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Open Source Underwater Distributed Sensor Network

Robotic platform for water quality sensors inspired by clams.

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With the politicalization of environmental science and cuts in research funding, it is important for NGOs and citizen scientists to fill the void with good data. The goal of this project is to build an open source and inexpensive sensor platform to create 3D maps of water quality for threatened bays and estuaries.

Water quality monitoring is essential for maintaining a healthy ecosystem. It is important for managing fisheries, measuring bacteria and algal blooms to protect public health, and pinpointing sources of pollution. Because of climate change, it is also important to get a baseline of data for water quality, in order to identify new and subtle trends.

This new sensor platform is designed so that citizen scientists and NGOs can supplement the work of government and academic organizations, in order to create a comprehensive database for all bodies of water. The platform is inspired by the simplicity of bivalves as a protective container, and will be open-source and 3D printed, so that a diverse group of individuals and organizations can collaborate in its development.

Researchers will deploy the sensor platforms (clams) in the same manner that shellfish are seeded. The clams will be spread across a body of water by boat. After they have been distributed, they will open their shells, releasing gas, and descend into the water column. As they descend, they will sample the water with their onboard sensors. Once they have reached the bottom of the water column, their bladders will fill with gas and they will ascend to the surface where they will be collected in nets. Their data will then be uploaded to create a 3D map of water quality for that body of water.

Once the clams are fully developed, future missions could have the clams deployed in the benthic zone. Instead of staying planktonic, the clams would settle out of the water column onto the sea bottom, and stay there for long periods taking measurements.

  • Saturometer & Siphon

    Michael Barton-Sweeney05/02/2018 at 01:27 0 comments

    The clam is a sensor platform for measuring water quality. So far, I have experimented with thermistors as stand-ins for more complex water quality sensors. I am developing a new saturometer, in order to bootstrap the capabilities of the clam. Saturometers are used to measure the total dissolved gas (TDG) in water. Monitoring TDG is important for understanding and mitigating issues related to supersaturation of water, which can cause large fish kills. I will take a naturalistic approach to how I develop the new saturometer probe, and will apply a machine learning technique, linear regression, for its calibration.

    Acknowledgements

    I am basing my work off of one of my dad's patents for the saturometer he developed in the early 1990's. I want to thank him for talking with me about my new design, and for letting me learn in his shop while I was a kid.

    Introduction

    My dad developed his saturometer before the internet was widespread. Powerful computers, SMD technology, and 3D printing were not widely available, nor was knowledge of machine learning techniques. My design for the clam is taking advantage of the developments over the last two decades. The redesign of the saturometer will focus on improving the ease of fabrication of the probe and improving the ease of calibration by incorporating linear regression, a simple machine learning technique.

    Saturometers are used to measure total dissolved gas (TDG) in water. It is important to measure TDG, in order to study and mitigate supersaturation (for example, in this study of using microbubbles). Supersaturation can be caused by spillways at dams, in water turbine vents, hatcheries and other man-made or natural structure that entrain air in water. Additionally, it can be caused by other processes, such as photosynthesis of algae. Gas bubble disease (GDB) is caused by supersaturation and can cause large fish kills. Fish have a limited ability to detect supersaturation and cannot avoid it if present, so it is imperative that we monitor and mitigate it.

    Sweeney Saturometer

    Saturometers are able to measure TDG by taking advantage of a property of silicone: permeation. Gases are able to pass through silicone tubing, so by measuring the pressure within the silicone tubing, the saturometer is able to measure the TDG within the fluid. The saturometer probe is composed of silicone tubing wound around a support structure and connected to a pressure sensor inside a protective mesh cover. The probe is attached to a metal tube that produces waterflow across the probe when moved in the water column. Waterflow is important for getting accurate readings. Here is a Youtube video of the saturometer in action.

    To calibrate the saturometer, it is necessary to use an external device. The probe can be calibrated without the silicone tubing using an air compressor, a manometer and a coupling. It can also be calibrated submerged in water with a controlled pressure and another saturometer.

    In order to make fast measurements, the thickness of the tubing needs to be decreased, and the surface area of the tubing increased by increasing the length of the tubing. The volume of the tubing can be decreased by inserting a filament like fishing line into the tubing. Additionally, by adjusting the calculations of the measurements and looking at the rate of change, fast estimates can be made before the pressures have reached equilibrium.

    Siphon: Initial Design & Fabrication

    My design for the saturometer probe will use a coil of silicone tubing without an armature. The tubing will be placed inside a silicone siphon, and be packed loosely. 

    I will use the same methods and materials that I used for the previous clam experiments. I will use the same electronic circuit but add op-amps and an absolute pressure sensor. I will pick through the old inventory of saturometer parts and use what is available. There are some inexpensive modern SMD pressure sensors that I would like to experiment with, but that part of the design can...

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  • Additional Material Considerations

    Michael Barton-Sweeney04/23/2018 at 18:54 0 comments

    In addition to the previous considerations about shells and batteries, the materials for the seals, bladders and circuits need to be considered too. All of the clams will be put in the water, and face the potential of getting lost. They all need to withstand the environment and not pollute it.

    Here are some thoughts on the different materials, and their durability, toxicity, accumulation in the environment, and fabrication. The choices available right now for rubbers and electronics are not ideal, but are adequate for this stage of the project. Further research should be conducted and a complete life-cycle assessment of the clam should be made.

    Seals and Bladders

    Silicone seems like the best rubber for the seals and bladders right now. It is extremely durable, has low toxicity, and it is easy to fabricate parts with it. On the other hand, because of its low degradation, it has very high accumulation in the environment.

    Silicone rubber is a siloxane made of long chains of silicon and oxygen with attached organic groups. It gets its durability from the silicon-oxygen bond. It is resistant to many chemicals, including salt water, hydrogen peroxide, acetic acid and sodium bicarbonate, so it is suitable to be used as part of the buoyancy system in the clam.

    High molecular weight siloxanes, like silicone rubber are not toxic, but low molecular weight siloxanes, like silicone fluid used in cosmetics and as defoaming agents, can be toxic. Because the clam will use high molecular weight siloxanes, toxicity to the environment is probably not a concern.

    On the other hand, accumulation in the environment is a major concern. As a result of the durability of silicone rubber, it has low degradation. It does not photodegrade or biodegrade, and is considered a 'very persistent chemical.' This is an area of active research, so I would like to find studies that look at it in a marine environment (here is an example study that I found for a lake).

    It would be nice to use a rubber that does not accumulate. I experimented with natural rubber latex, but I did not find it suitable. I did not vulcanize the rubber and it deteriorated rapidly in use.

    Natural rubber is made of polyisoprene chains. During vulcanization, polyisoprene chains are cross-linked with sulfur, making a more durable rubber. Natural rubber and vulcanized rubber can be degraded by a variety of mechanisms, including chlorine, metals, photodegradation and biodegradation

    Natural rubber in a marine environment has been extensively studied by the Navy, and the aging process is well understood. If a simple DIY vulcanization process could be figured out, it might be possible to use natural rubber for the seals and bladders. It would be beneficial to use natural rubber, but because of the difficulties involved in making it suitable, I will not be investigating it for now, but will use silicone instead.

    It is easy to fabricate parts with silicone. I used Oogoo for the seals for the clam, and laid them up in place by hand using tape. I like using Oogoo, because it is made with readily available silicone I caulk from the hardware store, but it contains cornstarch, which may make it unsuitable for long-term use. I did not notice any problems with the seals, but silicone is permeable and the cornstarch could attract microorganisms. I made the bladders by coating a form with rubber (natural rubber latex or Smooth-on Sorta-Clear).

    For the new design, I will translate the process, so that molds can be 3D printed. Instead of one seal between the shells, the clams will have two seals (one for each shell). The seals will be made by casting silicone on the lip of the shell, bounded by a 3D printed mold that will look like a mouth guard or dental tray. The bladders will either be cast in two parts and bonded, or they could be cast around a dissolvable filament form. Silicone does not perform well with terpenes, so the dissolvable filament will need to be PVA or Hydrofill and not HIPS. Another...

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  • Material Considerations

    Michael Barton-Sweeney04/15/2018 at 20:33 0 comments

    There are many concerns regarding what materials we choose to use for the clams. We have to assume that they will be lost and that animals will try to eat them. Additionally, an eventual goal is to develop clams that are benthic and can perform long-term missions. Instead of staying planktonic, the clams would settle out of the water column onto the seafloor, and either take measurements where they are situated, or periodically ascend to take measurements. Therefore, even in normal operation there is the potential for plastics to leach into the environment.

    For the initial prints, I believe that we should focus on using polylactic acid (PLA). It is a common filament for 3D printers and it is naturally derived and biodegradable. As of yet, I do not know it’s seaworthiness, but that should be a focus of testing. If anyone has a fish tank, saltwater and a PLA print that they are willing to sacrifice, I would be grateful for their observations about how well the PLA stands up over time. Future testing could use the sensors we incorporate into the clam to measure leaching, but for right now, sight and touch would be good enough to measure seaworthiness.

    In addition to knowing how well it stands up to saltwater, we need to know how well PLA performs with biofouling. Biofouling is a serious concern for water quality instruments. It is especially concerning for 3D prints, which tend to have significant gaps and crevices on their surfaces. This is another area where we will have to perform extensive testing.

    A common way for mitigating biofouling is to clean water quality instruments after use. It would be too laborious to require researchers to clean each clam individually, so we should try to design them to be cleaned in the dishwasher. As far as I know, PLA softens in dishwashers to a degree that might not be acceptable. We could try to design the shells, so that they can soften without losing their shape or impairing their function. This would also require testing.

    If we tried to use a different plastic that is higher temperature, we might lose the advantages of having a naturally derived and biodegradable plastic. A thin conformal coating of silicone or another high temperature plastic might be a good compromise that could fill the gaps to prevent biofouling, and protect the shells from melting and deforming.

    Alternatively, we could borrow a solution from natural clams and use calcium carbonate. I have done some experiments with mixing plastics (PLA and epoxy) with calcium carbonate, and it is a wonderful material. It feels like bone and shell, and it is very strong (here are links to vegan taxidermy I made with the material: antlers, scrimshaw).

    PLA and calcium carbonate filament is available, so using that material might be a good area to explore. Using calcium carbonate would not add any unnatural chemicals, and I believe that it might help with the dishwasher issue. Also, it might allow the clams to degrade somewhat gracefully, especially if we could figure out a way to build up the shells primarily in calcium carbonate with just a little PLA binder.

  • DevOps

    Michael Barton-Sweeney04/14/2018 at 21:44 0 comments

    This project is inspired by GNU, RepRap, and the free software/open source movement. I am using FreeCAD, KiCAD, and the GNU toolchain for my work. I will be setting up a public git repository, in order to share and collaborate. I am grateful for any criticism or help. In particular, right now, if there are any software developers who are skilled in DevOps, I would appreciate their insights.

    One of the big challenges for this project will be testing the clams and incorporating the feedback into the design. We need to lower the bar for participation, so that an individual without expert knowledge can print out and assemble a clam, test it, and then submit the results in a way that can be easily used by developers.

  • Initial Experiments

    Michael Barton-Sweeney04/11/2018 at 02:12 0 comments

    Shell

    Plastics

    For the initial experiments, I used blown acrylic sheet and tubing to make the clam body. The shells were blown using a plastics blow oven, and the internal structures were blown using a heat gun. The seals were made of silicone, the bladder was made of latex, and the different structures were assembled with epoxy.

    Stomach

    I used acrylic because it allows for a more direct process than prototyping with 3D printing. Ideas can be quickly tried out and modified with a bandsaw, sander, heat gun and hot knife, instead of working in a CAD file and printing new prototypes.

    Breadboard

    Electronics

    The clam's circuit is composed of a bluetooth module, atmega, push-pull circuits, dc-dc converters, batteries and a wireless charger. A thermistor was used as a stand-in for other sensors, and data-logging was not implemented. This circuit was enough for the clam to control the solenoids and communicate data between the clam and a bluetooth device.

    Free-form circuit

    After breadboarding the circuit, I free-form soldered the electronics and gave it a conformal coating of epoxy. Like free-blowing plastic, free-form soldering is an intuitive and direct way to prototype. Different circuits can be easily explored, instead of going through the process of designing and fabricating new PCBs.

    Clam top

    Bivalve

    In my experimentation, I was able to work out the design of the shell, hinge, and adductor to form the bivalve. The hinge is formed by teeth, like an exaggerated version of the hinge teeth of natural clams. It has two fixed states (opened and closed) that are held in position by permanent magnets. The solenoid for the adductor is only used to change state.

    Clam bottom

    In the closed state, the clam is sealed. In the open state, the clam has a gap to allow gas to release and water to flow in. Right now, that water inflow is what is used for sampling. It may be necessary to add a siphon to pump water into the clam for the sensors.

    Test Setup

    Bladder

    I experimented with chemical reactions to fill the bladder. I did not want to use a pressure chamber to store the gas, because I did not want to build something to maintain those forces, or have a consumable component like a CO2 cartridge. I experimented with acetic acid and sodium bicarbonate (vinegar and baking soda), as well as hydrogen peroxide and catalase (from yeast), and both worked well. My only concerns are that the chemicals are nontoxic, do not affect the sensors, and are easy to clean and replenish.

    Salt Water Battery Experiment

    Battery

    The initial idea was for the clams to have copper on one shell and zinc on another to make a salt water battery. I scrapped that idea because the batteries...

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Vishnu M Aiea wrote 4 days ago point

Congratulations for being selected on the first round of HaD Prize 2018 ;)

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donald murray wrote 7 days ago point

How about ultrasonic networking so they can just be placed there and stay there.....maybe finding a way to regenerate power from tidal action. This way you could tell it to surface maybe once a year for maintenance, etc..

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Michael Barton-Sweeney wrote 5 days ago point

Yeah, that would be awesome. I've looked a little into underwater communication but it seems like it would be difficult to build a robust system. I'm signed up for the WUWNET mailing list (http://wuwnet.org/), and am looking at what that community is creating, but if you have any suggestions, I'd love to hear. Ultimately, it seems like that would be the way to go.

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donald murray wrote 4 days ago point

I'd imagine if you used a cheap ultrasonic transducer like those made for arduino, you could develop a simple communication  protocol. Ultrasonics should work well under water.  https://www.ebay.com/itm/Arduino-Ultrasonic-Module-HC-SR04-Distance-Sensor-Measuring-Transducer/183197342385?hash=item2aa7699ab1:g:GWwAAOSwfo9a7B5v

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Lee Djavaherian wrote 04/15/2018 at 17:33 point

I like seeing water-related projects and like your use of materials, inspiration from nature, the acrylic shaping, the gas-filled bladder/bouyancy, the solenoid, and the creative circuit assembly.  Fascinating device and has lots of potential.  Looks like something fun to work with, too.  Great work!

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Michael Barton-Sweeney wrote 04/15/2018 at 19:24 point

Hey, Thanks! Your comment made my day. I think acrylic is an awesome material to work with; almost anything you make looks great. If you're interested, here's a link to a simple type of oven that I use to blow the bubbles:  https://hackaday.io/project/112181-plastics-blow-oven 

I'm a big fan of nature inspired technology too. Especially with marine invertebrates, it seems like so many technological solutions already exist that we can apply to our problems.

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ch.dugasduvillard wrote 04/11/2018 at 07:05 point

Nice project ! Have you think about using the wave and mouvement to charge your battery or as a power source?

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Michael Barton-Sweeney wrote 04/11/2018 at 20:22 point

Hi! That would be really interesting to explore. I think that if the clams were deployed for long missions that could be a great solution. Right now, these clams are planktonic, floating up and down in the water column, but if they were benthic we could harness the power of the tide. Maybe a different shellfish inspired sensor platform? :)

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Michael Barton-Sweeney wrote 04/11/2018 at 20:32 point

I could imagine a sensor platform that gets released and then attaches itself to rocks like mussels in the intertidal zone. It could be buoyant and use the force on its byssus threads to generate electricity. I'm not sure what would be the most efficient way to translate that force into electricity, but there is active research into how mussels produce byssus polymers, so we might get some inspiration for that part of the problem: https://phys.org/news/2017-03-mussel-byssus-threads-combination-self-assembly.html

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Vishnu M Aiea wrote 03/21/2018 at 17:19 point

I'm curious to know about type of sensors you're using for measure water quality. The circuit construction also seems really interesting and would love to see the schematic :)

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Michael Barton-Sweeney wrote 03/21/2018 at 17:39 point

Hi Vishnu! Right now, I am using a thermistor as a stand-in for other sensors. I am developing the platform so that the sensors are modular. I have done some experimentation with older chemical sensors for dissolved oxygen, but the goal would be to use newer optical sensors, in addition to pressure sensors for total dissolved gas. Optical sensors can be used to measure a variety of chemicals, like oxygen, oil, nitrates, as well as pH and turbidity.

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Michael Barton-Sweeney wrote 03/21/2018 at 17:42 point

I used free-form soldering and blown plastic for the first two prototypes, but I am switching to PCBs and 3-D printed bodies for the newer versions. I'll share the schematics in a project log.

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Vishnu M Aiea wrote 03/21/2018 at 17:48 point

Interesting! Looking forward to see the optical sensor in action. Are all those components covered in some water repellent epoxy just to be safe ? If yes, what material is it ? Or is it just glue ?

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Michael Barton-Sweeney wrote 03/21/2018 at 18:21 point

Hi Vishnu, yes, they have a conformal coating of epoxy. I have not developed optical sensors yet, but I have researched their operation and how to build them. I would want to team up with others to develop them, but until then, I am focusing on the platform and using older tech for the sensors.

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Vishnu M Aiea wrote 03/21/2018 at 18:24 point

Sounds great! I'll keep an eye on here becasue sensors have become a really interesting topic for me ;)

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