The impact of particle precipitation on the ion-neutral collision frequency analyzed with EISCAT measurements

Günzkofer, Florian; Stober, Gunter; Kero, Johan; Themens, David R.; Gulbrandsen, Njål; Tsutsumi, Masaki; Borries, Claudia

doi:https://doi.org/10.5194/egusphere-2024-2708

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https://doi.org/10.5194/egusphere-2024-2708

Preprints

10 Sep 2024

| 10 Sep 2024

The impact of particle precipitation on the ion-neutral collision frequency analyzed with EISCAT measurements

Florian Günzkofer, Gunter Stober, Johan Kero, David R. Themens, Njål Gulbrandsen, Masaki Tsutsumi, and Claudia Borries

Abstract. The ion-neutral collision frequency is a key parameter for the coupling of the neutral atmosphere and the ionosphere. Especially in the mesosphere lower-thermosphere (MLT), the collision frequency is crucial for multiple processes e.g. Joule heating, neutral dynamo effects, and momentum transport due to ion drag. Very few approaches exist to directly infer ion-neutral collision frequency measurements in that altitude range. We apply the recently demonstrated difference spectrum fitting method to obtain the ion-neutral collision frequency from dual-frequency measurements with the EISCAT incoherent scatter radars in Tromsø. A 60-hour-long EISCAT campaign was conducted in December 2022. Strong variations of nighttime ionization rates were observed with electron densities at 95 km altitude varying from N_e,95 ∼ 10⁹ − 10¹¹ m⁻³ which indicates varying levels of particle precipitation. A second EISCAT campaign was conducted on 16 May 2024 capturing a Solar Energetic Particle (SEP) event, exhibiting constantly increased ionization due to particle precipitation in the lower E region N_e,95 ≳ 5 · 10¹⁰ m⁻³. We demonstrate that the particle precipitation significantly impacts the ion-neutral collision frequency profile. Assuming a rigid-sphere particle model, we derive neutral density profiles and show that the particle precipitation heating causes a significant uplift of neutral gas between about 90–110 km altitude. We additionally test the sensitivity of the difference spectrum method to different a priori collision frequency profiles.

Received: 29 Aug 2024 – Discussion started: 10 Sep 2024

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Florian Günzkofer, Gunter Stober, Johan Kero, David R. Themens, Njål Gulbrandsen, Masaki Tsutsumi, and Claudia Borries

Status: final response (author comments only)

RC1:
'Comment on egusphere-2024-2708', Anonymous Referee #1, 29 Sep 2024

This study analyzed two datasets from collaborative measurements with the EISCAT UHF and VHF radars in Tromso, Norway, during moderately active conditions characterized by hard particle precipitation. By applying the difference spectrum fitting method developed in a previous study, the height profiles of the ion-neutral collision frequency in the MLT region were derived. The ion-neutral collision frequency is a critical physical parameter for understanding the ionosphere-thermosphere coupling process; however, its features have not been fully elucidated. Based on the derivation, this study presented the impacts of precipitating particle forcing on the ion-neutral collision frequency and discussed plausible causalities that produce variations in the collision frequency. However, the explanation of the calculation results and physical mechanism requires more rigorous and comprehensive analysis of data and consideration from multiple perspectives, as the current text is biased toward only certain aspects or interprets phenomena in an overly simplistic manner. These issues are summarized in the major comments. The accuracy of the calculations and discussion is significantly low, and the results of this study do not meet the standards for publication. Since the quality is unlikely to be improved by reanalysis, as mentioned in Major comment 1, the recommendation for the editor is to reject.
[Major comments]

1. Artificial discontinuity at 100 km altitude

In examining Figure 2b, a discontinuity in the collision frequency is observed at approximately 100 km altitude. This discrepancy is more evident in the line plot presented in Figure 3. The quick-look figure of the EISCAT measurements available in the Madrigal database clearly indicates a significant difference in the noise level of the UHF-measured electron density above and below 100 km. One of the conclusions of this study addresses the differential effects of thermospheric density variations at altitudes above 100 km. Based on the results presented in Figures 4b and 6b, this study corroborates that thermospheric density decreases and increases at altitudes below and above 100 km, respectively. However, the validity of this conclusion is subject to scrutiny given the apparent disparity in the quality of the EISCAT measurements, which constitute the primary data used to calculate the collision frequency.
While the manda pulse code employed in radar measurements exhibits an advantage in measuring lower-altitude electron density with high range resolution, it demonstrates reduced accuracy in measuring ionospheric parameters in the E region and above compared to other pulse codes. The analysis presented in this study does not account for this characteristic (at least, no explanation is provided in the text).
As illustrated in Figure 3, the collision frequency below 95-100 km altitude exhibits a strong dependence on a priori. The authors assert that the altitude region where the influence of the a priori is significant extends up to 95 km, and they have hatched this region with gray shadows (Figures 4 and 6). Figure 3 demonstrates that the upper altitude limit is contingent upon the choice of a priori, and the a priori should be considered dominant up to 97-100 km altitude. The noise level of the EISCAT measurements is elevated for collision frequencies above 100 km altitude, as noted above. Given these considerations, the calculated results for any altitude range are deemed unreliable for this dataset, and there appears to be no justification for the discussion and conclusions based on these ambiguous results. Consequently, the results, arguments, and conclusions drawn in this study based on the observed data are considered unreliable. It is recommended to utilize EISCAT UHF and VHF simultaneous observation data employing another pulse code rather than manda.

2. Physical parameters to affect on the ion-neutral collision frequency

The collision frequency is proportional to the thermospheric and ionospheric-plasma densities, as demonstrated in Equation 1. However, this equation represents a simplified model and is also dependent on temperature (Prolss, Physics of the Earth's Space Environment, 2004). Given that the event was observed during periods of high geomagnetic activity, it is logical that the temperature of the thermosphere and ionosphere increased due to particle heating and Joule heating. Rather than restricting the analysis to attributing all collision-frequency variations to the density variations, it would have been more comprehensive to incorporate temperature effects in this study.
The variation in thermospheric density is estimated from the increase or decrease in collision frequency (Figure 4b). As demonstrated in Equation 1, the collision frequency is a function of thermospheric density; however, it is also dependent on ionospheric plasma density. Lines 167-170 in the text briefly describe the derivation method, yet it remains unclear whether the thermospheric density was calculated considering the electron density measured by the EISCAT radar. If this factor had not been considered, it should have been incorporated into the calculations. If the collision frequency has been calculated taking this into account, the error in the atmospheric density should be determined by considering the error in the measured electron density and discussing its significance in relation to the magnitude of the thermospheric density variations.

3. Feature of the vertical motion in the lower thermosphere

It was previously mentioned that variations in collision frequency were not exclusively attributable to fluctuations in the thermospheric density. Even if density variation is presumed to be the primary factor governing the collision frequency variation, the explanation provided in the text would not align with the characteristics of vertical motion in the lower thermosphere. When examining the vertical motion of the lower thermosphere, it is essential to consider horizontal motion, particularly along isobars. In the lower thermosphere, where horizontal motion predominates, an upward displacement of the isobar in the heated region induces an apparent vertical component of the wind in geographic coordinates due to thermospheric winds flowing along the isobar. In instances of intense localized heating over brief periods, upwelling across the isobar may occur, but this phenomenon dissipates rapidly in conjunction with vertical oscillations. Upon cessation of heating, the isobar expansion terminates, and the apparent vertical component diminishes. However, during a transition process under force balance between buoyancy and gravity, the atmosphere undergoes oscillation (i.e., atmospheric gravity waves are generated), and vertical motion may persist for a duration. Nevertheless, this phenomenon does not result in an increase in the spatiotemporal mean density.
Figures 4b and 6b indicate that the atmospheric density increased above 100 km altitude irrespective of the electron density level at 95 km altitude employed in this study. During periods of high geomagnetic activity, characterized by high electron density, the atmospheric density above 100 km altitude may increase. However, the intermittent increase in electron density over the two and a half days of December 13-15 suggests that it is improbable that the energy flow from the magnetosphere to the polar thermosphere/ionosphere is sustained at a sufficient level to support the density increase. Considering that particle heating should have occurred at the same location as the aurora, and given the likely structured nature of the aurora, it is implausible to assume constant upwelling in the EISCAT radar beam, although Major comments 1 and 2 elucidate the unreliability of the calculation results. Even if the calculation results capture some degree of nature, the physical interpretation of this study cannot be objectively substantiated.

[Minor comments]

L3: "momentum transport" should be revised to "momentum transfer."
L13: "different a priori collision frequency profiles" may be better to say "various a priori collision frequency profiles."
L48-49: A magnetometer in Tromso, which can be checked at the IMAGE webpage, presents substorms during the high electron density periods selected in this study. The effects of Joule heating should be discussed, along with those of particle heating.
L60-61: According to the EISCAT QL from the Madrigal database, the transmitter powers of the UHF and VHF radars have not reached these numbers.
L66: "06-15 UT is analyzed" should be revised as "06-15 UT, is analyzed."
Section 5.1: The effects of the ambiguity of the beata parameter on the derived collision frequency should be evaluated in a quantitative manner.
L222-224: The explanation is incorrect, according to Figure 3.
Section 5.5: The meteor radar measures the horizontal wind, but what this study mentions is the density. To apply the meteor radar measurements, experimental evidence or theoretical support is required to link the wind and density in advance.

Citation: https://doi.org/10.5194/egusphere-2024-2708-RC1
- AC1:
  'Reply on RC1', Florian Günzkofer, 02 Oct 2024
  
  We thank the referee for taking the time to read and evaluate our paper. We agree that the presented analysis underlies considerable uncertainties which are, however, mostly discussed in the paper. We would be happy to extend the discussion to cover the points raised by the referee. As this paper presents a completely new approach to assessing the impact of particle precipitation in the lower thermosphere, we still think that the study is worth publication. Below, we address the major comments and some of the minor comments provided by the referee.
  Major comments
  1. EISCAT data quality
  The low signal-to-noise ratio (SNR) of EISCAT measurements in the lower thermosphere is indeed a major concern of this study and partly responsible for the considerable uncertainties of the results. However, as the referee states, the low SNR and the consequent impact of the a priori profile are discussed in the paper. It should be noted, that the noise level that the referee sees in the madrigal quicklooks above 100 km is limited to times of low ionization. These are also the conditions under which the discontinuity is observed in our collision frequency profiles at around 100 km altitude. It is therefore likely that increased noise levels cause the discontinuity. This is equivalent to the explanation given in the paper where we attribute the discontinuity to an increased SNR level. However, this does not invalidate the results obtained under particle precipitation conditions which are the main focus of this paper. The supplement zip folder contains plots of the UHF spectra at 95 km, 100 km, and 105 km for average and high N_e,95 values during the December 2022 campaign. It can be seen that despite the considerable noise in the spectrum wings, the ion line peak can be identified at all altitudes. The spectra therefore appear to have sufficient quality to perform the difference spectrum analysis for average ionization conditions. Due to the large statistics of multiple hours of measurements, single time points with high-noise measurements at all altitudes do not disturb the analysis result significantly.
  It should also be noted that the “difference in noise level above and below 100 km” that the referee noticed in the quicklooks is caused by changes in the settings of a priori parameters for the GUISDAP analysis of plasma parameters. For the UHF analysis, the plasma temperatures are taken from the a priori model below 100 km altitude though the exact altitude can be set differently in GUISDAP (for the VHF analysis the a priori temperatures are fixed even up to 120 km). However, for the difference spectrum method, the GUISDAP software is only applied to convert auto-correlation functions into incoherent scatter spectra. The a priori parameters and chosen settings do not affect the result of the difference spectrum analysis.
  The manda pulse code is, according to the EISCAT experiment documentation, designed to perform measurements in the lower thermosphere and would therefore be ideal for the presented analysis. We agree that the high altitude resolution of manda measurements and the consequently lower signal quality makes this mode presumably less suitable for difference spectrum measurements compared to other modes. Since this was not tested before, the presented measurements do have scientific value and this can be added to the conclusions of the paper following the referee's line of argument.
  2. Parameters that impact the collision frequency
  The referee is correct in pointing out that other parameters than the neutral density can potentially impact the collision frequency. However, as described by (Ieda, A. (2020) “Ion‐neutral collision frequencies for calculating ionospheric conductivity”), only the resonant ion-neutral collisions are temperature dependent. Non-resonant collisions are not temperature-dependent and dominate below 600 K (which is usually the case at the investigated altitudes, see Figure of EISCAT UHF ion temperature on May 16, 2024 in the supplement). However, we agree that the T<600 K condition does not trivially hold during intensified particle precipitation. We thank the referee for pointing this out to us. We will incorporate a quantitative analysis/discussion of the influence of resonant O₂ ⁺ - O₂ collisions on the calculated neutral densities in our revision.
  The plasma density impact on the ion-neutral collision frequency is apparent from Equation 1. However, it is clearly stated that since the plasma density is by far lower than the neutral density, it does not significantly impact the collision frequency and has therefore been neglected. A brief quantitative discussion of this can be added to the manuscript.
  In general, ion-neutral collisions can be described in multiple ways, e.g. as rigid-sphere collisions (Chapman (1956) “The Electrical Conductivity of the Ionosphere: a Review.”) which results in Equation 1, or as non-resonant Maxwell collisions (Schunk and Walker (1971) “Transport Processes in the E region of the Ionosphere”). As shown in our previous publication on the difference spectrum method (Günzkofer et al., 2023), these two approaches result in very similar neutral density profiles. (Thomas et al. (2024) “D-region ion-neutral collision frequency observed by incoherent scatter spectral width combined with LIDAR measurements”) in turn showed that the non-resonant collision frequency according to Ieda (2020) is nearly equivalent to the Schunk and Walker (1971) equation. As stated above, other parameters become significant for resonant ion-neutral collision frequencies (dominant at T>600 K).
  We are aware that we apply a simplified equation to describe the collision frequency and agree with the referee that this should be discussed in the manuscript in more detail. However, the applied collision frequency approach is in line with common literature in this field. We are happy to extend the discussion regarding the collision frequencies to address the referee’s concerns within our revision.
  3. Vertical motion in the lower thermosphere
  The referee states that localized heating can cause upwelling across the isobars (increasing thermosphere density) which diminishes shortly after the heating ceases. Therefore, the heating does not cause a general, persistent increase in the thermospheric density. We agree with the referee and see this as the main conclusion of our paper.
  “Figures 4b and 6b indicate that the atmospheric density increased above 100 km altitude irrespective of the electron density level at 95 km altitude employed in this study.”
  We would argue that the opposite is the case. Figures 4b and 6b show that the atmospheric density above 100 km altitude is increased for N_e,95 > 2*10¹⁰ (7*10¹⁰) m^-3 compared to N_e,95 <10¹⁰ m^-3.
  “During periods of high geomagnetic activity, characterized by high electron density, the atmospheric density above 100 km altitude may increase. However, the intermittent increase in electron density over the two and a half days of December 13-15 suggests that it is improbable that the energy flow from the magnetosphere to the polar thermosphere/ionosphere is sustained at a sufficient level to support the density increase.”
  As argued in the manuscript, the majority of N_e,95 > 2*10¹⁰ m^-3 conditions during December 13-15 2022 occur during the night from Dec 14 to 15 where the particle precipitation heating sustains over a longer time interval. As shown in Figure 4 a, the increase of atmospheric density is restricted to these conditions and significantly lower densities are found for non-heating conditions. This is equivalent to the referee's statement that the upwelling of the atmosphere ceases quickly after the heating stops.
  “…, it is implausible to assume constant upwelling in the EISCAT radar beam”
  We agree with this statement and do not see how our results would indicate a constant upwelling of the atmosphere. Our results explicitly show that the upwelling is only found for strong heating conditions, quantified by the electron density at 95 km altitude. The duration of the auroral precipitation events presented in (Grandin et al. (2024) “Statistical comparison of electron precipitation during auroral breakups occurring either near the open-closed field line boundary or in the central part of the auroral oval”) of roughly 20 min is within the range of the required atmosphere reaction time discussed in Section 5.7 of our paper.
  Minor comments
  The substorm conditions mentioned are also visible from the SME data shown in Figure 1. We agree with the referee that the Joule heating impact during this time should be discussed. However, as shown in (Baloukidis et al. (2023), “A Comparative Assessment of the Distribution of Joule Heating in Altitude as Estimated in TIE-GCM and EISCAT Over One Solar Cycle”) and (Günzkofer et al. (2024) “Evaluation of the Empirical Scaling Factor of Joule Heating Rates in TIE‐GCM With EISCAT Measurements”), the maximum of Joule heating occurs at 120-130 km altitude. Below 110 km altitude, the Joule heating only reaches significant values for Kp>4 conditions which needs to be considered in the presented case. We thank the referee for pointing this out and would be happy to add a discussion on this to the paper within our revision.
  The meteor radar measurements were applied to assess the tidal activity during the time of the December 2022. Since the tidal activity was considerably low in the horizontal wind, we followed that tidal waves do not affect the neutral density either. However, we would be happy to look into neutral density variations following (Stober et al. (2011) “Neutral air density variations during strong planetary wave activity in the mesopause region derived from meteor radar observations”).
  Regarding the remaining minor comments, we are happy to adjust the manuscript according to the referee’s suggestions.
  
  In summary, we would like to thank the referee again for the thorough review and for bringing up several points that indeed require a more detailed discussion in the manuscript. However, we strongly disagree with the statement that the results are completely unreliable. Though the results underly considerable uncertainties, they still provide relevant qualitative insight into the processes of the lower thermosphere. Given the low number of direct measurements of neutral atmosphere processes at these altitudes, the presented results are a relevant increment. The mentioned uncertainties of the results are (mostly) dutifully reported and discussed in the manuscript. As mentioned before, we are happy to address all of the referee’s points with a thorough revision.
  
  Citation: https://doi.org/10.5194/egusphere-2024-2708-AC1
  - RC2: 'Reply on AC1', Anonymous Referee #1, 12 Oct 2024
    
    The reviewer anticipated quantitative counterarguments rather than a vague qualitative response; however, it appears that more concrete evidence should have been provided in the initial comment. A brief analysis of the same EISCAT measurements examined in this study has been conducted, and these findings will be referenced to elucidate the reviewer's perspective.
    The attached Figure C1 was generated utilizing UHF and VHF radar data for December 13-15, 2022, obtained from the Madrigal database. The observed discontinuity is present exclusively in the UHF radar data (Figure C1a). This phenomenon is a recurrent issue that may arise when the manda pulse code is applied to the UHF radar during periods of low electron density, and the discontinuity is an artifact of this technical limitation. It is evident that the discontinuity observed in the collision frequency, as illustrated in Figure 2b of this study, originates from the UHF measurements. As the UHF radar measurements are not presented in this study, it is challenging for readers to discern the underlying cause. The figure should have been included to elucidate the reason clearly, thereby preventing any potential suspicion of intentional concealment.
    In this study, the electron density at an altitude of 95 km was utilized as a parameter to categorize the calculated collision frequencies. Specifically, the electron density at an altitude of 95 km was employed to ascertain the presence of a discontinuity effect at an altitude of 100 km. Consequently, it is imperative that the validity of this methodology be evaluated quantitatively and rigorously. The appropriateness of the threshold value (2x10^10 m-3) should have been quantitatively assessed through a comparative analysis of results derived using alternative thresholds.
    Figures C1b and C1d illustrate the EISCAT-measured electron density for periods when the electron density at an altitude of 95 km exceeds 2x10^10 m-3. For the majority of the selected periods, the electron density in this altitude range (85-110 km) exhibits an increase with altitude; however, this trend is not consistent across all time points (e.g., approximately 12 UT on 2022.Dec.13, 18 UT on 2022.Dec.14, 9-12 UT on 2022.Dec.14). This observation suggests that the measurement uncertainty in the upper layers may be greater than that in the lower layers, and adequate measurement accuracy at an altitude of 95 km may not necessarily ensure the accuracy of measurements in the upper layers. It is imperative to evaluate the validity of classification based on the 95 km altitude electron density for these exceptional cases.
    Assuming the aforementioned threshold and data selection method are appropriate, the time intervals for which reliable collision frequencies can be calculated are limited to those depicted in Figures C1b and C1d. Consequently, the collision frequencies for other time intervals lack reliability. Figure 2b presents collision frequencies for all time periods, potentially leading readers to erroneously conclude that collision frequency can be derived even for low electron densities. Figure 3 is categorized by time of day; however, it does not account for data classification based on the method applied in this study and calculates the average collision frequencies without considering the confidence level of the EISCAT data.
    Additional issues requiring quantitative analysis include heating due to particle precipitation and upwelling of the thermosphere. The text at L126-128 states that "Presumably, the atmospheric heating due to precipitating particles causes uplift of the neutral atmosphere, which in turn results in an increased neutral particle density and consequently an enhanced ion-neutral collision frequency for these altitudes." This statement implies that the particle heating energy generated during a particle precipitation event invariably produces sufficient thermal energy to cause upward flow in the lower thermosphere. The use of "Presumably" is inadequate to justify this assertion. This statement should be omitted. The conclusions that can be reliably drawn from the results of this study are as follows: 1) the collision frequency can be calculated by this method only during events of particle precipitation and high ionospheric density, and 2) the calculated collision frequency during this limited time interval is lower at lower layers and higher at upper layers compared to the climatological results. Regarding point (2), this study discusses thermospheric density fluctuations; however, these may be apparent fluctuations resulting from uncertainties in the climatological results. Even if density fluctuations do occur, they are not necessarily caused by upwelling generated by particle heating; they may be attributed to Joule heating, or they may be the result of advection from other regions. It is questionable whether the discussion in this study encompasses all possibilities. The conclusion that "the particle precipitation heating causes a significant uplift of neutral gas between about 90-110 km altitude" appears to be speculative and is not a comprehensive assessment based on quantitative consideration of the results.
    Based on the aforementioned analysis, this study exhibits critical deficiencies in the following areas: rigorous analysis considering data quality, methodology for assessing the confidence level of the calculated collision frequencies, and comprehensive discussion of the results and conclusions. Consequently, it is recommended that the editor rejects the study, as previously outlined in the initial comments. It should be noted that this assessment does not invalidate the method employed to derive the collision frequency.
    
    Citation: https://doi.org/10.5194/egusphere-2024-2708-RC2
    
    AC2: 'Reply on RC2', Florian Günzkofer, 17 Oct 2024
    
    We are grateful for the detailed review and take the highlighted data noise issue very seriously. We will speak to EISCAT staff about this matter. We will also look for other dual-frequency measurements without the mentioned data noise issue covering particle precipitation times and conduct the presented analysis. Depending on the obtained results, our paper will be adjusted accordingly. Should there be no such measurements, the paper will be adjusted to thoroughly discuss the data noise issue and the (quite serious) impacts on the presented analysis.
    
    Citation: https://doi.org/10.5194/egusphere-2024-2708-AC2
    
    AC6: 'Reply on RC2', Florian Günzkofer, 12 Dec 2024
    
    We thank the reviewer for taking the time to elaborate on their comments. However, we oppose the reviewer’s statement that our previous reply was purely qualitative.
    The supplemented ion temperature plot clearly showed that the limit for resonant ion-neutral collisions was not reached during the 16 May 2024 EISCAT campaign. Since the reviewer did not mention the initial major comment #2 again, we assume this issue has been adequately addressed. The revision will include the discussion outlined in our previous reply.
    Regarding major comment #3, the reviewer’s remaining concerns appear to be caused by a too-forward expression of our interpretation of the obtained results. We maintain that for us, a vertical uplift caused by thermosphere heating due to precipitating particles comes most naturally to mind as an explanation for the observed changes in the ion-neutral collision frequency profiles. Nevertheless, we admit this is an interpretation of the results, not underlined by quantitative evidence. We are happy to revise the conclusion section more carefully to highlight the conclusions drawn from quantitative results in contrast to our interpretations.
    The main remaining issue appears to be the initial major comment #1 regarding the discontinuity at 100 km. It is correct that there seems to be an issue with UHF manda measurements at low electron densities, which results in the discontinuity of the obtained collision frequency profiles at low electron densities. We discussed this issue with the EISCAT staff who confirmed that the manda-uhf noise is a consequence of the low electron densities in combination with the narrow altitude gates of the manda mode. They suggested a) increasing the integration window to 120s and b) increasing the altitude gates to 60 logarithmically spaced gates between 50 km and 210km altitude. They provided a quicklook plot of the parameters for Dec 14 which can be found in the supplement. It can be seen that the strong noise above 100 km is now restricted to the lowest electron densities and the data is far less noisy at 05 – 13 UT. Hence, we repeated the entire analysis for both UHF and VHF with the suggested settings and indeed, the discontinuity of the collision frequency is no longer present.
    That said, we agree with the referee that the collision frequency profiles for low electron density might better be discussed separately, showing the issue of the high noise data. However, as written in the previous reply, the obtained profiles for high electron densities remain valid. As a baseline profile to compare the collision frequency profiles for high electron density, the climatology profile could be used as well. The reviewer’s arguments regarding this are all very important and can be addressed with a thorough revision.
    Regarding the newly added comments about the validity of the chosen thresholds for electron density at 95 km altitude, we created a histogram of N_e,95 (see supplement). Applying logarithmic bin edges (10^x with x=9.0, 9.1, 9.,2, …, 11.0), a bimodal distribution is noticeable. The threshold for low electron densities is slightly larger than the left maximum thereby enclosing the majority of time points. The threshold for high electron density is approximately at the minimum in between the maxima, thereby ensuring the stability of the obtained profiles for small variations of the threshold. This can be seen in the attached plot of four collision frequency profiles obtained for different thresholds of high N_e,95. The original choice of thresholds was done qualitatively but we hope that this quantitative analysis provides the requested assessment of appropriateness.
    We thank the reviewer for explicitly stating that the method to derive collision frequencies is principally valid. Since we use valid EISCAT measurements, the results of this paper are valid as well, just affected by the UHF manda issue and generally large uncertainties that need to be discussed more carefully. However, as written in our previous reply, due to the extremely low number of studies addressing the collision frequency in this region and therefore the absence of a ground truth, our paper is a relevant contribution to the field.
    
    Citation: https://doi.org/10.5194/egusphere-2024-2708-AC6
RC3:
'Comment on egusphere-2024-2708', Anonymous Referee #2, 17 Oct 2024

The authors use simultaneous measurements from the EISCAT UHF and VHF incoherent scatter radars to examine the dependence of the ion-neutral collision frequency on particle precipitation. They purport to show a significant impact and that the particle heating causes a significant uplift of neutral gas between 90 and 110km.
This was a fascinating and worthy attempt to use the multifrequency data to extract information about the underlying neutral atmosphere. The technique and type of analysis involved was sensible and interesting. However, inspection of the underlying data has made me concerned as there seems to be some systematic noise issues that may persist even at high density levels and need to be properly identified and discussed. I feel the current discussion is not enough and misses some worrying features in the data (e.g. the UHF noise band from 100-110 km, the heightened noise spikes at all altitudes in the VHF).
I think that the fairest approach would be to ask the authors to conduct an analysis of the underlying data noise, speak to EISCAT staff about the measurements to check if there were additional issues (the system temperature on the VHF seemed rather high at times). This will give everyone more confidence in the data and the analysis. This could be done through rejection and request resubmission, though I am minded to recommend a major revision instead, unless the authors feel the timescale to carry this out would be too long? Even if there are fundamental issues with the underlying data there may be solutions for mitigating these that could make the study worth publishing even as those flaws are acknowledged.

Major comments
Data noise:
The underlying data as presented in figure 2 is somewhat noisy. I worry this may impact severely the analysis that the authors have done. Did they consider increasing the integration time and/or size of the range gates? I note that the noise issue is most pronounced in the UHF data, inspecting the MADRIGAL summary plots for 13 -15 December 2022) the UHF shows a persistent band of increased noise from 100-110 km altitude, which is worrying. The VHF shows highly noisy data below 110 km.
One would expect an increased level of relative noise in regions of lower density (i.e. low altitude) but for the data here it seems remarkably high with large multi-gate spikes. It is harder to tell if this persists when density is high though I note in figure 2b the first large precipitation event after noon on the 13/12/2022 there is a noticeable step change in the collision frequency that continues through the period. It appears to reduce during periods of very increased density, though this could be a color scale effect and so I am still wary. That the discontinuity manifests in the collision frequency data from the difference spectrum fitting method as well as in the GUISDAP analysed data suggests that it is an underlying data issue and not simply an analysis problem. If this is the case it would impact all of the data and so restricting analysis just to the high-density regions would not completely mitigate the problem. This needs thorough investigation.
I wondered if this may be that this is simply indicative of the transition from the a priori value to the measured value. However, this does not resolve the issue of the band of noise in the UHF density data that is suggestive of a bigger problem (and in the VHF manifesting in a different way).
The issue with the data is harder to see in May 2024, though the low altitude VHF data still shows unusual noise structure. I had a quick look at some older manda data in the Madrigal archive and the noise structure looks different (this is anecdotal and far from comprehensive), which makes me suspicious of these recent observations and whether there is an underlying issue in the latest version of the manda code. Did the authors discuss the data with the EISCAT staff? It would be worth identifying if this is a problem with the current implementation of manda or something else (some sort of aliasing problem with more contaminated range gates at higher altitudes?)
I think it is essential for the authors to conduct an analysis of the uncertainties and the level of variability (noise) in the data to identify any trends, or sharp changes with altitude and underlying density level. Expanding the analysis upwards beyond 110 km might be instructive in terms of identifying any additional discontinuities that would point to a problem in the noise level.

Minor to moderate comments:
Line 24: the assumption is made that the ion density is equal to the electron density; this is generally true at higher altitude but as one moves lower in the D region the negative ion density increases such that it may become appreciable (especially in darkness). How would this affect the use of Equation 1.
Line 69: “the UHF and VHF radars were operated in the manda zenith mode, also known as the Common Programme (CP) 6” – this is not accurate, it is similar to the CP6 mode. “Common Programme 6” has a very specific meaning beyond the pulse code and pointing direction. It would be more correct to say that “the UHF and VHF radars were operated pointed in the zenith using the manda pulse code, which is optimised for high resolution D-region measurements (as used in the EISCAT Common Programme 6)”
Line 130: a little more information on how the EISCAT climatology is constructed would be welcome to the reader who may not be familiar with EISCAT and climatologies. Given the way in which EISCAT data presents more explanation on how it is a straight line would be welcome. I assume this also indicates that the standard EISCAT analysis is not using NRLMSIS to provide the a priori data to the fit otherwise the two lines should be the same. Apologies if I have got this muddled but I think that demonstrates the need for further information on how this is constructed.
Line 164: The authors suggest that the detected uplift is due to direct particle heating. This may play a sizeable role; however, did the authors consider the role of Joule heating? This tends to maximise above the region of interest in this work but Baloukidis et al., 2023 (https://doi.org/10.1029/2023JA031526) showed that there can be appreciable heating towards the top of the region of interest and Deng et al., 2011 (https://doi.org/10.1029/2010JA016019) suggested that the uplift can start at lower altitudes. I think it unlikely that Joule heating alone could cause the potentially observed upwelling at the reported altitudes, but it is worth discussing this possibility with reference to the potential mechanisms and qualified assessment.
Line 189: “significantly” have you tested the result for significance. For example, a Kolmogorov-Smirnov test comparing the underlying data behind each profile with each other.
Line 199: “the difference between both profiles is within the measurement uncertainty and conclusions have to be drawn carefully” is a very sensible statement but have the authors attempted any significance testing of their results.
Line 205: I wonder is there an independent neutral temperature measurement over EISCAT at this time? There have been temperature mappers and lidar focused on the region though I admit I am uncertain of the data range that exists. Alternatively, is there any satellite data for the interval that could be used?
Line 222; the jump (or rather a kink in the profile) at 110 km appears in both cases in Figure 3, it is reduced when NRLMSIS is used but it is absolutely still there. Therefore, it is erroneous to state that “This jump is only found when the standard EISCAT… not when NRLMSIS climatology profile is used”. Please, correct this. I would also note that the jump is in all time sectors (fig 3a) but more pronounced in the noon and dusk sectors. The fact it persists at all times may suggest that the SNR problem is not just constrained to low density periods. In fig3b the jump is most pronounced in the dusk, then the noon and is indeed much reduced (to vanishing) in the two other sectors. This needs some thought and explanation; I suspect it may be connected to the SNR issue and how using NRLMSIS will mitigate that to a degree at higher densities, but I am unsure.
Line 245: fluxes and ionization rates are often presented in units of per cm cubed, but I recommend SI units. Leaves less room for mistakes. Same for neutral densities in Figure 6.
Lines 266 and 270; essentially saying the same thing twice in quick succession.
Lines 264 onwards: I am not clear on how the analysis of the tidal structures leads to the conclusion on line 275. Please provide more detail of the underlying mechanism.
Figure 6b: why not include error bars on the red line?

Citation: https://doi.org/10.5194/egusphere-2024-2708-RC3
- AC3: 'Reply on RC3', Florian Günzkofer, 17 Oct 2024
  
  We are grateful for the detailed review and take the highlighted data noise issue very seriously. We will speak to EISCAT staff about this matter. We will also look for other dual-frequency measurements without the mentioned data noise issue covering particle precipitation times and conduct the presented analysis. Depending on the obtained results, our paper will be adjusted accordingly. Should there be no such measurements, the paper will be adjusted to thoroughly discuss the data noise issue and the (quite serious) impacts on the presented analysis.
  
  Citation: https://doi.org/10.5194/egusphere-2024-2708-AC3
- AC5: 'Reply on RC3', Florian Günzkofer, 12 Dec 2024
  
  We would like to thank the referee for taking the time to read our paper and their detailed review.
  As suggested by the referee, we discussed the issue with EISCAT staff. The most likely explanation for the high noise levels and the discontinuities in the plasma parameters as well as in the collision frequency profiles is the low electron density in combination with too-narrow altitude gates and integration windows. Same as the referee, they suggested to a) increasing the integration window to 120s and b) increasing the altitude gates to 60 logarithmically spaced gates from 50 km to 210 km. The discontinuity at 100 km is caused by a change in the a priori parameter settings but increasing the altitude gates should reduce the noise far enough to avoid the discontinuity.
  With the new altitude gate settings, the high noise in the 100-110 km altitude band vanishes mostly (but remains for the lowest electron densities, see figure in supplement). The fact that the noise band is up to 110 km is because the original manda analysis increases the altitude gates upward 110 km just as we did now for lower altitudes as well. This was also why we originally limited our analysis up to 110 km. Another discontinuity at 130 km, also caused by the change of a priori parameter settings, is still present even with the new altitude gates and marks the upper limitation of our analysis.
  Regarding the high VHF system temperatures, the EISCAT staff informed us that there was a problem with one of the VHF signal lines (a and b). Quote: “At around 0100 there is notable hiccup and from there the "a" data starts having significantly higher system temperature than "b". This does not seem to have too much influence on the fitted results except for introducing some noise. There is, however, not really anything that can be done to fix the problem after the data has been collected.” We will add an according statement to the manuscript.
  
  Citation: https://doi.org/10.5194/egusphere-2024-2708-AC5
EC1:
'Comment on egusphere-2024-2708', Ana G. Elias, 17 Oct 2024

First, I would like to thank and highlight the meticulous and thorough reports provided by Reviewers #1 and Reviewer #2. I consider this discussion extremely important and productive, and I encourage the authors to proceed and follow the comments of both Reviewers, even if this requires significant time, as it surely is the case considering the data noise issue.
I have extended the discussion for additional 14 days.
I also thank the authors for considering Annales Geophysicae to publish the results of this interesting study, with its original contributions.
And, I would also like to remind researchers in this field that they are welcome to contribute to this discussion.

Citation: https://doi.org/10.5194/egusphere-2024-2708-EC1
- AC4: 'Reply on EC1', Florian Günzkofer, 12 Dec 2024
  
  We would like to thank the editor for extending the discussion deadline, thereby allowing us to thoroughly investigate the issues raised by the reviewers.
  
  Citation: https://doi.org/10.5194/egusphere-2024-2708-AC4

Florian Günzkofer, Gunter Stober, Johan Kero, David R. Themens, Njål Gulbrandsen, Masaki Tsutsumi, and Claudia Borries

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Short summary

The Earth’s magnetic field is not closed at high latitudes. Electrically charged particles can penetrate the Earth’s atmosphere, deposit their energy, and heat the local atmosphere-ionosphere. This presumably causes an upwelling of the neutral atmosphere which affects the atmosphere-ionosphere coupling. We apply a new analysis technique to infer the atmospheric density from incoherent scatter radar measurements. We show qualitatively how particle precipitation affects the neutral atmosphere.


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