Current atmospheric modeling represents both the biosphere and the atmosphere directly above the forest canopy as coarse boundary conditions. The biosphere is expressed as a 2-D surface that does not take into account specific qualities of the forest canopy (i.e. canopy height and crown size). Directly above the forest canopy, it is assumed that mixing allows us to ignore canopy heterogeneity. Present research suggests that a more high-resolution 3-D canopy is needed for a more accurate representation of the interaction between biosphere and atmosphere. This research will utilize the UMBS FASET and AmeriFlux sites to study the canopy structure and to further develop the RAFLES atmospheric modeling software developed by Dr. Bohrer. This software simulates the interactions among these canopy structures and wind, as well as fluxes of water vapor, heat, and CO2 using a biosphere-atmosphere high resolution large eddy simulation model that resolves 3-D explicit forest canopies. My hypothesis is that by taking the explicit 3D canopy structure into account, we will be able to model phenomena such as increased fluxes over gaps, tree-scale patterns of soil moisture, and modifications to the effective aerorodynamic roughness length of the forest. These phenomena, with strong effects on both the forest ecology and the atmosphere, cannot be resolved with a coarse model that does not resolve tree-scale structures at the biosphere-atmosphere interface. Along with atmospheric modeling, closed system automated chambers previously installed at the FASET and AmeriFlux sites at UMBS will be used to quantify links between soil respiration and the turbulent dynamics of the canopy.