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Observations from lidars and satellites have shown that large neutral temperature increases and decreases occur in the middle and low latitudes of the mesosphere and lower thermosphere region during geomagnetic storms. Here we undertake first-principles simulations of mesosphere and lower thermosphere temperature responses to storms using the Thermosphere Ionosphere Mesosphere Electrodynamics General Circulation Model to elucidate the nature and causes of these changes. Temperature variations were not uniform; instead, nighttime temperatures changed earlier than daytime temperatures, and temperatures changed earlier at high latitudes than at low ones. Furthermore, temperatures increased in some places/times and decreased in others. As the simulation behaves similar to observations, it provides an opportunity to understand physical processes that drive the observed changes. Our analysis has shown that they were produced mainly by adiabatic heating/cooling that was associated with vertical winds resulting from general circulation changes, with additional contributions from vertical heat advection.