Visualizing Hyporheic Flow Through Bedforms Using Dye Experiments and Simulation

Summary

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.

Abstract

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.

Introduction

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 zone^2,3. This zone is important because many nutrients and pollutants are stored, deposited, or transformed within the hyporheic zone^4-9. 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 ....

Protocol

1. Simulation Software

1. Use the software described in this section.
   1. Download and install the free/open-source multi-agent modeling language and simulation platform, NetLogo (Available: http://ccl.northwestern.edu/netlogo/, version 5.1 or later).
      Note: This software is available at no cost and runs on all major operating systems (Windows/Mac/Linux).
   2. Download the two specific simulation script files (mousedrop.nlogo and interface.nlogo) that accompany this laboratory procedure. (Available: http://modeling....

Results

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.......

Discussion

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.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Flume	Engineering Laboratory Design	Custom	Laboratory flume with clear sides for 24-48 hours. Alternatively a small teaching flume can be constructed for under 300 dollars following the guidelines provided in our supplementary materials.
Flowmeter	Rosemount	8800 vortex	This is located inside the recirculation loop of the flume
Sand	US. Silica	F30	Research-grade sand to form a layer 10-20 cm deep throughout the flume
Dye	Samples from food companies		Water-soluble food grade dye made into an aqueous solution. Dark colors like red, blue and green work best. (Avoid food dyes in propylene glycol.)
Syringe	HSW	4100.000V0	5-10 ml, e.g. HSW Norm-Ject 2-part disposable syringe
Pipetting Needle	Cadence Science	7942	14-gage, 6-in blunt end,  to inject the dye deep into the sand.
Digital Camera	Any		Digital camera with steady tripod. (Time lapse cameras can be used to collect rapid evenly spaced data.) We used a Nikon D7000.
Ruler	Any		Transparent is best.
Measuring Tape	Any
Netlogo Software	CCL		http://ccl.northwestern.edu/netlogo/
Mousedrop.nlogo	Netlogo Commons	4259	http://modelingcommons.org/browse/one_model/4259
Interface.nlogo	Netlogo Commons	4258	http://modelingcommons.org/browse/one_model/4258