Numerical simulations have been performed to model the neutral density response to two substorms in March 1979. Observations of density from the Satellite Electrostatic Triaxial Accelerometer (SETA) during this interval revealed neutral density waves propagating from high latitudes in response to the substorms. For the first substorm, waves were seen on both the day and nightside in the Northern Hemisphere, and for the second, only strong nightside waves were detected. The data also revealed the formation of deep neutral density “holes” at high latitudes. To simulate the response, a coupled thermosphere ionosphere model was driven by an empirical substorm model designed to follow the various phases of the substorms. By tuning the magnitude of the energy injection and, in one case, rotating the spatial distribution of the sources, both the wave features on the day and nightside, and the neutral density holes were reproduced. The neutral density waves were found to be consistent with the passage of atmospheric gravity waves with propagation speeds of 600 to 700 m/s. The neutral density holes are dynamically driven, created by the high velocity neutral winds from ion-drag. During strong geomagnetic activity momentum forcing resulting from ion-drag drives neutral winds of several hundreds of m/s. Inertial forces on the gas parcels cause a divergence in the vortex-like circulation. Backpressure induced by the divergent wind field does not completely balance the flow, and air rises within the vortex core, to maintain continuity, and cools adiabatically to produce a low temperature. Due to the cooling that takes place, in spite of the strong Joule heating that must accompany the ion-drag, the cold vortex core appears as a density hole. The physical model is able to reproduce the magnitude and location of the density holes. The study indicates that physical models, with well-defined magnetospheric inputs, will be able to improve neutral density specification for orbital tracking during period of high geomagnetic activity.