4. Interaction Weight (W)
Not all interactions contribute equally to the emergent phenotype. The interaction weight represents the functional or structural significance of a particular connection, scaled from --2 (inhibitory) to +2 (enhancing). These values can incorporate: Structural rigidity/flexibility (e.g., via RMSD shifts), Catalytic contribution (e.g., active-site residues), Stability enhancements (e.g., disulfide bridges).
The weighting schema enables simulation models to prioritize mutational paths that preserve or improve system function, acting as heuristics in evolutionary exploration.
5. Systemic Stability (S)
Stability is not merely thermodynamic; it is systemic, encompassing both internal consistency (e.g., folding robustness) and external adaptability (e.g., pH or temperature resilience). CAS models use: Standard deviation of output functionality across mutational cycles, Stability coefficients derived from Monte Carlo sampling or molecular dynamics.
By integrating stability as a multidimensional variable, the framework captures the homeostatic nature of evolved proteins, where robust functionality emerges from fluctuating microstates.
6. Emergent Output Function (O)
This is the phenotypic expression of the system, operationalized as:
Binding affinity to synthetic substrates (e.g., PET, PU),
Catalytic turnover rates (k_cat),
Degradation byproducts (e.g., terephthalate or EG for PET).
