Toward more mechanistic representations of biogeochemical processes in river networks: Implementation and demonstration of a multiscale model

Jan, Ahmad; Coon, Ethan; Painter, Scott

doi:10.1016/j.envsoft.2021.105166

Toward more mechanistic representations of biogeochemical processes in river networks: Implementation and demonstration of a multiscale model

Journal Article · 19 August 2021 · Environmental Modelling and Software

DOI:https://doi.org/10.1016/j.envsoft.2021.105166· OSTI ID:1819571

^[1]; ^[1]; ^[1]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Climate Change Science Institute, Environmental Sciences Division

A recently introduced multiscale model for representing the effects of small-scale hyporheic-zone biogeochemical processes is extended from the reach scale to river network scales. The model uses advection-dispersion-reaction equations for the channel network and one-dimensional advection-reaction subgrid models for the hyporheic zone. We summarize implementation in the integrated surface/subsurface hydrology modeling system Amanzi-ATS. The extension uses topologically defined meshes to represent stream/river networks and associates a hyporheic subgrid model with each channel grid cell. Biogeochemical reaction modeling capability residing in community software is accessed through an application programming interface. The implementation is verified against independent numerical solutions on a single reach. Mesh convergence studies show that commonly used semi-distributed representations can introduce significant spatial discretization error. Denitrification of farm runoff in a subbasin of the Portage River Basin in Ohio, USA is used to demonstrate the general-purpose reactive transport capability.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth and Environmental Systems Science Division

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1819571

Journal Information:: Environmental Modelling and Software, Vol. 145, Issue xx; ISSN 1364-8152

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (47)

Dynamic modeling of nitrogen losses in river networks unravels the coupled effects of hydrological and biogeochemical processes Alexander, Richard B.; Böhlke, John Karl; Boyer, Elizabeth W. Biogeochemistry, Vol. 93, Issue 1-2 https://doi.org/10.1007/s10533-008-9274-8	journal	January 2009
Surface storage dynamics in large rivers: Comparing three-dimensional particle transport, one-dimensional fractional derivative, and multirate transient storage models: SURFACE STORAGE DYNAMICS IN LARGE RIVERS Anderson, Eric J.; Phanikumar, Mantha S. Water Resources Research, Vol. 47, Issue 9 https://doi.org/10.1029/2010WR010228	journal	September 2011
Large area Hydrologic Modeling and Assessment part i: Model Development Arnold, J. G.; Srinivasan, R.; Muttiah, R. S. Journal of the American Water Resources Association, Vol. 34, Issue 1 https://doi.org/10.1111/j.1752-1688.1998.tb05961.x	journal	February 1998
Ambient groundwater flow diminishes nitrate processing in the hyporheic zone of streams: AMBIENT GROUNDWATER AND STREAM N-CYCLING Azizian, Morvarid; Boano, Fulvio; Cook, Perran L. M. Water Resources Research, Vol. 53, Issue 5 https://doi.org/10.1002/2016WR020048	journal	May 2017
Nutrient cycling in bedform induced hyporheic zones Bardini, L.; Boano, F.; Cardenas, M. B. Geochimica et Cosmochimica Acta, Vol. 84 https://doi.org/10.1016/j.gca.2012.01.025	journal	May 2012
Simulation of solute transport in a mountain pool-and-riffle stream: A transient storage model Bencala, Kenneth E.; Walters, Roy A. Water Resources Research, Vol. 19, Issue 3 https://doi.org/10.1029/WR019i003p00718	journal	June 1983
Scaling of dissolved organic carbon removal in river networks Bertuzzo, Enrico; Helton, Ashley M.; Hall,, Robert O. Advances in Water Resources, Vol. 110 https://doi.org/10.1016/j.advwatres.2017.10.009	journal	December 2017
Biogeochemical zonation due to intrameander hyporheic flow: INTRAMEANDER BIOGEOCHEMICAL ZONATION Boano, F.; Demaria, A.; Revelli, R. Water Resources Research, Vol. 46, Issue 2 https://doi.org/10.1029/2008WR007583	journal	February 2010
Reactive Solute Transport in an Acidic Stream: Experimental pH Increase and Simulation of Controls on pH, Aluminum, and Iron Broshears, Robert E.; Runkel, Robert L.; Kimball, Briant A. Environmental Science & Technology, Vol. 30, Issue 10 https://doi.org/10.1021/es960055u	journal	January 1996
Managing complexity in simulations of land surface and near-surface processes Coon, Ethan T.; David Moulton, J.; Painter, Scott L. Environmental Modelling & Software, Vol. 78 https://doi.org/10.1016/j.envsoft.2015.12.017	journal	April 2016
Contextualizing Wetlands Within a River Network to Assess Nitrate Removal and Inform Watershed Management Czuba, Jonathan A.; Hansen, Amy T.; Foufoula-Georgiou, Efi Water Resources Research, Vol. 54, Issue 2 https://doi.org/10.1002/2017WR021859	journal	February 2018
A parsimonious transport model of emerging contaminants at the river network scale Diamantini, Elena; Mallucci, Stefano; Bellin, Alberto Hydrology and Earth System Sciences, Vol. 23, Issue 1 https://doi.org/10.5194/hess-23-573-2019	journal	January 2019
Geochemical Exports to River From the Intrameander Hyporheic Zone Under Transient Hydrologic Conditions: East River Mountainous Watershed, Colorado Dwivedi, Dipankar; Steefel, Carl I.; Arora, Bhavna Water Resources Research, Vol. 54, Issue 10 https://doi.org/10.1029/2018WR023377	journal	October 2018
A multirate mass transfer model to represent the interaction of multicomponent biogeochemical processes between surface water and hyporheic zones (SWAT-MRMT-R 1.0) Fang, Yilin; Chen, Xingyuan; Gomez Velez, Jesus Geoscientific Model Development, Vol. 13, Issue 8 https://doi.org/10.5194/gmd-13-3553-2020	journal	January 2020
An improved process-based representation of stream solute transport in the soil and water assessment tools Femeena, Pandara V.; Chaubey, Indrajeet; Aubeneau, Antoine Hydrological Processes, Vol. 34, Issue 11 https://doi.org/10.1002/hyp.13751	journal	April 2020
Mesh Infrastructure for Coupled Multiprocess Geophysical Simulations Garimella, Rao V.; Perkins, William A.; Buksas, Mike W. Procedia Engineering, Vol. 82 https://doi.org/10.1016/j.proeng.2014.10.371	journal	January 2014
A hydrogeomorphic river network model predicts where and why hyporheic exchange is important in large basins Gomez-Velez, Jesus D.; Harvey, Judson W. Geophysical Research Letters, Vol. 41, Issue 18 https://doi.org/10.1002/2014GL061099	journal	September 2014
Denitrification in the Mississippi River network controlled by flow through river bedforms Gomez-Velez, Jesus D.; Harvey, Judson W.; Cardenas, M. Bayani Nature Geoscience, Vol. 8, Issue 12 https://doi.org/10.1038/ngeo2567	journal	October 2015
Comparing transient storage modeling and residence time distribution (RTD) analysis in geomorphically varied reaches in the Lookout Creek basin, Oregon, USA Gooseff, Michael N.; Wondzell, Steve M.; Haggerty, Roy Advances in Water Resources, Vol. 26, Issue 9 https://doi.org/10.1016/S0309-1708(03)00105-2	journal	September 2003
Denitrification and hydrologic transient storage in a glacial meltwater stream, McMurdo Dry Valleys, Antarctica Gooseff, Michael N.; McKnight, Diane M.; Runkel, Robert L. Limnology and Oceanography, Vol. 49, Issue 5 https://doi.org/10.4319/lo.2004.49.5.1884	journal	September 2004
Sensitivity analysis of conservative and reactive stream transient storage models applied to field data from multiple-reach experiments Gooseff, Michael N.; Bencala, Kenneth E.; Scott, Durelle T. Advances in Water Resources, Vol. 28, Issue 5 https://doi.org/10.1016/j.advwatres.2004.11.012	journal	May 2005
Analytical solution and simplified analysis of coupled parent-daughter steady-state transport with multirate mass transfer: TECHNICAL NOTE Haggerty, Roy Water Resources Research, Vol. 49, Issue 1 https://doi.org/10.1029/2012WR012821	journal	January 2013
Power-law residence time distribution in the hyporheic zone of a 2nd-order mountain stream Haggerty, Roy Geophysical Research Letters, Vol. 29, Issue 13 https://doi.org/10.1029/2002GL014743	journal	January 2002
Evaluating the performance of parallel subsurface simulators: An illustrative example with PFLOTRAN: Evaluating the Parallel Performance of Pflotran Hammond, G. E.; Lichtner, P. C.; Mills, R. T. Water Resources Research, Vol. 50, Issue 1 https://doi.org/10.1002/2012WR013483	journal	January 2014
Thinking outside the channel: modeling nitrogen cycling in networked river ecosystems Helton, Ashley M.; Poole, Geoffrey C.; Meyer, Judy L. Frontiers in Ecology and the Environment, Vol. 9, Issue 4 https://doi.org/10.1890/080211	journal	September 2010
An intermediate-scale model for thermal hydrology in low-relief permafrost-affected landscapes Jan, Ahmad; Coon, Ethan T.; Painter, Scott L. Computational Geosciences, Vol. 22, Issue 1 https://doi.org/10.1007/s10596-017-9679-3	journal	July 2017
Modelling one-dimensional reactive transport of toxic contaminants in natural rivers Kim, Byunguk; Seo, Il Won; Kwon, Siyoon Environmental Modelling & Software, Vol. 137 https://doi.org/10.1016/j.envsoft.2021.104971	journal	March 2021
Concurrent conservative and reactive tracer tests in a stream undergoing hyporheic exchange: Conservative and Reactive Tracer Tests in Streams Lemke, Dennis; Liao, Zijie; Wöhling, Thomas Water Resources Research, Vol. 49, Issue 5 https://doi.org/10.1002/wrcr.20277	journal	May 2013
Toward catchment hydro‐biogeochemical theories Li, Li; Sullivan, Pamela L.; Benettin, Paolo WIREs Water, Vol. 8, Issue 1 https://doi.org/10.1002/wat2.1495	journal	December 2020
Shape-free inference of hyporheic traveltime distributions from synthetic conservative and “smart” tracer tests in streams: INFERENCE OF HYPORHEIC TRAVEL TIMES Liao, Zijie; Cirpka, Olaf A. Water Resources Research, Vol. 47, Issue 7 https://doi.org/10.1029/2010WR009927	journal	July 2011
Modeling and inverting reactive stream tracers undergoing two-site sorption and decay in the hyporheic zone: Reactive Stream Tracer Modeling Liao, Zijie; Lemke, Dennis; Osenbrück, Karsten Water Resources Research, Vol. 49, Issue 6 https://doi.org/10.1002/wrcr.20276	journal	June 2013
Parameter Estimation of the Transient Storage Model for Stream–Subsurface Exchange Marion, Andrea; Zaramella, Mattia; Packman, Aaron I. Journal of Environmental Engineering, Vol. 129, Issue 5 https://doi.org/10.1061/(ASCE)0733-9372(2003)129:5(456)	journal	May 2003
Solute transport in rivers with multiple storage zones: The STIR model: STIR MODEL Marion, A.; Zaramella, M.; Bottacin-Busolin, A. Water Resources Research, Vol. 44, Issue 10 https://doi.org/10.1029/2008WR007037	journal	October 2008
A semianalytical three-dimensional process-based model for hyporheic nitrogen dynamics in gravel bed rivers: DIN DYNAMICS IN THE HYPORHEIC ZONE Marzadri, Alessandra; Tonina, Daniele; Bellin, Alberto Water Resources Research, Vol. 47, Issue 11 https://doi.org/10.1029/2011WR010583	journal	November 2011
Stream denitrification across biomes and its response to anthropogenic nitrate loading Mulholland, Patrick J.; Helton, Ashley M.; Poole, Geoffrey C. Nature, Vol. 452, Issue 7184 https://doi.org/10.1038/nature06686	journal	March 2008
Multiscale Framework for Modeling Multicomponent Reactive Transport in Stream Corridors Painter, S. L. Water Resources Research, Vol. 54, Issue 10 https://doi.org/10.1029/2018WR022831	journal	October 2018
Reactive Solute Transport in Streams: 1. Development of an Equilibrium-Based Model Runkel, Robert L.; Bencala, Kenneth E.; Broshears, Robert E. Water Resources Research, Vol. 32, Issue 2 https://doi.org/10.1029/95WR03106	journal	February 1996
Reactive solute transport in streams: A surface complexation approach for trace metal sorption Runkel, Robert L.; Kimball, Briant A.; McKnight, Diane M. Water Resources Research, Vol. 35, Issue 12 https://doi.org/10.1029/1999WR900259	journal	December 1999
A general real-time formulation for multi-rate mass transfer problems Silva, O.; Carrera, J.; Dentz, M. Hydrology and Earth System Sciences, Vol. 13, Issue 8 https://doi.org/10.5194/hess-13-1399-2009	journal	January 2009
Reactive transport modeling: An essential tool and a new research approach for the Earth sciences Steefel, C.; Depaolo, D.; Lichtner, P. Earth and Planetary Science Letters, Vol. 240, Issue 3-4 https://doi.org/10.1016/j.epsl.2005.09.017	journal	December 2005
A nitrogen model for European catchments: INCA, new model structure and equations Wade, A. J.; Durand, P.; Beaujouan, V. Hydrology and Earth System Sciences, Vol. 6, Issue 3 https://doi.org/10.5194/hess-6-559-2002	journal	January 2002
A semi-distributed ntegrated itrogen model for multiple source assessment in tchments (INCA): Part I — model structure and process equations Whitehead, P.; Wilson, E.; Butterfield, D. Science of The Total Environment, Vol. 210-211 https://doi.org/10.1016/S0048-9697(98)00037-0	journal	March 1998
Effect of flow-induced exchange in hyporheic zones on longitudinal transport of solutes in streams and rivers: EFFECT OF FLOW-INDUCED EXCHANGE Wörman, Anders; Packman, Aaron I.; Johansson, Håkan Water Resources Research, Vol. 38, Issue 1 https://doi.org/10.1029/2001WR000769	journal	January 2002
Autotrophic nitrate uptake in river networks: A modeling approach using continuous high-frequency data Yang, Xiaoqiang; Jomaa, Seifeddine; Büttner, Olaf Water Research, Vol. 157 https://doi.org/10.1016/j.watres.2019.02.059	journal	June 2019
Dissolved nutrient retention dynamics in river networks: A modeling investigation of transient flows and scale effects: DISSOLVED NUTRIENT RETENTION DYNAMICS IN RIVER NETWORKS Ye, Sheng; Covino, Timothy P.; Sivapalan, Murugesu Water Resources Research, Vol. 48, Issue 6 https://doi.org/10.1029/2011WR010508	journal	June 2012
Application of the transient storage model to analyze advective hyporheic exchange with deep and shallow sediment beds: HYPORHEIC EXCHANGE WITH SEDIMENT BEDS Zaramella, Mattia; Packman, Aaron I.; Marion, Andrea Water Resources Research, Vol. 39, Issue 7 https://doi.org/10.1029/2002WR001344	journal	July 2003
Coupled transport and reaction kinetics control the nitrate source-sink function of hyporheic zones: HYPORHEIC N SOURCE-SINK CONTROLS Zarnetske, Jay P.; Haggerty, Roy; Wondzell, Steven M. Water Resources Research, Vol. 48, Issue 11 https://doi.org/10.1029/2012WR011894	journal	November 2012

Similar Records

Toward more mechanistic representations of biogeochemical processes in stream and river networks: Implementation and demonstration of a multiscale model : Modeling Archive

Dataset · 2021 · OSTI ID:1785972

Jan, Ahmad; Coon, Ethan; Painter, Scott

On the Representation of Hyporheic Exchange in Models for Reactive Transport in Stream and River Corridors

Journal Article · 2021 · Frontiers in Water · OSTI ID:1765491

Painter, Scott

Related Subjects

54 ENVIRONMENTAL SCIENCES
58 GEOSCIENCES
97 MATHEMATICS AND COMPUTING
Reactive transport models
Hyporheic zone
River networks
Surface/subsurface hydrological models
Multiscale models

Toward more mechanistic representations of biogeochemical processes in river networks: Implementation and demonstration of a multiscale model

Citation Formats

References (47)

Similar Records

Related Subjects