DNA Supercoiling & Topoisomerase Simulator

Copying DNA is a topological problem, not just a chemical one: an advancing replication fork spins the helix ahead of it into tightly over-wound, positively supercoiled DNA while leaving under-wound, negatively supercoiled DNA behind — the twin supercoiled-domain model. This simulator renders a real 3D double helix whose local twist visibly tightens ahead of the fork and loosens behind it as the fork advances, tracks the linking-number change ΔLk and supercoil density σ live, and lets you dial in Topoisomerase I (single-strand swivel, ±1 turn per cycle) or Topoisomerase II / gyrase (double-strand-passage, ±2 turns per cycle, ATP-powered) to relieve the torsional strain. Push the fork speed up with both enzymes off and watch torque climb until the fork stalls — exactly what happens when a topoisomerase poison like ciprofloxacin or camptothecin blocks the enzyme in a living cell.