This page contains public data for the peer-reviewed publication:
Matthew B. Goss, Hannah S. Kenagy, Colette L. Heald, Jesse H. Kroll. “Re-examining chemical conditions of past chamber studies of secondary organic aerosol formation.” Submitted.
These data files are intended as additional supplementary information for this publication. If you would like to use any data herein in a publication, please contact the corresponding authors (Matthew Goss, [email protected], or Jesse Kroll, [email protected]) first.
Included below are the figure data, the starting conditions for model runs, and the Matlab files used to run the model. All starting conditions are read into Matlab via an excel file to allow for quick tuning of model inputs and to allow easy scalability to apply these methods to many chamber experiments. All modeling was carried out using Matlab R2023b and F0AM v4.3 (link). F0AM mechanism files are also included. These are based on the Master Chemical Mechanism (v3.3.1). All modifications to the mechanisms are noted in comments within the files.
If you have any more questions, please contact the corresponding authors.
All units are self-explanatory or abbreviated as part of column names. Please inquire with questions.
Figure 1 data:
Panel A:
Fig_1_measurement_timeseries.csv
Panel B/C:
Fig_1_oxidant_loss_timeseries.csv
Panel D/E
Figure 2 data:
Fig_2_fractional_oxidant_fates.csv
Figure 3 data:
Fig_3_fractional_ro2_fates.csv
Figure 4 data:
Fig_4_global_tau_bi_weighted_by_isop_ox.csv
Fig_4_model_tau_start_points.csv
Figure 5 data:
Fig_5_aerosol_yields_and_fractional_ox_and_RO2_chem.csv
Figure S2/S3 data:
Fig_S2_S3_model_timeseries.csv
Fig_S2_S3_experiment_timeseries.csv
Figure S5 to S12 data:
Fig_S5_to_S12_aerosol_yields_and_fractional_ox_and_RO2_chem.csv
All Matlab files and input files required to run the model are included below.
main_simulation_script_v12.m calls run_simulations_v12.m for each experiment. After all simulations have been run and analyzed, it aggregates and saves data to csvs in a folder called csv outputs.
run_simulations_v12.m extracts experimental conditions from an excel file (F0AM input conditions v12.xlsx) and runs F0AM. This excel file also controls various options for performing analysis or generating plots. F0AM mechanism files (linked below) must be found on the Matlab path. If desired, this runs an analysis script (run_analysis_v12.m) to compute metrics from the model output, and/or runs sensitivity tests, and/or produces a plot comparing real experimental timeseries to model timeseries. Experimental timeseries data are stored in a file Repository for real data in the working directory; this also includes files for the chamber light spectra. This script requires the symbolic math toolbox, and a function called clean_F0AM_output.m.
The excel file contains all model starting conditions, model control settings, and additional extraneous information for each experiment. print_basic_plots turns on code that generates a figure comparing model and measurement timeseries. print_all_plots turns on code that shows plots generated in the run_analysis_v12.m script. run_analysis controls whether the analysis script is run. run_sensitivity controls whether sensitivity testing is performed (note this slows down the run considerably).
F0AM input conditions v12.xlsx
find_maxes_and_mins.m is run by run_simulations_v12.m to find the range of values generated by the sensitivity testing
clean_F0AM_output.m is run by run_simulations_v12.m to generate an easier-to-work-with table of species concentrations over time, interpolated to 1s timesteps.
Modified mechanisms uploaded here include added isomerization reactions and mechanisms for species labeled by the suffix _tracer to enable removal of the influence of OH scavenger species on analysis.
All experimental data and chamber light spectra are stored in a file called Repository for real data.
run_analysis_v12.m performs assorted calculations related to RO2 and oxidant chemistry. Some of these are handled by subsequent scripts (calculate_RO2_parameters_update_v12.m, parse_ox_loss_rates_v12.m). This also contains code to plot a handful of related figures exploring this chemistry. Plotting can be turned on in the excel file, but note that this substantially slows down the total runtime. If plots are turned on, they are saved in a folder called Plots.