A new model for transport and fate of chemicals in the aquatic environment is presented. The tool, named ChemicalDrift, is integrated into the open-source Lagrangian framework OpenDrift and is hereby presented for organic compounds. The supported chemical processes include the degradation, the volatilization, and the partitioning between the different phases that a target chemical can be associated with in the aquatic environment, e.g. dissolved, bound to suspended particles, or deposited to the seabed sediments. The dependencies of the chemical processes on changes in temperature, salinity, and particle concentration are formulated and implemented. The chemical-fate modelling is combined with wide support for hydrodynamics by the integration within the Lagrangian framework which provides e.g. advection by ocean currents, diffusion, wind-induced turbulent mixing, and Stokes drift generated by waves. A flexible interface compatible with a wide range of available metocean data is made accessible by the integration, making the tool easily adaptable to different spatio-temporal scales and fit for modelling of complex coastal regions. Further inherent capabilities of the Lagrangian approach include the seamless tracking and separation of multiple sources, e.g. pollutants emitted from ships or from rivers or water treatment plants. Specific interfaces to a dataset produced by a model of emissions from shipping and to an unstructured-grid oceanographic model of the Adriatic Sea are provided. The model includes a database of chemical parameters for a set of poly-aromatic hydrocarbons and a database of emission factors for different chemicals found in discharged waters from sulfur emission abatement systems in marine vessels. A post-processing tool for generating mean concentrations of a target chemical, over customizable spatio-temporal grids, is provided. Model development and simulation results demonstrating the functionalities of the model are presented, while tuning of parameters, validation, and reporting of numerical results are planned as future activities. The ChemicalDrift model flexibility, functionalities, and potential are demonstrated through a selection of examples, introducing the model as a freely available and open-source tool for chemical fate and transport that can be applied to assess the risks of contamination by organic pollutants in the aquatic environment.
The negative effects of chemical pollution on the environment and human health have long been established
Lagrangian models
It is recognized that coastal environments are of particular concern due to the presence of multiple stressors (e.g. wastewater discharge, soil and sediment contamination, agricultural and municipal run-off and combustion of fossil fuels by civil and industrial activities)
The scrubbing process is implemented by leading the exhaust gas through a fine-water mist where
The present work is carried out under the scope of the Horizon 2020 EMERGE project, which aims to develop an integrated modelling framework to assess the combined impact of shipping emission-control options on the aquatic and atmospheric environment. Utilizing the open-source Lagrangian framework OpenDrift
This article is organized as follows: the relevant chemical processes implemented in ChemicalDrift are presented and formulated in Sect.
The new module ChemicalDrift is presented in this section, supported by a detailed description of the modelled chemical processes. The module is coded in Python and integrated into the open-source Lagrangian framework OpenDrift
Only the chemistry of non-ionizable organic compounds is described in this work, since the chemistry of metals has already been implemented in the Radionuclides OpenDrift module
The reactions implemented in ChemicalDrift include a partitioning scheme between the different phases that a target chemical can be associated with within the aquatic environment, the degradation of organic chemicals in the water column and in the sediments and the volatilization of dissolved chemicals from the water to the atmosphere. The dependencies of the each reaction on temperature and salinity changes are described and implemented based on the scientific literature. Sedimentation and resuspension are also presented in this section since these physical processes are strongly related to the chemical-phase partitioning.
Chemicals in the aquatic environment can be associated with different components of this medium (i.e. dissolved in the water or bound to dissolved organic carbon (DOC), suspended particle matter (SPM) or sediments) and are thereby exposed to different physical and chemical processes. For example, dissolved chemicals will be transported by advection due to water currents and by turbulent diffusion processes, such as wind-induced vertical mixing, while chemicals adsorbed to solid particles will also be affected by gravity and might sink towards the sea floor. Furthermore, the different distributions between dissolved and bound chemicals will also influence its availability to degradation processes like hydrolysis, biodegradation and photolysis. In computational models it is therefore crucial to process each of these components in distinct compartments.
In ChemicalDrift, each Lagrangian element represents a given mass of a target chemical, and the partitioning between the media components is implemented by assigning each element to a single corresponding model compartment. The partitioning is carried out dynamically, as opposed to a simpler steady-state approach, and transfer rates between compartments are calculated and applied at each time step. The dynamic approach is fit for the changing environmental conditions each Lagrangian element is exposed to (i.e. water temperature, salinity, SPM and DOC concentration), as it is transported in the media.
The dynamic partitioning scheme used in ChemicalDrift was first introduced by
The main phases considered in the algorithm (Fig.
The model compartments implemented in ChemicalDrift and the corresponding exchange processes and transfer rates adapted from
Transfer rates are calculated by adapting the equations described by
Transfer rates from the dissolved phase to the DOC, SPM and sediment compartments (i.e.
Parameters for the calculation of sediment-layer adsorption and desorption rates.
The stochastic method for calculating the probability of phase change between model compartments given the time step and the transfer rates is described by
The partitioning of organic chemicals to organic carbon has been reported as involving rapid adsorption to particle surfaces, followed by slow movement into, and out of, organic matter and porous aggregates
The solid–water partition coefficient
Given this context, Karickhoff and Morris
The value of
For organic chemicals it is assumed that the organic carbon fraction of solid particles (i.e. suspended particle matter and sediments) is almost entirely responsible for their sorbing capacity, and therefore
Typical values for
Relationships between
Experimental values of
Particle sedimentation and resuspension dynamics in ChemicalDrift are partly based on methods previously implemented in other OpenDrift modules. The vertical motion of Lagrangian elements representing dissolved chemicals or chemicals adsorbed to DOC is calculated as for a passive tracer by adding vertical currents (typically small compared to the other terms) to the vertical mixing associated with wind-induced or background turbulent diffusion.
Lagrangian elements associated with SPM are also affected by gravity and will sink towards the sea floor, and hence a third component has to be added to calculate the vertical motion. This term is referred to as the terminal velocity and is calculated from Stokes' law
When sinking particles reach the sea floor, the chemical elements are transferred to the sediment-layer compartments and thus can be subjected to either sediment burial or resuspension. Resuspension occurs when the horizontal current at the bottom is greater than a given threshold
Organic chemicals in the aquatic environment can be degraded due to various processes, such as biodegradation, photodegradation and hydrolysis. Modelling each of these reactions separately requires a large amount of information on the environmental behaviour of the target chemical and on the characteristics of the selected study area. Since these data are typically difficult to obtain with sufficient accuracy for a wide range of chemicals and case-study regions, a simpler approach is implemented in the current version of ChemicalDrift: degradation is implemented considering distinct overall reaction rates for the water column (subscript
Volatilization is modelled using the “stagnant boundary theory”, or two-film model, in which the target chemical must diffuse across both a stagnant water layer and a stagnant air layer to volatilize out of the water column
According to the literature
If pollutants can be assumed to have a negligible concentration in air (i.e.
Chemical parameters utilized for modelling the sorption, degradation, and volatilization of three organic compounds.
In the Lagrangian framework utilized by the proposed model, concentrations are not calculated at each time step, and hence the equivalent effect is obtained by applying an exponential decay to the mass
As reported above,
Here,
The diffusion rates of a chemical in these stagnant boundary layers can be related to the known diffusion rates of reference substances such as oxygen and water vapour
CMEMS products and data variables.
Emission fields from STEAM by
A database of parameters for a set of organic compounds and heavy metals has been compiled under the scope of the EMERGE project, based on an extensive review of data available in the literature. Mean values from the database for a selection of PAHs are integrated into the ChemicalDrift class method
Chemical simulation set-up and configuration.
Meteorological and oceanographic forcing is obtained from different sources. Several CMEMS products are utilized in this work, providing water temperature, salinity, current horizontal velocities, mixed-layer depth, ocean surface winds, and SPM concentration, as summarized in Table
Seeding elements and running simulation.
High-resolution 3-D currents, water temperature and salinity forcing over the northern Adriatic Sea including the Venice Lagoon are provided by the application of the unstructured hydrodynamic SHYFEM model
The SHYFEM simulations are forced by atmospheric fields from the global ECMWF reanalysis ERA5
The ChemicalDrift functionalities are demonstrated through a few modelling examples described in the following. The presented simulations are not meant to provide conclusive quantitative results as some of the input parameters are uncertain and the model remains to be validated. The examples are run with OpenDrift 1.9.0 (e.g.) and may not be functional in the far future.
A simple example of a ChemicalDrift simulation is presented with a description of the running script. The example is also available in the gallery section on the OpenDrift reference page (opendrift.github.io), where it is continuously updated with live forcing data. The simulation models the fate of a mass of an organic pollutant (phenanthrene) released outside the northern coast of Denmark over a period of 2 d. Simulation set-up is done as shown in the listing below by loading the OpenDrift modules, defining a ChemicalDrift instance, adding the necessary readers for forcing data and configuring a set of parameters. In detail, metocean forcing data including surface winds, ocean currents, sea water temperature and salinity are provided by the Norkyst800 model, while mixed-layer depth is set to a constant value of 40 m. Vertical mixing is activated, and the model used for the diffusivity profile is selected. Released chemicals are assumed to be 90 % in the dissolved fraction, and 10 % are adsorbed to particles. Degradation rates for phenanthrene are overridden in order to produce a clear effect in this short demo, and half-life constants are set to 6 h in the water column and 12 h in the sediment layer.
The model is configured at this stage. The next step is to seed the Lagrangian chemical elements and run the simulation. In this example, 500 chemical elements with a mass of 2000
Simulation results are illustrated in Fig.
Simulated transport and fate of a mass of phenanthrene released outside the northern coast of Denmark, showing horizontal advection
Exponential decay and mass distribution across the dissolved, adsorbed-to-SPM, and sediment phases for phenanthrene.
ChemicalDrift is demonstrated using input data from the STEAM model to simulate emissions of selected PAHs (i.e. naphthalene and benzo(a)pyrene) from open-loop scrubbers. The simulated region includes emissions for January 2019 in the area between 8 and 15
Emissions of naphthalene
Emissions of naphthalene
Modelling of emissions from multiple sources is demonstrated. The target chemical considered is benzo(a)pyrene, and emissions include discharges estimated in August 2019 from open-loop scrubber data derived from STEAM and discharges from 49 rivers obtained from water-quality monitoring data and river loads.
Snapshots of the simulation are shown in Fig.
Simulation results are further illustrated in Fig.
The example is also utilized to illustrate the dependency on temperature and salinity of the solid–water partition coefficient which is calculated according to Eqs. (
Emissions of benzo(a)pyrene from both open-loop scrubbers and rivers in the northern Adriatic Sea for August 2019, simulated in ChemicalDrift over a 2-month period, showing how the use of Lagrangian modelling allows for seamless separation of the different sources. Two time steps are shown, 8 August 2019
Emissions of benzo(a)pyrene from open-loop scrubbers and rivers in the northern Adriatic Sea. Total emitted mass
Effect on the desorption rate
ChemicalDrift is applied to open-loop scrubber emissions for the entire European region from January to March 2019. The target chemical is phenanthrene, and fate and transport modelling are calculated until December 2019. This example is utilized to demonstrate the method
We see that only a few ships with scrubbers were operating in the Mediterranean in 2019, since it was before global sulfur cap regulation. Dissolved chemicals are more diffused, while chemicals attached to particles sink and have smaller lateral diffusion, and hence ship routes are more easily observed.
Mean concentrations of phenanthrene emitted from open-loop scrubbers (January–March 2019). Concentrations are calculated separately for the dissolved
ChemicalDrift, a new Lagrangian model for transport and fate of chemicals in the aquatic environment, has been presented. The model is implemented as a new module and is fully integrated within the open-source framework OpenDrift in order to combine the newly implemented chemical processes with the framework's advanced hydrodynamical capabilities and to provide a flexible interface with most of the available metocean input data sources.
The modelled chemical processes include a dynamic partitioning between the different phases that pollutants can be associated with in the aquatic environment, chemical removal by degradation and volatilization, and sedimentation and resuspension of chemicals associated with suspended particles. Target chemicals are modelled as Lagrangian elements that are transported and exposed to changing environmental conditions, e.g. temperature and salinity. The dependencies of chemical processes on temperature and salinity changes are formulated and implemented.
The focus of the presented work has been on modelling organic pollutants in the marine and coastal regions. The model functionalities are demonstrated through a sequence of simulation examples. The presented examples are only for demonstration purposes, providing insights into the combined effect of the modelled physical and chemical processes and presenting the potential of the proposed model. Accurate tuning of input parameters, sensitivity analysis, model validation and quantitative modelling results are deferred to future publications. Specifically, in the scope of the Horizion 2020 EMERGE project, ChemicalDrift is planned for use in calculating concentrations of different pollutants, including PAHs and heavy metals, both at the European regional scale and at a finer scale in the northern Adriatic Sea and in the Øresund strait. Additionally, the model can also be applied to other case-study areas in the EMERGE project, namely the Piraeus port-case study and the Aveiro Lagoon case study, where the Delft3D suite will be utilized independently by other project partners, allowing one to compare the results between the two models. Datasets with measured concentrations of organic pollutants in sediments obtained from monitoring programmes in the Baltic region and in the northern Adriatic are identified and available and can be used in the future to attempt validation of the model.
Additional functionalities are also planned for the future, including support for hydrolysis, photolysis and biodegradation as distinct sub-processes, support for non-ionizable organic compounds and a more advanced resuspension scheme which will include the contribution of wave-induced stress to resuspension.
High flexibility is demonstrated by the presented examples, utilizing a selection of different input sources and at different spatio-temporal scales: an interface to the STEAM model for shipping emissions, including support for open-loop and close-loop scrubbers, is implemented and demonstrated. The Lagrangian framework offers seamless tracking and separation of chemicals emitted from different sources such as emissions from shipping or from rivers. The modelled chemical processes depend on a relatively large set of parameters, including e.g. the solid–water partitioning coefficient, the Henry law coefficients and the overall degradation rates. A database of chemical parameters for a set of PAHs is integrated into ChemicalDrift, and values for the three PAHs are presented.
The ChemicalDrift model is freely available at the OpenDrift github repository at
MA designed and developed the model, performed and analysed the simulations and wrote the manuscript draft. LC contributed with model design, compiled the input data and wrote the introduction section. CF provided the SHYFEM model results and wrote the description of the model in Sect.
The contact author has declared that none of the authors has any competing interests.
This work reflects only the authors’ view, and the European Climate, Infrastructure and Environment Executive Agency is not responsible for any use that may be made of the information it contains. Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Mattia Boscherini (Ca'Foscari University of Venice) and Isabel Hanstein (University of Heidelberg) are kindly thanked for the valuable support in the compilation of the PAH chemical property database. The authors are grateful to Jukka-Pekka Jalkanen (Finnish Meteorological Institute) for providing the results of the STEAM model used in this work.
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 874990 (EMERGE project). This research has also been supported by the Research Council of Norway (STIM-EU, project no. 334015).
This paper was edited by Andrew Yool and reviewed by two anonymous referees.