The Polychlorinated Biphenyl (PCB) Reactive Transport Model produces simulations of congener-specific PCB concentration in the aqueous and gas phase of laboratory-scale bioreactors containing PCB-contaminated sediment slurry. The script uses experimental passive sampler measurements and a minimization of least squares procedure to fit congener-specific adsorption and desorption coefficients to the model. Finally, the model can simulate the reduction in volatile release of PCBs from sediment slurry to air resulting from the presence of an aerobic PCB-degrading microorganism with a known PCB biotransformation rate.
This ReadMe file was generated on 2022-02-06 by Christain M. Bako (CMB) and last updated by CMB on 2022-02-08
Deposit Title: Polychlorinated Biphenyl (PCB) Reactive Transport Model
Contributor information:
Christian M. Bako, MS University of Iowa - Department of Civil & Environmental Engineering Iowa Superfund Research Program (ISRP) christian-bako@uiowa.edu ORCID: 0000-0001-9722-4964
Andres J. Martinez Araneda, PhD University of Iowa - Department of Civil & Environmental Engineering Iowa Superfund Research Program (ISRP) andres-martinez@uiowa.edu ORCID: 0000-0002-0572-1494
Principal Investigator: Timothy Mattes, PhD Principal Investigator email: tim-mattes@uiowa.edu
Date of Data Collection: 2021-05-19 to 2021-08-15
This work was supported by the National Institutes of Environmental Health Sciences (NIEHS) grant #P42ES013661. The funding sponsor did not have any role in study design; in collection, analysis, and/or interpretation of data; in creation of the dataset; and/or in the decision to submit this data for publication or deposit it in a repository.
Subject: Polychlorinated Biphenyls; Contaminant fate and transport; Paraburkholderia xenovorans LB400; Kinetic phase passive sampling; Bioremediation; Biodegradation; Biosurfactants; Bioavailability; GC-MS/MS
GeoLocation: The sediment used in this study was taken from a PCB-contaminated emergency overflow lagoon located in Altavista, VA (37°06'52"N, 79°16'21"W). Laboratory and analytical work was done at the University of Iowa in Iowa City, IA, USA.
Licenses/restrictions placed on the model documentation, or limitations of reuse: Open Data Commons Attribution License (ODC-By)
Recommended citation for the model documentation:
Bako, Christian M.; Martinez, Andres J. (2022): Polychlorinated Biphenyl (PCB) Reactive Transport Model. University of Iowa. (dataset). https://doi.org/reservedDOI
Citation for and links to publications that cite or use the model:
Bako, Christian M.; Martinez, Andres J.; Ewald, Jessica M.; Hua, Jason B.X.; Schnoor, Jerald L.; Mattes, Timothy E. (In preparation), "Aerobic Bioaugmentation to Decrease Polychlorinated Biphenyl (PCB) Emissions from Contaminated Sediments to Air"
Bako, Christian M.; Martinez, Andres J.; Marek, Rachel F.; Hornbuckle, Keri C.; Schnoor, Jerald L.; Mattes, Timothy E. (In preparation), "Aerobic, lab-scale biodegradation assay using passive samplers to screen microorganisms for the ability to reduce PCB volatilization from contaminated sediment slurry to air", MethodsX, doi:
This Iowa Research Online (IRO) Data Repository deposit describes documentation of code developed in "R" software for a "Polychlorinated Biphenyl (PCB) reactive transport model". The PCB Reactive Transport Model produces simulations of congener-specific PCB concentration in the aqueous and gas phase of laboratory-scale bioreactors containing PCB-contaminated sediment slurry. The script uses experimental passive sampler measurements and minimization of least squares procedures to fit congener-specific adsorption and desorption coefficients to the model. Finally, the model can simulate the reduction in volatile release of PCBs from sediment slurry to air resulting from the presence of an aerobic PCB-degrading microorganism with a known PCB biotransformation rate. As written, the model script calls data resulting from bioreactor experiments described in the peer-reviewed journal article ("Aerobic Bioaugmentation to Decrease Polychlorinated Biphenyl (PCB) Emissions from Contaminated Sediments to Air") linked to this IRO deposit. In this deposit, the full "R" script is available for PCB 52 to provide documentation for the underlying code and to provide a framework for future re-use. The code is documented and described in detail within an "R Markdown" (.RMD) file which can be viewed as .html, .pdf, or .docx. The purpose of this IRO deposit is to promote reuse of the underlying experimental dataset from the linked publication and the PCB reactive transport model. We hope other researches will use this model to conduct inform other analyses, investigations, and / or interpretive insights. It is recommended that a user first reads the linked publication and one of the R Markdown output files to interpret and contexualize the model script.
File Name: 00_PCB_ReactiveTransportModel_ReadMe File Size: 7.35kb File Format: .txt File description: Contains a brief description of the project, a description of files also associated with the IRO deposit, prerequisite software, installation instructions for software, and user contribution information.
File Name: 01_PCB_ReactiveTransportModel_R File Size: 11.5kb File Format: .R File description: Contains the raw code for the PCB Reactive Transport model in "R" which uses PCB 52 data from 08_Dataset_FinalPCBMass_2021-12-06.csv to compare simulated results to experimental observations.
File Name: 02_PCB_Reactive_Transport_Model_RMD File Size: 47.7kb File Format: .RMD File description: Contains the raw code for the model and detailed documentation in "R Markdown"; accessible using R studio.
File Name: 03_PCB_Reactive_Transport_Model_RMD_out_HTML File Size: 891kb File Format: .html File description: HTML file output of "R Markdown" document containing detailed description of model code; accessible using any web browser.
File Name: 04_PCB_Reactive_Transport_Model_RMD_out_pdf File Size: 422kb File Format: .pdf File description: PDF file output of "R Markdown" document containing detailed description of model code; accessible using Adobe Acrobat Reader or similar software.
File Name: 05_PCB_Reactive_Transport_Model_RMD_out_docx File Size: 66.9kb File Format: .docx File description: DOCX file output of "R Markdown" document containing detailed description of model code; accessible using Microsoft Word.
File Name: 06_PCB_Reactive_Transport_Model_RMD_References File Size: 15.1kb File Format: .bib File description: Contains the references cited in the "R Markdown"; accessible using a general text editor or LaTeX software.
File Name: 07_PCB_Reactive_Transport_Model_Metadata File Size: 2.63kb File Format: .json File description: Contains the metadata which describes this project. See https://codemeta.github.io/index.html for more information.
This section of the ReadMe file lists the necessary software and packages required to run the PCB reactive transport model in "R" and to view documentation provided in the "R Markdown" file, as well as in the various output files (e.g., .html, .pdf, and .docx).
For more information on "R Markdown" documentation please see: https://rmarkdown.rstudio.com/index.html
Software:
- Any web browser (e.g., Google Chrome, Microsoft Edge, Mozilla Firefox, etc.)
- R-studio for easily viewing, editing, and executing "R" code as a regular "R script" file and as an "R markdown" file: https://www.rstudio.com/products/rstudio/download/
- MiKTeX for outputting "R Markdown" file as a PDF: https://miktex.org/download
- Adobe Acrobat Reader for viewing PDF output of "R Markdown" file: https://get.adobe.com/reader/otherversions/
- Word for viewing .docx output of "R Markdown" file (requires software license)
R Packages:
- dplyr: Package used for reading and formatting data from files - https://dplyr.tidyverse.org/
- ggplot2: Package used for plotting data - https://ggplot2.tidyverse.org/
- reshape2: Package used for reshaping data (tall-narrow <-> short-wide) - https://cran.r-project.org/web/packages/reshape2/index.html
- deSolve: Package used for solving differential equations - http://desolve.r-forge.r-project.org/
- minpack.lm: Package for least squares fitting procedure with the levenberg-marquart algorithm - https://rdrr.io/cran/minpack.lm/
Other:
- Environmental Science & Technology citation style file (.csl) for including references in "R Markdown" file: https://www.zotero.org/styles
This section of the ReadMe file provides short instructions on how to download and install "R Studio". "R Studio" is an open source (no product license required) integrated development environment (IDE) for "R" and completely free to use. To install "R Studio" follow the instructions below:
- Visit the following web address: https://www.rstudio.com/products/rstudio/download/
- Click the "download" button beneath RStudio Desktop
- Click the button beneath "Download RStudio Desktop". This will download the correct installation file based on the operating system detected.
- Run the installation file and follow on-screen instructions.
https://github.com/valdiman/PCB-Reactive-Transport-Model
See the "07_PCB_Reactive_Transport_Model_Metadata.json" file for all available CodeMeta metadata.