{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:NN4GA5VLCSYGV4ROWVTES3YEAN","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":"6eb499d678b212e602688d577a4ff1fcf467be547f6e95a5d08dfaf4712d895c","cross_cats_sorted":["physics.bio-ph","physics.chem-ph"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.MN","submitted_at":"2024-04-22T16:55:35Z","title_canon_sha256":"4fef0adcc2c7e1f7cba2f6ffecaf4868b4307ca41b87a329892f9db289337408"},"schema_version":"1.0","source":{"id":"2404.14336","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2404.14336","created_at":"2026-07-05T08:11:04Z"},{"alias_kind":"arxiv_version","alias_value":"2404.14336v2","created_at":"2026-07-05T08:11:04Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2404.14336","created_at":"2026-07-05T08:11:04Z"},{"alias_kind":"pith_short_12","alias_value":"NN4GA5VLCSYG","created_at":"2026-07-05T08:11:04Z"},{"alias_kind":"pith_short_16","alias_value":"NN4GA5VLCSYGV4RO","created_at":"2026-07-05T08:11:04Z"},{"alias_kind":"pith_short_8","alias_value":"NN4GA5VL","created_at":"2026-07-05T08:11:04Z"}],"graph_snapshots":[{"event_id":"sha256:ed83f525a6158b7048184bf1e033630add170db41650eafbdabb0df565f42aa6","target":"graph","created_at":"2026-07-05T08:11:04Z","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/2404.14336/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Chemical reaction networks (CRNs) exhibit complex dynamics governed by their underlying network structure. In this paper, we propose a novel approach to study the dynamics of CRNs by representing them on species graphs (S-graphs). By scaling concentrations by conservation laws, we obtain a graph representation of transitions compatible with the S-graph, which allows us to treat the dynamics in CRNs as transitions between chemicals. We also define thermodynamic-like quantities on the S-graph from the introduced transitions and investigate their properties, including the relationship between spe","authors_text":"Dimitri Loutchko, Keisuke Sugie, Tetsuya J. Kobayashi","cross_cats":["physics.bio-ph","physics.chem-ph"],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.MN","submitted_at":"2024-04-22T16:55:35Z","title":"Transitions and Thermodynamics on Species Graphs of Chemical Reaction Networks"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2404.14336","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":"sha256:5a1d93fd90a557fc25dc3452b11a14070ca682d2e1b863b59d16c39df0a03184","target":"record","created_at":"2026-07-05T08:11:04Z","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":"6eb499d678b212e602688d577a4ff1fcf467be547f6e95a5d08dfaf4712d895c","cross_cats_sorted":["physics.bio-ph","physics.chem-ph"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.MN","submitted_at":"2024-04-22T16:55:35Z","title_canon_sha256":"4fef0adcc2c7e1f7cba2f6ffecaf4868b4307ca41b87a329892f9db289337408"},"schema_version":"1.0","source":{"id":"2404.14336","kind":"arxiv","version":2}},"canonical_sha256":"6b786076ab14b06af22eb566496f04036ae3c94e8a9ce14d631d5bacfb8f7389","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"6b786076ab14b06af22eb566496f04036ae3c94e8a9ce14d631d5bacfb8f7389","first_computed_at":"2026-07-05T08:11:04.999081Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T08:11:04.999081Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"QYeIlM/9HtG2tq80EJ+EHtfbnFFQ3UrU+mTI3jFjNCuBucEVB7Q3nQhG9I58CBgGd9/dyMZfgx3N+qk8RmNWCA==","signature_status":"signed_v1","signed_at":"2026-07-05T08:11:04.999625Z","signed_message":"canonical_sha256_bytes"},"source_id":"2404.14336","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:5a1d93fd90a557fc25dc3452b11a14070ca682d2e1b863b59d16c39df0a03184","sha256:ed83f525a6158b7048184bf1e033630add170db41650eafbdabb0df565f42aa6"],"state_sha256":"401a5e1bb88375671a9accd7dee39e9e94b4dcb6b0b97c7dd9e897492d2f58fa"}