffbe23bb6f2c62925f678c89fa0800ab99f798a7ebcd2ecc07de","schema_version":"1.0","event_id":"sha256:845822ffc0b0ffbe23bb6f2c62925f678c89fa0800ab99f798a7ebcd2ecc07de"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/T3PHHPBRBLO2CQSNG74JFB4A45/bundle.json","state_url":"https://pith.science/pith/T3PHHPBRBLO2CQSNG74JFB4A45/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/T3PHHPBRBLO2CQSNG74JFB4A45/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":"2026-05-28T19:52:40Z","links":{"resolver":"https://pith.science/pith/T3PHHPBRBLO2CQSNG74JFB4A45","bundle":"https://pith.science/pith/T3PHHPBRBLO2CQSNG74JFB4A45/bundle.json","state":"https://pith.science/pith/T3PHHPBRBLO2CQSNG74JFB4A45/state.json","well_known_bundle":"https://pith.science/.well-known/pith/T3PHHPBRBLO2CQSNG74JFB4A45/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2016:T3PHHPBRBLO2CQSNG74JFB4A45","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":"0cd306ac8a98e70ef23084f580d9714ce5ade19d084691bf1885154c3f389335","cross_cats_sorted":["physics.chem-ph","q-bio.BM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.soft","submitted_at":"2016-05-23T16:49:33Z","title_canon_sha256":"0de39046f921230d523de1c3022031547ea39ec05e3cd266ce1354326bff6a02"},"schema_version":"1.0","source":{"id":"1605.07090","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1605.07090","created_at":"2026-05-18T01:08:09Z"},{"alias_kind":"arxiv_version","alias_value":"1605.07090v1","created_at":"2026-05-18T01:08:09Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1605.07090","created_at":"2026-05-18T01:08:09Z"},{"alias_kind":"pith_short_12","alias_value":"T3PHHPBRBLO2","created_at":"2026-05-18T12:30:44Z"},{"alias_kind":"pith_short_16","alias_value":"T3PHHPBRBLO2CQSN","created_at":"2026-05-18T12:30:44Z"},{"alias_kind":"pith_short_8","alias_value":"T3PHHPBR","created_at":"2026-05-18T12:30:44Z"}],"graph_snapshots":[{"event_id":"sha256:845822ffc0b0ffbe23bb6f2c62925f678c89fa0800ab99f798a7ebcd2ecc07de","target":"graph","created_at":"2026-05-18T01:08:09Z","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 use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) (Tiwary and Berne, Proc. Natl. Acad. Sci 2016, 113, 2839 (2016)), to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Usin","authors_text":"B. J. Berne, Pratyush Tiwary","cross_cats":["physics.chem-ph","q-bio.BM"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.soft","submitted_at":"2016-05-23T16:49:33Z","title":"How wet should be the reaction coordinate for ligand unbinding?"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1605.07090","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":"sha256:638cec9d3638929aef0bfe6d4ae325d5e9a95c55287783ce325e795583e619a1","target":"record","created_at":"2026-05-18T01:08:09Z","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":"0cd306ac8a98e70ef23084f580d9714ce5ade19d084691bf1885154c3f389335","cross_cats_sorted":["physics.chem-ph","q-bio.BM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.soft","submitted_at":"2016-05-23T16:49:33Z","title_canon_sha256":"0de39046f921230d523de1c3022031547ea39ec05e3cd266ce1354326bff6a02"},"schema_version":"1.0","source":{"id":"1605.07090","kind":"arxiv","version":1}},"canonical_sha256":"9ede73bc310adda1424d37f8928780e74e2a3c6a95ed58cdb92a242c352cddf2","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"9ede73bc310adda1424d37f8928780e74e2a3c6a95ed58cdb92a242c352cddf2","first_computed_at":"2026-05-18T01:08:09.248869Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T01:08:09.248869Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"1s3wtHmh2Ph9epARBJNDtoNpabhnVhOSWBWWbadSIrTCHCrG/p8Bkh0TMpL/L02vCWsREZHPEILbY1wow5yOBA==","signature_status":"signed_v1","signed_at":"2026-05-18T01:08:09.249231Z","signed_message":"canonical_sha256_bytes"},"source_id":"1605.07090","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:638cec9d3638929aef0bfe6d4ae325d5e9a95c55287783ce325e795583e619a1","sha256:845822ffc0b0ffbe23bb6f2c62925f678c89fa0800ab99f798a7ebcd2ecc07de"],"state_sha256":"2b9fa0845ae2d9c298eda64622fca93470f9268cbb8c42920ef6765166da14af"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"UsJZ37gDgSKMov8w2Dz+yJCcLO735zLzqTycFiAilj1u1QFhLK26DoO0SbmiCUWeLJw7oGxJpW63PnZEwrqzBw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-28T19:52:40.659955Z","bundle_sha256":"0f22b1c2271879d7d0ee536c6cda8e57b630650db9da25b1bdc33ede55890f0e"}}