We have performed simulations using the Naval Research Laboratory's physics‐based model of the ionosphere, Sami3 is A Model of the Ionosphere (SAMI3), to illustrate how neutral wind dynamics is responsible for day‐to‐day variability of the ionosphere. We have used neutral winds specified from the extended version of the specified dynamics Whole Atmosphere Community Climate Model (SD‐WACCM‐X), in which meteorology below 92 km is constrained by atmospheric specifications from an operational weather forecast model and reanalysis. To assess the realism of the simulations against observations, we have carried out a case study during January–February 2009, a dynamically disturbed time characterized by a sudden stratospheric warming (SSW) commencing 24 January 2009. Model results are compared with total electron content (TEC) from Jet Propulsion Laboratory global ionospheric maps. We show that SAMI3/SD‐WACCM‐X captures longitudinal variability in the equatorial ionization anomaly associated with nonmigrating tides, with strongest contributions coming from the diurnal eastward wave number 2 (DE2) and DE3. Both migrating and nonmigrating tides contribute to significant day‐to‐day variability, with TEC varying up to 16%. Our simulation during the SSW period reveals that at the Jicamarca longitude (285°E) on 27 January 2009 nonmigrating tides contribute to an enhancement of the electron density in the morning followed by a decrease in the afternoon. An enhancement of the semidiurnal eastward wave number 2 (SE2) and SE3 nonmigrating tides, likely associated with the appearance of the SSW, suggests that these tides increase the longitudinal variability of the SSW impact on the ionosphere. The conclusion is that realistic meteorology propagating upward from the lower atmosphere influences the dynamo region and reproduces aspects of the observed variability in the ionosphere.
