Each backbone nucleotide sits at angle θi = i·twist (real B-DNA averages 34° per base pair, 10.4 bp per full turn) at a fixed rise of 0.34 nm per step. The two backbones are 180° out of phase — x = R·sin(θi), x = R·sin(θi+π) — which is exactly the parametric curve traced by a real double helix; strand depth (cos θi) darkens and thins whichever backbone is momentarily behind, giving the 2D drawing a rotating 3D look.
Each rung is a base pair: adenine always pairs with thymine (2 hydrogen bonds), guanine always with cytosine (3 bonds) — drawn in matching colors. The mutation slider randomly flags a rung as mismatched (flickering red) at a rate scaled by the slider.
Starting replication drives a fork downward through the base-pair list at a fixed rate: bases above the fork are drawn unzipped, splayed apart, each original strand shown re-growing a fresh complementary strand — the semi-conservative mechanism by which each daughter molecule keeps one old strand and gains one new one.