As seen in the figure (FIGURE), the biological processes of leaves and soil are studied in CloudRoots. Driven by the amount of direct and diffuse radiation reaching the canopy, the leaves control the stomatal aperture and photosynthesis rate. We use mechanistic models to study the intermittency of light (sun or cloud flecks) and how they influence radiation, in-canopy temperature and water vapor deficit. Two photosynthesis pathways are included (C3/C4). A novel aspect of CloudRoots is to include the diurnal variability of water vapor and carbon dioxide stable isotopologues to study the individual contributions of soil and plants. The variability of soil moisture and temperature is also taken into account in representing the exchange of soil carbon dioxide (heterotrophic) and soil evaporation and their response to soil moisture stress (droughts).