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Abstract A balloon borne Fabry Perot interferometer called High altitude Interferometer WIND observation (HIWIND) flew from Wanaka, New Zealand (44.69S, 169.14E) in April 2025 to observe mid‐latitude thermospheric winds in the southern hemisphere for the first time. The HIWIND results were compared with Thermosphere Ionosphere Electrodynamics General Circulation Model (TIEGCM) simulations. The HIWIND observed a stronger poleward (southward) meridional and eastward zonal wind during the daytime compared to the model. The ionospheric density profiles from TIEGCM were compared with those from the COSMIC 2 satellite observations. The peak heights of the ionospheric F2 layer electron density in the observations were lower than those in the model, suggesting that the meridional winds in the real world were stronger than those in the model, which is consistent with the HIWIND and TIEGCM wind comparisons. The source of the weaker simulated winds is not known and is a topic for future studies. 

K-mer-based analysis of genomic data is ubiquitous, but the presence of repetitive k-mers continues to pose problems for the accuracy of many methods. For example, the Mash tool (Ondov et al. 2016) can accurately estimate the substitution rate between two low-repetitive sequences from their k-mer sketches; however, it is inaccurate on repetitive sequences such as the centromere of a human chromosome. Follow-up work by Blanca et al. (2021) has attempted to model how mutations affect k-mer sets based on strong assumptions that the sequence is non-repetitive and that mutations do not create spurious k-mer matches. However, the theoretical foundations for extending an estimator like Mash to work in the presence of repeat sequences have been lacking. In this work, we relax the non-repetitive assumption and propose a novel estimator for the mutation rate. We derive theoretical bounds on our estimator’s bias. Our experiments show that it remains accurate for repetitive genomic sequences, such as the alpha satellite higher order repeats in centromeres. We demonstrate our estimator’s robustness across diverse datasets and various ranges of the substitution rate and k-mer size. Finally, we show how sketching can be used to avoid dealing with large k-mer sets while retaining accuracy. Our software is available at https://github.com/medvedevgroup/Repeat-Aware_Substitution_Rate_Estimator. 

Abstract We implement a nudging module into the Thermosphere Ionosphere Electrodynamics General Circulation Model (TIEGCM) to identify effective techniques for incorporating global‐scale tides and medium‐scale gravity waves (GWs) that induce ionospheric variability. Nudging the full fields of basic state variables minimizes contamination from spectral aliasing and mode coupling, ensuring the most accurate reproduction of each tidal component. In contrast, nudging solely diurnal tides has substantial spectral leakage into semidiurnal tides, leading to underestimations of their own amplitudes and day‐to‐day variabilities (DTDVs). Nudging both diurnal and semidiurnal tides mitigates such underestimations, establishing a minimal requirement for reproducing tidal dynamics and ionospheric DTDVs. Lower boundary forcing (LBF) causes significant deviations of tidal amplitudes and DTDVs near the boundary, but only a ∼10% underestimation above it. The DTDV of vertical ion drift gradually increases with more wave components incorporated and shows a ∼10% underestimation with LBF. Constraining geopotential height (Z*) is critical in TIEGCM to properly add GWs at lower levels. Model runs withZ* constrained exhibit reduced sensitivity to nudging levels: one‐level nudging and LBF runs show 20%–30% underestimations of TID magnitudes compared to a four‐scale‐height nudging run. Conversely, whenZ* is unavailable and onlyU,V,Tare constrained, one‐level nudging and LBF lead to 80%–90% underestimations of TIDs, with LBF entirely missing wave features. Therefore, multi‐level nudging, especially withZ* unconstrained, is recommended to incorporate GWs. Overall, nudging provides a powerful tool to realistically incorporate observed or simulated waves across medium to global scales into ionosphere‐thermosphere models, offering a data‐driven perspective of variability for lower boundary conditions. 

Abstract Penetrating and disturbed electric fields develop during geomagnetic storms and are effective in driving remarkable changes in the nightside low latitude ionosphere over varying time periods. While the former arrive nearly instantaneously with the changes in the solar wind electric field, the latter take more time, requiring auroral heating to modify upper atmospheric winds globally, leading to changes in the thermospheric wind dynamo away from the auroral zones. Such changes always differ from the quiet time state where the winds are usually patterned after daytime solar heating. We use the Multiscale Atmosphere‐Geospace Environment model (MAGE) and observations from the NASA Ionospheric Connection Explorer (ICON) mission to investigate both during the 7–8 July 2022 geomagnetic storm event. The model was able to simulate the penetrating and disturbed electric fields. The simulations showed enhanced westward winds and the wind dynamo induced upward ion drift confirmed by the ICON zonal wind and ion drift observations. The simulated zonal wind variations are slightly later in arrival at the low latitudes. We also see the penetrating electric field opposes or cancels the disturbed electric field in the MAGE simulation. 

Abstract We use the TIEGCM‐NG nudged by MAGIC gravity waves to study the impacts of a severe thunderstorm system, with a hundred tornado touchdowns, on the ionospheric and thermospheric disturbances. The generated waves induce a distinct concentric ring pattern on GNSS TIDs with horizontal scales of 150–400 km and phase speeds of 150–300 m/s, which is well simulated by the model. The waves show substantial vertical evolution in period, initially dominated by 0.5 hr at 200 km, shifting to 0.25 hr and with more higher‐frequency waves appearing at higher altitudes (∼400 km). The TADs reach amplitudes of 100 m/s, 60 m/s, 80 K, and 10% in horizontal winds, vertical wind, temperature, and relative neutral density, respectively. Significantly perturbations in electron density cause dramatic changes in its nighttime structure around 200 km and near the EIA crest. The concentric TIDs are also simulated in ion drifts and mapped from the Tornado region to the conjugate hemisphere likely due to neutral wind‐induced electric field perturbations. The waves manage to impact the ionosphere at altitudes of ICON and COSMIC‐2, which pass through the region of interest on a total of 8 separate orbits. In situ ion density observations from these spacecrafts reveal periodic fluctuations that frequently show good agreement with the TIEGCM‐NG simulation. The O⁺fraction observations from ICON indicate that the density fluctuations are the result of vertical transport of the ions in this region, which could result from either direct forcing by neutral winds or electrodynamic coupling. 

Abstract We provide observational evidence that the stability of the stratospheric Polar vortex (PV) is a significant driver of sub‐seasonal variability in the thermosphere during geomagnetically quiet times when the PV is anomalously strong or weak. We find strong positive correlations between the Northern Annular Mode (NAM) index and subseasonal (10–90 days) Global Observations of the Limb and Disk (GOLD) O/N₂perturbations at low to mid‐northern latitudes, with a largest value of +0.55 at ∼30.0°N when anomalously strong or weak (NAM >2.5 or < −2.1) vortex times are considered. Strong agreement for O/N₂variability and O/N₂‐NAM correlations is found between GOLD observations and the Whole Atmosphere Community Climate Model with thermosphere‐ionosphere eXtension (WACCM‐X) simulations, which is then used to delineate the global distribution of O/N₂‐NAM correlations. We find negative correlations between subseasonal variability in WACCM‐X O/N₂and NAM at high northern and southern latitudes (as large as −0.54 at ∼60.0°S during anomalous vortex times). These correlations suggest that PV driven upwelling at low latitudes is accompanied by corresponding downwelling at high latitudes in the lower thermosphere (∼80–120 km), which is confirmed using calculations of residual mean meridional circulation from WACCM‐X. 

Abstract Ultra‐low‐frequency (ULF) waves cause local Thermosphere‐Ionosphere (T‐I) perturbations, but their impacts on the global T‐I system including the generation of Traveling Atmospheric Disturbances (TADs) have never been evaluated. The mechanisms responsible for the TAD generation and propagation, whether through dynamic or thermal process, are not clear either. We present a model study of ULF wave impacts on the thermosphere using the Thermosphere‐Ionosphere‐Electrodynamics General Circulation Model. The model results indicate that ULF waves can trigger globally propagating TADs at ∼810 m/s. Thermal processes are the main driver for the TAD generation and propagation, with Joule heating and adiabatic processes taking effects inside the TAD source region, and adiabatic processes and heat conduction being the dominant processes outside. Model results also show that TAD propagation is almost independent of seasonal effects. This study reveals the physical connections between magnetospheric ULF waves and thermospheric disturbances for the first time. 

Abstract Magnetospheric forcing during geomagnetically “quiet” periods is generally assumed to have little impact on the low‐ and mid—latitude ionospheres, especially during solar minimums. However, recent observational evidence suggests that geomagnetic forcing can exert a measurable impact on the global ionosphere even during geomagnetically quiet times. In this study, the Whole Atmosphere Community Climate Model eXtended is employed to investigate how magnetospheric forcing affects the 30‐day average of ionospheric F2‐region peak electron density (NmF2) and height (HmF2) during a geomagnetically quiet period (average Kp 1.67). Four 5‐member ensemble simulations were conducted with different geomagnetic forcings: (a) no geomagnetic disturbances, (b) real Kp, (c) a constant low Kp of 1.67, and (d) a constant moderate Kp of 3.33, all under the same solar minimum condition with a constant F10.7 of 70 sfu. These ensemble runs were generated by introducing small neutral temperature perturbations. The results reveal that quiet‐time magnetospheric forcing alters the 30‐day mean NmF2 by up to 55% at low and mid latitudes. Daytime HmF2 rises by 20–50 km near the equatorial ionization anomaly crests but decreases by 20–30 km near the dip equator around local sunset. These variations are primarily driven by changes in neutral composition, winds, and plasma vertical E × B drifts. These findings demonstrate that magnetospheric forcing during quiet periods can substantially influence ionospheric NmF2. Our results highlight the need to account for the effects of quiet‐time magnetospheric forcing in space weather forecasts and scientific research. 

A new version of the US National Science Foundation National Center forAtmospheric Research (NSF NCAR) thermosphere-ionosphere-electrodynamicsgeneral circulation model (TIEGCM) has been developed and released. Thispaper describes the changes and improvements of the new version 3.0since its last major release (2.0) in 2016. These include: 1) increasingthe model resolution in both the horizontal and vertical dimensions, aswell as the ionospheric dynamo solver; 2) upward extension of the modelupper boundary to enable more accurate simulations of the topsideionosphere and neutral density in the lower exosphere; 3) improvedparameterization for thermal electron heating rate; 4) resolvingtransport of minor species N(2D); 5) treating helium as a major species;6) parameterization for additional physical processes, such as SAPS andelectrojet turbulent heating; 7) including parallel ion drag in theneutral momentum equation; 8) nudging of prognostic fields near thelower boundary from external data; 9) modification to the NO reactionrate and auroral heating rate; 10) outputs of diagnostic analysis termsof the equations; 11) new functionalities enabling model simulations ofcertain recurrent phenomena, such as solar flares and eclipse. Wepresent examples of the model validation during a moderate storm andcompare simulation results by turning on/off new functionalities todemonstrate the related new model capabilities. Furthermore, the modelis upgraded to comply with the new computer software environment at NSFNCAR for easy installation and run setup and with new visualizationtools. Finally, the model limitations and future development plans arediscussed.