Divergent convective outflow in large eddy simulations

Upper tropospheric outflow is analysed in cloud resolving large eddy simulations. Thereby, the role of convective organisation, latent heating and other factors in upper tropospheric divergent outflow variability from deep convection is diagnosed using a set of about 100 large eddy simulations, because the outflows are thought to be an important feedback from (organised) to large scale atmospheric flows: perturbations in those outflows may sometimes propagate into larger scale perturbations. Upper tropospheric divergence is found to be controlled by net latent heating and convective organisation. At low precipitation rates isolated convective cells have a stronger mass divergence than squall lines. The squall line divergence is the weakest (relative to the net latent heating) when the outflow is purely 2D, in case of an infinite length squall line. At high precipitation rates the mass divergence discrepancy between the various modes of convection reduces. Hence, overall the magnitude of divergent outflow is explained by the latent heating and the dimensionality of the outflow, which together create a non-linear relation.</p

Impact of urban imperviousness on boundary layer meteorology and air chemistry on a regional scale

It has been long understood that land cover change from natural to impervious modifies the surface energy balance and hence the dynamical properties of the overlying atmosphere. The urban heat island is manifested in the formation of an urban boundary layer with distinct thermodynamic features that in turn govern transport processes of air pollutants. While many studies already demonstrated the benefits of urban canopy models (UCM) for atmospheric modelling, work on the impact on urban air chemistry is scarce. This study uses the state-of-the-art coupled chemistry-climate modelling system MECO(n) to assess the impact of the COSMO UCM TERRA_URB on the dynamics and gas phase chemistry in the boundary layer of the urban agglomeration Rhine-Main in Germany. Comparing the model results to ground observations and satellite and ground based remote sensing data, we found that the UCM experiment reduces the bias in temperature at the surface and throughout the boundary layer. This is true for ground level NO2 and ozone distribution as well. The application of MECO(n) for urban planning purposes is discussed by designing case studies representing two projected scenarios in future urban planning – densification of central urban areas and urban sprawl. Averaged over the core urban region and 10‑days during a heat wave period in July 2018, model results indicate a warming of 0.7 K in surface temperature and 0.2 K in air temperature per 10 % increase in impervious surface area fraction. Within this period, a 50 % total increase of imperviousness accounts for a 3 K and 1 K spatially averaged warming respectively. This change in thermodynamic features results in a decrease of surface NO2 concentration by 10–20 % through increased turbulent mixing in areas with highest impervious fraction and highest emissions. In the evening and nighttime however, increased densification in the urban centre results in amplified canyon blocking, which in turn results in average increase in near surface NO2 concentrations of about 10 %, compared to the status quo. This work intends to analyse regional scale features of surface-atmosphere interactions in an urban boundary layer and can be seen as preparatory work for higher resolution street scale models

A fast stratospheric chemistry solver: the E4CHEM submodel for the atmospheric chemistry global circulation model EMAC

The atmospheric chemistry general circulation model ECHAM5/MESSy (EMAC) and the atmospheric chemistry box model CAABA are extended by a computationally very efficient submodel for atmospheric chemistry, E4CHEM. It focuses on stratospheric chemistry but also includes background tropospheric chemistry. It is based on the chemistry of MAECHAM4-CHEM and is intended to serve as a simple and fast alternative to the flexible but also computationally more demanding submodel MECCA. In a model setup with E4CHEM, EMAC is now also suitable for simulations of longer time scales. The reaction mechanism contains basic O3, CH4, CO, HOx, NOx, and ClOx gas phase chemistry. In addition, E4CHEM includes optional fast routines for heterogeneous reactions on sulphate aerosols and polar stratospheric clouds (substituting the existing submodels PSC and HETCHEM), and scavenging (substituting the existing submodel SCAV). We describe the implementation of E4CHEM into the MESSy structure of CAABA and EMAC. For some species the steady state in the box model differs by up to 100% when compared to results from CAABA/MECCA due to different reaction rates. After an update of the reaction rates in E4CHEM the mixing ratios in both boxmodel and 3-D model simulations are in satisfactory agreement with the results from a simulation where MECCA with a similar chemistry scheme was employed. Finally, a comparison against a simulation with a more complex and already evaluated chemical mechanism is presented in order to discuss shortcomings associated with the simplification of the chemical mechanism

Cold cloud microphysical process rates in a global chemistry–climate model

Microphysical processes in cold clouds which act as sources or sinks of hydrometeors below 0 degrees C control the ice crystal number concentrations (ICNCs) and in turn the cloud radiative effects. Estimating the relative importance of the cold cloud microphysical process rates is of fundamental importance to underpin the development of cloud parameterizations for weather, atmospheric chemistry, and climate models and to compare the output with observations at different temporal resolutions. This study quantifies and investigates the ICNC rates of cold cloud microphysical processes by means of the chemistry-climate model EMAC (ECHAM/MESSy Atmospheric Chemistry) and defines the hierarchy of sources and sinks of ice crystals. Both microphysical process rates, such as ice nucleation, aggregation, and secondary ice production, and unphysical correction terms are presented. Model ICNCs are also compared against a satellite climatology. We found that model ICNCs are in overall agreement with satellite observations in terms of spatial distribution, although the values are overestimated, especially around high mountains. The analysis of ice crystal rates is carried out both at global and at regional scales. We found that globally the freezing of cloud droplets and convective detrainment over tropical land masses are the dominant sources of ice crystals, while aggregation and accretion act as the largest sinks. In general, all processes are characterized by highly skewed distributions. Moreover, the influence of (a) different ice nucleation parameterizations and (b) a future global warming scenario on the rates has been analysed in two sensitivity studies. In the first, we found that the application of different parameterizations for ice nucleation changes the hierarchy of ice crystal sources only slightly. In the second, all microphysical processes follow an upward shift in altitude and an increase by up to 10 % in the upper troposphere towards the end of the 21st century

How non-equilibrium aerosol chemistry impacts particle acidity: the GMXe AERosol CHEMistry (GMXe--AERCHEM, v1.0) sub-submodel of MESSy

Aqueous-phase chemical processes in clouds, fog, and deliquescent aerosols are known to alter atmospheric composition and acidity significantly. Traditionally, global and regional models predict aerosol composition by relying on thermodynamic equilibrium models and neglect non-equilibrium processes. Here, we present the AERosol CHEMistry (GMXe–AERCHEM, v1.0) sub-submodel developed for the Modular Earth Submodel System (MESSy) as an add-on to the thermodynamic equilibrium model (i.e. ISORROPIA-II) used by MESSy's Global Modal-aerosol eXtension (GMXe) submodel. AERCHEM allows the representation of non-equilibrium aqueous-phase chemistry of varying complexity in deliquescent fine aerosols. We perform a global simulation for the year 2010 by using the available detailed kinetic model for the chemistry of inorganic and small oxygenated organics. We evaluate AERCHEM's performance by comparing the simulated concentrations of sulfate, nitrate, ammonium, and chloride to in situ measurements of three monitoring networks. Overall, AERCHEM reproduces observed concentrations reasonably well. We find that, especially in the USA, the consideration of non-equilibrium chemistry in deliquescent aerosols reduces the model bias for sulfate, nitrate, and ammonium when compared to simulated concentrations by ISORROPIA-II. Over most continental regions, fine-aerosol acidity simulated by AERCHEM is similar to the predictions by ISORROPIA-II, but simulated aerosol acidity tends to be slightly lower in most regions. The consideration of non-equilibrium chemistry in deliquescent aerosols leads to a significantly higher aerosol acidity in the marine boundary layer, which is in line with observations and recent literature. AERCHEM allows an investigation of the global-scale impact of aerosol non-equilibrium chemistry on atmospheric composition. This will aid in the exploration of key multiphase processes and improve the model predictions for oxidation capacity and aerosols in the troposphere

Apolipoprotein E-dependent load of white matter hyperintensities in Alzheimer’s disease: a voxel-based lesion mapping study

Introduction: White matter (WM) magnetic resonance imaging (MRI) hyperintensities are common in Alzheimer’s disease (AD), but their pathophysiological relevance and relationship to genetic factors are unclear. In the present study, we investigated potential apolipoprotein E (APOE)-dependent effects on the extent and cognitive impact of WM hyperintensities in patients with AD. Methods: WM hyperintensity volume on fluid-attenuated inversion recovery images of 201 patients with AD (128 carriers and 73 non-carriers of the APOE ε4 risk allele) was determined globally as well as regionally with voxel-based lesion mapping. Clinical, neuropsychological and MRI data were collected from prospective multicenter trials conducted by the German Dementia Competence Network. Results: WM hyperintensity volume was significantly greater in non-carriers of the APOE ε4 allele. Lesion distribution was similar among ε4 carriers and non-carriers. Only ε4 non-carriers showed a correlation between lesion volume and cognitive performance. Conclusion: The current findings indicate an increased prevalence of WM hyperintensities in non-carriers compared with carriers of the APOE ε4 allele among patients with AD. This is consistent with a possibly more pronounced contribution of heterogeneous vascular risk factors to WM damage and cognitive impairment in patients with AD without APOE ε4-mediated risk

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Chemistry-climate interactions of aerosol nitrate from lightning

Lightning represents one of the dominant emission sources for NOx in the troposphere. The direct release of oxidised nitrogen in the upper troposphere does not only affect ozone formation, but also chemical and microphysical properties of aerosol particles in this region. This study investigates the direct impact of LNOx emissions on upper-tropospheric nitrate using a global chemistry climate model. The simulation results show a substantial influence of the lightning emissions on the mixing ratios of nitrate aerosol in the upper troposphere of more than 50 %. In addition to the impact on nitrate, lightning substantially affects the oxidising capacity of the atmosphere with substantial implications for gas-phase sulfate formation and new particle formation in the upper troposphere. In conjunction with the condensation of nitrates, substantial differences in the aerosol size distribution occur in the upper troposphere as a consequence of lightning. This has implications for the extinction properties of the aerosol particles and for the cloud optical properties. While the extinction is generally slightly enhanced due to the LNOx emissions, the response of the clouds is ambiguous due to compensating effects in both liquid and ice clouds. Resulting shortwave flux perturbations are of   ∼ −100 mW m−2 as determined from several sensitivity scenarios, but an uncertainty range of almost 50 % has to be defined due to the large internal variability of the system and the uncertainties in the multitude of involved processes. Despite the clear statistical significance of the influence of lightning on the nitrate concentrations, the robustness of the findings gradually decreases towards the determination of the radiative flux perturbations