Histone Code 2D: Chromatin Fiber Compaction

Histone Modifications

Acetylation (HAT activity) 30%

H3K9 methylation (HP1 recruitment) 20%

Transcription factors 2

Live Readouts

Compaction

Accessibility

Radius of gyration

0.00

TF binding events

Accessible nucleosome (euchromatin)
Compacted nucleosome (heterochromatin)
Transcription factor (searching)
Transcription factor (bound)

How it works

DNA wraps around histone octamers to form nucleosomes — "beads on a string." Whether that string stays open or folds into a dense coil is set by chemical marks on the histone tails, not by the DNA sequence itself: this is epigenetics. This 2D version solves the identical chain physics as a planar polymer — a genuinely independent 2D N-body integration, not a flattened 3D render — so the fold pattern you see is computed directly from 2D positions and 2D forces.

Inter-nucleosome attraction:
ε_i = ε_max · [ (1 − A) + M · κ_i ]
Pair potential (Lennard-Jones-like, 2D):
U(r) = 4·ε_ij·[ (σ/r)^12 − (σ/r)^6 ]
Radius of gyration: Rg = sqrt( (1/N)·Σ|r_i − r_com|² )

Acetylation (A) — histone acetyltransferases (HATs) add acetyl groups to lysines on histone tails, neutralizing their positive charge. This weakens the electrostatic grip between nucleosomes (notably H4K16ac), loosening the chain into open, gene-accessible euchromatin.
H3K9 methylation (M) — methylated H3K9 recruits HP1, a protein that dimerizes and bridges neighboring nucleosomes, pulling the chain into a compact, transcriptionally silent heterochromatin coil.
κ_i — a fixed per-nucleosome susceptibility (models real sequence/CpG-context heterogeneity), so the same global enzyme activity compacts some stretches of the chain before others — exactly how real chromatin domains form.
Transcription factors — probes that random-walk in the 2D plane near the chain and can only dock at nucleosomes whose local neighbor density is low enough to be physically reachable, modeling how compaction gates gene expression without changing the DNA sequence.
Radius of gyration (Rg) — the standard polymer-physics measure of how spread out the chain is; compaction % is reported relative to the Rg of the fully extended chain.

Real-world relevance: this loosen/compact switch, driven by HAT/HDAC and HMT/demethylase enzymes, is how a skin cell and a neuron read the identical genome differently — and it's the mechanism targeted by HDAC-inhibitor cancer drugs (e.g. vorinostat).

Nucleosome chain (linker DNA)