Folding-unfolding behavior of proteins (e.g., under pH or solvent shifts),
Assembly/disassembly of multi-protein complexes,
The transition from non-functional polypeptides to catalytically competent enzymes.
In CAS modeling, these transitions are monitored by order parameters such as:
The folding order parameter \phi, based on root-mean-square deviation (RMSD),
Interaction entropy, derived from contact maps or energy landscapes,
Percolation threshold of intra-protein hydrogen bonds or hydrophobic cores.
Phase transitions are especially critical in synthetic systems where one seeks to design an enzyme that can switch states---for example, a plastic-degrading enzyme that is only active at specific temperatures or in acidic environments. Simulating and controlling phase transitions enables the engineering of environmental responsiveness, which is vital for applications in green biotechnology.
4. Mapping Emergence, Bifurcation, and Transitions onto CAS Variables
To integrate these concepts with our CAS variables, we propose the following mappings:
