A hierarchical time-splitting approach for solving finite-time optimal control problems

The self-cleaning or oxidation capacity of the atmosphere is principally controlled by hydroxyl (OH) radicals in the troposphere. Hydroxyl has primary (P) and secondary (S) sources, the former mainly through the photodissociation of ozone, the latter through OH recycling in radical reaction chains. We used the recent Mainz Organics Mechanism (MOM) to advance volatile organic carbon (VOC) chemistry in the general circulation model EMAC (ECHAM/MESSy Atmospheric Chemistry) and show that S is larger than previously assumed. By including emissions of a large number of primary VOC, and accounting for their complete breakdown and intermediate products, MOM is mass-conserving and calculates substantially higher OH reactivity from VOC oxidation compared to predecessor models. Whereas previously P and S were found to be of similar magnitude, the present work indicates that S may be twice as large, mostly due to OH recycling in the free troposphere. Further, we find that nighttime OH formation may be significant in the polluted subtropical boundary layer in summer. With a mean OH recycling probability of about 67 %, global OH is buffered and not sensitive to perturbations by natural or anthropogenic emission changes. Complementary primary and secondary OH formation mechanisms in pristine and polluted environments in the continental and marine troposphere, connected through long-range transport of O3, can maintain stable global OH levels

Autoimmunity in Long Covid and POTS.

Orthostatic intolerance and other autonomic dysfunction syndromes are emerging as distinct symptom clusters in Long Covid. Often accompanying these are common, multi-system constitutional features such as fatigue, malaise and skin rashes which can signify generalized immune dysregulation. At the same time, multiple autoantibodies are identified in both Covid-related autonomic disorders and non-Covid autonomic disorders, implying a possible underlying autoimmune pathology. The lack of specificity of these findings precludes direct interpretations of cause and association, but their prevalence with its supporting evidence is compelling

Improved simulation of isoprene oxidation chemistry with the ECHAM5/MESSy chemistry-climate model: lessons from the GABRIEL airborne field campaign

The GABRIEL airborne field measurement campaign, conducted over the Guyanas in October 2005, produced measurements of hydroxyl radical (OH) concentration which are significantly higher than can be simulated using current generation models of atmospheric chemistry. Based on the hypothesis that this "missing OH" is due to an as-yet undiscovered mechanism for recycling OH during the oxidation chain of isoprene, we determine that an OH recycling of about 40–50% (compared with 5–10% in current generation isoprene oxidation mechanisms) is necessary in order for our modelled OH to approach the lower error bounds of the OH observed during GABRIEL. Such a large amount of OH in our model leads to unrealistically low mixing ratios of isoprene. In order for our modelled isoprene mixing ratios to match those observed during the campaign, we also require that the effective rate constant for the reaction of isoprene with OH be reduced by about 50% compared with the lower bound of the range recommended by IUPAC. We show that a reasonable explanation for this lower effective rate constant could be the segregation of isoprene and OH in the mixed layer. Our modelling results are consistent with a global, annual isoprene source of about 500 Tg(C) yr<sup>−1</sup>, allowing experimentally derived and established isoprene flux rates to be reconciled with global models

The linear ubiquitin chain assembly complex regulates TRAIL-induced gene activation and cell death.

The linear ubiquitin chain assembly complex (LUBAC) is the only known E3 ubiquitin ligase which catalyses the generation of linear ubiquitin linkages de novo LUBAC is a crucial component of various immune receptor signalling pathways. Here, we show that LUBAC forms part of the TRAIL-R-associated complex I as well as of the cytoplasmic TRAIL-induced complex II In both of these complexes, HOIP limits caspase-8 activity and, consequently, apoptosis whilst being itself cleaved in a caspase-8-dependent manner. Yet, by limiting the formation of a RIPK1/RIPK3/MLKL-containing complex, LUBAC also restricts TRAIL-induced necroptosis. We identify RIPK1 and caspase-8 as linearly ubiquitinated targets of LUBAC following TRAIL stimulation. Contrary to its role in preventing TRAIL-induced RIPK1-independent apoptosis, HOIP presence, but not its activity, is required for preventing necroptosis. By promoting recruitment of the IKK complex to complex I, LUBAC also promotes TRAIL-induced activation of NF-κB and, consequently, the production of cytokines, downstream of FADD, caspase-8 and cIAP1/2. Hence, LUBAC controls the TRAIL signalling outcome from complex I and II, two platforms which both trigger cell death and gene activation

The atmospheric chemistry box model CAABA/MECCA-3.0

We present version 3.0 of the atmospheric chemistry box model CAABA/MECCA. In addition to a complete update of the rate coefficients to the most recent recommendations, a number of new features have been added: chemistry in multiple aerosol size bins; automatic multiple simulations reaching steady-state conditions; Monte-Carlo simulations with randomly varied rate coefficients within their experimental uncertainties; calculations along Lagrangian trajectories; mercury chemistry; more detailed isoprene chemistry; tagging of isotopically labeled species. Further changes have been implemented to make the code more user-friendly and to facilitate the analysis of the model results. Like earlier versions, CAABA/MECCA-3.0 is a community model published under the GNU General Public License

Surface and Boundary Layer Exchanges of Volatile Organic Compounds, Nitrogen Oxides and Ozone During the GABRIEL Campaign

Abstract. We present an evaluation of sources, sinks and turbulent transport of nitrogen oxides, ozone and volatile organic compounds (VOC) in the boundary layer over French Guyana and Suriname during the October 2005 GABRIEL campaign by simulating observations with a single-column chemistry and climate model (SCM) along a zonal transect. Simulated concentrations of O3 and NO as well as NO2 photolysis rates over the forest agree well with observations when a small soil-biogenic NO emission flux was applied. This suggests that the photochemical conditions observed during GABRIEL reflect a pristine tropical low-NOx regime. The SCM uses a compensation point approach to simulate nocturnal deposition and daytime emissions of acetone and methanol and produces daytime boundary layer mixing ratios in reasonable agreement with observations. The area average isoprene emission flux, inferred from the observed isoprene mixing ratios and boundary layer height, is about half the flux simulated with commonly applied emission algorithms. The SCM nevertheless simulates too high isoprene mixing ratios, whereas hydroxyl concentrations are strongly underestimated compared to observations, which can at least partly explain the discrepancy. Furthermore, the model substantially overestimates the isoprene oxidation products methlyl vinyl ketone (MVK) and methacrolein (MACR) partly due to a simulated nocturnal increase due to isoprene oxidation. This increase is most prominent in the residual layer whereas in the nocturnal inversion layer we simulate a decrease in MVK and MACR mixing ratios, assuming efficient removal of MVK and MACR. Entrainment of residual layer air masses, which are enhanced in MVK and MACR and other isoprene oxidation products, into the growing boundary layer poses an additional sink for OH which is thus not available for isoprene oxidation. Based on these findings, we suggest pursuing measurements of the tropical residual layer chemistry with a focus on the nocturnal depletion of isoprene and its oxidation products.JRC.H.2-Climate chang

The atmospheric chemistry general circulation model ECHAM5/MESSy1: consistent simulation of ozone from the surface to the mesosphere

International audienceThe new Modular Earth Submodel System (MESSy) describes atmospheric chemistry and meteorological processes in a modular framework, following strict coding standards. It has been coupled to the ECHAM5 general circulation model, which has been slightly modified for this purpose. A 90-layer model version up to 0.01 hPa was used at T42 resolution (~2.8 latitude and longitude) to simulate the lower and middle atmosphere. The model meteorology has been tested to check the influence of the changes to ECHAM5 and the radiation interactions with the new representation of atmospheric composition. A Newtonian relaxation technique was applied in the tropospheric part of the domain to weakly nudge the model towards the analysed meteorology during the period 1998?2005. It is shown that the tropospheric wave forcing of the stratosphere in the model suffices to reproduce the Quasi-Biennial Oscillation and major stratospheric warming events leading e.g. to the vortex split over Antarctica in 2002. Characteristic features such as dehydration and denitrification caused by the sedimentation of polar stratospheric cloud particles and ozone depletion during winter and spring are simulated accurately, although ozone loss in the lower polar stratosphere is slightly underestimated. The model realistically simulates stratosphere-troposphere exchange processes as indicated by comparisons with satellite and in situ measurements. The evaluation of tropospheric chemistry presented here focuses on the distributions of ozone, hydroxyl radicals, carbon monoxide and reactive nitrogen compounds. In spite of minor shortcomings, mostly related to the relatively coarse T42 resolution and the neglect of interannual changes in biomass burning emissions, the main characteristics of the trace gas distributions are generally reproduced well. The MESSy submodels and the ECHAM5/MESSy1 model output are available through the internet on request

Hydroxyl radicals in the tropical troposphere over the Suriname rainforest: comparison of measurements with the box model MECCA

As a major source region of the hydroxyl radical OH, the Tropics largely control the oxidation capacity of the atmosphere on a global scale. However, emissions of hydrocarbons from the tropical rainforest that react rapidly with OH can potentially deplete the amount of OH and thereby reduce the oxidation capacity. The airborne GABRIEL field campaign in equatorial South America (Suriname) in October 2005 investigated the influence of the tropical rainforest on the HOx budget (HOx = OH + HO2). The first observations of OH and HO2 over a tropical rainforest are compared to steady state concentrations calculated with the atmospheric chemistry box model MECCA. The important precursors and sinks for HOx chemistry, measured during the campaign, are used as constraining parameters for the simulation of OH and HO2. Significant underestimations of HOx are found by the model over land during the afternoon, with mean ratios of observation to model of 12.2 ± 3.5 and 4.1 ± 1.4 for OH and HO2, respectively. The discrepancy between measurements and simulation results is correlated to the abundance of isoprene. While for low isoprene mixing ratios (above ocean or at altitudes \u3e3 km), observation and simulation agree fairly well, for mixing ratios \u3e200 pptV (rainforest) the model tends to underestimate the HOx observations as a function of isoprene. Box model simulations have been performed with the condensed chemical mechanism of MECCA and with the detailed isoprene reaction scheme of MCM, resulting in similar results for HOx concentrations. Simulations with constrained HO2 concentrations show that the conversion from HO2 to OH in the model is too low. However, by neglecting the isoprene chemistry in the model, observations and simulations agree much better. An OH source similar to the strength of the OH sink via isoprene chemistry is needed in the model to resolve the discrepancy. A possible explanation is that the oxidation of isoprene by OH not only dominates the removal of OH but also produces it in a similar amount. Several additional reactions which directly produce OH have been implemented into the box model, suggesting that upper limits in producing OH are still not able to reproduce the observations (improvement by factors of ≈2.4 and ≈2 for OH and HO2, respectively). We determine that OH has to be recycled to 94% instead of the simulated 38% to match the observations, which is most likely to happen in the isoprene degradation process, otherwise additional sources are required

Isoprene-derived secondary organic aerosol in the global aerosol–chemistry–climate model ECHAM6.3.0–HAM2.3–MOZ1.0

Within the framework of the global chemistry climate model ECHAM–HAMMOZ, a novel explicit coupling between the sectional aerosol model HAM-SALSA and the chemistry model MOZ was established to form isoprene-derived secondary organic aerosol (iSOA). Isoprene oxidation in the chemistry model MOZ is described by a semi-explicit scheme consisting of 147 reactions embedded in a detailed atmospheric chemical mechanism with a total of 779 reactions. Semi-volatile and low-volatile compounds produced during isoprene photooxidation are identified and explicitly partitioned by HAM-SALSA. A group contribution method was used to estimate their evaporation enthalpies and corresponding saturation vapor pressures, which are used by HAM-SALSA to calculate the saturation concentration of each iSOA precursor. With this method, every single precursor is tracked in terms of condensation and evaporation in each aerosol size bin. This approach led to the identification of dihydroxy dihydroperoxide (ISOP(OOH)2) as a main contributor to iSOA formation. Further, the reactive uptake of isoprene epoxydiols (IEPOXs) and isoprene-derived glyoxal were included as iSOA sources. The parameterization of IEPOX reactive uptake includes a dependency on aerosol pH value. This model framework connecting semi-explicit isoprene oxidation with explicit treatment of aerosol tracers leads to a global annual average isoprene SOA yield of 15&thinsp;% relative to the primary oxidation of isoprene by OH, NO3 and ozone. With 445.1&thinsp;Tg (392.1&thinsp;Tg&thinsp;C) isoprene emitted, an iSOA source of 138.5&thinsp;Tg (56.7&thinsp;Tg&thinsp;C) is simulated. The major part of iSOA in ECHAM–HAMMOZ is produced by IEPOX at 42.4&thinsp;Tg (21.0&thinsp;Tg&thinsp;C) and ISOP(OOH)2 at 78.0&thinsp;Tg (27.9&thinsp;Tg&thinsp;C). The main sink process is particle wet deposition, which removes 133.6 (54.7&thinsp;Tg&thinsp;C). The average iSOA burden reaches 1.4&thinsp;Tg (0.6&thinsp;Tg&thinsp;C) in the year 2012.</p

Airborne glyoxal measurements in the marine and continental atmosphere: comparison with TROPOMI observations and EMAC simulations

We report on airborne limb and nadir measurements of vertical profiles and total vertical column densities (VCDs) of glyoxal (C2H2O2) in the troposphere, which were performed aboard the German research aircraft HALO (High Altitude and LOng Range) in different regions and seasons around the globe between 2014 and 2019. The airborne nadir and integrated limb profiles agree excellently among each other. Our airborne observations are further compared to collocated glyoxal measurements of the TROPOspheric Monitoring Instrument (TROPOMI), with good agreement between both data sets for glyoxal observations in (1) pristine terrestrial, (2) pristine marine, (3) mixed polluted, and (4) biomass-burning-affected air masses with high glyoxal concentrations. Exceptions to the overall good agreement are observations of (1) faint and aged biomass burning plumes over the oceans and (2) of low-lying biomass burning or anthropogenic plumes in the terrestrial or marine boundary layer, both of which contain elevated glyoxal that is mostly not captured by TROPOMI. These differences in airborne and satellite-detected glyoxal are most likely caused by the overall small contribution of plumes of a limited extent to the total glyoxal absorption in the atmosphere and the difficulty in remotely detecting weak absorbers located close to low reflective surfaces (e.g. the ocean in the visible wavelength range) or within dense aerosol layers. Observations of glyoxal in aged biomass burning plumes (e.g. observed over the tropical Atlantic off the coast of West Africa in summer 2018, off the coast of Brazil by the end of the dry season 2019, and the East China Sea in spring 2018) could be traced back to related wildfires, such as a plume crossing over the Drake Passage that originated from the Australian bushfires in late 2019. Our observations of glyoxal in such aged biomass burning plumes confirm recent findings of enhanced glyoxal and presumably secondary organic aerosol (SOA) formation in aged wildfire plumes from yet-to-be-identified, longer-lived organic precursor molecules (e.g. aromatics, acetylene, or aliphatic compounds) co-emitted in the fires. Furthermore, elevated glyoxal (median 44 ppt – parts per trillion), as compared to other marine regions (median 10–19 ppt), is observed in the boundary layer over the tropical oceans, which is well in agreement with previous reports. The airborne data sets are further compared to glyoxal simulations performed with the global atmosphere chemistry model EMAC (ECHAM/MESSy Atmospheric Chemistry). When using an EMAC set up that resembles recent EMAC studies focusing on complex chemistry, reasonable agreement is found for pristine air masses (e.g. the unperturbed free and upper troposphere), but a notable glyoxal overestimation of the model exists for regions with high emissions of glyoxal and glyoxal-producing volatile organic compounds (VOCs) from the biosphere (e.g. the Amazon). In all other investigated regions, the model underpredicts glyoxal to varying degrees, in particular when probing mixed emissions from anthropogenic activities (e.g. over continental Europe, the Mediterranean, and East China Sea) and potentially from the sea (e.g. the tropical oceans). Also, the model tends to largely underpredict glyoxal in city plumes and aged biomass burning plumes. The potential causes for these differences are likely to be multifaceted, but they all point to missing glyoxal sources from the degradation of the mixture of potentially longer-chained organic compounds emitted from anthropogenic activities, biomass burning, and from the organic microlayer of the sea surface.</p