The Penumbra · Working model

Where light goes in a leaf

A leaf absorbs blue light. Each packet of that energy then has three exits: it drives photosynthesis, it leaves as heat, or it leaves as a faint red glow. The three compete, so when one takes more, the others get less. Every particle below is routed by the published equations for that competition.

absorbed light electrons onward →

incoming photosynthesis regulated heat unregulated heat red glow

Pause

Reaction centers open 100%

Rings in the band. A closed center is still busy with its last packet and can't take another.

Protective heat dump (NPQ) 0.00

0 in a dark-rested leaf. Typical plants reach 0.5 to 3.5 in full light.

Example states

Dark-rested leaf Flash on rested leaf Full sun, protected Full sun, unprotected

The split, right now

Large number: the equation. Small number: what the particles above have actually done since your last change.

Photosynthesis Y(II)

0%sim —

Regulated heat Y(NPQ)

0%sim —

Unregulated heat part of Y(NO)

0%sim —

Red glow fluorescence, part of Y(NO)

0%sim —

What is computed

The share of packets sent to each exit. Each absorbed packet takes an exit with the probability the equations give, so the simulated counts converge on the computed percentages. The rings that count as open, and the four rates behind every number, come from the model.

What is styling

Positions, speeds, trail lengths, colors and the shape of the band. Real chlorophyll sits in stacked membranes far smaller than anything drawn here, and energy hops between molecules in billionths of a second. The picture is a schematic. The proportions are the claim.

Assumptions

• ModelA shared pool of chlorophyll feeding many reaction centers (the "lake model"), with four competing exits, each a fixed rate. The yield of an exit is its rate divided by the sum of all four.
• SourcedThe ratio of photosynthesis rate to the other rates is set so a dark-rested leaf scores Fv/Fm = 0.83, the typical healthy value.
• CalibratedHow the unregulated loss splits between red glow and heat is not set by these sources. It is chosen (8% glow) so that total glow stays in the 1 to 2% of absorbed light that the sources report. This is the least certain number on the page.
• SimplifiedYou set the open fraction and NPQ directly. A real leaf sets both from light intensity, temperature and its own history over minutes, which this model leaves out. Photosystem I and its small glow are ignored.

Sources

1. Maxwell, K. & Johnson, G. N. (2000). Chlorophyll fluorescence: a practical guide. Journal of Experimental Botany 51, 659–668. doi.org/10.1093/jexbot/51.345.659. The three exits and their competition, glow at 1 to 2% of absorbed light, Fv/Fm near 0.83, NPQ of 0.5 to 3.5.
2. Klughammer, C. & Schreiber, U. (2008). Complementary PS II quantum yields calculated from simple fluorescence parameters. PAM Application Notes 1, 27–35. walz.com PDF. The four-rate model and Y(II) + Y(NPQ) + Y(NO) = 1.
3. Cited through the two papers above, not read directly: Kitajima & Butler (1975), the Fv/Fm ratio; Genty, Briantais & Baker (1989), the photosynthesis yield; Björkman & Demmig (1987), the 0.83 benchmark.