{
  "kind": "executed computational sensitivity; not biological validation",
  "question": "How does assumed cell\u2013matrix contact energy change organization of an idealized hepatic cell cluster at a gel interface?",
  "use_case": "HepG2/C3A\u2013GelMA liver-tissue design context; generic cells and a rigid matrix surface, not a calibrated cell line or gel formulation",
  "relationship_to_oxygen": "Complementary mechanism test, NOT coupled to the saved whole-gel oxygen solution",
  "geometry": {
    "lattice": [
      40,
      40,
      28
    ],
    "matrix_z": [
      0,
      3
    ],
    "cells": 18,
    "target_cell_volume_voxels": 125
  },
  "units": {
    "length": "lattice sites; no micrometre mapping",
    "time": "Monte Carlo steps; no hour mapping",
    "contact_energy": "model units; no ligand-density or stiffness mapping"
  },
  "fixed_parameters": {
    "J_cell_cell": 8,
    "J_cell_medium": 16,
    "J_matrix_medium": 16,
    "temperature": 5,
    "lambda_volume": 4,
    "neighbor_order": 2,
    "steps": 600,
    "processors": 1
  },
  "conditions": {
    "matrix_favoring": 2,
    "matrix_disfavoring": 24
  },
  "seeds": [
    17,
    29,
    43
  ],
  "excluded_mechanisms": [
    "growth",
    "death",
    "oxygen",
    "gel elasticity",
    "remodeling",
    "fluid flow",
    "hepatic function"
  ],
  "sources": [
    "https://compucell3dreferencemanual.readthedocs.io/en/latest/contact_plugin.html",
    "https://compucell3dreferencemanual.readthedocs.io/en/4.9.0/connectivity.html"
  ],
  "acceptance": [
    "18 connected cells persist in every exported frame",
    "cell volumes remain within 10% of target",
    "frozen matrix does not change",
    "no cell touches non-matrix domain boundary",
    "same-seed repeat matches saved arrays and metrics",
    "report all seed outcomes without selecting a winner"
  ],
  "source_hashes": {
    "run.py": "7db0d71f7ddd24da2afde1bc1dbcd0ce3942f9d866fb68b66d9e7d9ac6e12c58",
    "steppable.py": "24bf3e40203704d51587c361b4ad730701f94aed952228fc9b35493c8553f17b"
  },
  "runs": [
    {
      "directory": "matrix_favoring-17",
      "J_cell_matrix": 2,
      "seed": 17,
      "completion": {
        "engine": "CompuCell3D",
        "version": "4.6.0",
        "last_mcs": 600,
        "frames": 13
      }
    },
    {
      "directory": "matrix_favoring-29",
      "J_cell_matrix": 2,
      "seed": 29,
      "completion": {
        "engine": "CompuCell3D",
        "version": "4.6.0",
        "last_mcs": 600,
        "frames": 13
      }
    },
    {
      "directory": "matrix_favoring-43",
      "J_cell_matrix": 2,
      "seed": 43,
      "completion": {
        "engine": "CompuCell3D",
        "version": "4.6.0",
        "last_mcs": 600,
        "frames": 13
      }
    },
    {
      "directory": "matrix_disfavoring-17",
      "J_cell_matrix": 24,
      "seed": 17,
      "completion": {
        "engine": "CompuCell3D",
        "version": "4.6.0",
        "last_mcs": 600,
        "frames": 13
      }
    },
    {
      "directory": "matrix_disfavoring-29",
      "J_cell_matrix": 24,
      "seed": 29,
      "completion": {
        "engine": "CompuCell3D",
        "version": "4.6.0",
        "last_mcs": 600,
        "frames": 13
      }
    },
    {
      "directory": "matrix_disfavoring-43",
      "J_cell_matrix": 24,
      "seed": 43,
      "completion": {
        "engine": "CompuCell3D",
        "version": "4.6.0",
        "last_mcs": 600,
        "frames": 13
      }
    },
    {
      "directory": "matrix_favoring_repeat-17",
      "J_cell_matrix": 2,
      "seed": 17,
      "completion": {
        "engine": "CompuCell3D",
        "version": "4.6.0",
        "last_mcs": 600,
        "frames": 13
      }
    }
  ]
}