Geophysical Research Letters: Small-scale waves originating from the lower atmosphere have been shown to propagate into the thermosphere. To study their effects a high-resolution whole atmosphere model has been employed. Using this high-resolution model, which can partially resolve the small-scale waves, we can directly quantify the force exerted by these waves on the general circulation in the thermosphere. We found that such force is strong, and affects the thermospheric circulation in both winter and summer hemisphere. This consequently changes the distribution of important thermospheric species. One measure of the thermospheric composition is the ratio of atomic oxygen and molecular nitrogen, which is an indicator of the relative abundance of atomic and molecular species. This ratio has been grossly over-estimated in previous modeling studies. It is reduced as a result of the circulation change, and is in much better agreement with observations.