Hydrophobic Collapse 2D: Polymer Folding & Rg Trace

This simulation drives a coarse-grained bead-chain polymer through the hydrophobic collapse that initiates globular protein folding, computed and rendered natively in two dimensions: a heteropolymer of hydrophobic (H) and polar (P) beads, connected by harmonic bonds, evolves under overdamped 2D 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 chain folds itself into a compact 2D globule with a buried hydrophobic core and a polar rim — the same energetic asymmetry that drives real proteins to collapse in water, replayed here as a planar packing problem rather than a projected 3D structure. A live strip chart traces the radius of gyration through time alongside readouts for the collapse ratio and hydrophobic-contact count, while a sequence-pattern selector shows how the arrangement of H/P residues along the backbone controls whether a well-packed 2D core is even reachable.