How do we quantify the coupling of the carbon, water and energy cycles at the surface, in the boundary layer and in atmospheric vertical transports?

Photosynthesis is coupled to transpiration but not to surface evaporation off wet soils and wet canopies. The BL diurnal cycle and daily equilibrium involves all the surface fluxes and the radiation balance. The vertical transports are coupled especially through convective clouds, and cloud forcing feeds back on the SW and LW surface energy budget. We need to evaluate and quantify this coupled system in earth system models.