🔦 Singlet Oxygen Dose Simulator (3D)

Why a depth-resolved 3D volume adds something the 2D lab can't show

The 2D Singlet Oxygen Dose Simulator walks through the photophysics stage by stage — ground state, excitation, triplet-triplet energy transfer, cytotoxic reaction, cumulative dose — as a flat narrative. This 3D companion keeps the same underlying photochemistry (photosensitizer excitation → intersystem crossing → Type II energy transfer to molecular oxygen → localized biomolecule oxidation) but places it inside an actual tissue volume with a real depth axis, so the single variable the 2D version can't visualize — how far light actually reaches before it's used up — becomes something you can orbit around and inspect directly.

Photons spawn at the irradiated surface and travel downward through the slab. Each step, a Beer-Lambert-style stochastic attenuation check removes photons with a probability set by the tissue attenuation coefficient — which the Wavelength slider controls directly, matching the real clinical pattern where shorter red wavelengths near 630 nm are absorbed within roughly a millimeter while longer red / near-infrared wavelengths near 700 nm reach several millimeters deeper. The readout panel's "Penetration 1/e" figure is that depth, computed directly from the slider rather than fit after the fact.

Photosensitizer molecules scattered through the volume only excite when a photon happens to be absorbed near them; excited triplet molecules then hunt for a nearby ³O₂ molecule (whose local density you set with the Tissue Oxygenation slider) to complete the spin-conserving energy transfer into cytotoxic ¹O₂, visible as a red flash. That singlet oxygen survives only a short simulated window before it either oxidizes a nearby lipid, protein or DNA target — turning it violet — or is quenched by the surrounding medium, mirroring the nanometer-scale reach and microsecond lifetime described in the 2D lab's biochemistry stage.