{
  "schema_version": "2.0",
  "released_on": "2026-07-14",
  "release": {
    "version": "1.0.0",
    "data_revision": "e62ffa1e99122f8fbbeb3df7586f4050c4ff5c58",
    "manuscript_science_revision": "fde25e17187bc3f247b36ce411f6f14eb93d52cf",
    "figure_source_revision": "c0bfc431a19b81b1c45363dea472c29a745ad055",
    "simulator_revision": "7c2a09b24fdebb9000b9b996eb34150d6de5ed17"
  },
  "paper": {
    "title": "Chemotaxis models with signal-dependent sensitivity and a logistic-type source. III: Bifurcation",
    "authors": [
      "Le Chen",
      "Ian Ruau",
      "Wenxian Shen"
    ],
    "manuscript_working_file": "04-02-2026-CRS-3.tex",
    "status": "active submission manuscript"
  },
  "evidence_policy": {
    "validated_current": "The named artifact passed the checks frozen in this manifest and may support only its stated semidiscrete claim.",
    "provenance_only": "The object is retained to document earlier work but is excluded from the reader-facing numerical evidence."
  },
  "stationary_validation": {
    "id": "paper3-stationary-continuation-v1",
    "title": "Amplitude-constrained stationary continuation",
    "status": "validated_current",
    "quantitative_use": true,
    "claim_scope": "Finite-difference validation of the local branch direction and the coefficient beta_n0/alpha_n0 for four Paper III parameter sets.",
    "bundle_path": "docs/results/paper-iii/stationary-continuation/v1",
    "checksums_path": "docs/results/paper-iii/stationary-continuation/v1/SHA256SUMS",
    "method": "Prescribe the signed first-cosine amplitude, solve the stationary equations, and fit chi-chi_star_disc=c2*A^2+c4*A^4.",
    "design": {
      "meshes": [
        40,
        80,
        160
      ],
      "amplitudes": [
        -0.02,
        -0.01,
        -0.005,
        -0.0025,
        0.0025,
        0.005,
        0.01,
        0.02
      ],
      "state_count": 96
    },
    "acceptance": {
      "passed": true,
      "gates_passed": 780,
      "gates_total": 780,
      "max_full_stationary_residual": 8.50945980346296e-11,
      "max_elliptic_residual": 1.1404210908949608e-10,
      "max_mass_error": 3.3306690738754696e-16,
      "observed_order_min": 1.9984495528615873,
      "observed_order_max": 2.009423448648791
    },
    "paper_figure_id": "paper3-stationary-continuation",
    "paper_figure": {
      "source_manuscript_commit": "fde25e17187bc3f247b36ce411f6f14eb93d52cf",
      "preview_path": "docs/assets/images/paper3-stationary-continuation.png",
      "preview_sha256": "3560d2ccd1fa46737d6ee8b236ef54236cadfa4b40db9de1a57b852db466e08c",
      "vector_path": "docs/assets/images/paper3-stationary-continuation.pdf",
      "vector_sha256": "432761bcdadd6cca9d06954c533eec7c1334ea5d26cfd4b8d5e4714b0b25e7d7"
    },
    "cases": [
      {
        "id": "nonminimal-a10-beta0",
        "title": "Non-minimal a=10, beta=0",
        "classification": "supercritical",
        "alpha_n0": 9.080003316496247,
        "beta_n0": 0.07650308051520315,
        "theory_c2": 0.00842544631852886,
        "fits": [
          {
            "mesh": 40,
            "c2": 0.008370760765781244,
            "observed_order": null
          },
          {
            "mesh": 80,
            "c2": 0.008411801148577492,
            "observed_order": 2.0027693774459787
          },
          {
            "mesh": 160,
            "c2": 0.008422057235434008,
            "observed_order": 2.009423448648791
          }
        ]
      },
      {
        "id": "nonminimal-beta3",
        "title": "Non-minimal beta=3",
        "classification": "subcritical",
        "alpha_n0": 0.1135000414562031,
        "beta_n0": -2.232172436126313,
        "theory_c2": -19.666710315587455,
        "fits": [
          {
            "mesh": 40,
            "c2": -19.318560593702777,
            "observed_order": null
          },
          {
            "mesh": 80,
            "c2": -19.579579296748616,
            "observed_order": 1.9984495528615873
          },
          {
            "mesh": 160,
            "c2": -19.64492609095355,
            "observed_order": 1.9999026486399063
          }
        ]
      },
      {
        "id": "minimal-m1-g1",
        "title": "Minimal m=1, gamma=1",
        "classification": "supercritical",
        "alpha_n0": 0.4540001658248124,
        "beta_n0": 0.8730377411877027,
        "theory_c2": 1.9229899169785474,
        "fits": [
          {
            "mesh": 40,
            "c2": 1.9130168027041174,
            "observed_order": null
          },
          {
            "mesh": 80,
            "c2": 1.9204956382538594,
            "observed_order": 1.9994213920153865
          },
          {
            "mesh": 160,
            "c2": 1.92236644735955,
            "observed_order": 2.0002315231020047
          }
        ]
      },
      {
        "id": "minimal-m2-g2",
        "title": "Minimal m=2, gamma=2",
        "classification": "subcritical",
        "alpha_n0": 0.9080003316496248,
        "beta_n0": -1.0429176776256086,
        "theory_c2": -1.1485873311641532,
        "fits": [
          {
            "mesh": 40,
            "c2": -1.1795328096525204,
            "observed_order": null
          },
          {
            "mesh": 80,
            "c2": -1.1563262402309178,
            "observed_order": 1.9995265165374327
          },
          {
            "mesh": 160,
            "c2": -1.1505222060103328,
            "observed_order": 1.9998899565433161
          }
        ]
      }
    ]
  },
  "time_integration_cases": [
    {
      "id": "time-nonminimal-a10-beta0",
      "title": "Quasi-linear supercritical time evolution",
      "status": "validated_current",
      "quantitative_use": true,
      "claim_scope": "Near-threshold semidiscrete trajectories: below-threshold decay and symmetry-related patterned trajectories above threshold.",
      "paper_figure_id": "paper3-supercritical-quasilinear",
      "paper_figure": {
        "source_manuscript_commit": "c0bfc431a19b81b1c45363dea472c29a745ad055",
        "preview_path": "docs/assets/images/paper3-supercritical-quasilinear.png",
        "preview_sha256": "e96975dbaa9a3a81f22c23ef7f1f76e85b485b8180f443817d409c49d0bb7575",
        "vector_path": "docs/assets/images/paper3-supercritical-quasilinear.pdf",
        "vector_sha256": "dc1d3705e6a43b524d583bc244de741be17096bd96a5b44a50362d1126989b92"
      },
      "legacy_preview_policy": "Per-run summaries retain obsolete annotations and are provenance only; only the hashed paper_figure assets are reader-facing.",
      "raw_path": "docs/results/quasilinear/supercritical/a10_b1_alpha1_m1_beta0_gamma1_mu1_nu1_L1_n1",
      "constants_path": "docs/results/quasilinear/supercritical/a10_b1_alpha1_m1_beta0_gamma1_mu1_nu1_L1_n1/constants.json",
      "archive_assertions": {
        "classification": "supercritical",
        "chi_star_mode_n0": 2.1882816237512737,
        "beta_n0": 0.07650308051520315
      },
      "featured_runs": [
        {
          "role": "below-threshold positive seed",
          "run_path": "docs/results/quasilinear/supercritical/a10_b1_alpha1_m1_beta0_gamma1_mu1_nu1_L1_n1/runs/chi2-1656_ep0-0010_p/run.npz",
          "metadata_path": "docs/results/quasilinear/supercritical/a10_b1_alpha1_m1_beta0_gamma1_mu1_nu1_L1_n1/runs/chi2-1656_ep0-0010_p/run_meta.json",
          "legacy_preview_path": "docs/results/quasilinear/supercritical/a10_b1_alpha1_m1_beta0_gamma1_mu1_nu1_L1_n1/runs/chi2-1656_ep0-0010_p/run_summary6.png"
        },
        {
          "role": "above-threshold positive branch",
          "run_path": "docs/results/quasilinear/supercritical/a10_b1_alpha1_m1_beta0_gamma1_mu1_nu1_L1_n1/runs/chi2-2102_ep0-0010_p/run.npz",
          "metadata_path": "docs/results/quasilinear/supercritical/a10_b1_alpha1_m1_beta0_gamma1_mu1_nu1_L1_n1/runs/chi2-2102_ep0-0010_p/run_meta.json",
          "legacy_preview_path": "docs/results/quasilinear/supercritical/a10_b1_alpha1_m1_beta0_gamma1_mu1_nu1_L1_n1/runs/chi2-2102_ep0-0010_p/run_summary6.png"
        },
        {
          "role": "above-threshold negative branch",
          "run_path": "docs/results/quasilinear/supercritical/a10_b1_alpha1_m1_beta0_gamma1_mu1_nu1_L1_n1/runs/chi2-2102_ep0-0010_m/run.npz",
          "metadata_path": "docs/results/quasilinear/supercritical/a10_b1_alpha1_m1_beta0_gamma1_mu1_nu1_L1_n1/runs/chi2-2102_ep0-0010_m/run_meta.json",
          "legacy_preview_path": "docs/results/quasilinear/supercritical/a10_b1_alpha1_m1_beta0_gamma1_mu1_nu1_L1_n1/runs/chi2-2102_ep0-0010_m/run_summary6.png"
        }
      ]
    },
    {
      "id": "time-nonminimal-m2-beta1-gamma2",
      "title": "Nonlinear-mobility supercritical time evolution",
      "status": "validated_current",
      "quantitative_use": true,
      "claim_scope": "Near-threshold semidiscrete trajectories for nonlinear mobility and signal production.",
      "paper_figure_id": "paper3-supercritical-nonlinear",
      "paper_figure": {
        "source_manuscript_commit": "c0bfc431a19b81b1c45363dea472c29a745ad055",
        "preview_path": "docs/assets/images/paper3-supercritical-nonlinear.png",
        "preview_sha256": "66333a7ffdd4c06afdb17d735412aa50158ceb289ad5ab5cf3cda86d217077c3",
        "vector_path": "docs/assets/images/paper3-supercritical-nonlinear.pdf",
        "vector_sha256": "7b5f03c9cbf7097c330321700d7d7c9b15255169580d8ef2e2e756287fa74405"
      },
      "legacy_preview_policy": "Per-run summaries retain obsolete annotations and are provenance only; only the hashed paper_figure assets are reader-facing.",
      "raw_path": "docs/results/nonlinear_beta_gamma/supercritical/a1_b1_alpha1_m2_beta1_gamma2_mu1_nu1_L1_n1",
      "constants_path": "docs/results/nonlinear_beta_gamma/supercritical/a1_b1_alpha1_m2_beta1_gamma2_mu1_nu1_L1_n1/constants.json",
      "archive_assertions": {
        "classification": "supercritical",
        "chi_star_mode_n0": 11.970925584731697,
        "beta_n0": 9.508880363384589
      },
      "featured_runs": [
        {
          "role": "below-threshold positive seed",
          "run_path": "docs/results/nonlinear_beta_gamma/supercritical/a1_b1_alpha1_m2_beta1_gamma2_mu1_nu1_L1_n1/runs/chi11-8424_ep0-0010_p/run.npz",
          "metadata_path": "docs/results/nonlinear_beta_gamma/supercritical/a1_b1_alpha1_m2_beta1_gamma2_mu1_nu1_L1_n1/runs/chi11-8424_ep0-0010_p/run_meta.json",
          "legacy_preview_path": "docs/results/nonlinear_beta_gamma/supercritical/a1_b1_alpha1_m2_beta1_gamma2_mu1_nu1_L1_n1/runs/chi11-8424_ep0-0010_p/run_summary6.png"
        },
        {
          "role": "above-threshold positive branch",
          "run_path": "docs/results/nonlinear_beta_gamma/supercritical/a1_b1_alpha1_m2_beta1_gamma2_mu1_nu1_L1_n1/runs/chi12-0906_ep0-0010_p/run.npz",
          "metadata_path": "docs/results/nonlinear_beta_gamma/supercritical/a1_b1_alpha1_m2_beta1_gamma2_mu1_nu1_L1_n1/runs/chi12-0906_ep0-0010_p/run_meta.json",
          "legacy_preview_path": "docs/results/nonlinear_beta_gamma/supercritical/a1_b1_alpha1_m2_beta1_gamma2_mu1_nu1_L1_n1/runs/chi12-0906_ep0-0010_p/run_summary6.png"
        },
        {
          "role": "above-threshold negative branch",
          "run_path": "docs/results/nonlinear_beta_gamma/supercritical/a1_b1_alpha1_m2_beta1_gamma2_mu1_nu1_L1_n1/runs/chi12-0906_ep0-0010_m/run.npz",
          "metadata_path": "docs/results/nonlinear_beta_gamma/supercritical/a1_b1_alpha1_m2_beta1_gamma2_mu1_nu1_L1_n1/runs/chi12-0906_ep0-0010_m/run_meta.json",
          "legacy_preview_path": "docs/results/nonlinear_beta_gamma/supercritical/a1_b1_alpha1_m2_beta1_gamma2_mu1_nu1_L1_n1/runs/chi12-0906_ep0-0010_m/run_summary6.png"
        }
      ]
    }
  ],
  "provenance_only": [
    {
      "id": "legacy-minimal-m1-g1-time-run",
      "title": "Historical minimal m=1, gamma=1 time integration",
      "status": "provenance_only",
      "quantitative_use": false,
      "reader_facing": false,
      "reason": "The archived above-threshold trajectory has unacceptable mass drift; the replacement stationary continuation is the validated evidence.",
      "raw_path": "docs/results/minimal_model/subcritical/u1_beta1_m1_gamma1_mu1_nu1_L1_n1",
      "constants_path": "docs/results/minimal_model/subcritical/u1_beta1_m1_gamma1_mu1_nu1_L1_n1/constants.json"
    },
    {
      "id": "legacy-minimal-m2-g2-time-run",
      "title": "Historical minimal m=2, gamma=2 time integration",
      "status": "provenance_only",
      "quantitative_use": false,
      "reader_facing": false,
      "reason": "This archive predates the corrected subcritical classification; the replacement stationary continuation is the validated evidence.",
      "raw_path": "docs/results/minimal_model/supercritical/u1_beta1_m2_gamma2_mu1_nu1_L1_n1",
      "constants_path": "docs/results/minimal_model/supercritical/u1_beta1_m2_gamma2_mu1_nu1_L1_n1/constants.json"
    },
    {
      "id": "legacy-nonminimal-beta3-misseeded",
      "title": "Historical beta=3 coefficient-dependent branch seeds",
      "status": "provenance_only",
      "quantitative_use": false,
      "reader_facing": false,
      "reason": "The branch seeds used an obsolete asymptotic coefficient; the v1 stationary continuation is the validated replacement.",
      "raw_path": "docs/results/quasilinear/subcritical/a1_b1_alpha1_m1_beta3_gamma1_mu1_nu1_L1_n1",
      "constants_path": "docs/results/quasilinear/subcritical/a1_b1_alpha1_m1_beta3_gamma1_mu1_nu1_L1_n1/constants.json"
    },
    {
      "id": "legacy-nonminimal-beta1-misseeded",
      "title": "Reclassified all-ones coefficient-dependent branch seeds",
      "status": "provenance_only",
      "quantitative_use": false,
      "reader_facing": false,
      "reason": "The case is supercritical, while its A_rel files were generated from an obsolete negative coefficient.",
      "raw_path": "docs/results/quasilinear/subcritical/a1_b1_alpha1_m1_beta1_gamma1_mu1_nu1_L1_n1",
      "constants_path": "docs/results/quasilinear/subcritical/a1_b1_alpha1_m1_beta1_gamma1_mu1_nu1_L1_n1/constants.json"
    }
  ]
}
