Improvements of organic aerosol representations and their effects in large-scale atmospheric models

Organics dominate the composition of the atmospheric aerosol, especially in the fine mode, influencing some of its characteristics such as the hygroscopicity, which is of climatic relevance for the Earth system. This study targets an improvement in the description of organic aerosols suitable for large-scale modelling, making use of recent developments based on laboratory and field measurements. In addition to the organic mass and particle number distribution, the proposed method keeps track of the oxidation state of the aerosol based on the OH exposure time, describing some of its chemical characteristics. This study presents the application of the method in a global chemistry climate model, investigates the sensitivity to process formulations and emission assignments, provides a comparison with observations and analyses the climate impact. <br></br> Even though the organic aerosol mass distribution is hardly affected by the new formulation, it shows impacts (regionally of the order of 10 % to 20 %) on parameters directly influencing climate via the direct and indirect aerosol effects. Furthermore, the global distribution of the organic O:C ratio is analysed in detail, leading to different regimes in the oxidation state: low O:C ratios over the tropical continents due to small OH concentrations caused by OH depletion in chemical reactions, and enhanced oxidation states over the tropical oceans based on less OH scavengers and at high altitudes due to longer atmospheric residence time. Due to the relation between O:C ratio and the aerosol hygroscopicity the ageing results in a more physically and chemically consistent description of aerosol water uptake by the organic aerosol. In comparison with observations reasonable agreement for the O:C ratio within the limits of a global model of the simulations is achieved

Lightning and convection parameterisations ? uncertainties in global modelling

International audienceThe simulation of convection, lightning and consequent NOx emissions with global atmospheric chemistry models is associated with large uncertainties since these processes are heavily parameterised. Each parameterisation by itself has deficiencies and the combination of these substantially increases the uncertainties compared to the individual parameterisations. In this study several combinations of state-of-the-art convection and lightning parameterisations are used in simulations with the global atmospheric chemistry general circulation model ECHAM5/MESSy, and are evaluated against lightning observations. A wide range in the spatial and temporal variability of the simulated flash densities is found, attributed to both types of parameterisations. Some combinations perform well, whereas others are hardly applicable. In addition to resolution dependent rescaling parameters, each combination of lightning and convection schemes requires individual scaling to reproduce the observed flash frequencies. The resulting NOx profiles are inter-compared, however definite conclusions about the most realistic profiles can currently not be drawn

Technical note: A new comprehensive SCAVenging submodel for global atmospheric chemistry modelling

International audienceWe present the new scavenging scheme SCAV, simulating the removal of trace gases and aerosol particles by clouds and precipitation in global atmospheric chemistry models. The scheme is quite flexible and can be used for various purposes, e.g. long term chemistry simulations as well as detailed cloud and precipitation chemistry calculations. The presence of clouds can substantially change the chemical composition of the atmosphere. We present a new method of mechanistically coupling gas phase, aerosol, cloud and precipitation chemistry, which enables studies of feedbacks between multiphase chemistry and transport processes

Technical Note: Simulation of detailed aerosol chemistry on the global scale using MECCA-AERO

International audienceWe present the MESSy submodel MECCA-AERO, which simulates both aerosol and gas phase chemistry within one comprehensive mechanism. Including the aerosol phase into the chemistry mechanism increases the stiffness of the resulting set of differential equations. The numerical aspects of the approach followed in MECCA-AERO are presented. MECCA-AERO requires input of an aerosol dynamical/microphysical model to provide the aerosol size and particle number information of the modes/bins for which the chemistry is explicitly calculated. Additional precautions are required to avoid the double counting of processes, especially for sulphate in the aerosol dynamical and the chemistry model. This coupling is explained in detail. To illustrate the capabilities of the new aerosol submodel, examples for species usually treated in aerosol dynamical models are shown. The aerosol chemistry as provided by MECCA-AERO is very sumptuous and not readily applicable for long-term simulations, though it provides a reference to evaluate simplified approaches

DNA methylation profiling of the human major histocompatibility complex: A pilot study for the Human Epigenome Project

The Human Epigenome Project aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena. Occurring naturally on cytosine bases at cytosine-guanine dinucleotides, DNA methylation is intimately involved in diverse biological processes and the aetiology of many diseases. Differentially methylated cytosines give rise to distinct profiles, thought to be specific for gene activity, tissue type, and disease state. The identification of such methylation variable positions will significantly improve our understanding of genome biology and our ability to diagnose disease. Here, we report the results of the pilot study for the Human Epigenome Project entailing the methylation analysis of the human major histocompatibility complex. This study involved the development of an integrated pipeline for high-throughput methylation analysis using bisulphite DNA sequencing, discovery of methylation variable positions, epigenotyping by matrix-assisted laser desorption/ionisation mass spectrometry, and development of an integrated public database available at http://www.epigenome.org. Our analysis of DNA methylation levels within the major histocompatibility complex, including regulatory exonic and intronic regions associated with 90 genes in multiple tissues and individuals, reveals a bimodal distribution of methylation profiles (i.e., the vast majority of the analysed regions were either hypo- or hypermethylated), tissue specificity, inter-individual variation, and correlation with independent gene expression data

Aproximación analítica de consumo de combustible y comportamiento periódico para un vehículo que viaja a través de una serie de semáforos

In this paper, we present a piecewise smooth system, that describes the dynamics of a single vehicle moving through a street that has a sequence of lights that turn on and off with a specific frequency. The model presents three dynamic ways: accelerated, decelerated and zero state. Besides, we show the description of the mathematical model used to simulate the system. The simulation was developed under an event-based scheme and implemented in Matlab. To make the numerical analysis, we take as a parameter study the cycle traffic light, which provides benefits to vehicular traffic system due to its configuration is achieved implementing optimization strategies for the phenomenon of green wave and reduces the travel time as the vehicle minimizes the number of stops along the road. Also, the stability was studied for the periodic orbits one and two. Finally, we made an approximation of fuel consumption. We assume that this is proportional to the mechanical energy produced by the motor. From this point of view, it can be concluded that it is possible to apply modeling and simulation strategies based on dynamic systems to understand the complex behaviors associated with the travel of vehicles in a traffic controlled by traffic lights.En el siguiente artículo, se presenta un sistema suave por tramos que describe la dinámica de un vehículo que se mueve a través de una calle con semáforos que se encienden y apagan con una frecuencia específica. El modelo presenta tres comportamientos dinámicos: acelerado, desacelerado y detenido. Además, se muestra la descripción del modelo matemático utilizado para simular el sistema. La simulación se desarrolló bajo un esquema basado en eventos y se implementó en Matlab. Para realizar el análisis numérico, se toma como parámetro el ciclo de los semáforos, que mejora el sistema de tráfico vehicular debido a que con su configuración se logran implementar estrategias de optimización permitiendo que los vehículos se desplacen en ola verde y reduzcan el tiempo de viaje, minimizando así, el número de paradas a lo largo del camino y reduciendo el consumo de combustible debido a las paradas y aceleradas. Además, se estudió la estabilidad de las órbitas periódicas uno y dos que presenta el modelo de simulación, así como sus implicaciones dinámicas. Finalmente, se presenta una propuesta para calcular el consumo de combustible, asumiendo que es proporcional a la energía mecánica producida por el motor, resulta en una propuesta novedosa que permite a las secretarias de movilidad comprender los comportamientos de los vehículos en vías principales de las ciudades. Desde este punto de vista, se puede concluir que es posible aplicar estrategias de modelado y simulación basadas en sistemas dinámicos para comprender los comportamientos complejos asociados al desplazamiento de los vehículos en una via controlada por semáforos

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

Technical Note: An implementation of the dry removal processes DRY DEPosition and SEDImentation in the Modular Earth Submodel System (MESSy)

International audienceWe present the submodels DRYDEP and SEDI for the Modular Earth Submodel System (MESSy). Dry deposition of gases and aerosols is calculated within DRYDEP, whereas SEDI deals with aerosol particle sedimentation. Dry deposition velocities depend on the near-surface turbulence and the physical and chemical properties of the surface cover (e.g. the roughness length, soil pH or leaf stomatal exchange). The dry deposition algorithm used in DRYDEP is based on the big leaf approach and is described in detail within this Technical Note. The sedimentation submodel SEDI contains two sedimentation schemes: a simple upwind zeroth order scheme and a first order approach

Global cloud and precipitation chemistry and wet deposition: tropospheric model simulations with ECHAM5/MESSy1

International audienceThe representation of cloud and precipitation chemistry and subsequent wet deposition of trace constituents in global atmospheric chemistry models is associated with large uncertainties. To improve the simulated trace gas distributions we apply the new submodel SCAV, which includes detailed cloud and precipitation chemistry and present results of the atmospheric chemistry general circulation model ECHAM5/MESSy1. A good agreement with observed wet deposition fluxes for species causing acid rain is obtained. The new scheme enables prognostic calculations of the pH of clouds and precipitation, and these results are also in accordance with observations. We address the influence of detailed cloud and precipitation chemistry on trace constituents based on sensitivity simulations. The results confirm previous results from regional scale and box models, and we extend the analysis to the role of aqueous phase chemistry on the global scale. Some species are directly affected through multiphase removal processes, and many also indirectly through changes in oxidant concentrations, which in turn have an impact on the species lifetime. While the overall effect on tropospheric ozone is relatively small (3 can reach ?20%, and several important compounds (e.g., H2O2, HCHO) are substantially depleted by clouds and precipitation

Technical Note: Coupling of chemical processes with the Modular Earth Submodel System (MESSy) submodel TRACER

International audienceThe implementation of processes related to chemistry into Earth System Models and their coupling within such systems requires the consistent description of the chemical species involved. We provide a tool (written in Fortran95) to structure and manage information about constituents, hereinafter referred to as tracers, namely the Modular Earth Submodel System (MESSy) generic (i.e., infrastructure) submodel TRACER. With TRACER it is possible to define a multitude of tracer sets, depending on the spatio-temporal representation (i.e., the grid structure) of the model. The required information about a specific chemical species is split into the static meta-information about the characteristics of the species, and its (generally in time and space variable) abundance in the corresponding representation. TRACER moreover includes two submodels. One is TRACER_FAMILY, an implementation of the tracer family concept. It distinguishes between two types: type-1 families are usually applied to handle strongly related tracers (e.g., fast equilibrating species) for a specific process (e.g., advection). In contrast to this, type-2 families are applied for tagging techniques. Tagging means the artificial decomposition of one or more species into parts, which are additionally labelled (e.g., by the region of their primary emission) and then processed as the species itself. The type-2 family concept is designed to conserve the linear relationship between the family and its members. The second submodel is TRACER_PDEF, which corrects and budgets numerical negative overshoots that arise in many process implementations due to the numerical limitations (e.g., rounding errors). The submodel therefore guarantees the positive definiteness of the tracers and stabilises the integration scheme. As a by-product, it further provides a global tracer mass diagnostic. Last but not least, we present the submodel PTRAC, which allows the definition of tracers via a Fortran95 namelist, as a complement to the standard tracer definition by application of the TRACER interface routines in the code. TRACER with its submodels and PTRAC can readily be applied to a variety of models without further requirements. The code and a documentation are included in the electronic supplement