When light energy from the sun is absorbed by a chlorophyll molecule within a sample, the electronic configuration of the molecule is temporarily altered. This excited configuration is inherently unstable and short lived (typically less than 10^-8 sec) as several processes compete to dissipate the absorbed energy. In photosynthetic systems the processes by which this energy is dissipated are either photochemical or non-photochemical processes.

Photochemical processes utilise absorbed energy for photochemistry, during which electron donation from pigment to an acceptor molecule occurs. Such processes direct energy for the chemical work involved in photosynthesis.

Non-photochemical processes dissipate energy from the photosynthetic apparatus in a manner which does not drive photosynthesis. Energy is usually re-emitted from the sample in the form of infra-red radiation (heat) and red/far-red radiation which is known as chlorophyll fluorescence.

The competition between these processes for absorbed energy ensures that a reduction in the rate of one process will be associated with a corresponding increase in the rates of competing processes e.g. a reduction in the dissipation of energy by photochemistry will be reflected in an increase in energy dissipation by non-photochemical processes such as heat production and chlorophyll fluorescence.

Any forms of biotic or abiotic stress which have an effect on the photosynthetic performance of the sample e.g. effects the leaf’s ability to channel solar energy through the photochemical pathways, will therefore alter the intensity of the chlorophyll fluorescence emission.

Consequently measurement of changes in the extent of fluorescence emission can be used to infer information about changes in the efficiency of light use for photochemistry (Reviewed in Krause and Weis 1991* and Govindjee 1995**) allowing samples to be screened effectively for particular types of stress factors which limit the photosynthetic performance of the sample.

Since the work of Emerson et al. (1932)*** it has been widely accepted that there are two separate photochemical steps during photosynthesis which are associated with different groups of pigments; these groups have become known as photosystem I and photosystem II. In practice differences in the functionality of photosystem I and II mean that at least 95% of the chlorophyll fluorescence signal observed under physiological temperatures is derived from chlorophyll molecules associated with photosystem II (PSII).