01 Introduction — what you're about to explore
A from-scratch, interactive reconstruction of a quantum-biology paper. No physics background needed — start here.
Microtubule tryptophan networks · arXiv:2602.02868v1 · interactive reconstruction
How does a flicker of light travel — and linger — inside a cell's skeleton?
Microtubules are hollow protein tubes that give cells their shape and act as internal railways. They're studded with tryptophan, an amino acid that absorbs ultraviolet light and behaves like a tiny antenna. Packed close together, these antennas couple into a shared quantum network.
This site attempts to reproduce a 2026 paper that asks: when one antenna lights up, how does that excitation — and the quantum correlations it carries — flow, get shared, and leak away? Everything here is computed live from a from-scratch simulation, not pre-rendered.
Eight tryptophans per tubulin building block — each a light-driven dipole with a fixed position and orientation.
Some collective modes radiate super-fast (superradiant): they broadcast the energy outward almost at once.
Others are nearly dark (subradiant): they trap the excitation and hold its correlations far longer.
The seven views ahead
Each tab is a live step of the reconstruction — drag, scrub, hover. Click a card to jump in.
Spot something unclear, off, or explained at the wrong abstraction level? Use the Feedback button (bottom-right) on any view.
01 Geometry — Trp sites & dipoles
Eight tryptophan chromophores extracted from PDB 1JFF, each an indole-ring centroid with its ¹Lₐ transition dipole. Drag to orbit · scroll to zoom.
02 Couplings — Δ and G matrices
Coherent dipole coupling Δ (Eq. 9) and collective radiative decay G (Eq. 10), in units of the single-site rate γ. Hover a cell for the value.
03 Spectrum — bright & dark modes
Excitonic eigenmodes classified by collective radiative rate Γj/γ. Above the dashed line are superradiant (bright); below, subradiant (dark).
04 Dynamics — Lindblad evolution
Trace-preserving evolution of the five preparations. Scrub or play the timeline; watch populations, pairwise coherence and entanglement flow.
05 Embeddings — routing across scale
Top-4 focal-tubulin pairwise coherences as the environment grows from a single tubulin to a three-tubulin segment (Fig. 8).
06 Non-Markovian backflow
Trace-distance Dk(t) between two preparations of a two-tubulin subsystem. Rising intervals (shaded) are information flowing back from the surrounding tubulins (Fig. 9).
07 Lifetime scaling & disorder
Super/subradiant radiative lifetimes vs assembly size. Ordered lattices reach the millisecond range; disorder collapses the contrast (Fig. 12).