in silico
Phase 1: In Silico Validation
- Objective
- To rapidly test the core dynamical systems hypothesis using computational models, identifying if the proposed negative feedback loop can theoretically generate stable limit cycles under the specified boundary conditions.
- Estimated cost
- €0-2k (primarily compute time if using cloud/HPC)
- Estimated duration
- 4-8 weeks
- Success criteria
- Existence of a stable limit cycle in the ODE model · Model produces sustained oscillations (non-damping) for >100 cycles within the predicted τ range (10-1000 s) for at least one set of parameters within the specified variable ranges. · (Numerical integration of ODEs; calculation of Lyapunov exponents or Poincaré maps to confirm limit cycle stability.)
- Sensitivity to key intermediate · Forcing constant, saturating coverage of the driving intermediate (O*) in the model collapses the oscillation amplitude (Δθ) to < 0.01 ML. · (Model perturbation test: clamp the O* coverage variable and observe the time evolution of θ.)
- Go if
- Both success criteria are met. The model robustly predicts limit cycles under plausible conditions, validating the theoretical feasibility of the mechanism.
- No-go if
- No parameter set yields stable oscillations, or oscillations only occur outside all specified boundary conditions (e.g., above Tammann temperature). The core feedback loop is theoretically invalid.
- Pivot if
- Oscillations require unrealistic parameters (Ea > 1.5 eV, coupling strength not physically plausible). The hypothesis may need reformulation (e.g., different intermediate, modified mechanism).
- Risks
- Model predictions are overly sensitive to poorly known kinetic parameters (e.g., pre-exponential factors).Probability: mediumMitigation: Use Bayesian parameter estimation with literature priors and perform global sensitivity analysis (Sobol indices) to identify critical parameters. Focus on qualitative bifurcation behavior rather than exact numbers.
- Mean-field approximation fails to capture crucial spatial effects (facet coupling, diffusion).Probability: lowMitigation: Implement the optional agent-based kMC simulation for a subset of conditions to cross-validate the mean-field results.