EGU General Assembly 2020
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the Creative Commons Attribution 4.0 License.

A Pore-Scale Reactive Transport Model Approach for Investigating the Effect of Soil Physical Properties on Biogeochemical Processes

Amir Golparvar1, Matthias Kästner2, and Martin Thullner1
Amir Golparvar et al.
  • 1Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Leipzig, Germany
  • 2Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology, Leipzig, Germany

The vadose zone hosts a wide range of various microorganisms which provide different soil ecosystem services from nutrient cycling to biodegradation of harmful chemical substances. The efficiency of such in-situ biodegradation is influenced by different biotic and abiotic factors ranging from physical properties of the soil to the redox conditions controlled by the activity of the involved chemical compounds. One important feature of the soil system is the dynamical and simultaneous interplay of these factors, boosting or deteriorating the residing microbial community’s abundance and/or activity and hence shaping biodegradation of vadose zone contaminants. Physical properties of porous media – e.g. the pore geometry, pore size distribution, connectivity as well as the water content – play a major role in enhancing or restricting the bioavailable concentration of contaminants and other reaction partners. Pore-scale phenomena have been shown to be considerably affecting the macro-scale processes, therefore a quantitative bottom-top approach of these mechanisms in situ is adamant. Hence it is of paramount importance to understand the effect of soil physical properties on microbial activity and biodegradation of carbon compounds in soil.

Pore scale reactive transport processes have a complex, nonlinear dependency on the aforementioned factors, which severely challenges the experimental and/or numerical investigation of biodegradation at in in-situ conditions. However, the recent technological advances, specifically the imaging techniques, have made it easier to study biological and microbial evolution in porous media, but there is still a need for putting all these information together. For this purpose, numerical methods would offer the possibility of simulating a variable/controllable water saturation conditions and considering water/air dynamics and advective and diffusive micro-scale transport of all components in both, air and water phase, in porous medium structures directly obtained from CT scanned samples. Up to now, such pore-sale model approaches considering also the fate of biogeochemically reactive compounds are scarce. In this work we propose a novel reactive transport modelling technique combining the pore-scale numerical characterization of water flow and solute transport in unsaturated porous media and of biogeochemical process. For a variably saturated porous system, the presented model approach is solving the Navier Stokes equation and scalar transport equations for any arbitrary geometry and is simulating the dynamics of biogeochemical processes with any degree of complexity. Simulations are compared to experimental data to assess the effect of soil physical properties on the transport and degradation of contaminants in soil.

How to cite: Golparvar, A., Kästner, M., and Thullner, M.: A Pore-Scale Reactive Transport Model Approach for Investigating the Effect of Soil Physical Properties on Biogeochemical Processes, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-7738,, 2020

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Presentation version 2 – uploaded on 06 May 2020
Typo's error are corrected
  • CC1: Comment on EGU2020-7738, Arjun Chakrawal, 06 May 2020

    Hey Amir,

    Thank you for this very interesting poster. I wonder how long it takes to run your transport simulation? Are the simulations based on PN-BNRS ()?  Is your model also written in Matlab?

    I am very interested in pore-scale modeling in the context of soil C cycling if you think there is a possibility of collaboration please write back. I have a few crazy ideas that might be worth testing using your framework!


    Arjun (


    • AC1: Reply to CC1, Amir Golparvar, 06 May 2020

      Hi Arjun


      Thanks for the comment. Didn't see you in the live session.

      I'm using BRNS for building the reaction network coupling it to my c++ fluid flow solver. I;m writing the whole thing up within openfoam environment.

      C cycling is quite interesting and practical actually, so yeah let me know what you have in mind :) we prolly can do something together.




      • CC2: Reply to AC1, Arjun Chakrawal, 06 May 2020

        Great. Could you please provide your email!

        Yes, the live session with all the chat madness is not really helping (personal opinion). 

        • AC2: Reply to CC2, Amir Golparvar, 07 May 2020

Presentation version 1 – uploaded on 06 May 2020 , no comments