Amphibian and mammalian rods can both detect single photons of light even though they differ greatly in physical dimensions, mammalian rods being much smaller in diameter than amphibian rods. To understand the changes in physiology and biochemistry required by such large differences in outer segment geometry, we developed a computational approach, taking into account the spatial organization of the outer segment divided into compartments, together with molecular dynamics simulations of the signaling cascade. We generated simulations of the single-photon response together with intrinsic background fluctuations in toad and mouse rods. Combining this computational approach with electrophysiological data from mouse rods, we determined key biochemical parameters. On average around one phosphodiesterase (PDE) molecule is spontaneously active per mouse compartment, similar to the value for toad, which is unexpected due to the much smaller diameter in mouse. A larger number of spontaneously active PDEs decreases dark noise, thereby improving detection of single photons; it also increases cGMP turnover, which accelerates the decay of the light response. These constraints explain the higher PDE density in mammalian compared with amphibian rods that compensates for the much smaller diameter of mammalian disks. We further find that the rate of cGMP hydrolysis by light-activated PDE is diffusion limited, which is not the case for spontaneously activated PDE. As a consequence, in the small outer segment of a mouse rod only a few activated PDEs are sufficient to generate a signal that overcomes noise, which permits a shorter lifetime of activated rhodopsin and greater temporal resolution.phototransduction | mathematical modeling | analysis | stochastic S ignal transduction at a single molecular level requires controlled biochemical events occurring in constrained cellular microdomains. Furthermore, intrinsic fluctuations in the events of the transduction pathway generate a noisy background, which sets the limit of detection. Of all of the G-protein cascades in nature, the best understood are those initiated by the absorption of a photon in Drosophila microvilli (1, 2) and in the outer segment (OS) of vertebrate rod photoreceptors (1, 3, 4). Much of the research on vertebrate transduction has used either amphibians or mammals. The rods of both species have been shown to have the remarkable ability to detect single photons of light above background noise (5, 6); and for both a photon closes about 5% of the channels open in darkness. However, amphibian and mammalian rods differ in concentrations and biochemical properties of proteins involved in the light response and by as much as an order of magnitude in the diameter of their disk membranes, where the reactions of the cascade take place. It remains largely unknown how the biochemistry and the rod geometry adapt to guarantee a reliable macroscopic response initiated by a single molecular event.To explore this fundamental question, we developed a model that combines spatially res...