Mechanisms for Atmospheric chemistry: GeneratioN, Interpretation and FidelitY - MAGNIFY

Lead Research Organisation: University of York
Department Name: Chemistry

Abstract

The chemistry of the troposphere underlies a range of environmental issues, which have substantial societal and economic impacts. Whether it is a changing climate, a reduction in air quality affecting human health or the degradation of ecosystems due to air pollution the details of the chemistry determines the severity of the impact. Numerical models of atmospheric chemistry are essential to our ability to understand, predict and hence mitigate these problems. The description of the chemistry occurring within these models is known as the 'mechanism'. Different models use different levels of chemical complexity in deriving these mechanisms, depending on their individual foci. However, there is an overarching need for a 'gold standard' or benchmark mechanism, which contains as full a representation of our fundamental 'state of science' understanding of atmospheric chemistry as is possible. For the last decade this benchmark mechanism, both in the UK and internationally, has been the Master Chemical Mechanism (MCM).

The MCM provides a highly comprehensive representation of atmospheric volatile organic compound (VOC) degradation chemistry, which is extensively used by the atmospheric science community in a wide variety of science and policy applications where chemical detail is required. The MCM is an internationally recognised resource, with registered users worldwide, and thus represents a highly regarded flagship facility for atmospheric science in the UK. Much of its success stems from the availability of the MCM database on the web, along with the provision of a range of tools to facilitate its use.

However, both the MCM itself and its supporting infrastructure are now becoming dated. It is clear that the enormous task of bringing the entire mechanism fully up to date, and maintaining it in that condition, is becoming increasingly difficult within the resources and methods that are currently available. It is recognised, therefore, that sustainable development of the MCM as a whole requires a fundamental revision in the methods applied to its maintenance to ensure that updates/changes can be carried out thoroughly and efficiently, and which can be more readily sustained through changes of personnel in the future. Without such changes, it is probable that the MCM will stagnate, gradually fall from use and eventually become obsolete, and hence no longer a highly regarded flagship facility for atmospheric science in the UK.

The MAGNIFY project puts in place a comprehensive strategic work plan (including a number of important scientific deliverables) in order to make the MCM more sustainable, updating its construction rules and opening it up more to community, building upon its success and maintaining it as the "gold standard" benchmark mechanism for atmospheric chemistry.

This proposal will:
1) build a fully updated and revised mechanism development protocol, for the generation of a new version of the MCM (v4.0)
2) put in place a range of quality assurance methods to ensure high quality updates and changes into the future
3) develop an international community tasked with supporting the continual development of the MCM mechanism and framework.
4) investigate automated methods for mechanism generation that will reduce workload and error, ensuring responsive, efficient generation of mechanisms into the future
5) further develop and enhance the successful open access web platform used by the MCM for access, archiving and interrogation not only of the MCM and its successors, but also a range of mechanisms used by a range of NERC / MO / DEFRA supported activities and for a range of models world wide
6) provide a comprehensive evaluation methodology of all mechanisms stored in the system against the updated benchmark MCM and its successors with an emphasis on assessing those models currently being used for policy (air quality and climate) related work within the UK.

Planned Impact

MAGNIFY has impacts on 5 key groups and activities; air quality and climate policy; operational weather and climate groups running forecast models; scientists running research models of atmospheric composition; laboratory atmospheric chemical kinetics and field groups; education.

i) Impacts on policy
Chemical mechanisms provide the route by which emissions of pollutants lead to impacts on socially important processes such as climate, air quality, food security etc. Our ability to accurately predict and understand these phenomena depends on the quality and fidelity of these simulations. A more accurate simulation will lead to better policy making. This proposal will provide a benchmark mechanism to compare simpler mechanism against, put in place the computational infrastructure to host a range of mechanisms and to automate the comparison of these mechanisms under a range of conditions. Ultimately this will lead to better mechanisms being implemented into policy models.

ii) Operational weather and climate groups
These are the organisations that run air quality and climate models as a core part of their remit. This proposal will improve the quality of the chemical mechanisms they use by providing them with a readily accessible way to assess the fidelity of their mechanism against a benchmark mechanism and other mechanisms being used by science and operational agencies.

iii) Scientists running research models of atmospheric composition
By providing a readily accessible mechanism with which to test, assess and update chemical mechanisms MAGNIFY will allow research science to progress more rapidly and to adopt updates to process understanding in an enhanced way.

iv) Laboratory and field groups
These groups have typically found it difficult to impact policy directly as numerical models are needed to fully interpret both field and laboratory measurements. Often to interpret these new results fully, new or updated mechanisms need to be generated and then comparisons made with previous mechanisms. MAGNIFY will significant decrease the time it takes to compose new mechanisms and to evaluate the impact of new results from kinetics and field studies.

v) Education
MAGNIFY will continue the open access model used for the MCM. This has proven useful for atmospheric chemistry education where students are able to explore the mechanism using the tools on the website, and can generate models for exploring the mechanisms themselves. MAGNIFY will enhance this capability by allowing students to explore a range of mechanisms and to appreciate the uncertainty associated with science.

New educational tools and resources for teachers and students will be developed and assessed in conjunction with our project partner the Royal Society of Chemistry in order to enhance the teaching and learning of the impacts of atmospheric chemistry on air quality and climate change to high school age students.

Publications

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Jenkin M (2019) The CRI v2.2 reduced degradation scheme for isoprene in Atmospheric Environment

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Newland MJ (2019) Photochemistry of 2-butenedial and 4-oxo-2-pentenal under atmospheric boundary layer conditions. in Physical chemistry chemical physics : PCCP

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Newland MJ (2017) Elucidating the fate of the OH-adduct in toluene oxidation under tropospheric boundary layer conditions. in Proceedings of the National Academy of Sciences of the United States of America

 
Description The ambitious MAGNIFY project has put in place a comprehensive strategic work plan in order to make the Maser Chemical Mechanism more sustainable, updating its construction rules and opening it up more to community, building upon its success and maintaining it as the "gold standard" benchmark mechanism for atmospheric chemistry.

More specifically:

1) A range of fully updated and revised mechanism development protocols have been developed in order to build the next generation of atmospheric chemical mechanisms (several have been published in peer review literature)
2) The new and updated protocol rules have been tested for use with automated methods for mechanism generation (the MCM/GECKO-A mechanism) that will reduce workload and error, ensuring responsive, efficient generation of mechanisms into the future
5) The successful open access web platform used by the MCM for access, archiving and interrogation has been sustainably developed at the University of York, where it can support the next generation of the MCM and its successors
Exploitation Route Over the last decade the MCM has been hugely influential on the global atmospheric chemistry community, where it is extensively used in a wide variety of science and policy applications, where chemical detail is required to assess issues related to atmospheric composition. The work carried out as part of this project is fundamental to the future development of atmospheric chemical mechanisms and the MCM, in particular the automatic generation of a range of atmospheric chemical mechanisms.

For example, much of the MAGNIFY work feeds directly into the work of the US Coordination Research Council Project on the "Development and Evaluation of Databases and Estimation Methods for Predicting Air Quality Impacts of Emitted Organic Compound" for the development of future air quality modelling initiatives.

The MCM and new versions of it will continue to be used directly as a state of the science tool (facilitated by the new tools to make using it easier), or as a benchmark "gold standard' against which to develop, optimise and test the fidelity of chemical schemes used in chemical transport models (e.g. GEOS-CHEM, and CMAQ)
Sectors Chemicals,Education,Environment

URL http://mcm.york.ac.uk
 
Description (EUROCHAMP-2020) - Integration of European Simulation Chambers for Investigating Atmospheric Processes - Towards 2020 and beyond
Amount € 9,289,955 (EUR)
Funding ID 730997 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 12/2016 
End 11/2020
 
Title New sustainable website for the Master Chemical Mechanism and CRI variants (CVRIv2.2) 
Description The MCM provides a highly comprehensive representation of atmospheric volatile organic compound (VOC) degradation chemistry, which is extensively used by the atmospheric science community in a wide variety of science and policy applications where chemical detail is required. The MCM is an internationally recognised resource, with registered users worldwide, and thus represents a highly regarded flagship facility for atmospheric science in the UK. Much of its success stems from the availability of the MCM database on the web, along with the provision of a range of tools to facilitate its use. A new sustainable version of the MCM website is now available at york. It has also been updated to the latest version of the reduced CRI mechanism (CRIv2.2) 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? Yes  
Impact The MCM is an internationally recognised resource, with registered users worldwide, and thus represents a highly regarded flagship facility for atmospheric science in the UK. Much of its success stems from the availability of the MCM database on the web, along with the provision of a range of tools to facilitate its use. 
URL http://mcm.york.ac.uk
 
Title Development of MCM website at the University of York 
Description Master Chemical Mechanism Database and website has developed at the University of York. It has been re-developed, cleaned up and moved to be backed up by IT services in York. New CRIv2.2 reduced mechanism has been added 
Type Of Material Computer model/algorithm 
Year Produced 2019 
Provided To Others? Yes  
Impact A better performing website and database, ready for the new MCM/GECKO-A schemes to be added 
URL http://mcm.york.ac.uk
 
Title Master Chemical Mechanism Development Protocols 
Description New protocols for estimation of rate coefficients and branching ratios for gas-phase reactions of OH with aliphatic and aromatic organic compounds for use in automated mechanism construction - including recommended kinetic databases (see publications) 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact These new protocols and their associated chemical kinetic databases will form the basis of the new MCM/GECKO-A autogenerated chemical mechanisms 
 
Description CEAM 
Organisation Centre for Environmental Studies of the Mediterranean (Centro de Estudios Ambientales del Mediterráneo)
Country Spain 
Sector Academic/University 
PI Contribution Experimental design, data analysis 2 EU funded Trans National Access experimental campaigns funded through the EUROCHAMP2020 programme in order to look at (1) the structural dependence of alkenes on the stabilisation yield of Criegee intermediates from ozonolysis, (2) the kinetics and mechanisms of beta-dicarbonyl photolysis. These experiments have been carried out in line with work being carried out as part of the MAGNIFY project
Collaborator Contribution Chamber infrastructure support, measurements, data analysis
Impact 3 collaborative publications in high impact peer reviewed journals (see publications). Further collaborations/infrastructure support on other chamber experiments in EUPHORE and other EUROCHAMP2020 chambers
Start Year 2013
 
Description Development of a new advanced photolysis protocol for auto-generated chemical mechanisms 
Organisation NCAR National Center for Atmospheric Research
Country United States 
Sector Academic/University 
PI Contribution Development of a new advanced photolysis protocol for auto-generated chemical mechanisms Update and development of the TUV photolysis model code
Collaborator Contribution Provision of the TUV photolysis modelling code Assistance in the development of a new advanced photolysis protocol for auto-generated chemical mechanisms
Impact Report on the development of a new advanced photolysis protocol for auto-generated chemical mechanisms and associated database available at: https://github.com/wacl-york/MCMphotolysis
Start Year 2015
 
Description Development of the Atchem2 modelling toolkit for use with the MCM 
Organisation University of Birmingham
Department School of Geography, Earth and Environmental Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism. It was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies
Collaborator Contribution AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism. It was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies
Impact The AtChem2 code and documentation are available at https://github.com/AtChem/ An accompanying peer reviewed publication in the GeoScientific Model Development journal has been published: https://doi.org/10.5194/gmd-13-169-2020
Start Year 2017
 
Description Development of the Atchem2 modelling toolkit for use with the MCM 
Organisation University of Leeds
Department School of Chemistry Leeds
Country United Kingdom 
Sector Academic/University 
PI Contribution AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism. It was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies
Collaborator Contribution AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism. It was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies
Impact The AtChem2 code and documentation are available at https://github.com/AtChem/ An accompanying peer reviewed publication in the GeoScientific Model Development journal has been published: https://doi.org/10.5194/gmd-13-169-2020
Start Year 2017
 
Description Development of the Atchem2 modelling toolkit for use with the MCM 
Organisation University of Leeds
Department School of Computing Leeds
Country United Kingdom 
Sector Academic/University 
PI Contribution AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism. It was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies
Collaborator Contribution AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism. It was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies
Impact The AtChem2 code and documentation are available at https://github.com/AtChem/ An accompanying peer reviewed publication in the GeoScientific Model Development journal has been published: https://doi.org/10.5194/gmd-13-169-2020
Start Year 2017
 
Description Development of the Atchem2 modelling toolkit for use with the MCM 
Organisation University of Leicester
Country United Kingdom 
Sector Academic/University 
PI Contribution AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism. It was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies
Collaborator Contribution AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism. It was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies
Impact The AtChem2 code and documentation are available at https://github.com/AtChem/ An accompanying peer reviewed publication in the GeoScientific Model Development journal has been published: https://doi.org/10.5194/gmd-13-169-2020
Start Year 2017
 
Description development of automatically generated chemical mechanisms 
Organisation University of Paris-Est
Country France 
Sector Academic/University 
PI Contribution Development of chemical mechanism construction protocols for coding into the autogeneration expert system Reduction protocols Evaluation of auto-generated mechanisms in models Future updates and development of the MCM/GECKO-A chemical mechanism, and variants of
Collaborator Contribution Provision and development of automatic mechanisms generation expert system code Application of new chemical mechanism development protocols Reduction of system complexities Evaluation of explicit mechanisms using bespoke zero-dimensional box models
Impact 2 publications on the estimation of rate coefficients and branching ratios for gas-phase reactions of OH with aliphatic and aromatic organic compounds for use in automated mechanism construction (see publications). Contributions to a major expert perspective on the development and applications of structure activity relationships in atmospheric mechanism development (see publications). Collaborative project work on the Horizons 2020 project - EUROCHAMP-2020: Integration of European Simulation Chambers for Investigating Atmospheric Processes - Towards 2020 and beyond (grant number 730997).
Start Year 2015
 
Title new york mcm website 
Description new mcm website developed at york 
Type Of Technology Webtool/Application 
Year Produced 2019 
Open Source License? Yes  
Impact new mcm website available at york 
URL http://mcm.york.ac.uk
 
Description Conference Organisation 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Organisation of The Royal Society of Chemistry's 24th International Symposium on Gas Kinetics and Related Phenomena,York, 17th to the 21st July 2016. Over 160 scientists from 22 countries participated in a programme consisting of over 160 presentations on themes as diverse as combustion chemistry, reaction dynamics, experimental methods, modelling
of complex systems, nanoparticles and aerosols and, of course, atmospheric chemistry. The four day conference consisted of a combination of invited plenary and contributed oral and poster presentations, providing an open forum for discussion of the latest scientific advances in various fields related to chemical kinetics and dynamics.
Year(s) Of Engagement Activity 2016
URL https://www.york.ac.uk/chemistry/research/physical/gaskineticsconf2016/