The driving mechanisms of particle precipitation during the moderate geomagnetic storm of 7 January 2005

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Ann. Geophys., 25, 2053–2068, 2007 © European Geosciences Union 2007 Annales Geophysicae The driving mechanisms of particle precipitation during the moderate geomagnetic storm of 7 January 2005 N. Longden1, F. Honary1, A. J. Kavanagh1, and J. Manninen2 1Department of Communication Systems, Lancaster University, UK 2Sodankyla¨ Geophysical Observatory, Sodankyla¨, Finland Received: 29 March 2007 – Revised: 20 July 2007 – Accepted: 18 September 2007 – Published: 2 October 2007 Abstract. The arrival of an interplanetary coronal mass ejection (ICME) triggered a sudden storm commencement (SSC) at ∼09:22 UT on the 7 January 2005. The ICME followed a quiet period in the solar wind and interplanetary magnetic field (IMF). We present global scale observations of energetic electron precipitation during the moderate geomagnetic storm driven by the ICME. Energetic electron precipitation is inferred from increases in cosmic noise absorption (CNA) recorded by stations in the Global Riometer Array (GLORIA). No evidence of CNA was observed during the first four hours of passage of the ICME or following the sudden commencement (SC) of the storm. This is consistent with the findings of Osepian and Kirkwood (2004) that SCs will only trigger precipitation during periods of geomagnetic activity or when the magnetic perturbation in the magnetosphere is substantial. CNA was only observed following enhanced coupling between the IMF and the magnetosphere, resulting from southward oriented IMF. Precipitation was observed due to substorm activity, as a result of the initial injection and particles drifting from the injection region. During the recovery phase of the storm, when substorm activity diminished, precipitation due to density driven increases in the solar wind dynamic pressure (Pdyn) were identified. A number of increases in Pdyn were shown to drive sudden impulses (SIs) in the geomagnetic field. While many of these SIs appear coincident with CNA, SIs without CNA were also observed. During this period, the threshold of geomagnetic activity required for SC driven precipitation was exceeded. This implies that solar wind density driven SIs occurring during storm recovery can drive a different response in particle precipitation to typical SCs. Keywords. Ionosphere (Particle precipitation) – Magnetospheric physics (Solar wind-magnetosphere interaction; Storms and substorms) Correspondence to: N. Longden ( 1 Introduction Riometers enable the investigation of precipitation of energetic electrons into the D-region of the ionosphere through measurement of the absorption of cosmic noise (CNA). One mechanism for the enhancement of precipitation in the auroral zones is the compression of the magnetosphere as a result of an increase in the dynamic pressure (Pdyn) of the solar wind (Brown et al., 1961). Compression of the magnetosphere results in the stimulation of VLF waves, which in turn drive the pitch-angle diffusion necessary for trapped particles to precipitate into the ionosphere (Perona, 1972). Magnetospheric compression can be observed as an impulsive perturbation in the horizontal component of the geomagnetic field measured on the ground; i.e. a sudden commencement (SC). When followed by a geomagnetic storm, the event is termed a sudden storm commencement (SSC), and when not a sudden impulse (SI). Conversely, when the solar wind pressure decreases the magnetosphere can experience rapid expansion. The signature of expansion is a negative sudden impulse (SI−) in the horizontal component of the geomagnetic field measured at mid to low latitudes (e.g. Takeuchi et al., 2002). Precipitation driven by a SC can be observed by riometers as short-lived CNA coincident with the onset of the SC, known as Sudden Commencement Absorption (SCA) (Brown et al., 1961). CNA observed following an SI is termed Sudden Impulse Absorption (SIA). When observed, SCA and SIA exhibit a geomagnetic latitude and local time dependency, with probability of occurrence maximising around local noon between 65 and 70 magnetic latitude (Perona, 1972). Osepian and Kirkwood (2004) have determined that a storm SC event during a period of activity, defined as a period when the geomagnetic index Kp is two or greater, will result in SCA proportional to the magnitude of the magnetic impulse observed at equatorial latitudes. However, a storm SC event during a period of quiet activity (Kp<2) would only result in SCA if the magnitude of the Published by Copernicus Publications on behalf of the European Geosciences Union. 2054 N. Longden et al.: Particle precipitation during 7 January 2005 storm magnetic impulse exceeded a threshold of around 30 nT. In their study, SCA was evident during active periods irrespective of the local time of the observing riometer. However, at quiet times, the local time sector altered the threshold of magnetic field perturbation required for SCA to occur, with a greater perturbation required for SCA in the local afternoon than local morning. Magnetospheric compression has been linked to substorm processes, such as reducing the period of southward IMF required for substorm activity to occur (Burch, 1972) and the triggering of substorms (Brown, 1978). Precipitation due to substorms has been linked to a number of forms of CNA (e.g. Stauning, 1996, and references therein), including CNA around local midnight, presumably close to the injection region of the substorm, and in the morning sector, due to the drift of injected electrons. Interplanetary Coronal Mass Ejections (ICME) are the interplanetary (IP) counterpart of Coronal Mass Ejections (CME). When earthward directed, ICMEs are known to drive geomagnetic storms with levels of activity ranging from the most intense storms observed (Richardson et al., 2001) to relative inactivity (Gosling et al., 1991). Taylor et al. (1994) have shown that ICMEs are the most likely drivers for SSC events. In this paper we study the global-scale effects on particle precipitation of a moderate geomagnetic storm triggered by an ICME that collided with the magnetosphere on 7 January 2005 and consider the effects in the context of the survey of SSC-related absorption by Osepian and Kirkwood (2004). The ICME followed a period of low activity in both the solar wind and magnetosphere indicating little energy coupling into the system. The storm developed over the course of two days and exhibited at least two periods of substorm activity, observed by the Los Alamos National Laboratory (LANL) satellites at geosynchronous orbit. The recovery phase of the storm on the 8 January 2005 was accompanied by a number of solar wind density-driven sudden impulses that led to precipitation confined mostly to the dayside magnetosphere. There was an advantageous configuration of riometers with coverage of both magnetic noon and midnight at the time of the sudden commencement and during a good portion of the recovery phase of the storm making this an interesting case study on the effects of an ICME on energetic electron precipitation on global scales. 2 Instrumentation Observations of the solar wind and IMF during the event are taken from the ACE satellite, in orbit around the L1 point, and the Geotail satellite. During this event, Geotail was located off the dawn flank moving towards noon close to the Earth. The solar wind velocities and magnetic structure observed by the ACE satellite are consistent with those observed by Geotail, indicating that Geotail is located outside the bow shock and magnetosphere, directly in the solar wind throughout this event. The IMF data are obtained from the ACE magnetic fields experiment (MAG) instrument (Smith et al., 1998) and the Geotail Magnetic Field Measurement (MGF) instrument (Kokubun et al., 1994). The ACE solar wind data are obtained from the Solar Wind Electron Proton Alpha Monitor (SWEPAM) instrument (McComas et al., 1998) and the Geotail solar wind data are obtained from the Comprehensive Plasma Instrument (CPI) (Frank et al., 1994). The global scale effects of the ICME in the ionosphere were investigated using two riometer chains; the NORSTAR riometer chain (formerly CANOPUS), covering CANADA, and the SGO riometer chain in Fennoscandia. Data from the central beam (beam 25) of the imaging riometer (IRIS) located at Kilpisja¨rvi was also used. These riometers are detailed in Table 1 and form part of the GLORIA project (Global Riometer Array). Magnetic latitudes are given in the Corrected Geomagnetic (CGM) coordinate system using the International Geomagnetic Reference Field (IGRF) model for 2005 (e.g. Maus et al., 2005). GLORIA aims to link the data from riometers located throughout the Northern and Southern Hemispheres to enable investigation of the effect of electron precipitation simultaneously across the globe. Small errors in the calculation of the quiet day curves for the riometers at Abisko and Rovaniemi could result in errors of the absolute magnitude of CNA of the order of 0.1 to 0.2 dB during this event. The geomagnetic field local to the riometers was investigated using data from ground based magnetometers. The IMAGE magnetometer chain is located close to the SGO chain of riometers and the CARISMA magnetometer chain (formerly CANOPUS) is located close to the NORSTAR riometers. Three of the magnetometer stations used are not located in the region of one of the riometers detailed in Table 1. These are at Muonio (station code MUO), Rørvik (station code RVK) and Ouluja¨rvi (station code OUJ). These stations have a geographic latitude and longitude of 68.02 N, 23.53 E, 64.94 N, 10.98 E and 64.52 N, 27.23 E respectively. Pi2 pulsations were investigating using the lowest latitude CARISMA station (Pinawa) and the York magnetometer (station code YOR) from the SAMNET magnetometer chain, located at 53.95 N, 1.05 W (geographic). Geosynchronous particle flux intensity measurements are taken from the Synchronous Orbit Particle Analyzer (SOPA) instrument (Belian et al., 1992) on board the LANL satellites. At the time of the ICME, data was available from five LANL satellites with SOPA instrumentation; 084, 095, 97A, 01A and 02A. These satellites were located at geographic longitudes of 166.13 W, 38.54 W, 145.36 E, 8.16 E and 69.30 E, respectively, during this event. Figure 1 indicates the geographic location of the GLORIA riometers used in this study. The geographic longitude of the five LANL satellites are shown in red. Ann. Geophys., 25, 2053–2068, 2007 N. Longden et al.: Particle precipitation during 7 January 2005 storm 2055 3 Observations of the ICME in the solar wind At approximately 08:42 UT on the 7 January 2005, the signature of an ICME was first observed in the solar wind and IMF data from the ACE satellite at the L1 point. Figure 2 shows the solar wind and IMF data observed by ACE and Geotail on the 7 and 8 January 2005. Panels (a) to (c) show the IMF total magnetic field strength, the magnetic field strength component in the Y direction GSM (East-West), and the magnetic field strength component in the Z direction GSM (North-South), respectively. Panels (d) and (e) give the solar wind velocity in the X direction GSM and the proton number density in the solar wind from both satellites. Panel (f) displays the solar wind dynamic pressure from Geotail only and panel (g) shows the ratio between the helium alpha number density and the proton number density in the solar wind from ACE only. The ICME arrival was evident at Geotail at ∼09:24 UT, indicated by the vertical line on Fig. 2. Solar wind conditions returned to ambient levels by the 9 January 2005. Comparison of the IMF data from ACE and Geotail indicates a consistent magnetic structure in the solar wind. The best cross-correlation between the datasets of the satellites is achieved when the ACE data are delayed by ∼42.6 min. The ACE data given in Fig. 2 has been shifted in time by this amount. This value is close to the mean delay time between the satellites of ∼45 min, calculated according to their separation and the velocity of the solar wind (e.g. Khan and Cowley, 1999). The ACE solar wind data are unavailable for the period from ∼20:59 UT (∼21:41 UT at Geotail) on the 7 January to ∼03:11 UT (∼03:53 UT at Geotail) on the 8 January 2005 whereas the Geotail solar wind dataset is complete. Data from both satellites are shown as ACE provides information about the helium alpha particle content of the solar wind. With the onset of the ICME, the solar wind velocity increases from approximately 500 km s−1 to 600 km s−1. This is followed by a decrease to pre-ICME levels over the duration of the event. The IMF exhibits two periods of extended southward orientation, the first between ∼13:38 and ∼15:47 UT on the 7 January and the second between ∼21:41 UT on the 7 January and ∼02:00 UT on the 8 January. The Pdyn is highly variable and elevated from ambient levels throughout the event, during periods of both northward and southward IMF. It should be noted that the Pdyn is calculated for Geotail CPI assuming that the helium alpha particle number density of the solar wind is constantly 5% of the proton number density. From the limited data set available from ACE SWEPAM, it can be seen that the ratio of helium alpha number density to proton number density exceeds this for extended periods throughout the event, reaching levels of approximately 0.34. Therefore, the Pdyn will at times be underestimated in the Geotail data set. 4 Observations of the SSC At ∼09:22 UT on 7 January, a global scale SC signature was identified in ground based magnetometer readings in the Northern Hemisphere, confirmed by the NOAA NGDC (National Oceanic and Atmospheric Administration National Geophysical Data Center1). The SC signature was identified in mid to low latitude ground based magnetometers. The magnitude of the perturbation of the horizontal component of the geomagnetic field ranged from −4 nT to −6.6 nT at stations from the SAMNET array. The SC was initiated by the step increase in the Pdyn at the start of the ICME as the velocity of the solar wind rises sharply. Of the ten stations that recorded the SC, four magnetometers recorded a class B event (defined as “Fair, ordinary but unmistakable” by the NOAA) while the six remaining magnetometers recorded a class C event (defined as “Very poor, doubtful observation”). The magnetometers located at magnetic latitudes of ∼47 N and above recorded a preliminary reverse impulse (PRI) where the magnetic perturbation was observed to decrease before the main positive impulse (MI), determined as the SC* signature by Araki (1977). Below these latitudes, the standard SC signature of a positive impulse only was observed by the magnetometer stations. The stations at which the SC signature was observed are detailed in Table 2. Quiet conditions were observed prior to the SC; the Kp index did not exceed a value of 0+ between 00:00 and 09:00 UT on the 7 January 2005. This suggests that the magnetosphere was in a relatively unprimed state before the arrival of the ICME. We define unprimed as without sufficient trapped particles for precipitation to be identified in riometer CNA. The Kp index on the 7 and 8 January 2005 is shown in the top panel of Fig. 3. The SC was followed by a moderate geomagnetic storm; the definition of a moderate storm as when minimum Dst falls in the range of −50 to −100 nT (Gonzalez et al., 1994) has been used. The Dst index during the 7 and 8 January 2005 is given in the second panel of Fig. 3. It should be noted that Dst is not the most appropriate index with which to identify certain types of geomagnetic activity. Fast solar wind streams, for example, cause little deflection in Dst but still input significant energy to the system (e.g. Borovsky and Denton, 2006; Denton et al., 2006). However, Dst is considered an appropriate index to use in the identification of ICME driven storms. The storm develops in two phases with partial recovery between minima; Kamide et al. (1998) termed this a type 2 storm as opposed to a sharp decrease in Dst and a gradual recovery (type 1). The first Dst minimum occurs at 16:00 UT on the 7 January, with a magnitude of −46 nT. It should be 1 DATA/RELATED INDICES/Geomagnetic PDF Files/Geomagnetic Storm Sudden Commencements 0501.pdf Ann. Geophys., 25, 2053–2068, 2007 2056 N. Longden et al.: Particle precipitation during 7 January 2005 storm Table 1. GLORIA stations used in this study ordered by descending magnetic latitude. Code TAL CON RAN FCH RAB KIL DAW ABK IVA SOD ROV OUL PIN JYV Station Taloyoak Contwoyto Rankin Inlet Fort Churchill Rabbit Lake Kilpisja¨rvi Dawson Abisko Ivalo Sodankyla¨ Rovaniemi Oulu Pinawa Jyva¨skyla¨ Geographic Latitude 69.54 N 65.75 N 62.82 N 58.76 N 58.23 N 69.05 N 64.05 N 68.40 N 68.55 N 67.42 N 66.78 N 65.09 N 50.20 N 62.42 N Geographic Longitude 93.56 W 111.26 W 92.11 W 94.09 W 103.68 W 20.79 E 139.11 W 18.90 E 27.28 E 26.39 E 25.94 E 25.89 E 96.04 W 25.28 E Magnetic Latitude 78.59 N 73.00 N 72.53 N 68.62 N 67.08 N 65.98 N 65.92 N 65.41 N 65.17 N 64.06 N 63.42 N 61.69 N 60.24 N 58.95 N MLT (at 00:00 UT) ∼17:19 ∼15:43 ∼17:35 ∼17:28 ∼16:37 ∼02:44 ∼13:32 ∼02:31 ∼02:59 ∼02:53 ∼02:50 ∼02:47 ∼17:22 ∼02:40 L Shell 11.86 11.25 7.63 6.68 6.12 6.09 5.86 5.75 5.30 5.07 4.51 4.12 3.81 78oN 084 72oN 66oN 60oN NORSTAR Chain TAL DAW CON RAN RAB FCH 54oN 48oN PIN 180oW 120oW 095 60oW 01A SGO Chain 02A 0o 60oE 97A 120oE 180oW Fig. 1. Geographic location of the GLORIA stations used in this study. The geographic longitude of the five LANL satellites in orbit on the 7 January 2005 are shown in red for all riometer latitudes. Red dots indicate the approximate footprint of a equilibrium value of MeCpG steps (,+14 deg.) [31,44]. In comparison, methylation has a significantly lower stability cost when happening at major groove positions, such as 211 and 21 base pair from dyad (mutations 9 and 12), where the roll of the nucleosome bound conformation (+10 deg.) is more compatible with the equilibrium geometry of MeCpG steps. The nucleosome destabilizing effect of cytosine methylation increases with the number of methylated cytosines, following the same position dependence as the single methylations. The multiple-methylation case reveals that each major groove meth- PLOS Computational Biology | 3 November 2013 | Volume 9 | Issue 11 | e1003354 DNA Methylation and Nucleosome Positioning ylation destabilizes the nucleosome by around 1 kJ/mol (close to the average estimate of 2 kJ/mol obtained for from individual methylation studies), while each minor groove methylation destabilizes it by up to 5 kJ/mol (average free energy as single mutation is around 6 kJ/mol). This energetic position-dependence is the reverse of what was observed in a recent FRET/SAXS study [30]. The differences can be attributed to the use of different ionic conditions and different sequences: a modified Widom-601 sequence of 157 bp, which already contains multiple CpG steps in mixed orientations, and which could assume different positioning due to the introduction of new CpG steps and by effect of the methylation. The analysis of our trajectories reveals a larger root mean square deviation (RMSD) and fluctuation (RMSF; see Figures S2– S3 in Text S1) for the methylated nucleosomes, but failed to detect any systematic change in DNA geometry or in intermolecular DNA-histone energy related to methylation (Fig. S1B, S1C, S4–S6 in Text S1). The hydrophobic effect should favor orientation of the methyl group out from the solvent but this effect alone is not likely to justify the positional dependent stability changes in Figure 2, as the differential solvation of the methyl groups in the bound and unbound states is only in the order of a fraction of a water molecule (Figure S5 in Text S1). We find however, a reasonable correlation between methylation-induced changes in hydrogen bond and stacking interactions of the bases and the change in nucleosome stability (see Figure S6 in Text S1). This finding suggests that methylation-induced nucleosome destabilization is related to the poorer ability of methylated DNA to fit into the required conformation for DNA in a nucleosome. Changes in the elastic deformation energy between methylated and un-methylated DNA correlate with nucleosomal differential binding free energies To further analyze the idea that methylation-induced nucleosome destabilization is connected to a worse fit of methylated DNA into the required nucleosome-bound conformation, we computed the elastic energy of the nucleosomal DNA using a harmonic deformation method [36,37,44]. This method provides a rough estimate of the energy required to deform a DNA fiber to adopt the super helical conformation in the nucleosome (full details in Suppl. Information Text S1). As shown in Figure 2, there is an evident correlation between the increase that methylation produces in the elastic deformation energy (DDE def.) and the free energy variation (DDG bind.) computed from MD/TI calculations. Clearly, methylation increases the stiffness of the CpG step [31], raising the energy cost required to wrap DNA around the histone octamers. This extra energy cost will be smaller in regions of high positive roll (naked DNA MeCpG steps have a higher roll than CpG steps [31]) than in regions of high negative roll. Thus, simple elastic considerations explain why methylation is better tolerated when the DNA faces the histones through the major groove (where positive roll is required) that when it faces histones through the minor groove (where negative roll is required). Nucleosome methylation can give rise to nucleosome repositioning We have established that methylation affects the wrapping of DNA in nucleosomes, but how does this translate into chromatin structure? As noted above, accumulation of minor groove methylations strongly destabilizes the nucleosome, and could trigger nucleosome unfolding, or notable changes in positioning or phasing of DNA around the histone core. While accumulation of methylations might be well tolerated if placed in favorable positions, accumulation in unfavorable positions would destabilize the nucleosome, which might trigger changes in chromatin structure. Chromatin could in fact react in two different ways in response to significant levels of methylation in unfavorable positions: i) the DNA could either detach from the histone core, leading to nucleosome eviction or nucleosome repositioning, or ii) the DNA could rotate around the histone core, changing its phase to place MeCpG steps in favorable positions. Both effects are anticipated to alter DNA accessibility and impact gene expression regulation. The sub-microsecond time scale of our MD trajectories of methylated DNAs bound to nucleosomes is not large enough to capture these effects, but clear trends are visible in cases of multiple mutations occurring in unfavorable positions, where unmethylated and methylated DNA sequences are out of phase by around 28 degrees (Figure S7 in Text S1). Due to this repositioning, large or small, DNA could move and the nucleosome structure could assume a more compact and distorted conformation, as detected by Lee and Lee [29], or a slightly open conformation as found in Jimenez-Useche et al. [30]. Using the harmonic deformation method, we additionally predicted the change in stability induced by cytosine methylation for millions of different nucleosomal DNA sequences. Consistently with our calculations, we used two extreme scenarios to prepare our DNA sequences (see Fig. 3): i) all positions where the minor grooves contact the histone core are occupied by CpG steps, and ii) all positions where the major grooves contact the histone core are occupied by CpG steps. We then computed the elastic energy required to wrap the DNA around the histone proteins in unmethylated and methylated states, and, as expected, observed that methylation disfavors DNA wrapping (Figure 3A). We have rescaled the elastic energy differences with a factor of 0.23 to match the DDG prediction in figure 2B. In agreement with the rest of our results, our analysis confirms that the effect of methylation is position-dependent. In fact, the overall difference between the two extreme methylation scenarios (all-in-minor vs all-in-major) is larger than 60 kJ/mol, the average difference being around 15 kJ/ mol. We have also computed the elastic energy differences for a million sequences with CpG/MeCpG steps positioned at all possible intermediate locations with respect to the position (figure 3B). The large differences between the extreme cases can induce rotations of DNA around the histone core, shifting its phase to allow the placement of the methylated CpG steps facing the histones through the major groove. It is illustrative to compare the magnitude of CpG methylation penalty with sequence dependent differences. Since there are roughly 1.5e88 possible 147 base pairs long sequence combinations (i.e., (4n+4(n/2))/2, n = 147), it is unfeasible to calculate all the possible sequence effects. However, using our elastic model we can provide a range of values based on a reasonably large number of samples. If we consider all possible nucleosomal sequences in the yeast genome (around 12 Mbp), the energy difference between the best and the worst sequence that could form a nucleosome is 0.7 kj/mol per base (a minimum of 1 kJ/mol and maximum of around 1.7 kJ/mol per base, the first best and the last worst sequences are displayed in Table S3 in Text S1). We repeated the same calculation for one million random sequences and we obtained equivalent results. Placing one CpG step every helical turn gives an average energetic difference between minor groove and major groove methylation of 15 kJ/ mol, which translates into ,0.5 kJ/mol per methyl group, 2 kJ/ mol per base for the largest effects. Considering that not all nucleosome base pair steps are likely to be CpG steps, we can conclude that the balance between the destabilization due to CpG methylation and sequence repositioning will depend on the PLOS Computational Biology | 4 November 2013 | Volume 9 | Issue 11 | e1003354 DNA Methylation and Nucleosome Positioning Figure 3. Methylated and non-methylated DNA elastic deformation energies. (A) Distribution of deformation energies for 147 bplong random DNA sequences with CpG steps positioned every 10 base steps (one helical turn) in minor (red and dark red) and major (light and dark blue) grooves respectively. The energy values were rescaled by the slope of a best-fit straight line of figure 2, which is 0.23, to source of circulating FGF-21. The lack of association between circulating and muscle-expressed FGF-21 also suggests that muscle FGF-21 primarily works in a local manner regulating glucose metabolism in the muscle and/or signals to the adipose tissue in close contact to the muscle. Our study has some limitations. The number of subjects is small and some correlations could have been significant with greater statistical power. Another aspect is that protein levels of FGF-21 were not determined in the muscles extracts, consequently we cannot be sure the increase in FGF-21 mRNA is followed by increased protein expression. In conclusion, we show that FGF-21 mRNA is increased in skeletal muscle in HIV patients and that FGF-21 mRNA in muscle correlates to whole-body (primarily reflecting muscle) insulin resistance. These findings add to the evidence that FGF-21 is a myokine and that muscle FGF-21 might primarily work in an autocrine manner. Acknowledgments We thank the subjects for their participation in this study. 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