Week 1 HW: Final Project Ideas

(ryan-hutton-Jztmx9yqjBw-unsplash.jpg)

HTBAA Homework #1

For your first homework, propose and describe one idea for something you would like to biomanufacture. This could be medicine, material, food, energy, an art, design, or architectural artifact, or beyond. Draw from your own background and interests for inspiration.

1. I want to try something I haven’t done before; make cellulose bricks(or cubes) inside a bioreactor. I want to try using microbes to produce specific shapes made out of cellulose or another biomaterial inside the system. A few reasons why I want to try this are to try something new that will help me learn, build a system to test biomanufacturing shapes, and try out making a sort of manufacturing line of bio-based bricks. This idea might have been done in some form already. I’m guessing kombucha SCOBY or plant leather might have something similar. Mycelium can already be grown in brick forms.
2. I want to try it with Baker’s yeast. Plant waste and sugar would go in with engineered yeast taking the plant waste cellulose and secreting it into a shape(?). Still working that out.
3. Automated bioreactor that manages living conditions. An automated harvesting system to separate bricks from the microbe cultures without damaging them would be nice.
4. Probably at least half a pound of plast waste. May depend on how easy the plant is to decompose. 4b. A lot of bricks, but starting off with a 100 as a test would be nice.
5. How to structure yeast to produce specific shapes may be one. I’m assuming there’s a way to structure them or an initial substrate they can use to produce a specific shape.

Include in detail:

(1) What you would like to biomanufacture and why?

Describe the target product or output you would like to make.

Why are you interested in making it? Your motivation might be utilitarian—for example, addressing a problem in health, sustainability, food, energy, or manufacturing—but it does not need to be. Your project might instead have a social, cultural, artistic, or personal motivation.

Clearly articulate what you want to make, who or what it is for, and why you think it is interesting or important.

(2) What living system would you use?

Propose at least one living-system manufacturing chassis that could produce your target—for example, a microbial, mammalian, or cell-free system.

At a high level, describe how the system would make your target product. What goes into the system? What biological process or processes occur? What comes out?

You do not need to design the complete biological system yet. Make reasonable assumptions where necessary and identify them.

(3) How would you use automation?

Identify at least one automation technology that you would combine with your living system.

This could include a large-scale Cloud Lab, a desktop liquid-handling robot such as an Opentrons, a programmable microfluidics platform such as Nuclera’s, or another automation technology.

Describe what part of the biomanufacturing workflow you would automate and why. For example, you might automate liquid handling, culturing, assembly, screening, sampling, measurement, optimization, or another step.

(4) How much would you need to make, and how long would it take?

Perform a back-of-the-envelope calculation estimating what it would take to manufacture your target at a meaningful scale.

(a) How much?

Define a scale relevant to your project and calculate approximately how much of your target product you would need to manufacture.

For example, if you are producing a medicine, you might estimate the amount required to treat 1,000 people, everyone in Massachusetts, or everyone in the world. If you are producing a building material, you might calculate the amount required for one structure or an entire neighborhood. If you are producing an art or design artifact, define an appropriate scale yourself.

Clearly show your calculation, including units, assumptions, and sources for important numbers.

(b) How long?

Using your proposed living system and automation technology, estimate how long it would take to manufacture that amount.

Consider quantities such as production rate, yield, volume, number of parallel experiments or reactors, automation throughput, or whatever parameters are most appropriate for your system.

You may discover that the automation technology you would use to prototype your system is very different from what you would use to manufacture at scale. If so, describe both.

Again, we are looking for a reasonable engineering estimate. Show your assumptions and calculations.

5. What don’t you know yet?

After completing your analysis, identify the 2–3 biggest technical unknowns, bottlenecks, or assumptions in your proposed biomanufacturing system.

What would you need to learn, measure, or experimentally determine to know whether your idea could actually work?

AI

Feel free to use AI and our learning tools to be shared in recitation to assist you, but remember that you will present in class, so make sure you have a solid understanding of your responses.

Please also cite your AI client and prompts.

Readings:

Asin-Garcia, E., Fawcett, J. D., Batianis, C., & Martins dos Santos, V. A. P. (2025). A snapshot of biomanufacturing and the need for enabling research infrastructure. Trends in Biotechnology, 43(5), 1000–1014. https://doi.org/10.1016/j.tibtech.2024.10.014

Averesch, N. J. H., Berliner, A. J., Nangle, S. N., Zezulka, S., Vengerova, G. L., Ho, D., Casale, C. A., Lehner, B. A. E., Snyder, J. E., Clark, K. B., Dartnell, L. R., Criddle, C. S., & Arkin, A. P. (2023). Microbial biomanufacturing for space-exploration—what to take and when to make. Nature Communications, 14, 2311. https://doi.org/10.1038/s41467-023-37910-1

Karim, A. S. & Jewett, M. C. (2021). “Toward sustainable, cell-free biomanufacturing.” Current Opinion in Biotechnology 69, 136–144. DOI: 10.1016/j.copbio.2020.12.012.

Petzold, C. J., & Mukhopadhyay, A. (2025). From bench to biofactory: High-throughput technologies and automated workflows to accelerate biomanufacturing. Current Opinion in Biotechnology, 94, 103320. https://doi.org/10.1016/j.copbio.2025.103320

Yap, W. S., Choudhury, D., & Suntornnond, R. (2023). Towards biomanufacturing of cultured meat. Trends in Biotechnology, 41(3), 292–294. https://doi.org/10.1016/j.tibtech.2023.01.014

Ye, J.-W., Lin, Y.-N., Yi, X.-Q., Yu, Z.-X., Liu, X., & Chen, G.-Q. (2023). Synthetic biology of extremophiles: A new wave of biomanufacturing. Trends in Biotechnology, 41(3), 342–357. https://doi.org/10.1016/j.tibtech.2022.11.010

Zhang, Y.-H. P., Sun, J., & Ma, Y. (2017). Biomanufacturing: History and perspective. Journal of Industrial Microbiology & Biotechnology, 44, 773–784. https://doi.org/10.1007/s10295-016-1863-2

Readings Folder:

https://drive.google.com/drive/folders/1wX9w_MaJ3TFwHMyPp51b2vJ4mxkUNibf?usp=sharing

Final Project