Pore network model - PNBRNS

Developing Team: Mehdi Gharasoo, Falk Heße, Florian Centler

Natural porous media like soils or aquifers are characterized by heterogeneities at various scales which influence the transport of chemical species and the spatial distribution of microorganisms. These heterogeneities are thus relevant for the dynamic or redox processes, including biodegradation of organic contaminants, many of them controlled by microorganisms. The accessibility of the chemical species to the resident microbial populations may be limited, altering the efficiency of the biodegradation process. Hence, biogeochemical reaction rates in porous media at large scales do not only depend on the metabolic activitry of the indigenous microbial population but also on the heterogeneities of the media at smaller scales. It is thus important to establish a link between effective reaction rates and various structural features of porous media which can be directly observed or measured. This link is urgently needed because explicit resolution of heterogeneities within large-scale reactive transport models is still limited by the available computational capacities.

For this purpose, a pore network model, which simulates flow and advective–diffusive transport of chemical species in heterogeneous pore networks has developed and coupled to the Biogeochemical Reaction Network Simulator (BRNS) and subsequently to an individual-based module for bacterial chemotaxis. The resulting coupled model (PN-BRNS) is able to simulate the reactive transport of solutes and the distribution of microbial communities in heterogeneous pore assemblies.


Gharasoo, M., Centler, F., Fetzer, I., Thullner, M. (2014): How the chemotactic characteristics of bacteria can determine their population patterns Soil Biol. Biochem. 69, 346 - 358

Stolpovsky, K., Gharasoo, M., Thullner, M. (2012): The impact of pore-size heterogeneities on the spatiotemporal variation of microbial activity in porous media Soil Sci. 177 (2), 98 - 110

Gharasoo, M., Centler, F., Regnier, P., Harms, H., Thullner, M. (2012): A reactive transport modeling approach to simulate biogeochemical processes in pore structures with pore-scale heterogeneities Environ. Modell. Softw. 30 (1), 102 - 114


The manual can be downloaded here .

The Matlab source code of a self-contained demo version can be downloaded here .