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Absorbed photon flux is the rate at which a specified sample absorbs photons. Number-based flux counts photons per second; amount-based flux counts moles of photons per second. The absorbed rate differs from the incident rate and supplies the denominator of a rate-based photochemical quantum yield. For monochromatic light passing through a homogeneous absorbing sample,where $q_0$ is incident photon flux and $A(\lambda )$ is the decadic absorbance at the excitation wavelength. Reflection and scattering must be absent or accounted for before transmission loss is interpreted entirely as absorption.^[ref]

For example, $q_0=2\mu \mathrm{mol}{\mathrm{s}}^{-1}$ and $A=0.30$ giveA product-formation rate of $0.20\mu \mathrm{mol}{\mathrm{s}}^{-1}$ would then give photochemical quantum yield approximately $0.20/0.998=0.200$, whereas division by incident flux gives $0.10$. The two calculations answer different questions.

The distinction also matters during an experiment: if absorbance changes as a reactant is consumed, one initial flux value cannot represent the whole exposure. Absorbed photon amount is the time integral of the absorbed rate. If the numerator is a change of concentration per second, divide the total absorbed amount rate by the illuminated sample volume as well. A photon rate, a rate per unit area and a rate per unit volume have different dimensions; the word flux alone should not conceal that distinction.^[ref]

Photoisomerization is a light-induced conversion between molecular isomers: absorption of a photon initiates a change in molecular arrangement without requiring a change in elemental composition. The resulting isomers can have different shapes, spectra or interactions even though they contain the same kinds and numbers of atoms.

A biological example occurs in rhodopsin. Its bound 11-cis-retinal chromophore changes toward all-trans-retinal after light absorption, initiating changes in the receptor that can activate transducin. This converts a molecular rearrangement into a signaling event.^[ref]

The change is an example of cis-trans isomerism, not fragmentation of retinal into smaller molecules. “Light-induced” also does not mean that every photon entering a sample produces one permanent isomerization. Absorption, competing excited-state processes and subsequent reactions can affect the measured outcome.

An idealized photochemical quantum yield for a specified primary product is $\Phi =N_{\mathrm{product}}/N_{\mathrm{absorbed}\mathrm{photons}}$. If 100 photons are absorbed and 30 product-forming events are counted under a defined low-conversion assay, $\Phi =0.30$. Counting incident rather than absorbed photons would answer a different question. The example is bookkeeping, not a measured rhodopsin yield.

The surrounding protein can influence the chromophore's behavior by controlling its local environment. A free molecule's light response therefore need not be identical to its behavior inside a receptor. The useful mechanism is the full chain from absorption to rearrangement to altered interaction with other molecules.