Terrachip PALS – Designing a project

Written by Rachel Shen and Janice Tjan

Developing a project is difficult, but keeping a project going after moving off campus due to COVID-19 is even trickier. What does developing a project look like during remote learning and lack of access to any laboratory equipment? In this blog post, we’ll walk through what that process looked like for our group!

During the first half of the spring semester of 2020, we (Rachel Shen, Janice Tjan, and Melody Wu) started ideation of our project in NEET Living Machines (https://neet.mit.edu/faq), which is a 3-year interdisciplinary engineering program with threads in different fields. In 20.051, the sophomore class in the Living Machines thread we learned how to make microfluidic chips, which are devices that take advantage of the properties of substances on a small scale for a variety of applications. In this project, we decided to study soil salinity, a major problem in agriculture in which salts accumulate in the soil, affecting the complex ecosystem of microbes around plant roots, called the rhizosphere. To do this, we created a simulated microfluidic platform to the rhizosphere in a salinity gradient, with different velocities, and combinations of common microbes in the rhizosphere. We wanted to simulate the effects of different irrigation techniques on the rhizosphere as an effect of altered salt profiles simulating soil profiles in agriculture and in natural systems and better understand the rhizosphere in a wide variety of different soil environments.

Before we left campus due to COVID-19, we had started the ideation session. We had determined that we wanted to work on a chip to simulate soil gradients and how they affect the rhizosphere. We had done a literature review and began the preliminary experimental design, but had yet to develop the chip itself.  We had sketched out a rough idea of how to mix bacteria and growth media for the plants:

A good start.

Getting yeeted off campus

The night that Boston Biogen announced that they had hosted patient zero of the outbreak in the Cambridge area, we were sitting around a table at Next House eating DIY mini-omelettes and drafting up a proposal for our group project. The same day we started to feel the creeping impact of COVID-19 closing in on MIT, the beginnings of Terrachip came to be (the name was a nod at the chip brand and the fact that our chip simulated soil conditions).

Once yeeted off campus, we would not be able to see each other on campus for a long time, nor would we be able to use campus facilities. The initial goal for the semester was to manufacture a chip of our design. This would have involved using MIT.nano clean room facilities, which we were really excited about. 

Now, the goals of the semester would have to change. Rather than go through the manufacturing process, we would explore simulating our device in more depth with COMSOL. Nevertheless, the project remained a group effort. 

Slack had been used for class announcements earlier, so it became the natural outlet for all our class communications once everything became virtual. However, while Slack was the place for getting formal feedback, it was not the best place to *slack* off. We had a messenger group chat for that sort of stuff and became our main line of communication.

We were determined to take away some experience from this project. Having group meetings over Zoom was not as nice as eating mini-omelettes at someone’s dorm, but it was nice to talk to have some face to face time with each other and even chat about other developments outside of the project.

Seeing the development of other group’s projects also kept motivating us to take advantage of the change to simulate our chip more thoroughly. We would come together as a class weekly and share updates about our progress. We wanted to make sure that we would always have a new development to share about TerraChip. As we prepared for new presentations week to week, we noticed the visible changes between versions and clear improvements between simulations. Having more time to think about the design of the chip gave us more time to experiment with different forms and to properly define what made our device unique.

Iterating our device

Idea 1 – Mixing bacteria in a complicated way

We wanted to study the effect of different combinations of bacteria on the rhizosphere, so we started off simple by looking at devices that did a simple function, such as mixing two different fluids.

A simple 2-inlet serpentine channel. This was before a room chamber was in the picture.
We added a T-junction so we could mix four different microbial species and a room chamber for the plant roots to grow. 

Our initial idea was to study different interactions between combinations of microbes.We then added a chamber for the plant and four inlets for our different microbes. However, this made any sort of microfluidic feature (eg. serpentine channels) pretty obsolete since as a result it would be easy to just mix four microbes with a pipette, making the microfluidic device a difficult way to do a relatively easy thing. Back to the drawing board to figure out why bother using a microfluidic device in the first place!

Idea 2: Maximizing the utility of a microfluidic device by creating gradients

A better use of serpentine channels was to make some sort of gradient. After some reading, we learned about salt gradients in agriculture. When plants are irrigated, the salts in the soil can be drawn up to the growing zone of the root. However, where the salts accumulate isn’t uniformly spread out; instead, it forms a gradient. This could affect the delicate microbial community in the rhizosphere by restricting where different microbes could live in the root zone. This is a really interesting problem that we realized we could study with our microfluidic chip, which was both clear for easy imaging and could quickly build a clear gradient! We elaborated on our initial design a bit by turning the serpentine channels into a christmas tree design: 

The separation part at the beginning makes a triangle shape that looks sort of like a Christmas tree. It takes in a very concentrated salt solution in one inlet (the diagonal channel on the far left) and unsalted growth media in the other. As both solutions move through the channels, they mix in different concentrations as they move through the device, eventually creating a gradient that transfers to the growth chamber where we will add our plant.

Oops. Where’s the gradient?

As you can see here, we struggled at first to make COMSOL do our bidding. There should be a gradient here. It turned out we forgot to pair the effects of both diffusion and fluid flow. 

Much better!

Thanks to help from Dr. Mehdi Salek, our instructor for 20.051, we got Comsol to work by linking the effects of both diffusion and fluid flow and created this lovely gradient. The colors represent the concentration of salt in a particular area. 

The plant grows in the top circular chamber while the roots grow down across the gradient.

Finally, we added a small chamber for the plant to grow down into the gradient and switched where we put the salt solution and the growth media to accommodate the initial plant chamber. We also simplified the outlet channel to a single outlet rather than our original six. 

The final design we presented to the class looked like this.

We also made a conceptual sketch of what our device would look like with different species of bacteria and arabdopsis plant growing in the root chambers.

Presentation

Iteration happened with more than just our project; iteration and improvement was important in communicating our project as well. 

A major deliverable was a weekly presentation for feedback from the NEET instructors. During our first presentation, it became evident that our initial message was unclear – we received questions about what our project accomplished with microfluidics that other methods (such as growing the plants directly in pots) could not. 

The next week, we returned with a restructured presentation. In this second round, we started off by emphasizing that the gradient, not the salt concentration itself was what was being studied, and included a slide that pointed out the drawbacks that our device could solve.

Following feedback from the BE communications lab, we also made many of the slide titles into sentences that told a story, such as changing “Bacterial interactions” to “Observing bacterial interactions with roots in generated salt gradient with flow.”

These changes were simple but they helped a lot with our final presentation. Our audience grasped the point of the presentation more fully and as a result we had much more helpful feedback and more engaging questions. We even presented our project to Professor Jennifer Brophy at Stanford upon Prof. Griffith’s recommendation! 

What’s next?

Once we return to campus, we plan to create our initial microfluidic chip and do initial tests with dye to see how the gradient forms! We’re also planning on better simulating the texture of the soil by adding pegs, and hoping to incorporate the fact that plants grow downward by creating a vertical chip. There is a lot of work to do, but it is temporarily on hold until we can get back on campus. 

A conceptual sketch of what could be the next iteration.

Biomaking design process

Our experience in making this project in NEET LM taught us about the design process in both biomaking and pitching that idea to others. Through designing, building, testing, then using what we learned to iterate and improve, we came up with a project that was much improved compared to our initial design. In the Biomakerspace, we are looking forward to improving even more! 

1 thought on “Terrachip PALS – Designing a project

  1. I am very much interested in the microfludics devise for soil studies. Do you have a prototype ready? If yes, how do you intend to deliver to other researchers? Will this be commercial or you would like to collaborate?

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