High-resolution simulation of free-surface flow and tracer retention over streambeds with ripples

Almeida, 1990, Laser-doppler measurements of fully developed turbulent channel flow, 5th International Symposia on Applications of Laser Techniques to Fluid Mechanics Bardini, 2012, Nutrient cycling in bedform induced hyporheic zones, Geochim. Cosmochim. Acta, 84, 47, 10.1016/j.gca.2012.01.025 Boano, 2006, Sinuosity-driven hyporheic exchange in meandering rivers, Geophys. Res. Lett., 33, L18406, 10.1029/2006GL027630 Boano, 2007, Bedform-induced hyporheic exchange with unsteady flows, Adv. Water Resour., 30, 148, 10.1016/j.advwatres.2006.03.004 Buffington, 2009, Hyporheic exchange in mountain rivers ii: Effects of channel morphology on mechanics, scales, and rates of exchange, Geogr. Compass, 3, 1038, 10.1111/j.1749-8198.2009.00225.x Buss, 2009 Cardenas, 2008, The effect of river bend morphology on flow and timescales of surface water groundwater exchange across pointbars, J. Hydrol., 362, 134, 10.1016/j.jhydrol.2008.08.018 Cardenas, 2008, Constraining denitrification in permeable wave-influenced marine sediment using linked hydrodynamic and biogeochemical modeling, Earth Planet. Sci. Lett., 275, 127, 10.1016/j.epsl.2008.08.016 Cardenas, 2007, Dunes, turbulent eddies, and interfacial exchange with permeable sediments, Water Resour. Res., 43, W08412, 10.1029/2006WR005787 Cardenas, 2007, Hydrodynamics of coupled flow above and below a sediment-water interface with triangular bedforms, Adv. Water Resour., 30, 301, 10.1016/j.advwatres.2006.06.009 Chanson, 1995, Characteristics of undular hydraulic jumps: experimental apparatus and flow patterns, J. Hydraul. Eng., 121, 129, 10.1061/(ASCE)0733-9429(1995)121:2(129) Chen, 2015, Three-dimensional versus two-dimensional bed form-induced hyporheic exchange, Water Resour. Res, 51, 2923, 10.1002/2014WR016848 Dahm, 1998, Nutrient dynamics at the interface between surface waters and groundwaters, Freshw. Biol., 40, 427, 10.1046/j.1365-2427.1998.00367.x Elliott, 1997, Transfer of nonsorbing solutes to a streambed with bed forms: theory, Water Resour. Res., 33, 123, 10.1029/96WR02784 Fehlman, 1985 Greenshields, 2010 Harvey, 1998, Effect of enhanced manganese oxidation in the hyporheic zone on basin-scale geochemical mass balance, Water Resour. Res., 34, 623, 10.1029/97WR03606 Hinkelmann, 2005 Hirt, 1981, Volume of fluid (VOF) method for the dynamics of free boundaries, J. Comput. Phys., 39, 201, 10.1016/0021-9991(81)90145-5 Janssen, 2012, A comparative experimental and multiphysics computational fluid dynamics study of coupled surface-subsurface flow in bed forms, Water Resour. Res., 48, W08514, 10.1029/2012WR011982 Jirka, 2007 Kinzelbach, 1992 Lane, 2002, High-resolution numerical modelling of three-dimensional flows over complex river bed topography, Hydrol. Process., 16, 2261, 10.1002/hyp.5034 Packman, 2001, Hyporheic exchange of solutes and colloids with moving bed forms, Water Resour. Res., 37, 2591, 10.1029/2001WR000477 Revelli, 2008, Intrameander hyporheic flow in alluvial rivers, Water Resour. Res., 44, W12428, 10.1029/2008WR007081 Rodrigues, 2011, Theophylline polymorphs by atomization of supercritical antisolvent induced suspensions, J. Supercrit. Fluids, 58, 303, 10.1016/j.supflu.2011.05.012 Schulze, 2014, The multiphase capabilities of the CFD toolbox openfoam for hydraulic engineering applications, ICHE 2014, Hamburg. Bundesanstalt für Wasserbau Shen, 2008, Application of two- and three-dimensional computational fluid dynamics models to complex ecological stream flows, J. Hydrol., 348, 195, 10.1016/j.jhydrol.2007.09.060 Stoesser, 2008, Turbulence structures in flow over two-dimensional dunes, J. Hydraul. Eng., 134, 42, 10.1061/(ASCE)0733-9429(2008)134:1(42) Stonedahl, 2010, A multiscale model for integrating hyporheic exchange from ripples to meanders, Water Resour. Res., 46, W12539, 10.1029/2009WR008865 Thibodeaux, 1987, Bedform-generated convective transport in bottom sediment, Nature, 325, 341, 10.1038/325341a0 Tonina, 2007, Hyporheic exchange in gravel bed rivers with pool-riffle morphology: laboratory experiments and three-dimensional modeling, Water Resour. Res., 43, W01421, 10.1029/2005WR004328 Tonina, 2009, Hyporheic exchange in mountain rivers i: Mechanics and environmental effects, Geogr. Compass, 3, 1063, 10.1111/j.1749-8198.2009.00226.x Tonina, 2009, A three-dimensional model for analyzing the effects of salmon redds on hyporheic exchange and egg pocket habitat, Can. J. Fish. Aquat. Sci., 66, 2157, 10.1139/F09-146 Trauth, 2013, Coupled 3-d stream flow and hyporheic flow model under varying stream and ambient groundwater flow conditions in a pool-riffle system, Water Resour. Res., 49, 5834, 10.1002/wrcr.20442 Trauth, 2014, Hyporheic transport and biogeochemical reactions in pool-riffle systems under varying ambient groundwater flow conditions, J. Geophys. Res. Biogeosci., 119, 910, 10.1002/2013JG002586 Trauth, 2015, Hydraulic controls of in-stream gravel bar hyporheic exchange and reactions, Water Resour. Res., 51, 2243, 10.1002/2014WR015857 Young, 2010 Yue, 2005, Large eddy simulation of turbulent open-channel flow with free surface simulated by level set method, Phys. Fluids, 17, 10.1063/1.1849182