Nucleosome chain (linker DNA)
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The same DNA sequence can be read as active or silent depending only on chemical marks stamped onto the histone proteins it's wrapped around. This simulator renders a chain of nucleosomes as a real physical system: adjacent beads are linked by springs modeling linker DNA, and non-adjacent beads attract through a Lennard-Jones-like potential whose strength depends on two sliders — histone acetylation, which neutralizes tail charge and opens the fiber, and H3K9 methylation, which recruits HP1-style bridging and compacts it. Each nucleosome carries a fixed, sequence-like susceptibility, so heterochromatin domains emerge unevenly along the chain exactly as they do in a real nucleus. Transcription-factor probes random-walk through the scene and can only dock where local compaction is low enough to be physically accessible, and live readouts track overall compaction, chromatin accessibility, and cumulative TF binding events as you tune the two enzyme activities.