BottomRedoxModel / Wiki

Description of the group structure

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Welcome to the Bottom RedOx model wiki!

Bottom RedOx Model(BROM) is a group of coupled benthic-pelagic models for simulation of water and sediment biogeochemistry. BROM is compatible with the Framework for Aquatic Biogeochemical Models FABM.

It consists of transport models:

• BROM_transport coupled benthic-pelagic model (details in Yakushev et al., 2017)
• 2DBP - 2 dimensional transport coupled benthic-pelagic model (details in Yakushev et al., 2020)
• SPBM - Sympagic Bethic Pelagic Model (details in Yakubov et al., 2019)

and biogeochemical models:

• BROM_biogeochemistry O-C-Si-N-P-Fe-Mn-S model consisting from modules for elements transfomation parameterization (details in Yakushev et al., 2017)
• OxyDep - Oxygen Depletion Model to parameterize basic processes of organic mattercycling and oxygen depletion (a light N-O verion of BROM) (details in Berezina et al., 2020)

Besides this there are available modules that can be coupled to BROM and Oxydep for modeling fate of Hg, Ni, Microplastics, Fish Farm waste, Chemical Oxygen Demand, minerals precipitation/dissolution, CO2 bubbling etc.

Publicatons (BROM related):

1. Yakushev, E. V., Protsenko, E. A., Bruggeman, J., Wallhead, P., Pakhomova, S. V., Yakubov, S. Kh., Bellerby, R. G. J., and Couture, R.-M. 2017: Bottom RedOx Model (BROM v.1.1): a coupled benthic–pelagic model for simulation of water and sediment biogeochemistry, Geosci. Model Dev., 10, 453-482, doi:10.5194/gmd-10-453-2017, 2017.
2. Pakhomova S., Yakushev E., Protsenko E., Rigaud S., Cossa D., Knoery J., Couture, R.M., Radakovith O., Yakubov Sh., Krzeminska D., Newton A. Modeling the Influence of Eutrophication and Redox Conditions on Mercury Cycling at the Sediment-Water Interface in the Berre Lagoon. Frontiers in Marine Science, V.5, Art. 291, published: 21 August 2018, doi: 10.3389/fmars.2018.00291
3. Yakubov S., Wallhead P, Protsenko E., Yakushev E., Pakhomova S, Brix H. 2019. A 1-Dimensional Sympagic–Pelagic–Benthic Transport Model (SPBM): Coupled Simulation of Ice, Water Column, and Sediment Biogeochemistry, Suitable for Arctic Applications. Water. 2019, 11, 1582; doi:10.3390/w11081582
4. Yakushev E., Wallhead Ph., Renault P., Ilinskaya A., Protsenko E., Yakubov Sh., Pakhomova S. Sweetman A., Dunlop K., Berezina A., Bellerby R., Dale T. 2020.Understanding the Biogeochemical Impacts of Fish Farms using a Benthic-Pelagic Model. Water, 2020, 12, 2384; doi:10.3390/w12092384
5. Pakhomova S., Yakushev E., Schaanning M.T. Modeling nickel leaching from abandoned mine tailing deposits in Jøssingfjorden. Water, 2021, 13(7): 967.
6. Yakushev, E.V., Nøst, O.A., Bruggeman, J., Ghaffari, P. and Protsenko, E., 2020. Modelling Biogeochemical and Physicochemical Regime Changes During the Drying Period of Lake Urmia. In: The Handbook of Environmental Chemistry. Springer, Berlin, Heidelberg. https://doi.org/10.1007/698_2020_485
7. Yakushev E., Blomberg A.E.A., Eek E., Protsenko E., Totland C., Staalstrøm A., Waaru I.-K. Modeling of biogeochemical consequences of a CO2 leak in the water column with bottom anoxia. International Journal of Greenhouse Gas Control. 2021. 111: 103464.
8. Gurova, Y.S., Yakushev, E.V., Berezina, A.V., Novikov, M.O., Gurov, K.I. and Orekhova, N.A., Numerical Modelling of RedOx Condition Dynamics at the Water-Sediment Interface in Sevastopol Bay. Ecological Safety of Coastal and Shelf Zones of Sea. No. 2. 2023 doi: 0.22449/2413-5577-2023-2-71-90

Publicatons (OxyDep related):

1. Yakushev, E. V., E. I. Debolskaya, I. S. Kuznetsov, and A. Staalstrøm. "Modelling of the meromictic fjord Hunnbunn (Norway) with an Oxygen Depletion model (OxyDep)." In Chemical Structure of Pelagic Redox Interfaces, pp. 235-251. Springer, Berlin, Heidelberg, 2011.
2. Daewel U., Yakushev E.V., Schrum C., Nizzetto L., Mikheeva E. 2020. Understanding the role of organic matter cycling for the spatio-temporal structure of PCBs in the North Sea. Water. 2020, 12, 817; doi:10.3390/w12030817(https://www.researchgate.net/publication/216683346_Modelling_of_the_Meromictic_Fjord_Hunnbunn_Norway_with_an_Oxygen_Depletion_Model_OxyDep)
3. Berezina A., Yakushev E., Drivsdal M., Vogelsang C., Staalstrøm A., Savchuk O. 2021. Modelling the Influence from Biota and Organic Matter on the Transport Dynamics of Microplastics in the Water Column and Bottom Sediments in the Oslo Fjord. Water, 13(19): 2690.

Published versions of the code:

• BROM_transport
• BROM_biogeochemistry
• SPBM

Since publications, the code has been significantly changed. Here are current versions of BROM_transport, BROM_biogeochemistry and SPBM.

Case scenarios:

Case scenarios for different geographical positions are in repositories with names "data_Name_of_case"

1. Urmia lake data_urmia
2. Berre lagoon data_berre
3. Hardangerfjord data_hardangerfjord
4. Eastern Baltic Sea data_baltic
5. Lindesnes data_lindesnes
6. Laptev Sea, SPBM + BROM_biogeochemistry data_spbm_laptev

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