The application of an Eulerian chemical and transport model (CMAQ) at fine scale resolution to the UK

Present-day numerical air quality models are considered essential tools for predicting future air pollutant concentrations and depositions, contributing to the development of new effective strategies for the control and the reduction of pollutant emissions. They simulate concentrations and depositions of pollutants on a wide range of scales (global, national, urban scale) and they are used for identifying critical areas, integrating measurements and achieving a deeper scientific understanding of the physical and chemical processes involving air pollutants in the atmosphere. The use of comprehensive air quality models started in the late 1970s and since then their development has increased rapidly, hand in hand with the rapid increase in computational resources. Today more and more complex and computationally expensive numerical models are available to the scientific community. One of these tools is the Community Multi-Scale Air Quality System (CMAQ), developed in the 1990s by the US Environmental Protection Agency (EPA) and currently widely applied across the world for air pollution studies. This work focuses on the application of CMAQ to the United Kingdom, for estimating concentrations and depositions of acidifying pollutants (NOX, NHX, SOX) on a national scale. The work is divided into seven chapters, the first one describing the main issues related to the emission and dispersion in the atmosphere of acidifying species. It also includes a brief overview of the main international policies signed in the last thirty years in order to reduce the problem of acidification in Europe, as well as a brief description of some models mentioned in this thesis. The second one describes the main features of CMAQ and addresses some issues such as the use of a nesting process for achieving temporally and spatially resolved boundary concentrations, and the implementation of the model on parallel machines, essential for reducing the simulation computing time. It also describes how this study is part of a wider context, which includes the application of CMAQ in the United Kingdom by other users with different scientific purposes (aerosols processes, air quality in the urban area of London, contribution of UK power stations to concentrations and depositions etc.). The third part of the thesis focuses on the application and evaluation over the United Kingdom of the 5th Generation Mesoscale Model MM5, used for providing 3D meteorological input fields to CMAQ. This study was performed assuming that an accurate representation of depositions and concentrations of chemical species cannot be achieved without a good estimate of the meteorological parameters involved in most of the atmospheric processes (transport, photochemistry, aerosol processes, cloud processes etc.). The fourth part of the thesis describes the preliminary implementation of the Sparse Matrix Operational Kernel Emission System (SMOKE) in the United Kingdom. The processor provides input emissions to CMAQ. The use of SMOKE is usually avoided in CMAQ applications of outside America, and CMAQ input emission files are prepared by the application of other software. The reason is that the model requires radical changes for being applied outside Northern and Central America. Some of these changes have been made in this study such as the adaptation of the European emission inventory EMEP and the UK National Inventory NAEI to the modelling system for point and area sources, the introduction of new European emission temporal profiles in substitution of the American ones and the introduction of new geographical references for the spatial allocation of emissions. In the fifth chapter the results of CMAQ application over the UK are discussed. The study focuses on NOX, SO2, NH3 and + 4 NH . Maps of concentration are presented and modelled data are compared to measurements from two different air quality networks in the UK. An analysis of the performance of CMAQ over the UK is also performed. In the final chapter an annual inter-comparison between CMAQ and the Lagrangian transport model FRAME is carried out. Maps of annual wet deposition fluxes of NHX, NOY and SOX for year 1999 are presented. The results of both models are compared to one another and they are also compared to values from the UK official data set CBED. Finally, the last chapter suggests the work that has to be done in the future with CMAQ and it summarizes the conclusions

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

A tool to evaluate air quality model performances in regulatory applications

This paper describes the details of the DELTA Tool and Benchmarking service for air quality models, recently developed in the framework of FAIRMODE (Forum for Air Quality Modelling in Europe). One of the main objectives of the FAIRMODE activities is the development of a procedure for the evaluation and benchmarking of air quality modelling applications for regulatory purposes. The DELTA Tool is a specific software which provides summary statistics (i.e. BIAS, RMSE, correlation coefficient) as well as scatter-plots, time series plots, Taylor, Target and other diagrams providing an overview of the quality of model results with respect to monitored data. Moreover, the benchmarking service implemented in DELTA produces summary reports containing performance indicators related to a given model application in the frame of the EU Air Quality directive 2008.This work describes the structure of the DELTA tool and template for reporting model performances. Some examples of application are also briefly presented.JRC.H.2-Air and Climat

Performance criteria to evaluate air quality modeling applications

A set of statistical indicators fit for air quality model evaluation is selected based on experience and literature: The Root Mean Square Error (RMSE), the bias (Bias), the standard Deviation (SD) and the correlation factor (R) are selected. Among these the RMSE is proposed as the key one for the description of the model skill. Model Performance Criteria (MPC) to investigate whether a model results are ‘good enough’ for a given application are calculated based on the observation uncertainty (U). The basic concept is to allow for model results a similar margin of tolerance (in terms of uncertainty) as for observations. U is pollutant, concentration level and station dependent, therefore the proposed MPC are normalized by U. Some existing composite diagrams are adapted to visualize model performance in terms of the proposed MPC and are illustrated in a real modeling application. The Target diagram, used to visualize the RMSE, is adapted with a new normalization on its axis, while complementary diagrams are proposed. In this first application the dependence of U on concentrations level and station is ignored, and an assumption on the pollutant dependent relative error is made. The advantages of this new approach are finally described.JRC.H.2-Air and Climat

A tool to evaluate air quality model performances in regulatory applications

This paper describes the details of the DELTA Tool and Benchmarking service for air quality models, recently developed in the framework of FAIRMODE (Forum for Air Quality Modelling in Europe). One of the main objectives of the FAIRMODE activities is the development of a procedure for the evaluation and benchmarking of air quality modelling applications for regulatory purposes. The DELTA Tool is a specific software which provides summary statistics (i.e. BIAS, RMSE, correlation coefficient) as well as scatterplots, time series plots, Taylor, Target and other diagrams providing an overview of the quality of model results with respect to monitored data. Moreover, the benchmarking service implemented in DELTA produces summary reports containing performance indicators related to a given model application in the frame of the EU Air Quality Directive (AQD, 2008). This work describes the structure of the DELTA tool and template for reporting model performances. Some examples of application are also briefly presented

Concentration Reduction Apportionment (CRA) Approach: a new methodology to define effective air quality plans.

Decision Support Systems (DSSs) are key tools to help the decision makers in the development of effective strategies to reduce atmospheric pollution. This is especially true for secondary atmospheric pollutants, which are generated in the atmosphere through complex non-linear reactions, involving anthropogenic and biogenic precursor emissions. In this work, a new methodology called Concentration Reduction Apportionment (CRA) technique, is formalized and applied to support decision makers in air quality planning. The feasible potential impacts and costs of the application of emission abatement measures in different clusters of anthropic activities on PM10 concentrations are assessed and a case study in Northern Italy is then presented