Modeling complex multi-component reactive-transport systems: towards a simulation environment based on the concept of a Knowledge Base

Regnier, Pierre; O’Kane, J. P.; Steefel, Carl I.; Vanderborght, Jean-Pierre

doi:10.1016/s0307-904x(02)00047-1

Cited by 78 publications

(66 citation statements)

References 13 publications

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“…The reaction-transport model calculations were carried out with the Biogeochemical Reaction Network Simulator (BRNS), a flexible modeling environment for one-dimensional simulations (Regnier et al, 2003;Aguilera et al, 2005;Jourabchi et al, 2005). In the BRNS, the chemical species, reaction stoichiometries, kinetic parameters, boundary conditions, and transport parameters are specified by the user through a MAPLE software or web-based interface (Chilakapati, 1995;Amberg et al, 1999;Regnier et al, 2002Regnier et al, , 2003). An executable program, which consists of a set of standard routines for iteratively solving the reaction and transport equations, is then generated automatically.…”

Section: Model Formulationmentioning

confidence: 99%

Organic matter mineralization in sediment of a coastal freshwater lake and response to salinization

Canavan

Slomp

Jourabchi

et al. 2006

Geochimica et Cosmochimica Acta

113

108

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Solid phase and pore water chemical data collected in a sediment of the Haringvliet Lake are interpreted using a multi-component reactive transport model. This freshwater lake, which was formed as the result of a river impoundment along the southwestern coast of the Netherlands, is currently targeted for restoration of estuarine conditions. The model is used to assess the present-day biogeochemical dynamics in the sediment, and to forecast possible changes in organic carbon mineralization pathways and associated redox reactions upon salinization of the bottom waters. Model results indicate that oxic degradation (55%), denitrification (21%), and sulfate reduction (17%) are currently the main organic carbon degradation pathways in the upper 30 cm of sediment. Unlike in many other freshwater sediments, methanogenesis is a relatively minor carbon mineralization pathway (5%), because of significant supply of soluble electron acceptors from the well-mixed bottom waters. Although ascorbate-reducible Fe(III) mineral phases are present throughout the upper 30 cm of sediment, the contribution of dissimilatory iron reduction to overall sediment metabolism is negligible. Sensitivity analyses show that bioirrigation and bioturbation are important processes controlling the distribution of organic carbon degradation over the different pathways. Model simulations indicate that sulfate reduction would rapidly suppress methanogenesis upon seawater intrusion in the Haringvliet, and could lead to significant changes in the sediment's solid-state iron speciation. The changes in Fe speciation would take place on time-scales of 20-100 years.

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Section: Model Formulationmentioning

confidence: 99%

Organic matter mineralization in sediment of a coastal freshwater lake and response to salinization

Canavan

Slomp

Jourabchi

et al. 2006

Geochimica et Cosmochimica Acta

113

108

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“…The early diagenesis model (EDM) was developed by means of the Biogeochemical Reaction Network Simulator (BRNS) (Regnier et al, 2002) through a knowledgebased reactive transport model application (Aguilera et al, 2005). In the present application we used a simplified version of the EDM identified for the northern Adriatic Sea by Brigolin et al (2011).…”

Section: Model Theory: Mussel Farm Deposition Model and Early Diagenementioning

confidence: 99%

“…The Lagrangian equation for the deposition model was solved following Jusup et al (2007). The set of partial differential equations in the EDM was numerically solved by means of an implicit method; details on the operator splitting technique -a sequential non-iterative approach -and the definition of the function residuals and the Jacobian matrix are provided in Aguilera et al (2005) and Regnier et al (2002). Model runs were performed in SC-SCF (www.dais.unive.it/scscf), a multiprocessor cluster system owned by Ca' Foscari University of Venice running under GNU/Linux.…”

Section: Model Theory: Mussel Farm Deposition Model and Early Diagenementioning

confidence: 99%

Modelling biogeochemical processes in sediments from the north-western Adriatic Sea: response to enhanced particulate organic carbon fluxes

et al. 2018

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Abstract. This work presents the result of a study carried out in the north-western Adriatic Sea, by combining two different types of biogeochemical models with field sampling efforts. A longline mussel farm was taken as a local source of perturbation to the natural particulate organic carbon (POC) downward flux. This flux was first quantified by means of a pelagic model of POC deposition coupled to sediment trap data, and its effects on sediment bioirrigation capacity and organic matter (OM) degradation pathways were investigated constraining an early diagenesis model by using original data collected in sediment porewater. The measurements were performed at stations located inside and outside the area affected by mussel farm deposition. Model-predicted POC fluxes showed marked spatial and temporal variability, which was mostly associated with the dynamics of the farming cycle. Sediment trap data at the two sampled stations (inside and outside of the mussel farm) showed average POC background flux of 20.0-24.2 mmol C m −2 d −1 . The difference of organic carbon (OC) fluxes between the two stations was in agreement with model results, ranging between 3.3 and 14.2 mmol C m −2 d −1 , and was primarily associated with mussel physiological conditions. Although restricted, these changes in POC fluxes induced visible effects on sediment biogeochemistry. Observed oxygen microprofiles presented a 50 % decrease in oxygen penetration depth (from 2.3 to 1.4 mm), accompanied by an increase in the O 2 influx at the station below the mussel farm (19-31 versus 10-12 mmol O 2 m −2 d −1 ) characterised by higher POC flux. Dissolved inorganic carbon (DIC) and NH + 4 concentrations showed similar behaviour, with a more evident effect of bioirrigation underneath the farm. This was confirmed through constraining the early diagenesis model, of which calibration leads to an estimation of enhanced and shallower bioirrigation underneath the farm: bioirrigation rates of 40 yr −1 and irrigation depth of 15 cm were estimated inside the shellfish deposition footprint versus 20 yr −1 and 20 cm outside. These findings were confirmed by independent data on macrofauna composition collected at the study site. Early diagenesis model results indicated a larger organic matter mineralisation below the mussel farm (11.1 versus 18.7 mmol m −2 d −1 ), characterised by similar proportions between oxic and anoxic degradation rates at the two stations, with an increase in the absolute values of oxygen consumed by OM degradation and reduced substances re-oxidation underneath the mussel farm.

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“…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:…”

Section: Model Descriptionmentioning

confidence: 99%

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

Spiteri

Slomp

Regnier

et al. 2007

Journal of Contaminant Hydrology

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A 1D reactive transport model (RTM) is used to obtain a mechanistic understanding of the fate of phosphorus (P) in the saturated zone of two contrasting aquifer systems. We use the field data from two oxic, electron donor-poor, wastewater-impacted, sandy Canadian aquifers, (Cambridge and Muskoka sites) as an example of a calcareous and non-calcareous groundwater system, respectively, to validate our reaction network. After approximately 10 years of wastewater infiltration, P is effectively attenuated within the first 10 m downgradient of the source mainly through fast sorption onto calcite and Fe oxides. Slow, kinetic sorption contributes further to P removal, while precipitation of phosphate minerals (strengite, hydroxyapatite) is quantitatively unimportant in the saturated zone. Nitrogen (N) dynamics are also considered, but nitrate behaves essentially as a conservative tracer in both systems. The model-predicted advancement of the P plume upon continued wastewater discharge at the calcareous site is in line with field observations. Model results suggest that, upon removal of the wastewater source, the P plume at both sites will persist for at least 20 years, owing to desorption of P from aquifer solids and the slow rate of P mineral precipitation. Sensitivity analyses for the noncalcareous scenario (Muskoka) illustrate the importance of the sorption capacity of the aquifer solids for P in modulating groundwater N:P ratios in oxic groundwater. The model simulations predict the breakthrough of groundwater with high P concentrations and low N:P ratios after 17 years at 20 m from the source for an aquifer with low sorption capacity (b 0.02% w/w Fe(OH) 3 ). In this type of system, denitrification plays a minor role in lowering the N:P ratios because it is limited by the availability of labile dissolved organic matter.

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Modeling complex multi-component reactive-transport systems: towards a simulation environment based on the concept of a Knowledge Base

Cited by 78 publications

References 13 publications

Organic matter mineralization in sediment of a coastal freshwater lake and response to salinization

Organic matter mineralization in sediment of a coastal freshwater lake and response to salinization

Modelling biogeochemical processes in sediments from the north-western Adriatic Sea: response to enhanced particulate organic carbon fluxes

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

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