Recent observations have revealed unambiguous signatures of the impact of terrestrial weather on the upper atmosphere. The manifestation are either spatial, indicating a longitude dependence in ionospheric features, or temporal, indicating multi-day periodicities from planetary wave forcing. A new model of Integrated Dynamics through Earth's Atmosphere (IDEA) that self-consistently combines a Whole Atmosphere Model (WAM) with a Global Ionosphere Plasmasphere (GIP), together with a solution of global electrodynamics has been used to begin to interpret the observations. The model was developed under a NASA sponsored collaborative project between the University of Colorado and National Weather Service's (NWS) Environmental Modeling and Space Environment Centers. The model was specifically designed to understand and interpret the recent observations, and determine the physical processes responsible for the longitude dependent ionospheric spatial structure and planetary wave (PW) modulation of the upper atmosphere. The model simulates ionospheric variability and is used to begin to quantify and separate the impact of either neutral dynamics, composition, and electrodynamics at mid and low latitudes.