{
  "meta": {
    "schema": "rosettaq-archive/v1",
    "file_name": "RosettaQ__RUN__EXP-0007-003__20260724T2154Z__ctqw-vs-diffusion--allostery-2hhb-c8.0-t0.5_8.0.json",
    "file_id": "EXP-0007-003",
    "type": "RUN",
    "is_demo": false,
    "scope_note": "Sweep de robustez 2HHB (Cleveland Clinic). cutoff=8.0A, ventana [0.5,8.0], 16 tiempos. CTQW vs difusion clasica; bolsillo 2,3-BPG documentado como arbitro.",
    "content_hash": "sha256:cf8b897df2f55dd3620964416fc8a92734bd503a6f34f2a08ed9ab7b5874931d"
  },
  "w6": {
    "que": {
      "recipe_id": "RQ-0007",
      "recipe_name": "Allosteric site identification via quantum signal propagation",
      "problem_class": "Molecular simulation / allostery",
      "instance": "2HHB_ca_cutoff8.0_t0.5-8.0",
      "quantum_side": {
        "method": "continuous-time quantum walk, U(t)=exp(-iAt), integrated",
        "allosteric_percentile": 75.67,
        "runtime_s": 4.656
      },
      "classical_side": {
        "method": "continuous-time diffusion, p(t)=exp(-Lt), integrated",
        "allosteric_percentile": 73.65,
        "runtime_s": 1.925
      },
      "ground_truth": {
        "active_site": [
          [
            "A",
            87
          ],
          [
            "C",
            87
          ],
          [
            "B",
            92
          ],
          [
            "D",
            92
          ]
        ],
        "allosteric": [
          [
            "B",
            2
          ],
          [
            "B",
            82
          ],
          [
            "B",
            143
          ],
          [
            "D",
            2
          ],
          [
            "D",
            82
          ],
          [
            "D",
            143
          ]
        ],
        "ref": "Arnone 1972; textbook 2,3-BPG allosteric pocket of deoxyhemoglobin",
        "n_active_matched": 4,
        "n_allosteric_matched": 6
      },
      "outcome": "quantum win",
      "metric": "percentil medio de residuos alostericos verdaderos en el mapa de propagacion (entre residuos distales, >6A del sitio activo); 100=top",
      "scores": {
        "quantum_percentile": 75.67,
        "classical_percentile": 73.65
      }
    },
    "como": {
      "protocol": "juez-v1: misma red de residuos + mismo par fuente/tiempos; sitios alostericos documentados como arbitro (ninguno los define)",
      "instance_params": {
        "pdb": "2HHB",
        "cutoff_A": 8.0,
        "n_residues": 574,
        "time_window": [
          0.5,
          8.0
        ],
        "n_times": 16
      },
      "sweep_note": "parte del sweep de robustez de EXP-0007 sobre 2HHB; ground truth y protocolo identicos a EXP-0007-001, solo varian cutoff/ventana",
      "lib_versions": {
        "prody": "2.6.1",
        "numpy": "2.4.4",
        "scipy": "1.16.3",
        "python": "3.11.15"
      },
      "compute": "contenedor cloud Cowork (CPU, Linux)",
      "harness": "allo_sweep.py",
      "raw_data_url": "pendiente de publicacion en repo"
    },
    "cuando": {
      "started_at": "2026-07-24T21:54:55.174517+00:00",
      "archived_at": "2026-07-24T21:54:55.174542+00:00",
      "timezone_note": "UTC; equipo en America/Punta_Arenas"
    },
    "donde": {
      "quantum_backend": "CTQW por matrix-exponential (simulacion exacta; ruta NISQ = Hamiltonian simulation gate-based)",
      "classical_backend": "difusion por matrix-exponential del Laplaciano",
      "protein_source": "RCSB PDB 2HHB via ProDy",
      "region": "cloud sandbox Anthropic"
    },
    "porque": {
      "hypothesis": "si CTQW realmente identificara mejor los sitios alostericos, deberia ganar de forma estable a lo largo de cutoffs y ventanas; el sweep prueba robustez, no una config afortunada",
      "question": "A cutoff=8.0A y ventana [0.5,8.0], CTQW vs difusion: cual rankea mas alto el bolsillo 2,3-BPG?",
      "ledger_goal": "robustez del veredicto RQ-0007; insumo de la propuesta Fase I Cleveland"
    },
    "quien": {
      "operator": "Nicholas",
      "agents": [
        "Claude (Cowork cloud)",
        "allo_sweep.py"
      ],
      "judge_protocol_version": "juez-v1",
      "org": "Rosetta Quantum",
      "team": "Rosetta Quantum"
    }
  },
  "storage": {
    "policy": "triple-copia identica; verificar con content_hash",
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    "self_note": "Este archivo es una de las 3 copias listadas. Si el hash difiere, esa copia no es valida."
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