Name: visualizing hyporheic flow through bedforms using dye experiments and simulation
Uploaded: 2015-11-18T15:00:00
Description: Watch this Scientific Journal Video about Visualizing Hyporheic Flow Through Bedforms Using Dye Experiments and Simulation at JoVE.com

This material is based upon work supported by National Science Foundation grants EAR-0810270, EAR-1215898, and EAR-1344280, as well as an&#160;NSF Graduate Research Fellowship.

1. Simulation Software
<ol>
	<li>Use the software described in this section.
	<ol>
		<li>Download and install the free/open-source multi-agent modeling language and simulation platform, NetLogo (Available: <a href="http://ccl.northwestern.edu/netlogo/">http://ccl.northwestern.edu/netlogo/</a>, version 5.1 or later). 
		Note: This software is available at no cost and runs on all major operating systems (Windows/Mac/Linux).</li>
		<li>Download the two specific simulation script files (mousedrop.nlogo and <e...

<ol>
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W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reactive+uptake+of+trace+metals+in+the+hyporheic+zone+of+a+mining-contaminated+stream,+Pinal+Creek,+Arizona.">Reactive uptake of trace metals in the hyporheic zone of a mining-contaminated stream, Pinal Creek, Arizona.</a> Environ Sci Technol. 34, 1150-1155 (2000).</li><li>Jones, J. B., Mulholland, P. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Streams and Ground Waters. , (1999).</li><li>McKnight, D. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spectrofluorometric+characterization+of+dissolved+organic+matter+for+indication+of+precursor+organic+material+and+aromaticity.">Spectrofluorometric characterization of dissolved organic matter for indication of precursor organic material and aromaticity.</a> Limnol Oceanogr. 46, 38-48 (2001).</li><li>Mulholland, P. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Inter-biome+comparison+of+factors+controlling+stream+metabolism.">Inter-biome comparison of factors controlling stream metabolism.</a> Freshwater Biol. 46, 1503-1517 (2001).</li><li>Peterson, B. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Control+of+nitrogen+export+from+watersheds+by+headwater+streams.">Control of nitrogen export from watersheds by headwater streams.</a> Science. 292, 86-90 (2001).</li><li>Goolsby, D. A., Battaglin, W. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Long-term+changes+in+concentrations+and+flux+of+nitrogen+in+the+Mississippi+River+Basin,+USA.">Long-term changes in concentrations and flux of nitrogen in the Mississippi River Basin, USA.</a> Hydrol Process. 15, 1209-1226 (2001).</li><li>Rabalais, N. N., Smith, L. E., Harper, D. 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L., Haggerty, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Residence+time+of+bedform-driven+hyporheic+exchange.">Residence time of bedform-driven hyporheic exchange.</a> Adv Water Resour. 31, 1382-1386 (2008).</li><li>Stonedahl, S. H., Harvey, J. W., Detty, J., Aubeneau, A., Packman, A. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Physical+controls+and+predictability+of+stream+hyporheic+flow+evaluated+with+a+multiscale+model.">Physical controls and predictability of stream hyporheic flow evaluated with a multiscale model.</a> Water Resour Res. 48, (2012).</li><li>Stonedahl, S. H., Harvey, J. W., W&#246;rman, A., Salehin, M., Packman, A. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+multiscale+model+for+integrating+hyporheic+exchange+from+ripples+to+meanders.">A multiscale model for integrating hyporheic exchange from ripples to meanders.</a> Water Resour Res. 46, (2010).</li><li>W&#246;rman, A., Packman, A. I., Marklund, L., Harvey, J. W., Stone, S. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fractal+topography+and+subsurface+water+flows+from+fluvial+bedforms+to+the+continental+shield.">Fractal topography and subsurface water flows from fluvial bedforms to the continental shield.</a> Geophys Res Lett. 34, (2007).</li><li>Tonina, D., Buffington, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+three-dimensional+model+for+analyzing+the+effects+of+salmon+redds+on+hyporheic+exchange+and+egg+pocket+habitat.">A three-dimensional model for analyzing the effects of salmon redds on hyporheic exchange and egg pocket habitat.</a> Can J Fish Aquat Sci. 66, 2157-2173 (2009).</li><li>Elliott, A. H., Brooks, N. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transfer+of+nonsorbing+solutes+to+a+streambed+with+bed+forms:+Theory.">Transfer of nonsorbing solutes to a streambed with bed forms: Theory.</a> Water Resour Res. 33, 123-136 (1997).</li><li>Elliott, A. H., Brooks, N. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transfer+of+nonsorbing+solutes+to+a+streambed+with+bed+forms:+Laboratory+experiments.">Transfer of nonsorbing solutes to a streambed with bed forms: Laboratory experiments.</a> Water Resour Res. 33, 137-151 (1997).</li><li>W&#246;rman, A., Packman, A. I., Marklund, L., Harvey, J. W., Stone, S. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Exact+three-dimensional+spectral+solution+to+surface-groundwater+interactions+with+arbitrary+surface+topography.">Exact three-dimensional spectral solution to surface-groundwater interactions with arbitrary surface topography.</a> Geophys Res Lett. 33, (2006).</li><li>Janssen, F., Cardenas, M. B., Sawyer, A. H., Dammrich, T., Krietsch, J., de Beer, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+comparative+experimental+and+multiphysics+computational+fluid+dynamics+study+of+coupled+surface-subsurface+flow+in+bed+forms.">A comparative experimental and multiphysics computational fluid dynamics study of coupled surface-subsurface flow in bed forms.</a> Wat Resour Res. 48, (2012).</li><li>Shen, H. W., Fehlman, H. M., Mendoza, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bed+Form+Resistances+in+Open+Channel+Flows.">Bed Form Resistances in Open Channel Flows.</a> J Hydraul Eng-Asce. 116, 799-815 (1990).</li><li>Ma, J., Nickerson, J. 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J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Conceptual+change+in+science+and+in+science+education.">Conceptual change in science and in science education.</a> Synthese. 80, 163-183 (1989).</li><li>Magin, D., Kanapathipillai, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Engineering+students'+understanding+of+the+role+of+experimentation.">Engineering students' understanding of the role of experimentation.</a> European Journal of Engineering Education. 25, 351-358 (2000).</li><li>Shin, D., Yoon, E. S., Lee, K. Y., Lee, E. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+web-based,+interactive+virtual+laboratory+system+for+unit+operations+and+process+systems+engineering+education:+issues,+design+and+implementation.">A web-based, interactive virtual laboratory system for unit operations and process systems engineering education: issues, design and implementation.</a> Comput Chem Eng. 26, 319-330 (2002).</li><li>Smith, P. R., Pollard, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Role+of+Computer-Simulations+in+Engineering-Education.">The Role of Computer-Simulations in Engineering-Education.</a> Comput Educ. 10, 335-340 (1986).</li><li>Gillet, D., Ngoc, A. V. N., Rekik, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Collaborative+web-based+experimentation+in+flexible+engineering+education.">Collaborative web-based experimentation in flexible engineering education.</a> Ieee T Educ. 48, 696-704 (2005).</li><li>Subramanian, R., Marsic, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ViBE:+Virtual+biology+experiments.">ViBE: Virtual biology experiments.</a> Proceedings of the 10th international conference on World Wide Web. , 316-325 (2001).</li><li>Blikstein, P., Fuhrmann, T., Greene, D., Salehi, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bifocal+Modeling:+Mixing+Real+and+Virtual+Labs+for+Advanced+Science+Learning.">Bifocal Modeling: Mixing Real and Virtual Labs for Advanced Science Learning.</a> Proceedings of Idc 2012: The 11th International Conference on Interaction Design and Children. , 296-299 (2012).</li><li>Freeze, R. A., Cherry, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Groundwater. , (1979).</li><li>Todd, D. K., Mays, L. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Groundwater Hydrology. , (2005).</li><li>Box, G. E., Draper, N. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Empirical Model-Building and Response Surfaces. , (1987).</li><li>Flavell, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Metacognition+and+cognitive+monitoring:+A+new+area+of+cognitive&#8211;developmental+inquiry.">Metacognition and cognitive monitoring: A new area of cognitive&#8211;developmental inquiry.</a> American Psychologist. 34, 906 (1979).</li><li>Bransford, J. D., Brown, A. L., Cocking, R. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> How People Learn. , (2000).</li><li>Pintrich, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+metacognitive+knowledge+in+learning,+teaching,+and+assessing.">The role of metacognitive knowledge in learning, teaching, and assessing.</a> Theor Pract. 41 (4), 219-225 (2002).</li><li>Zohar, A., Ben David, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Paving+a+clear+path+in+a+thick+forest:+a+conceptual+analysis+of+a+metacognitive+component.">Paving a clear path in a thick forest: a conceptual analysis of a metacognitive component.</a> Metacogn Learn. 4, 177-195 (2009).</li><li>Fox, A., Boano, F., Arnon, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impact+of+losing+and+gaining+streamflow+conditions+on+hyporheic+exchange+fluxes+induced+by+dune-shaped+bed+forms.">Impact of losing and gaining streamflow conditions on hyporheic exchange fluxes induced by dune-shaped bed forms.</a> Water Resour Res. 50, 1895-1907 (2014).</li><li>Norman, F. A., Cardenas, M. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Heat+transport+in+hyporheic+zones+due+to+bedforms:+An+experimental+study.">Heat transport in hyporheic zones due to bedforms: An experimental study.</a> Water Resour Res. 50, 3568-3582 (2014).</li><li>Precht, E., Huettel, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+wave-driven+advective+pore+water+exchange+in+a+permeable+coastal+sediment.">Rapid wave-driven advective pore water exchange in a permeable coastal sediment.</a> J Sea Res. 51, 93-107 (2004).</li><li>Salehin, M., Packman, A. I., Paradis, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hyporheic+exchange+with+heterogeneous+streambeds:+Laboratory+experiments+and+modeling.">Hyporheic exchange with heterogeneous streambeds: Laboratory experiments and modeling.</a> Water Resour Res. 40, (2004).</li><li>Cardenas, M. B., Wilson, J. L., Zlotnik, V. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impact+of+heterogeneity,+bed+forms,+and+stream+curvature+on+subchannel+hyporheic+exchange.">Impact of heterogeneity, bed forms, and stream curvature on subchannel hyporheic exchange.</a> Water Resour Res. 40, (2004).</li><li>Sawyer, A. H., Cardenas, M. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hyporheic+flow+and+residence+time+distributions+in+heterogeneous+cross-bedded+sediment.">Hyporheic flow and residence time distributions in heterogeneous cross-bedded sediment.</a> Water Resour Res. 45, (2009).</li><li>Boano, F., Camporeale, C., Revelli, R., Ridolfi, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sinuosity-driven+hyporheic+exchange+in+meandering+rivers.">Sinuosity-driven hyporheic exchange in meandering rivers.</a> Geophys Res Lett. 33, (2006).</li><li>Cardenas, M. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+model+for+lateral+hyporheic+flow+based+on+valley+slope+and+channel+sinuosity.">A model for lateral hyporheic flow based on valley slope and channel sinuosity.</a> Water Resour Res. 45, (2009).</li><li>Tonina, D., Buffington, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hyporheic+exchange+in+gravel+bed+rivers+with+pool-riffle+morphology:+Laboratory+experiments+and+three-dimensional+modeling.">Hyporheic exchange in gravel bed rivers with pool-riffle morphology: Laboratory experiments and three-dimensional modeling.</a> Water Resour Res. 43, (2007).</li><li>Harbaugh, A. W., Banta, E. R., Hill, M. C., McDonald, M. 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In conjunction, the flume demonstration and particle tracking simulations provide a comprehensive introduction to hyporheic flow for a range of audiences. Participants of all levels are provided visual evidence for the occurrence of hyporheic exchange induced by bedforms, and the strong variability in subsurface flow paths under bedforms. These procedures can be used as a simple demonstration of porewater flow for undergraduates or K-12 students, or it can be used in graduate courses in conjunction with a more in-depth p...

As surface water moves in a stream, river, or tidal zone it creates head gradients that drive water into and out of the sediments1. In fluvial systems the portion of the streambed sediments where this exchange occurs is known as the hyporheic zone2,3. This zone is important because many nutrients and pollutants are stored, deposited, or transformed within the hyporheic zone4-9. The amount of time a tracer spends in the sediment is called a residence time. Both residence times and the locations of the flow paths affect the transformation processes. Improved understanding of the processes affecting flow through the sediment is needed to predict solute transport in rivers and address large environmental problems resulting from propagation of materials such as nutrients (e.g., coastal hypoxia10,11). In spite of the significance of hyporheic exchange, it is often not described in undergraduate courses in hydrology, fluid mechanics, hydraulics, etc. Educators wishing to add hyporheic exchange to their courses could find it useful to have experimental and numerical visualizations that clearly show this process.
Stream channel sinuosity, surrounding groundwater levels, and streambed topography (i.e., bars, bedforms, and biogenic mounds) all affect hyporheic exchange to varying degrees12-17. This study focused on bedforms, such as dunes and ripples, which are usually key geomorphic features affecting hyporheic flow14,15. We created a numerical simulation and laboratory experiment to visualize flow through a regular series of bedforms. This simulation is based on a body of previous research relating hyporheic flow paths to readily observable system characteristics15,18-21. As this research forms the scientific background for the simulation, a brief summary of the key aspects of the theory follows. Bedform topography, T(x), is given by:
Equation 1: 
<img alt="Equation 1" src="/files/ftp_upload/53285/53285eq1.jpg" />
where H is twice the amplitude of the bedform, k is the wavenumber, and x is the longitudinal dimension parallel to the average streambed surface. An example of this bedform topography is shown in Figure 1.
<img alt="Figure 1" src="/files/ftp_upload/53285/53285fig1.jpg" /> 
Figure 1. Parameter definitions and settings controlled by the user. In Interface, tracer particles are released in a flux-weighted manner at the water/sediment interface and tracked through the sediment. If show-paths? is &#8220;on&#8221; the water tracers mark where they have been, showing their paths. When a tracer returns to the surface water, this changes the total number of tracers in the system, when re-drop? is set to &#8220;off&#8221;. The cumulative residence time distribution plot shows this change by plotting the ratio of the number of tracers remaining in the sediment bed to the initial number as a function of time. If re-drop? is &#8220;on&#8221; then tracers that leave the system are replaced in the same flux-weighted manner as original particles, and the cumulative plot is disabled. <a href="https://www.jove.com/files/ftp_upload/53285/53285fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<table fo:keep-together.within-page="1">
	<tbody>
		<tr>
			<td>Parameter Name</td>
			<td>Units</td>
			<td colspan="3">Definition</td>
			<td>Interface</td>
			<td>Mousedrop</td>
		</tr>
		<tr>
			<td>Lambda (&#955;)</td>
			<td>cm</td>
			<td colspan="3">Wavelength of bedform (see Figure 1)</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>BedformHeight (H)</td>
			<td>cm</td>
			<td colspan="3">Twice the bedform amplitude (see Figure 1)</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>BedDepth (D)</td>
			<td>cm</td>
			<td colspan="3">Depth of the sediments (see Figure 1)</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>HydrCond (K)</td>
			<td>cm/s</td>
			<td colspan="3">Hydraulic Conductivity</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>Porosity (&#952;)</td>
			<td></td>
			<td colspan="3">Porosity</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>ChannelVelocity (U)</td>
			<td>cm/s</td>
			<td colspan="3">Mean velocity in the surface water or channel</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>Depth (d)</td>
			<td>cm</td>
			<td colspan="3">Water depth (see Figure 1)</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>Slope (S)</td>
			<td></td>
			<td colspan="3">Slope of the bedforms and water surface</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>NumParticles</td>
			<td></td>
			<td colspan="3">The number of particles released into the system.</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td></td>
		</tr>
		<tr>
			<td>TimeX (Time1, Time2..)</td>
			<td>min</td>
			<td colspan="3">Time at which each color change occurs</td>
			<td></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>Simulation Buttons</td>
			<td></td>
			<td colspan="3">Definition</td>
			<td>Interface</td>
			<td>Mousedrop</td>
		</tr>
		<tr>
			<td>Setup</td>
			<td></td>
			<td colspan="3">Set&#8217;s up the simulation using parameters shown</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>go/stop</td>
			<td></td>
			<td colspan="3">Starts and stops the simulation</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>Step</td>
			<td></td>
			<td colspan="3">Clicking step causes one time step to pass.&#160; This allows users to slow down the code and see exactly what happens in 100 sec.</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td></td>
		</tr>
		<tr>
			<td>clear paths</td>
			<td></td>
			<td colspan="3">Clears all he blue particle paths from the screen</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>Advance to next time</td>
			<td></td>
			<td colspan="3">This causes the program to run until the next color change time (TimeX)</td>
			<td></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>mouse-drop</td>
			<td></td>
			<td colspan="3">This button must be clicked before particles may be placed in the subsurface by clicking on locations in the subsurface.</td>
			<td></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>show-paths?</td>
			<td></td>
			<td colspan="3">If show-paths? is &#8220;on&#8221; the water particles leave a trail of blue showing where they have been (see Figure 1).</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
		</tr>
		<tr>
			<td>re-drop?</td>
			<td></td>
			<td colspan="3">If re-drop? is &#8220;on&#8221; the particles are replaced in a flux weighted manner for every particle, which exits the system, and the cumulative plot does not work.&#160; When a particle exits the hyporheic zone the number of particles in the system decreases if re-drop? is &#8220;off&#8221; (see Figure 1).</td>
			<td><img alt="checkmark" src="/files/ftp_upload/53285/checkmark.jpg" /></td>
			<td></td>
		</tr>
	</tbody>
</table>
Table 1. Hyporheic Parameters and Simulation Controls. Each parameter, button, and slider that can be adjusted by the user is given in this table along with a definition.
In this simulation, two processes induce fluid velocity in the sand bed. The first is due to the interactions of the stream flow with bedforms. The velocity head at the water/sediment interface induced by bedforms is also approximately sinusoidal, and shifted by a quarter wavelength from the bedform itself22. The amplitude of the velocity head function at the surface-subsurface interface has been approximated from measurements as16:
Equation 2: 
<img alt="Equation 2" src="/files/ftp_upload/53285/53285eq2.jpg" />
where U is the mean surface water velocity, g is the gravitational constant, and d is the depth of the water (shown in Figure 1). The velocity head function is then given by:
Equation 3: 
<img alt="Equation 3" src="/files/ftp_upload/53285/53285eq3.jpg" />
This head function can then be used to calculate the bedform-based component of the subsurface velocity functions by solving the Laplace equation with a constant sand bed depth20. The second component of the porewater velocity is determined by the slope of the system, S, which corresponds to a gravitational head gradient that yields flow in the downstream direction proportional to <img alt="S/sqrt(1 + S^2)" src="/files/ftp_upload/53285/53285eq_S_inline.jpg" />. The final functions for porewater velocity are:
Equation 4: 
<img alt="Equation 4" src="/files/ftp_upload/53285/53285eq4.jpg" />
Equation 5: 
<img alt="Equation 5" src="/files/ftp_upload/53285/53285eq5.jpg" />
where u is the longitudinal velocity component, v is the vertical velocity component, K is the average hydraulic conductivity of the sediment, is the average porosity of the sediments, y is the vertical coordinate, and D is the depth of the sediments.
Particle tracking simulations were created, which use the NetLogo modeling language and simulation platform23. The two implementations (Mousedrop.nlogo and Interface.nlogo) use these equations to model hyporheic flow with the same simulation core. The primary difference is the initial locations of the tracer particles. Mousedrop allows the user to place simulated tracer anywhere within the subsurface. Subsurface velocity equations 4 and 5 are used to move the tracer to simulate dye injection experiments. In Interface, tracer is always placed along the surface/subsurface boundary in a flux-weighted manner. This mimics the delivery of dissolved and suspended material from the surface water into the porewater, which is crucial to understanding hyporheic exchange. The tracer then moves within the subsurface until it again reaches the stream water. Tracing the dye paths in the flume and simulating the paths using NetLogo yields the streamlines of the flowfield, as long as the flow conditions and bedform morphology remain steady during the period of observation. Interface.nlogo creates a cumulative residence time distribution, which shows the ratio of the number of tracer particles remaining in the sediments to the initial number of tracer particles placed at time 0 as a function of time.
As discussed in a recent literature survey24, there remains considerable debate within the educational research community about the relative merits of hands-on laboratory experiments versus simulated labs and computer models. On the one hand, some feel that &#8220;hands-on experience is at the heart of learning&#8221;25, and caution that cost-savings arguments may be fueling the replacement of hands-on lab activities by computer-based simulations, to the detriment of student understanding26. On the other hand, some researchers in science/engineering education argue that simulations are at least as effective as traditional hands-on labs27, or discuss the benefits of computer-simulation in fostering student-centered &#8220;discovery learning&#8221;28. While consensus has not been reached, many researchers have concluded that, ideally, computer simulations should supplement, rather than supplant, hands-on laboratory experiments29,30. There have also been initiatives within science and engineering education to simultaneously couple physical experimentation and real-world sensing with computer simulations of the phenomena; see, e.g., &#8220;bifocal modeling&#8221;31.
Students can gain a deeper conceptual knowledge and a better understanding of the scientific research process by interacting with both a physical system, and a computer-based simulation of that system. This procedure involves having students perform a solute transport experiment that demonstrates gravitational and bedform-induced hyporheic exchange flow, and match their own experimental setup and results with a computer simulation of the same phenomena. This comparison facilitates important student-learning outcomes, and a deeper discussion of the scientific method, and interplay between model/theory-building and empirical validation through data collection. After performing this comparison, students can also take advantage of the benefits of computer-based simulation to quickly explore a multitude of alternative scenarios by changing model parameters.

<table border="0" cellpadding="0" cellspacing="0" width="1244">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:117px;">Flume</td>
			<td style="width:199px;">Engineering Laboratory Design</td>
			<td style="width:125px;">Custom</td>
			<td style="width:804px;">Laboratory flume with clear sides for 24-48 hours</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Flowmeter</td>
			<td>Rosemount&#160;</td>
			<td>8800 vortex&#160;</td>
			<td style="width:804px;">This is located inside the recirculation loop of the flume</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sand</td>
			<td>US. Silica</td>
			<td>F30</td>
			<td style="width:804px;">Research-grade sand to form a layer 10-20 cm deep throughout the flume</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">Dye</td>
			<td>Samples from food companies</td>
			<td></td>
			<td style="width:804px;">Water-soluble food grade dye made into an aqueous solution.&#160; Dark colors like red, blue and green work best. (Avoid food dyes in propylene glycol)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Syringe</td>
			<td>HSW</td>
			<td>4100.000V0</td>
			<td style="width:804px;">5-10 mL, e.g. HSW Norm-Ject 2-part disposable syringe</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Pipetting Needle</td>
			<td>Cadence Science</td>
			<td>7942</td>
			<td>14-gage, 6-in blunt end,&#160; to inject the dye deep into the sand.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">Digital Camera</td>
			<td>Any</td>
			<td></td>
			<td style="width:804px;">Digital camera with steady tripod (Time lapse cameras can be used to collect rapid evenly spaced data.)&#160; We used a Nikon D7000.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ruler</td>
			<td>Any</td>
			<td></td>
			<td style="width:804px;">Transparent is best.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Measuring Tape</td>
			<td>Any</td>
			<td></td>
			<td style="width:804px;"></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Netlogo Software</td>
			<td>CCL</td>
			<td></td>
			<td><a href="http://ccl.northwestern.edu/netlogo/">http://ccl.northwestern.edu/netlogo/</a></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Mousedrop.nlogo</td>
			<td>Netlogo Commons</td>
			<td align="right">4259</td>
			<td><a href="http://modelingcommons.org/browse/one_model/4259">http://modelingcommons.org/browse/one_model/4259</a></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Interface.nlogo</td>
			<td>Netlogo Commons</td>
			<td align="right">4258</td>
			<td><a href="http://modelingcommons.org/browse/one_model/4258">http://modelingcommons.org/browse/one_model/4258</a></td>
		</tr>
	</tbody>
</table>

visualizing hyporheic flow through bedforms using dye experiments and simulation

Advective exchange between the pore space of sediments and the overlying water column, called hyporheic exchange in fluvial environments, drives solute transport in rivers and many important biogeochemical processes. To improve understanding of these processes through visual demonstration, we created a hyporheic flow simulation in the multi-agent computer modeling platform NetLogo. The simulation shows virtual tracer flowing through a streambed covered with two-dimensional bedforms. Sediment, flow, and bedform characteristics are used as input variables for the model. We illustrate how these simulations match experimental observations from laboratory flume experiments based on measured input parameters. Dye is injected into the flume sediments to visualize the porewater flow. For comparison virtual tracer particles are placed at the same locations in the simulation. This coupled simulation and lab experiment has been used successfully in undergraduate and graduate laboratories to directly visualize river-porewater interactions and show how physically-based flow simulations can reproduce environmental phenomena. Students took photographs of the bed through the transparent flume walls and compared them to shapes of the dye at the same times in the simulation. This resulted in very similar trends, which allowed the students to better understand both the flow patterns and the mathematical model. The simulations also allow the user to quickly visualize the impact of each input parameter by running multiple simulations. This process can also be used in research applications to illustrate basic processes, relate interfacial fluxes and porewater transport, and support quantitative process-based modeling.

The use of a simulation in conjunction with experiments allows students to observe the similarities and differences between idealized mathematical models and more complex real systems. Figure 4 shows an example comparing dye injection photographs with Mousedrop simulations. The initial photograph is used to determine the placement of the simulated dye tracer at time zero, and then the simulation is run for 34.2 min and compared with a photograph taken at that time. Overall the model does an exce...

Watch this Scientific Journal Video about Visualizing Hyporheic Flow Through Bedforms Using Dye Experiments and Simulation at JoVE.com

Visualizing Hyporheic Flow Through Bedforms Using Dye Experiments and Simulation

This manuscript describes how to create regular bedforms in a flume, visualize flow through the bedforms, and use computer simulations to simulate the hyporheic flow. The computer simulations compare well with the experimental observations. This coupled simulation and experiment is well-suited for both research and educational purposes.

Advective exchange between the pore space of sediments and the overlying water column, called hyporheic exchange in fluvial environments, drives solute ...

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