I spent this morning adding a couple more sliders and switches to our model as extra features for the user to play around with. In the afternoon, Ethan and I met again to combine our code one last time for our final model. Seeing the final model was really cool as it really showed how much we’ve done these past two weeks. Here’s a before and after:
Before:
After:
Yesterday, I spent most of my day commenting on my code and play-testing our model.
Since I added a lot of new bits of code to the existing code, I had to add comments so that anyone who looks at my code in the future will be able to easily understand it.
I then began play-testing our model in both the web-based version of NetLogo and the offline version. Basically, I was trying to find conditions that would yield “interesting” scenarios like the bacteria overpopulating or the fungi overpopulating.
Here’s a version where the bacteria overpopulate–the bacteria is all the green stuff, by the way.
And here’s a version where the fungi overpopulate–the fungi is the dark blue stuff.
This morning, Ethan and I met with Dr. Aziz and Leah to provide an update on our work from the past couple of days. These past couple of days, we’ve made some really great progress on the model, and things are starting to come together.
I spent the remainder of the day on three main things: debugging my code for lignin degradation, writing up tasks and the information page for the model, and designing the user interface.
Debugging the lignin code entailed a ton of trial and error with numbers. I went back and forth between my code and the interface multiple times, first to make sure the lignin was decreasing (since it’s being consumed) and not increasing, then to slow the fungal reproduction so that fungi didn’t dominate.
Since our model may eventually be used as a virtual experiment for middle and high schoolers or an educational game, I then worked on writing up the introduction page and some challenges that future players could try.
Lastly, after poking around on the web-based version of NetLogo, I realized that our user interface needed some re-designing since the graphs were really condensed in the web-based version, making them hard to read. Here’s the re-designed interface:
Talk about crazy colors haha! Let’s just say a lot is going on in the fungal filter and leave it at that…
Today, Ethan and I merged the code we had been working on for the past four days. It was so cool seeing our work finally come together into one model.
Check out our combined model in the works!
I spent the remainder of the day working on the lignin aspect of the model to make it more closely resemble reality. Right now, the code is set so that fungi consume lignin, even though it’s actually enzymes that the fungi produce (LiP) that break the lignin down to glucose.
-Emily
I spent the bulk of my day today fine-tuning some of the enzyme kinetics aspects in my code and incorporating dissolved oxygen, which is a key component in cellular respiration. First, I had to add into my code directions so that the dissolved oxygen would be consumed. In a physical experiment, there might be bubblers to add more dissolved oxygen to the water as organisms consume the oxygen, so I had to also add that aspect into my code. Unfortunately, it was difficult to see on the model if my code was working, so I decided to write code so that the background would change colors to indicate how much oxygen was left. That solved my problem! And it was cool seeing all the colors.
Look at all the colors! The different shapes represent different elements in the model (fungi, bacteria, enzymes, and contaminants), and the blue background represents nutrient-rich water.
-Emily
This morning, Ethan and I met with Dr. Aziz and Leah again. We shared our work from the previous day and began discussing some more ideas about how to make this fungi model more realistic. We had a very interesting discussion about different mathematical equations that could be used to model various variables’ effects on the reaction rate (e.g. temperature, pH, UV light, and dissolved oxygen) and ways to model water flow (in the real system, water would be flowing through the fungi filter).
After our meeting, to get a better context for our research, I spent some time reading a journal article that Leah shared detailing the different mechanisms that the fungi’s enzymes use to break down pollutants.
I spent the bulk of my day fine-tuning the enzyme kinetics aspect of the model (shoutout to Mr. Rushin–iykyk). I was working on writing code to incorporate the relationships between temperature, pH, UV light, and dissolved oxygen into the model. For each of the variables, there’s a sweet spot, where the rate is the fastest and enzymes function best. Then, on either side of the sweet spot, the rate decreases.
Look at all my bell curves! Each of these is for one of the variables. You can see the sweet spot is at the peak of the curve and the curve tapers off on both sides.
Below, you can see how the different conditions affect the rate of the reaction. On the left is when all of the variables are set to the optimal conditions. On the right is when the conditions are too acidic, so the enzymes don’t do their job 🙁
-Emily
This morning, Ethan and I met with Dr. Aziz and his graduate student Leah. Leah explained the research that she is working on. Basically, she’s trying to design a water filter that will use fungus to chemically convert harmful pollutants in water into something less harmful.
We then spent the remainder of the day playing around with NetLogo, which is the software that we’ll mainly be using to create simulations. We explored the Wolf-Sheep Predation model and the Enzyme Kinetics model and modified the parameters on the models to see how the changes would affect the results.
The Wolf-Sheep model showed how the populations of wolves, sheep, and grass changed based on various parameters, and the Enzyme Kinetics model showed how various parameters affected the concentrations of substrate, complex, and product.
Below is an image of the Enzyme Kinetics model.
