Which processes drive observed variations of HCHO columns over India?

We interpret HCHO column variations observed by the Ozone Monitoring Instrument (OMI), aboard the NASA Aura satellite, over India during 2014 using the GEOS-Chem atmospheric chemistry and transport model. We use a nested version of the model with a horizontal resolution of approximately 25 km. HCHO columns are related to local emissions of volatile organic compounds (VOCs) with a spatial smearing that increases with the VOC lifetime. Over India, HCHO has biogenic, pyrogenic, and anthropogenic VOC sources. Using a 0-D photochemistry model, we find that isoprene has the largest molar yield of HCHO which is typically realized within a few hours. We also find that forested regions that neighbour major urban conurbations are exposed to high levels of nitrogen oxides. This results in depleted hydroxyl radical concentrations and a delay in the production of HCHO from isoprene oxidation. We find that propene is the only anthropogenic VOC emitted in major Indian cities that produces HCHO at a comparable (but slower) rate to isoprene. The GEOS-Chem model reproduces the broad-scale annual mean HCHO column distribution observed by OMI (<i>r</i> = 0.6), which is dominated by a distinctive meridional gradient in the northern half of the country, and by localized regions of high columns that coincide with forests. Major discrepancies are noted over the Indo-Gangetic Plain (IGP) and Delhi. We find that the model has more skill at reproducing observations during winter (JF) and pre-monsoon (MAM) months with Pearson correlations <i>r</i> &gt; 0.5 but with a positive model bias of  <mo form="infix">≃</mo> 1×10¹⁵ molec cm⁻². During the monsoon season (JJAS) we reproduce only a diffuse version of the observed meridional gradient (<i>r</i> = 0.4). We find that on a continental scale most of the HCHO column seasonal cycle is explained by monthly variations in surface temperature (<i>r</i> = 0.9), suggesting a role for biogenic VOCs, in agreement with the 0-D and GEOS-Chem model calculations. We also find that the seasonal cycle during 2014 is not significantly different from the 2008 to 2015 mean seasonal variation. There are two main loci for biomass burning (the states of Punjab and Haryana, and northeastern India), which we find makes a significant contribution (up to 1×10¹⁵ molec cm⁻²) to observed HCHO columns only during March and April over northeastern India. The slow production of HCHO from propene oxidation results in a smeared hotspot over Delhi that we resolve only on an annual mean timescale by using a temporal oversampling method. Using a linear regression model to relate GEOS-Chem isoprene emissions to HCHO columns we infer seasonal isoprene emissions over two key forest regions from the OMI HCHO column data. We find that the a posteriori emissions are typically lower than the a priori emissions, with a much stronger reduction of emissions during the monsoon season. We find that this reduction in emissions during monsoon months coincides with a large drop in satellite observations of leaf phenology that recovers in post monsoon months. This may signal a forest-scale response to monsoon conditions

Quantification of the depletion of ozone in the plume of Mount Etna

Volcanoes are an important source of inorganic halogen species into the atmosphere. Chemical processing of these species generates oxidised, highly reactive, halogen species which catalyse considerable O3 destruction within volcanic plumes. A campaign of ground-based in situ O3, SO2 and meteorology measurements was undertaken at the summit of Mount Etna volcano in July/August 2012. At the same time, spectroscopic measurements were made of BrO and SO2 columns in the plume downwind. Depletions of ozone were seen at all in-plume measurement locations, with average O3 depletions ranging from 11–35 nmol mol 1 (15–45 %). Atmospheric processing times of the plume were estimated to be between 1 and 4 min. A 1-D numerical model of early plume evolution was also used. It was found that in the early plume O3 was destroyed at an approximately constant rate relative to an inert plume tracer. This is ascribed to reactive halogen chemistry, and the data suggests the majority of the reactive halogen that destroys O3 in the early plume is generated within the crater, including a substantial proportion generated in a high-temperature “effective source region” immediately after emission. The model could approximately reproduce the main measured features of the ozone chemistry. Model results show a strong dependence of the near-vent bromine chemistry on the presence or absence of volcanic NOx emissions and suggest that near-vent ozone measurements can be used as a qualitative indicator of NOx emission

Halogen chemistry in volcanic plumes: a 1D framework based on MOCAGE 1D (version R1.18.1) preparing 3D global chemistry modelling

HBr emissions from volcanoes lead rapidly to the formation of BrO within volcanic plumes and have an impact on tropospheric chemistry, at least at the local and regional scales. The motivation of this paper is to prepare a framework for further 3D modelling of volcanic halogen emissions in order to determine their fate within the volcanic plume and then in the atmosphere at the regional and global scales. The main aim is to evaluate the ability of the model to produce a realistic partitioning of bromine species within a grid box size typical of MOCAGE (Model Of atmospheric Chemistry At larGE scale) 3D (0.5×0.5). This work is based on a 1D single-column configuration of the global chemistry-transport model MOCAGE that has low enough computational cost to allow us to perform a large set of sensitivity simulations. This paper uses the emissions from the Mount Etna eruption on 10 May 2008. Several reactions are added to MOCAGE to represent the volcanic plume halogen chemistry. A simple plume parameterisation is also implemented and tested. The use of this parameterisation tends to only slightly limit the efficiency of BrO net production. Both simulations with and without the parameterisation give results for the partitioning of the bromine species, of ozone depletion and of the BrO/SO2 ratio that are consistent with previous studies. A series of test experiments were performed to evaluate the sensitivity of the results to the composition of the emissions (primary sulfate aerosols, Br radical and NO) and to the effective radius assumed for the volcanic sulfate aerosols. Simulations show that the plume chemistry is sensitive to all these parameters. We also find that the maximum altitude of the eruption changes the BrO production, which is linked to the vertical variability of the concentrations of oxidants in the background air. These sensitivity tests display changes in the bromine chemistry cycles that are generally at least as important as the plume parameterisation. Overall, the version of the MOCAGE chemistry developed for this study is suitable to produce the expected halogen chemistry in volcanic plumes during daytime and night-time

A glycan gate controls opening of the SARS-CoV-2 spike protein.

SARS-CoV-2 infection is controlled by the opening of the spike protein receptor binding domain (RBD), which transitions from a glycan-shielded 'down' to an exposed 'up' state to bind the human angiotensin-converting enzyme 2 receptor and infect cells. While snapshots of the 'up' and 'down' states have been obtained by cryo-electron microscopy and cryo-electron tomagraphy, details of the RBD-opening transition evade experimental characterization. Here over 130 µs of weighted ensemble simulations of the fully glycosylated spike ectodomain allow us to characterize more than 300 continuous, kinetically unbiased RBD-opening pathways. Together with ManifoldEM analysis of cryo-electron microscopy data and biolayer interferometry experiments, we reveal a gating role for the N-glycan at position N343, which facilitates RBD opening. Residues D405, R408 and D427 also participate. The atomic-level characterization of the glycosylated spike activation mechanism provided herein represents a landmark study for ensemble pathway simulations and offers a foundation for understanding the fundamental mechanisms of SARS-CoV-2 viral entry and infection