A knowledge‐based reactive transport approach for the simulation of biogeochemical dynamics in Earth systems

Abstract

[1] A Knowledge-Based Reactive Transport Model (KB-RTM) for simulation of coupled transport and biogeochemical transformations in surface and subsurface flow environments is presented (http:// www.geo.uu.nl/$kbrtm). The scalable Web-distributed Knowledge Base (KB), which combines Information Technology (IT), an automatic code generator, and database management, facilitates the automated construction of complex reaction networks from comprehensive information stored at the level of biogeochemical processes. The reaction-centric approach of the KB-RTM system offers full flexibility in the choice of model components and biogeochemical reactions. The procedure coupling the reaction networks to a generalized transport module into RTMs is also presented. The workings of our KB-RTM simulation environment are illustrated by means of two examples of redox and acid-base chemistry in a typical shelf sediment and an aquifer contaminated by landfill plumes.

pH-Dependent iron oxide precipitation in a subterranean estuary

“…Although it would be possible to incorporate pH and O 2 as master variables in the RTM (e.g. Aguilera et al, 2005), the current data set for Waquoit Bay does not allow the reaction network required to model these variables to be fully constrained. Instead, both O 2 and pH are implemented as forcing functions, either as constant values or as a longitudinal gradient along the flow line ( Table 2).…”

“…The processes included in the Biogeochemical Reaction Network Simulator (BRNS), a flexible 1D RTM (Regnier et al, 2003;Aguilera et al, 2005), are pHdependent oxidative precipitation of Fe(II), APO 4 adsorption onto Fe-oxides and advective plus dispersive groundwater transport (Table 1). At the upstream boundary (x = 0 m), a Dirichlet boundary condition is applied, which fixes the concentration of Fe(II), O 2 , APO 4 and pH at the freshwater side of the domain ( Table 2).…”

Modelling the geochemical fate and transport of wastewater-derived phosphorus in contrasting groundwater systems

“…The biogeochemical processes that determine groundwater N and P dynamics are incorporated in the Biogeochemical Reaction Network Simulator (BRNS), a flexible modelling environment for one-dimensional simulations in groundwater, sediments and surface waters (Regnier et al, 2002(Regnier et al, , 2003Aguilera et al, 2005). In the model, the transport and reaction of solutes are described by:…”

“…The latter can handle mixed kineticequilibrium reaction systems. Further details can be found in Aguilera et al (2005). (Table 1).…”

“…For O 2 concentrations below kmo2, the reaction is limited by O 2 , while denitrification is simultaneously activated. Further details on the implementation of the rate laws for organic matter degradation can be found in Van Cappellen and Wang (1996), Hunter et al (1998) and Aguilera et al (2005).…”