{
  "schema": "stromalytix.biofab-oxygen-verification/v1",
  "config": {
    "id": "biofab-static-gel-oxygen-v1",
    "question": "Which printed gel thickness should we test first, and does measured oxygen agree with the transport prediction?",
    "status": "Proposed reference experiment; actual cell lot, lab and hardware not yet confirmed",
    "cell_model": "HepG2/C3A engineering reference; not primary human hepatocytes",
    "material": "GelMA reference; actual lot, formulation and photocuring require qualification",
    "hardware_evidence": "Recovered September 1 founder photo inspected September 25: label says Creality CR-10, rated build size 300 x 300 x 400 mm. This identifies the donor printer; current motion, controller and conversion status require physical qualification.",
    "base_inputs": {
      "well_radius_mm": 3.2,
      "liquid_height_mm": 2.0,
      "gel_radius_mm": 0.8,
      "gel_height_mm": 0.2,
      "cells_per_ml": 10000000.0,
      "uptake_mol_cell_s": 4.76e-16,
      "km_mol_m3": 0.0063,
      "gel_diffusivity_m2_s": 2e-09,
      "medium_diffusivity_m2_s": 3.8e-09,
      "surface_oxygen_mol_m3": 0.18,
      "comparison_threshold_mol_m3": 0.02,
      "nr": 32,
      "nz": 40
    },
    "heights_mm": [
      0.2,
      0.6,
      1.0
    ],
    "sensitivity": {
      "uptake_mol_cell_s": [
        3e-17,
        4.76e-16
      ],
      "gel_diffusivity_m2_s": [
        1.5e-09,
        2.5e-09
      ],
      "surface_oxygen_mol_m3": [
        0.15,
        0.2
      ]
    },
    "parameter_provenance": [
      {
        "fields": [
          "uptake_mol_cell_s",
          "km_mol_m3",
          "medium_diffusivity_m2_s"
        ],
        "source": "bhise-2016",
        "location": "Numerical simulations, printed page 4",
        "status": "Published modeling assumptions, not measurements of our cell lot"
      },
      {
        "fields": [
          "sensitivity.uptake_mol_cell_s"
        ],
        "source": "existing-o2-library",
        "location": "qo2_011 plus Bhise modeling assumption",
        "status": "Sensitivity stress test spanning materially different literature assumptions; not a measured population interval"
      },
      {
        "fields": [
          "gel_diffusivity_m2_s",
          "sensitivity.gel_diffusivity_m2_s"
        ],
        "source": "existing-o2-library",
        "location": "do2_014 and do2_015",
        "status": "Estimated gel transport; direct measurement required"
      },
      {
        "fields": [
          "well_radius_mm",
          "liquid_height_mm",
          "gel_radius_mm",
          "heights_mm",
          "cells_per_ml",
          "surface_oxygen_mol_m3",
          "sensitivity.surface_oxygen_mol_m3",
          "comparison_threshold_mol_m3"
        ],
        "source": "proposed-design",
        "status": "Explicit engineering choices for this reference experiment, not extracted paper values or confirmed hardware dimensions"
      }
    ],
    "sources": [
      {
        "id": "bhise-2016",
        "title": "A liver-on-a-chip platform with bioprinted hepatic spheroids",
        "doi": "10.1088/1758-5090/8/1/014101",
        "pmid": "26756674",
        "url": "https://escholarship.org/content/qt9f546248/qt9f546248.pdf",
        "verified_at": "2026-09-25",
        "scope": "Published hepatic-printing context and transport-model assumptions; our geometry and boundary conditions differ"
      },
      {
        "id": "mcmurtrey-2016",
        "title": "Analytic Models of Oxygen and Nutrient Diffusion, Metabolism Dynamics, and Architecture Optimization in Three-Dimensional Tissue Constructs",
        "doi": "10.1089/ten.TEC.2015.0375",
        "pmid": "26650970",
        "url": "https://pubmed.ncbi.nlm.nih.gov/26650970/",
        "verified_at": "2026-09-25",
        "scope": "Dimensional diffusion/consumption framework; does not validate our numerical implementation or experiment"
      },
      {
        "id": "existing-o2-library",
        "path": "data/parameters/o2_transport.json",
        "scope": "Existing parameter assumptions, preserved with their uncertainty labels"
      }
    ],
    "assumptions": [
      "Axisymmetric printed cylinder with uniform cell density; individual spheroids are not resolved.",
      "Static well with zero oxygen flux through its floor and side wall; top concentration must be measured.",
      "Steady-state transport and constant cell number, not a time-course or a growth/death simulation.",
      "Gel and medium diffusivities are constant within each region; no flow, drug binding or remodeling.",
      "Gel/medium oxygen partition coefficient is assumed to be one, with zero interfacial resistance.",
      "The 20 micromolar line is an engineering comparison level, not an asserted survival threshold.",
      "Oxygen, viability, albumin, urea and CYP activity are distinct measurements. Only oxygen is predicted here."
    ],
    "execution_dependencies": [
      "CR-10 actual motion envelope, controller and conversion qualification",
      "syringe/nozzle and extrusion calibration",
      "plate SKU and measured well geometry",
      "cell lot and lab-approved culture SOP",
      "gel lot/formulation and calibrated photocuring",
      "oxygen measurement method and calibration",
      "qualified lab access"
    ]
  },
  "execution_fingerprint": {
    "code_sha256": {
      "core/oxygen_verification.py": "a8653a8f387d28a4fc0f982159fd38a0de35e28c3d4a06a013987bb6565daef0",
      "data/parameters/o2_transport.json": "8327612473d2e214ccc17ab0e30d19fbc6625cf05f579ef54fd321bc44696734"
    },
    "python": "3.13.13",
    "numpy": "2.4.2",
    "scipy": "1.17.1"
  },
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          "gel_height_mm": 0.2,
          "cells_per_ml": 10000000.0,
          "uptake_mol_cell_s": 4.76e-16,
          "km_mol_m3": 0.0063,
          "gel_diffusivity_m2_s": 2e-09,
          "medium_diffusivity_m2_s": 3.8e-09,
          "surface_oxygen_mol_m3": 0.18,
          "comparison_threshold_mol_m3": 0.02,
          "nr": 32,
          "nz": 40
        },
        "kinetics": "michaelis_menten",
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  "numerical_checks_passed": true,
  "biological_validation": "Not performed",
  "hardware_execution": "Not performed",
  "envelope_meaning": "Corners of explicit input assumptions, not a confidence interval",
  "result_sha256": "67f4272f0fb6bbf3042526484f0bc3862145a9949c2f4454d4079967165e2202",
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}