DNA polymerase follows the replication fork, reading each template strand and adding the complementary base (A↔T, G↔C) to build two new daughter duplexes from one original molecule.
P(mutation per base) = mutRate
Fork position(t) = clamp(fork + speed·dt, 0, N)
CRISPR-Cas9: cut at target → NHEJ repair
P(clean repair) = 70%, P(indel) = 30%
- Replication speed — bases added per second by the polymerase; real cells run ~1000 bp/s per fork.
- Mutation rate — chance each newly synthesized base is miscopied (shown in magenta), modelling replication error.
- Strand length — number of base pairs in the template; longer strands take proportionally longer to fully replicate.
- Fire CRISPR-Cas9 — sends the Cas9 protein to cut both strands at a target site ahead of the fork; NHEJ usually repairs cleanly but sometimes leaves a small insertion/deletion.
- Reset strand — restarts the fork from the beginning, reseeds a random sequence and clears the counters.
Real-world relevance: replication fidelity and CRISPR repair outcomes underpin everything from cancer-causing mutations to gene-therapy edits used to treat sickle-cell disease.