Base Editor Repair Outcome Simulator

Cytosine base editing converts a single C:G base pair to T:A without cutting both DNA strands — but the raw chemistry only creates a uracil intermediate, and what the cell does with that uracil determines whether the edit actually lands. This simulator renders a 3D B-form DNA helix with a Cas9-nickase-deaminase complex parked on a target cytosine, then runs the downstream repair race as a stochastic model: each trial launches a particle from the target base toward one of four outcome bins — unedited, precise C→T conversion, silent reversion back to C, or an indel from error-prone repair of the abasic site — with landing odds set by whether a uracil glycosylase inhibitor (UGI) is fused to the editor and whether the opposite strand carries a directing nick, exactly the two design choices that separate early, impure base editors from modern high-fidelity ones.