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Coarse-Grained Two-State Stochastic Dynamics on a Reference Bead Configuration

  • Task ID: biology.protein_folding_go_model
  • Domain: biology
  • Subdomain: biophysics
  • Status: final
  • Benchmark set: seed42 (60 tasks)
  • Tags: langevin, multi_temperature, free_energy, heat_capacity, coarse_grained, stochastic_dynamics

Runtime and requirements

  • Estimated time: 45-90 minutes
  • Python: >=3.11
  • Packages: numpy>=2.0, scipy>=1.11, matplotlib>=3.7
  • GPU required: no
  • Network required: no

Public input and output contract

Inputs

  • data/parameters.json (data): Run parameters (neutral schema): n_beads, friction, dt_reduced, temperature_list, n_steps_per_T, save_interval, contact_cutoff, min_seq_separation
  • data/target_coords.npy (data): Reference bead configuration (N x 3 Cartesian coordinates in arbitrary length units)

Outputs

  • simulation.py (code): Agent-written simulation and analysis code
  • final_coords.npy (data): End-of-run configuration at the lowest temperature
  • order_parameter_trajectory.npy (data): Per-temperature order parameter time series with n_temperatures rows; the checkpoint count may include an initial sample and otherwise follows n_steps_per_T and save_interval
  • order_parameter_histograms.npy (data): Normalized histograms of the order parameter at each temperature
  • heat_capacity_curve.npy (data): Row 0 = temperature grid, Row 1 = specific heat C_v(T)
  • temperature_observables.json (data): Per-temperature means/variances of Q and energy, direct heat capacity estimates, and Q-energy correlations
  • transition_free_energy_profile.npy (data): Row 0 = Q bin centers, Row 1 = shifted F(Q)/kBT at the transition temperature
  • q_energy_joint_histograms.npy (data): Per-temperature joint probability-mass histograms of Q and z-scored energy; Q bins cover [0,1], energy z bins cover [-3,3]
  • native_contact_probability.npy (data): Matrix of per-temperature native-contact formation probabilities using the reference-contact ordering defined by contact_cutoff and min_seq_separation
  • transition_analysis.json (data): Structured summary: transition_temperature, peak_heat_capacity, order_parameter_at_transition_modes, mode_separation, free_energy_barrier_kT, reference_contact_jaccard, warnings
  • visualization.png (figure): Multi-panel figure: final configuration, order-parameter histograms, C_v(T), free-energy landscape at the transition

Public repository files

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Provenance

This task is included in the current seed42 benchmark set at dataset revision f11a199f71fb4b854ac43a1bf548d5df519141a9.

This page is generated only from files tracked in the public ASI-Bench repository at commit f18382f03faf. Submission bundles, run logs, private scoring configuration, and private reference answers are not read by this page generator.