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A4 : Due by 11:30 AM, Oct. 22 via Catalyst

1. Implement rock/paper/scissors in gro. Use three signal types and three states. If a cell is in state ROCK and is expressing the signal rock, it will die if it senses too much paper signal, and so on. Use a different fluorescent marker for each sate.

a) Run the system starting with three spatially distributed sub-colonies that merge into each other. Describe the dynamic and show snapshots.
b) Start with a single cell in state ROCK. At a low rate, have the cells switch randomly to another state. Run this version in the chemostat. Show several different behaviors that can arise from different choices of the parameters. Describe the dynamic and plot the number of cells in each state versus time.

2. Design a system that implements a NAND gate (as in fig. 3d of this paper) using three types of cells. You don't have to model the details of the biochemistry, just the logic of what each cell type does. And, obviously, you can use simulated bacteria instead of simulated yeast. Show how the system works in gro with a simulated mixture of cells of each type. Show that you get the desired truth table.

3. Consider the problem of "majority". A group each has a different opinion, say either 0 or 1. They must communicate with each other and switch their opinions until they all agree on what opinion was initially the majority. In this problem, you will come up with a consensus protocol for bacteria and show it works in gro. Start with a grid of 100 or so of non-growing bacteria (as in the quorum sensing example in Lecture 10). Initialize each to have an integer variable q that is either 0 or 1 by putting

q := rand(2); // assigns q to either 0 or 1

in the initialization for the cell (you might consider biasing this assignment so there is a clear majority initially). Make each state glow a different color. Then devise a strategy for emitting signals and switching states that eventually makes all of the bacteria to take on whatever is the majority value.

4. Graduate students only: Find a paper on synthetic biology that is interesting to you. By the end of the course you need to (a) turn in a written report of the paper and (b) present your report to the class. Reports should by brief and address the following:

What is the background or context of the paper?
What is the main contribution of the paper?
How do the results in the paper address at least one of the "five hard truths"?

The report is due Wednesday of the 12/12. Your presentation will be 10 minutes (strictly time) and should be sent to Kevin in powerpoint format the night before your give it. Presentations will be 11/30, 12/3, and 12/5. You should definitely chat with Eric about your ideas of which paper you want to review, or to get ideas in the first place. By the way, starting with the papers listed on the course wiki, and following references, authors, etc. is a good place to start.

Turn in A4 here: https://catalyst.uw.edu/collectit/assignment/koishi/23996/97143