Parameter Provenance Audit — h09 Phase 4 + cross-hypothesis
Purpose: every hardcoded constant in models/hydrogel_phase*.py catalogued against its claimed source. Columns: parameter → value → claimed source → pdf-have? → target paper to download.
Status legend: ✅ sourced (pdf + paper note exist) · ⚠ claimed but no pdf · ❌ no claim, pure estimate.
Phase 1 — self-assembly (hydrogel_phase1_self_assembly.py)
Const Value Claimed source Status Target paper KB_T_KCAL0.593 @ 310K physical constant ✅ — COCHLEA_STB_LENGTH_MM32.0 cochlear anatomy ⚠ Salt simulator reference values BASAL_OHC_DEPTH_MM1.5 — ❌ Salt simulator APEX_DEPTH_MM30.0 — ❌ Salt simulator HTC_PER_STEREOCILIUM6 — ⚠ Verpy 2011 (have), Tobin 2019 (NEED) HTC_SPACING_NM8.0 — ⚠ Verpy 2011 SI, Tobin 2019 K_HTC_PN_PER_NM7.5 ”Tobin 2019” ⚠ Tobin 2019 — NEED WT_BUNDLE_STIFFNESS_PN_PER_NM1400 — ❌ Tobin 2019 / Beurg / Dulon — NEED HUMAN_SCALA_TYMPANI_VOLUME_UL70 — ⚠ Salt & Plontke simulator (NEED) BETA_STRAND_AA_LEN_NM0.35 — ✅ textbook constant
Phase 4d — F-actin bundling (hydrogel_phase4d_factin_bundling_model.py)
Const Value Claimed source Status Target paper WH2_KD_GACTIN_M100 nM ”Chereau 2005, Husson 2010” ⚠ Chereau 2005 PNAS — NEED · Husson 2010 — NEED WH2_KD_FACTIN_M5 μM ”estimated 5-25× weaker” ❌ NEED Pollard side-binding proteins reviewRADA16_MONOMERS_PER_NM_FIBRIL4.35 ”Zhang MIT” ⚠ Yokoi/Kinoshita/Zhang 2005 PNAS — NEED FACTIN_SUBUNITS_PER_NM13/36 ≈ 0.361 standard ✅ — FACTIN_DIAMETER_NM7.0 standard ✅ — FACTIN_PERSISTENCE_NM10000 standard Isambert ✅ — STEREOCILIA_INTER_FILAMENT_NM12.0 — ⚠ Barr-Gillespie proteomics / Tilney — NEED decision_volume_nm10.0 (inline) — ❌ geometry argument fibril_length_nm1000 — ⚠ RADA16 AFM length distribution
Phase 4e — Cochlear PK/PD (hydrogel_phase4e_cochlear_pkpd.py)
Const Value Claimed source Status Target paper PEPTIDE_MW_KDA14.2 computed ✅ — PERILYMPH_VOL_UL70 ”human cochlea” ⚠ Salt & Plontke — NEED K_CLEAR_MIDDLE_EAR0.35/h (t½ 2h) “mucociliary” ⚠ Salt RWM review — NEED K_RWM0.02/h for 14 kDa ”Salt 2011” ⚠ Salt 2011 RWM permeability — NEED K_PERILYMPH_CLEAR0.35/h ”cochlear aqueduct” ⚠ Salt simulator — NEED K_PROTEOLYSIS1.4/h (t½ 30min) “conservative” ❌ any PuraMatrix PK study — NEED KD_TMEM145_M100 nM ”Phase 3 ipTM 0.68” ❌ computational estimate — flag as such
Phase 4h — Endogenous STRC competition
Const Value Claimed source Status Target paper STRC_NORMAL_OHC_M1 μM — ⚠ Barr-Gillespie stereocilia proteomics — NEED E1659A Kd scenarios 10nM-1mM scan sensitivity analysis ✅ — (scenario scan, OK)
Cross-hypothesis parameters (reusable in h01, h02, h03, h05, h26)
These should live in literature-params/ so every hypothesis pulls from one canonical spot:
Parameter Candidates Hypotheses using Cochlear fluid volumes Salt & Plontke h01 (drug delivery), h03 (AAV spread), h05 (acoustic), h09 RWM permeability by MW Salt 2011 h03, h04 (mRNA), h06, h09 Stereocilia actin geometry Barr-Gillespie, Tilney h02 (piezo), h03, h09, h26 Stereocilia stiffness WT Tobin 2019, Dulon 2019 h02, h03, h09, h26 STRC-TMEM145 Kd (real SPR) Derstroff SI, Verpy SI h03, h09, h26 WH2 × G-actin kinetics Chereau 2005, Husson 2010, Pollard h09, any actin binder RADA16 β-sheet geometry Zhang 1993, Yokoi 2005 h09 only Peptide proteolysis in perilymph PuraMatrix, Landegger h09, h06
Delegated retrieval assignments (2026-04-23)
Domain 1 — Cochlear PK/PD → Sonnet agent (target: Salt, Plontke, Landegger, Borenstein)Domain 2 — Actin / WH2 → Sonnet agent (target: Chereau, Husson, Pollard, Barr-Gillespie)Domain 3 — Stereocilia biomech → Sonnet agent (target: Tobin 2019, Verpy SI, Derstroff SI)Domain 4 — RADA16 materials → Sonnet agent (target: Zhang 1993, Yokoi 2005, PuraMatrix, Stupp)
Each agent writes to shared /tmp/strc-lit-params-domain{N}.md. After all return, consolidate into literature-params/*.md topic files.
Connections