Folding Funnel Energy Landscape

This simulator renders the free-energy surface that energy-landscape theory says a protein actually explores while folding: a funnel-shaped landscape over the fraction of native contacts Q, narrowing and deepening toward the native state at its base. An ensemble of conformations, each an instanced sphere colour-coded by its own progress toward Q=1, undergoes overdamped Langevin dynamics on this surface — diffusing under thermal noise while being pulled downhill by the funnel's energetic bias, and occasionally trapped by the energetic roughness ("frustration") layered on top. Live controls for temperature, ruggedness, funnel steepness and ensemble size, plus running statistics on the fraction folded and mean folding time, let you explore why a smooth, sufficiently steep funnel resolves Levinthal's paradox while a rugged or shallow one produces slow, glassy, multi-pathway folding.