Hydrophobic Collapse: Protein Folding Molecular Dynamics

This simulation drives a coarse-grained bead-chain polymer through the hydrophobic collapse that initiates globular protein folding: a heteropolymer of hydrophobic (H) and polar (P) beads, connected by harmonic bonds, evolves under overdamped Langevin dynamics with a Lennard-Jones attraction restricted to H–H pairs and a purely repulsive Weeks-Chandler-Andersen potential everywhere else. Raise the hydrophobic well depth or lower the solvent temperature and the extended coil folds itself into a compact molten globule with a buried hydrophobic core and a polar surface — the same energetic asymmetry that drives real proteins to collapse in water before secondary and tertiary structure lock in. Live readouts track the radius of gyration, its ratio to the fully extended chain, and the number of hydrophobic contacts, while a sequence-pattern selector shows how the arrangement of H/P residues along the backbone controls whether a well-packed core is even reachable.