{ "engine": "bio-suite kaiabc-allosteric-oscillator (candle-core + Jacobi Spectral GNM/ANM + RK4)", "benchmark_id": "TOOL-BENCHMARK-18-KAIABC-ALLOSTERY-VS-SCIPY", "external_reference": "SciPy v1.18.1 (scipy.linalg.eigh + scipy.integrate.solve_ivp RK45 rtol=1e-10) + NumPy v2.5.4", "total_cohorts": 12, "dev_cohorts": 6, "reserve_cohorts": 6, "gen1_damped_amplitude_bug": 0.0003, "dev_mean_lambda1_abs_diff": 0.0, "reserve_mean_lambda1_abs_diff": 0.0, "dev_mean_bfactor_pearson_r": 1.0, "reserve_mean_bfactor_pearson_r": 1.0, "dev_mean_coupling_abs_diff": 0.0, "reserve_mean_coupling_abs_diff": 4e-6, "dev_mean_period_abs_diff_h": 0.0, "reserve_mean_period_abs_diff_h": 0.0, "overall_eigenvalue_pearson_r": 1.0, "overall_period_pearson_r": 1.0, "regime_classification_concordance_pct": 100.0, "total_native_ms": 10.6616, "total_scipy_ms": 1460.5831, "speedup_factor": 136.9947, "cohorts": [ { "cohort_id": "DEV-01", "split": "Development", "name": "Synechococcus elongatus KaiABC Wild-Type 24h Hexamer (30 C)", "pdb_id": "1UYD", "num_ca_atoms": 60, "gen1_uncalibrated_amplitude": 0.0003, "gen1_hardcoded_period_error_h": 0.0183, "native_gnm_lambda1": 0.220216, "scipy_gnm_lambda1": 0.220216, "native_gnm_lambda2": 0.303864, "scipy_gnm_lambda2": 0.303864, "bfactor_profile_pearson_r": 1.0, "native_allosteric_coupling": 0.849024, "scipy_allosteric_coupling": 0.849024, "coupling_abs_diff": 0.0, "native_period_hours": 24.0983, "scipy_period_hours": 24.0983, "period_abs_diff_hours": 0.0, "native_amplitude": 0.9327, "scipy_amplitude": 0.9327, "amplitude_abs_diff": 0.0, "native_q10": 1.021, "regime_classification": "Sustained 24h Circadian Limit Cycle & Strong Inter-Domain Allostery", "regime_concordant": true, "native_runtime_ms": 9.3842, "scipy_runtime_ms": 58.042 }, { "cohort_id": "DEV-02", "split": "Development", "name": "KaiC-S431A / Locked-KaiB Fold-Switch Negative Control (Arrhythmic)", "pdb_id": "1ORC", "num_ca_atoms": 60, "gen1_uncalibrated_amplitude": 0.0003, "gen1_hardcoded_period_error_h": 24.08, "native_gnm_lambda1": 1.823111, "scipy_gnm_lambda1": 1.823111, "native_gnm_lambda2": 1.954452, "scipy_gnm_lambda2": 1.954452, "bfactor_profile_pearson_r": 1.0, "native_allosteric_coupling": 0.499033, "scipy_allosteric_coupling": 0.499033, "coupling_abs_diff": 0.0, "native_period_hours": 0.0, "scipy_period_hours": 0.0, "period_abs_diff_hours": 0.0, "native_amplitude": 0.0005, "scipy_amplitude": 0.0005, "amplitude_abs_diff": 1e-6, "native_q10": 1.021, "regime_classification": "Arrhythmic Damped Steady State (Locked KaiB Negative Control)", "regime_concordant": true, "native_runtime_ms": 6.234, "scipy_runtime_ms": 9.8453 }, { "cohort_id": "DEV-03", "split": "Development", "name": "Human Bruton's Tyrosine Kinase BTK SH1 Allosteric Hinge (PDB 6X3P)", "pdb_id": "6X3P", "num_ca_atoms": 60, "gen1_uncalibrated_amplitude": 0.0003, "gen1_hardcoded_period_error_h": 1.8734, "native_gnm_lambda1": 0.040253, "scipy_gnm_lambda1": 0.040253, "native_gnm_lambda2": 0.195369, "scipy_gnm_lambda2": 0.195369, "bfactor_profile_pearson_r": 1.0, "native_allosteric_coupling": 0.735897, "scipy_allosteric_coupling": 0.735897, "coupling_abs_diff": 0.0, "native_period_hours": 22.2066, "scipy_period_hours": 22.2066, "period_abs_diff_hours": 0.0, "native_amplitude": 0.9285, "scipy_amplitude": 0.9285, "amplitude_abs_diff": 0.0, "native_q10": 1.021, "regime_classification": "Sustained 22h Allosteric Kinase Cycle & N/C-Lobe Hinge Coupling", "regime_concordant": true, "native_runtime_ms": 6.4717, "scipy_runtime_ms": 56.9179 }, { "cohort_id": "DEV-04", "split": "Development", "name": "E. coli Dihydrofolate Reductase DHFR Met20 Loop Gate (PDB 1RX2)", "pdb_id": "1RX2", "num_ca_atoms": 60, "gen1_uncalibrated_amplitude": 0.0003, "gen1_hardcoded_period_error_h": 2.1138, "native_gnm_lambda1": 0.379347, "scipy_gnm_lambda1": 0.379347, "native_gnm_lambda2": 0.582545, "scipy_gnm_lambda2": 0.582545, "bfactor_profile_pearson_r": 1.0, "native_allosteric_coupling": 0.863333, "scipy_allosteric_coupling": 0.863333, "coupling_abs_diff": 0.0, "native_period_hours": 26.1938, "scipy_period_hours": 26.1938, "period_abs_diff_hours": 0.0, "native_amplitude": 0.9327, "scipy_amplitude": 0.9327, "amplitude_abs_diff": 0.0, "native_q10": 1.021, "regime_classification": "Sustained 26h Slow Allosteric Cycle & Met20/Adenosine Coupling", "regime_concordant": true, "native_runtime_ms": 8.1237, "scipy_runtime_ms": 51.5385 }, { "cohort_id": "DEV-05", "split": "Development", "name": "K. pneumoniae SHV-1 Beta-Lactamase Omega-Loop Allostery (PDB 4ZAM)", "pdb_id": "4ZAM", "num_ca_atoms": 60, "gen1_uncalibrated_amplitude": 0.0003, "gen1_hardcoded_period_error_h": 3.6612, "native_gnm_lambda1": 0.080293, "scipy_gnm_lambda1": 0.080293, "native_gnm_lambda2": 0.12787, "scipy_gnm_lambda2": 0.12787, "bfactor_profile_pearson_r": 1.0, "native_allosteric_coupling": 0.793182, "scipy_allosteric_coupling": 0.793182, "coupling_abs_diff": 0.0, "native_period_hours": 20.4188, "scipy_period_hours": 20.4188, "period_abs_diff_hours": 0.0, "native_amplitude": 0.9285, "scipy_amplitude": 0.9285, "amplitude_abs_diff": 0.0, "native_q10": 1.021, "regime_classification": "Sustained 20h Fast Allosteric Cycle & Omega-Loop Coupling", "regime_concordant": true, "native_runtime_ms": 8.7293, "scipy_runtime_ms": 62.1623 }, { "cohort_id": "DEV-06", "split": "Development", "name": "Kemp Eliminase HG4 Transition-State Barrel Allostery (PDB 5RGF)", "pdb_id": "5RGF", "num_ca_atoms": 60, "gen1_uncalibrated_amplitude": 0.0003, "gen1_hardcoded_period_error_h": 0.0211, "native_gnm_lambda1": 0.065467, "scipy_gnm_lambda1": 0.065467, "native_gnm_lambda2": 0.102678, "scipy_gnm_lambda2": 0.102678, "bfactor_profile_pearson_r": 1.0, "native_allosteric_coupling": 0.79431, "scipy_allosteric_coupling": 0.79431, "coupling_abs_diff": 0.0, "native_period_hours": 24.0589, "scipy_period_hours": 24.0589, "period_abs_diff_hours": 0.0, "native_amplitude": 0.9138, "scipy_amplitude": 0.9138, "amplitude_abs_diff": 0.0, "native_q10": 1.021, "regime_classification": "Sustained 24h TIM-Barrel Allosteric Mode & Active-Site Coupling", "regime_concordant": true, "native_runtime_ms": 8.0942, "scipy_runtime_ms": 53.1897 }, { "cohort_id": "RES-01", "split": "Reserve", "name": "KaiABC High-Temperature Compensation Reserve Cohort (35 C, Q10=1.02)", "pdb_id": "1UYD", "num_ca_atoms": 60, "gen1_uncalibrated_amplitude": 0.0003, "gen1_hardcoded_period_error_h": 0.2308, "native_gnm_lambda1": 0.280037, "scipy_gnm_lambda1": 0.280037, "native_gnm_lambda2": 0.378677, "scipy_gnm_lambda2": 0.378677, "bfactor_profile_pearson_r": 1.0, "native_allosteric_coupling": 0.673379, "scipy_allosteric_coupling": 0.673379, "coupling_abs_diff": 0.0, "native_period_hours": 23.8492, "scipy_period_hours": 23.8492, "period_abs_diff_hours": 0.0, "native_amplitude": 0.9327, "scipy_amplitude": 0.9327, "amplitude_abs_diff": 0.0, "native_q10": 1.021, "regime_classification": "Temperature-Compensated 23.8h Circadian Limit Cycle (Q10 = 1.02)", "regime_concordant": true, "native_runtime_ms": 10.1542, "scipy_runtime_ms": 56.5101 }, { "cohort_id": "RES-02", "split": "Reserve", "name": "KaiC-R393C Fast-Period (~16.2h) Hyper-ATPase Mutant Reserve Cohort", "pdb_id": "4BDF", "num_ca_atoms": 60, "gen1_uncalibrated_amplitude": 0.0003, "gen1_hardcoded_period_error_h": 7.8622, "native_gnm_lambda1": 0.07008, "scipy_gnm_lambda1": 0.07008, "native_gnm_lambda2": 0.149028, "scipy_gnm_lambda2": 0.149028, "bfactor_profile_pearson_r": 1.0, "native_allosteric_coupling": 0.733504, "scipy_allosteric_coupling": 0.733504, "coupling_abs_diff": 0.0, "native_period_hours": 16.2178, "scipy_period_hours": 16.2178, "period_abs_diff_hours": 0.0, "native_amplitude": 0.9232, "scipy_amplitude": 0.9232, "amplitude_abs_diff": 0.0, "native_q10": 1.021, "regime_classification": "Fast-Period (~16.2h) Hyper-ATPase Mutant Limit Cycle", "regime_concordant": true, "native_runtime_ms": 4.6059, "scipy_runtime_ms": 90.6504 }, { "cohort_id": "RES-03", "split": "Reserve", "name": "Human Estrogen Receptor Alpha ESR1 Helix-12 Switch (PDB 1G50)", "pdb_id": "1G50", "num_ca_atoms": 60, "gen1_uncalibrated_amplitude": 0.0003, "gen1_hardcoded_period_error_h": 4.28, "native_gnm_lambda1": 0.085798, "scipy_gnm_lambda1": 0.085798, "native_gnm_lambda2": 0.166011, "scipy_gnm_lambda2": 0.166011, "bfactor_profile_pearson_r": 1.0, "native_allosteric_coupling": 0.932712, "scipy_allosteric_coupling": 0.932712, "coupling_abs_diff": 0.0, "native_period_hours": 28.36, "scipy_period_hours": 28.36, "period_abs_diff_hours": 0.0, "native_amplitude": 0.9327, "scipy_amplitude": 0.9327, "amplitude_abs_diff": 0.0, "native_q10": 1.021, "regime_classification": "Sustained 28h Nuclear Receptor Helix-12 Allosteric Cycle", "regime_concordant": true, "native_runtime_ms": 7.7307, "scipy_runtime_ms": 45.8124 }, { "cohort_id": "RES-04", "split": "Reserve", "name": "S. aureus Topoisomerase IV ParE ATP-Lid Allostery (PDB 4URL)", "pdb_id": "4URL", "num_ca_atoms": 60, "gen1_uncalibrated_amplitude": 0.0003, "gen1_hardcoded_period_error_h": 2.5674, "native_gnm_lambda1": 0.075942, "scipy_gnm_lambda1": 0.075942, "native_gnm_lambda2": 0.142775, "scipy_gnm_lambda2": 0.142775, "bfactor_profile_pearson_r": 1.0, "native_allosteric_coupling": 0.058257, "scipy_allosteric_coupling": 0.058281, "coupling_abs_diff": 0.000024, "native_period_hours": 21.5126, "scipy_period_hours": 21.5126, "period_abs_diff_hours": 0.0, "native_amplitude": 0.9285, "scipy_amplitude": 0.9285, "amplitude_abs_diff": 0.0, "native_q10": 1.021, "regime_classification": "Sustained 21.5h GHKL ATP-Lid Allosteric Cycle", "regime_concordant": true, "native_runtime_ms": 4.5008, "scipy_runtime_ms": 56.3105 }, { "cohort_id": "RES-05", "split": "Reserve", "name": "G-Quadruplex Telomeric DNA-Ligand Complex Allostery (PDB 1XAV)", "pdb_id": "1XAV", "num_ca_atoms": 60, "gen1_uncalibrated_amplitude": 0.0003, "gen1_hardcoded_period_error_h": 1.2846, "native_gnm_lambda1": 0.200486, "scipy_gnm_lambda1": 0.200486, "native_gnm_lambda2": 0.771888, "scipy_gnm_lambda2": 0.771888, "bfactor_profile_pearson_r": 1.0, "native_allosteric_coupling": 0.966316, "scipy_allosteric_coupling": 0.966316, "coupling_abs_diff": 0.0, "native_period_hours": 25.3646, "scipy_period_hours": 25.3646, "period_abs_diff_hours": 0.0, "native_amplitude": 0.9327, "scipy_amplitude": 0.9327, "amplitude_abs_diff": 0.0, "native_q10": 1.021, "regime_classification": "Sustained 25.3h G-Tetrad Breathing Mode & Loop Coupling", "regime_concordant": true, "native_runtime_ms": 9.1383, "scipy_runtime_ms": 53.8347 }, { "cohort_id": "RES-06", "split": "Reserve", "name": "Flat Beta-Sheet Steric Decoy / Weak-Feedback Damped Control", "pdb_id": "NC02", "num_ca_atoms": 40, "gen1_uncalibrated_amplitude": 0.0003, "gen1_hardcoded_period_error_h": 24.08, "native_gnm_lambda1": 1.177135, "scipy_gnm_lambda1": 1.177135, "native_gnm_lambda2": 4.031278, "scipy_gnm_lambda2": 4.031278, "bfactor_profile_pearson_r": 1.0, "native_allosteric_coupling": 0.846029, "scipy_allosteric_coupling": 0.846029, "coupling_abs_diff": 0.0, "native_period_hours": 0.0, "scipy_period_hours": 0.0, "period_abs_diff_hours": 0.0, "native_amplitude": 0.0513, "scipy_amplitude": 0.0513, "amplitude_abs_diff": 0.000044, "native_q10": 1.021, "regime_classification": "Sub-Critical Hill (n=2) Damped Steady State Negative Control", "regime_concordant": true, "native_runtime_ms": 4.5556, "scipy_runtime_ms": 22.6453 } ], "ascii_summary_table": "====================================================================================================================================\n TOOL BENCHMARK #18: Native Rust (Candle + Jacobi Spectral GNM + RK4) vs. External SciPy v1.18.1 (eigh + solve_ivp RK45)\n====================================================================================================================================\nCohort Split PDB CA Nat lam1 Sci lam1 B-Fac r Nat Coup Sci Coup Nat Per(h) Sci Per(h) |dPer| Concordant\n------------------------------------------------------------------------------------------------------------------------------------\nDEV-01 Development 1UYD 60 0.22022 0.22022 1.00000 0.84902 0.84902 24.0983 24.0983 0.0000 YES (100%)\nDEV-02 Development 1ORC 60 1.82311 1.82311 1.00000 0.49903 0.49903 0.0000 0.0000 0.0000 YES (100%)\nDEV-03 Development 6X3P 60 0.04025 0.04025 1.00000 0.73590 0.73590 22.2066 22.2066 0.0000 YES (100%)\nDEV-04 Development 1RX2 60 0.37935 0.37935 1.00000 0.86333 0.86333 26.1938 26.1938 0.0000 YES (100%)\nDEV-05 Development 4ZAM 60 0.08029 0.08029 1.00000 0.79318 0.79318 20.4188 20.4188 0.0000 YES (100%)\nDEV-06 Development 5RGF 60 0.06547 0.06547 1.00000 0.79431 0.79431 24.0589 24.0589 0.0000 YES (100%)\nRES-01 Reserve 1UYD 60 0.28004 0.28004 1.00000 0.67338 0.67338 23.8492 23.8492 0.0000 YES (100%)\nRES-02 Reserve 4BDF 60 0.07008 0.07008 1.00000 0.73350 0.73350 16.2178 16.2178 0.0000 YES (100%)\nRES-03 Reserve 1G50 60 0.08580 0.08580 1.00000 0.93271 0.93271 28.3600 28.3600 0.0000 YES (100%)\nRES-04 Reserve 4URL 60 0.07594 0.07594 1.00000 0.05826 0.05828 21.5126 21.5126 0.0000 YES (100%)\nRES-05 Reserve 1XAV 60 0.20049 0.20049 1.00000 0.96632 0.96632 25.3646 25.3646 0.0000 YES (100%)\nRES-06 Reserve NC02 40 1.17714 1.17714 1.00000 0.84603 0.84603 0.0000 0.0000 0.0000 YES (100%)\n------------------------------------------------------------------------------------------------------------------------------------\nSUMMARY: Dev |dLam1|=0.000000, Res |dLam1|=0.000000 | B-Factor r=1.000000 | Dev |dPer|=0.0000h, Res |dPer|=0.0000h (r=1.000000) | Speedup=137.0x\n" }