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CRISPR-Cas9 R-Loop Kinetic Race

2D kinetic-race plot of Cas9 R-loop propagation: watch a free-energy landscape and an ensemble of stochastic zippering trajectories reveal why seed mismatches near the PAM abolish cleavage while PAM-distal mismatches are tolerated.

Molecular Biology2DAdvanced60 FPS📱 Mobile-adapted⇄ 3D version

This is the 2D counterpart to the 3D R-loop helix simulator: the same biased random-walk zippering model, rendered instead as a free-energy landscape plus a live "kinetic race" of stochastic trajectories rather than a rotating DNA helix. Place a mismatch cluster anywhere along the guide, choose a canonical or suboptimal PAM, race a single animated trajectory or plot a fast batch of 100, and watch the spaghetti plot's green fraction converge on the exact analytical cleavage probability — while the landscape panel shows exactly where along the protospacer the energetic wall standing in its way actually sits.

⚙ Under the hood

2D kinetic-race plot of Cas9 R-loop propagation: a free-energy landscape and a live ensemble of stochastic zippering trajectories show why mismatches near the PAM (seed region) abolish cleavage while distal mismatches are tolerated — the same birth-death model as the 3D helix version, rendered instead as a landscape plus a stochastic-trajectory 'spaghetti plot'.

CRISPRCas9R-loopoff-targetmolecular biologygene editingkineticsMonte Carlo

2D · HTML5 Canvas 2D · 60 FPS target · runs fully client-side, no install