scholarly journals Semantically enhanced provenance capture for chamber model development with a master chemical mechanism

2008 ◽  
Vol 367 (1890) ◽  
pp. 987-990 ◽  
Author(s):  
Chris J Martin ◽  
Mohammed H Haji ◽  
Peter M Dew ◽  
Michael J Pilling ◽  
Peter K Jimack
Keyword(s):  
Atmospheric Chemistry ◽  
Model Development ◽  
Computational Modelling ◽  
Chemical Mechanism ◽  
Scientific Communities ◽  
Chamber Model ◽  
Master Chemical Mechanism ◽  
Semantically Enhanced ◽  
Chemistry Community

The development and maintenance of benchmark databases within scientific communities is reliant on interactions with database users. We explore the role of semantically enhanced provenance for computational modelling processes that make use of one such database: the master chemical mechanism, a key resource within the atmospheric chemistry community.

scholarly journals AtChem, an open source box-model for the Master Chemical Mechanism

2019 ◽  
Author(s):  
Roberto Sommariva ◽  
Sam Cox ◽  
Chris Martin ◽  
Kasia Borońska ◽  
Jenny Young ◽  
...  
Keyword(s):  
Open Source ◽  
Atmospheric Chemistry ◽  
Web Application ◽  
Box Model ◽  
Chemical Mechanism ◽  
Control Software ◽  
Sensitivity Studies ◽  
Master Chemical Mechanism ◽  
Field Campaigns ◽  
Set Up

Abstract. 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 (MCM, http://mcm.york.ac.uk/). AtChem was initially developed within the EUROCHAMP project as a web application (AtChem-online, https://atchem.leeds.ac.uk/webapp/) for modelling environmental chamber experiments; it was recently upgraded and further developed into a standalone 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. AtChem is installed, set up and configured using semi-automated scripts and simple text configuration files, making it easy to use even for non-experienced users. A key feature of AtChem is that it can easily be constrained to observational data which may have different timescales, thus retaining all the information contained in the observations. Implementation of a continuous integration workflow, coupled with a comprehensive suite of tests and version control software, makes the AtChem codebase robust, reliable and traceable. The AtChem2 code and documentation are available at https://github.com/AtChem/, under the open source MIT license.

scholarly journals The community atmospheric chemistry box model CAABA/MECCA-4.0

2019 ◽  
Vol 12 (4) ◽  
pp. 1365-1385 ◽  
Author(s):  
Rolf Sander ◽  
Andreas Baumgaertner ◽  
David Cabrera-Perez ◽  
Franziska Frank ◽  
Sergey Gromov ◽  
...  
Keyword(s):  
Atmospheric Chemistry ◽  
Box Model ◽  
Chemical Mechanism ◽  
Chemical Mechanisms ◽  
Community Model ◽  
Volatile Organic ◽  
Master Chemical Mechanism ◽  
New Feature ◽  
User Friendly ◽  
Skeletal Mechanism

Abstract. We present version 4.0 of the atmospheric chemistry box model CAABA/MECCA that now includes a number of new features: (i) skeletal mechanism reduction, (ii) the Mainz Organic Mechanism (MOM) chemical mechanism for volatile organic compounds, (iii) an option to include reactions from the Master Chemical Mechanism (MCM) and other chemical mechanisms, (iv) updated isotope tagging, and (v) improved and new photolysis modules (JVAL, RADJIMT, DISSOC). Further, when MECCA is connected to a global model, the new feature of coexisting multiple chemistry mechanisms (PolyMECCA/CHEMGLUE) can be used. Additional 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-4.0 is a community model published under the GNU General Public License.

scholarly journals Development of a chlorine chemistry module for the Master Chemical Mechanism

2015 ◽  
Vol 8 (6) ◽  
pp. 4823-4849
Author(s):  
L. K. Xue ◽  
S. M. Saunders ◽  
T. Wang ◽  
R. Gao ◽  
X. F. Wang ◽  
...  
Keyword(s):  
Atmospheric Chemistry ◽  
Southern China ◽  
Oxidative Capacity ◽  
Early Morning ◽  
Chemical Mechanism ◽  
Atmospheric Photochemistry ◽  
Nitryl Chloride ◽  
Chemistry Research ◽  
Master Chemical Mechanism ◽  
Chemistry Module

Abstract. The chlorine atom (Cl·) has a high potential to perturb atmospheric photochemistry by oxidizing volatile organic compounds (VOCs), but the exact role it plays in the polluted troposphere remains unclear. The Master Chemical Mechanism (MCM) is a near explicit mechanism that has been widely applied in the atmospheric chemistry research. While it addresses comprehensively the chemistry initiated by the OH, O3 and NO3 radicals, its representation of the Cl· chemistry is incomplete as it only considers the reactions for alkanes. In this paper, we develop a more comprehensive Cl· chemistry module that can be directly incorporated within the MCM framework. A suite of 199 chemical reactions describes the Cl·-initiated degradation of alkenes, aromatics, aldehydes, ketones, alcohols, and some organic acids and nitrates, along with the inorganic chemistry involving Cl· and its precursors. To demonstrate the potential influence of the new chemistry module, it was incorporated into a MCM box model to evaluate the impacts of nitryl chloride (ClNO2), a product of nocturnal halogen activation by nitrogen oxides (NOx), on the following-day's atmospheric photochemistry. With constraints of recent observations collected at a coastal site in Hong Kong, southern China, the modeling analyses suggest that the Cl· produced from ClNO2 photolysis may substantially enhance the atmospheric oxidative capacity, VOC oxidation, and O3 formation, particularly in the early morning period. The results demonstrate the critical need for photochemical models to include more fully chlorine chemistry in order to better understand the atmospheric photochemistry in polluted environments subject to intense emissions of NOx, VOCs and chlorine-containing constituents.

A user-orientated approach to provenance capture and representation for in silico experiments, explored within the atmospheric chemistry community

2009 ◽  
Vol 367 (1898) ◽  
pp. 2753-2770 ◽  
Author(s):  
Chris J. Martin ◽  
Mohammed H. Haji ◽  
Peter K. Jimack ◽  
Michael J. Pilling ◽  
Peter M. Dew
Keyword(s):  
Atmospheric Chemistry ◽  
In Silico ◽  
Model Development ◽  
Design Development ◽  
Laboratory Notebook ◽  
Iterative Model ◽  
Science Domain ◽  
And Storage ◽  
Chemistry Community

We present a novel user-orientated approach to provenance capture and representation for in silico experiments, contrasted against the more systems-orientated approaches that have been typical within the e-Science domain. In our approach, we seek to capture the scientist's reasoning in the form of annotations as an experiment evolves, while using the scientist's terminology in the representation of process provenance. Our user-orientated approach is applied in a case study within the atmospheric chemistry domain: we consider the design, development and evaluation of an electronic laboratory notebook, a provenance capture and storage tool, for iterative model development.

scholarly journals AtChem (version 1), an open-source box model for the Master Chemical Mechanism

2020 ◽  
Vol 13 (1) ◽  
pp. 169-183 ◽  
Author(s):  
Roberto Sommariva ◽  
Sam Cox ◽  
Chris Martin ◽  
Kasia Borońska ◽  
Jenny Young ◽  
...  
Keyword(s):  
Open Source ◽  
Atmospheric Chemistry ◽  
Web Application ◽  
Box Model ◽  
Chemical Mechanism ◽  
Code Base ◽  
Sensitivity Studies ◽  
Master Chemical Mechanism ◽  
Field Campaigns ◽  
Set Up

Abstract. 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 (MCM, http://mcm.york.ac.uk/, last access: 16 January 2020). AtChem was initially developed within the EUROCHAMP project as a web application (AtChem-online, https://atchem.leeds.ac.uk/webapp/, last access: 16 January 2020) for modelling environmental chamber experiments; 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. AtChem is installed, set up and configured using semi-automated scripts and simple text configuration files, making it easy to use even for inexperienced users. A key feature of AtChem is that it can easily be constrained to observational data which may have different timescales, thus retaining all the information contained in the observations. Implementation of a continuous integration workflow, coupled with a comprehensive suite of tests and version control software, makes the AtChem code base robust, reliable and traceable. The AtChem2 code and documentation are available at https://github.com/AtChem/ (last access: 16 January 2020) under the open-source MIT License.

scholarly journals Improvement in Modeling of OH and HO2 Radical Concentrations during Toluene and Xylene Oxidation with RACM2 Using MCM/GECKO-A

Atmosphere ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 732
Author(s):  
Victor Lannuque ◽  
Barbara D’Anna ◽  
Florian Couvidat ◽  
Richard Valorso ◽  
Karine Sartelet
Keyword(s):  
Air Quality ◽  
Atmospheric Chemistry ◽  
Oxidation Mechanism ◽  
Chemical Mechanism ◽  
Flow Tube ◽  
Quality Models ◽  
Pollutant Formation ◽  
Master Chemical Mechanism ◽  
Kinetics Of ◽  
Ho2 Radical

Due to their major role in atmospheric chemistry and secondary pollutant formation such as ozone or secondary organic aerosols, an accurate representation of OH and HO2 (HOX) radicals in air quality models is essential. Air quality models use simplified mechanisms to represent atmospheric chemistry and interactions between HOX and organic compounds. In this work, HOX concentrations during the oxidation of toluene and xylene within the Regional Atmospheric Chemistry Mechanism (RACM2) are improved using a deterministic–near-explicit mechanism based on the Master Chemical Mechanism (MCM) and the generator of explicit chemistry and kinetics of organics in the atmosphere (GECKO-A). Flow tube toluene oxidation experiments are first simulated with RACM2 and MCM/GECKO-A. RACM2, which is a simplified mechanism, is then modified to better reproduce the HOX concentration evolution simulated by MCM/GECKO-A. In total, 12 reactions of the oxidation mechanism of toluene and xylene are updated, making OH simulated by RACM2 up to 70% more comparable to the comprehensive MCM/GECKO-A model for chamber oxidation simulations.

scholarly journals Development of a chlorine chemistry module for the Master Chemical Mechanism

2015 ◽  
Vol 8 (10) ◽  
pp. 3151-3162 ◽  
Author(s):  
L. K. Xue ◽  
S. M. Saunders ◽  
T. Wang ◽  
R. Gao ◽  
X. F. Wang ◽  
...  
Keyword(s):  
Atmospheric Chemistry ◽  
Southern China ◽  
Oxidative Capacity ◽  
Early Morning ◽  
Chemical Mechanism ◽  
Atmospheric Photochemistry ◽  
Nitryl Chloride ◽  
Chemistry Research ◽  
Master Chemical Mechanism ◽  
Chemistry Module

Abstract. The chlorine atom (Cl·) has a high potential to perturb atmospheric photochemistry by oxidizing volatile organic compounds (VOCs), but the exact role it plays in the polluted troposphere remains unclear. The Master Chemical Mechanism (MCM) is a near-explicit mechanism that has been widely applied in the atmospheric chemistry research. While it addresses comprehensively the chemistry initiated by the OH, O3 and NO3 radicals, its representation of the Cl· chemistry is incomplete as it only considers the reactions for alkanes. In this paper, we develop a more comprehensive Cl· chemistry module that can be directly incorporated within the MCM framework. A suite of 205 chemical reactions describes the Cl·-initiated degradation of alkenes, aromatics, alkynes, aldehydes, ketones, alcohols, and some organic acids and nitrates, along with the inorganic chemistry involving Cl· and its precursors. To demonstrate the potential influence of the new chemistry module, it was incorporated into a MCM box model to evaluate the impacts of nitryl chloride (ClNO2), a product of nocturnal halogen activation by nitrogen oxides (NOX), on the following day's atmospheric photochemistry. With constraints of recent observations collected at a coastal site in Hong Kong, southern China, the modeling analyses suggest that the Cl· produced from ClNO2 photolysis may substantially enhance the atmospheric oxidative capacity, VOC oxidation and O3 formation, particularly in the early morning period. The results demonstrate the critical need for photochemical models to include more detailed chlorine chemistry in order to better understand the atmospheric photochemistry in polluted environments subject to intense emissions of NOX, VOCs and chlorine-containing constituents.

scholarly journals Measurement of isoprene nitrates by GCMS

2016 ◽  
Vol 9 (9) ◽  
pp. 4533-4545 ◽  
Author(s):  
Graham P. Mills ◽  
Glyn D. Hiatt-Gipson ◽  
Sean P. Bew ◽  
Claire E. Reeves
Keyword(s):  
Atmospheric Chemistry ◽  
Production Efficiency ◽  
Chemical Mechanism ◽  
Ozone Production ◽  
Gas Chromatography Mass Spectrometry ◽  
Nitrate Radical ◽  
Calibration Methods ◽  
Isoprene Nitrates ◽  
Ambient Concentrations ◽  
Master Chemical Mechanism

Abstract. According to atmospheric chemistry models, isoprene nitrates play an important role in determining the ozone production efficiency of isoprene; however this is very poorly constrained through observations as isoprene nitrates have not been widely measured. Measurements have been severely restricted largely due to a limited ability to measure individual isoprene nitrate isomers. An instrument based on gas chromatography/mass spectrometry (GCMS) and the associated calibration methods are described for the speciated measurements of individual isoprene nitrate isomers. Five of the primary isoprene nitrates which formed in the presence of NOx by reaction of isoprene with the hydroxyl radical (OH) in the Master Chemical Mechanism are identified using known isomers on two column phases and are fully separated on the Rtx-200 column. Three primary isoprene nitrates from the reaction of isoprene with the nitrate radical (NO3) are identified after synthesis from the already identified analogous hydroxy nitrate. A Tenax adsorbent-based trapping system allows the analysis of the majority of the known hydroxy and carbonyl primary isoprene nitrates, although not the (1,2)-IN isomer, under field-like levels of humidity and showed no impact from typical ambient concentrations of NOx and ozone.

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