Week 1 HW: Final Project Ideas

(1) What would you 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.

I would like to explore biomanufacturing a biodegradable hydrogel that could be used as a wound-care material. Hydrogels are soft, water-containing materials that can help maintain a moist environment around a wound. I am interested in this because wound care is an area where materials science and medicine overlap. I have become interested in how scientific ideas can be turned into practical tools that improve healthcare.

My goal would be to investigate whether a biological system could produce the material that forms the basis of a wound-care hydrogel. I think this is interesting because it would combine biology, materials science, and engineering. I would also want to investigate whether the material could be produced efficiently enough to make it useful at a larger scale.

(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.

For a first prototype, I would propose using a microbial system, such as bacteria, to produce a biological polymer that could be processed into a hydrogel. Bacteria can grow using nutrients supplied to them and can produce molecules or materials as part of their normal biological processes. At a high level, nutrients would be supplied to the bacteria, the bacteria would grow and produce the desired polymer, and the polymer would then be collected and processed into a hydrogel. I would need to determine which bacterial system and polymer would be most appropriate for this application. I would also need to test whether the resulting material has useful properties, such as its ability to hold water and maintain its structure.

(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.

I would use an automated liquid-handling system to test different conditions for producing the polymer. The robot could prepare cultures with different nutrient concentrations, transfer liquids between samples, and collect samples at different times. Automation would be useful because I could test many conditions more consistently than I could by doing every step manually. For example, I could compare different nutrient concentrations and growth times to determine which conditions result in the greatest amount of polymer production. This would allow me to collect quantitative data and use the results to improve the production process. For a prototype, I would use a small automated system with multiple experimental cultures. At a larger manufacturing scale, I would likely need larger bioreactors and automated systems designed to control and monitor many cultures at once.

(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?

For this estimate, I will define a meaningful scale as enough hydrogel to make 100 prototype wound-care patches. Assumption: each prototype patch requires approximately 5 g of hydrogel. 10 patches × 5 g/patch = 50 g of hydrogel Therefore, I would need approximately 500 g of hydrogel for 100 prototype patches. This is an estimate rather than a clinical requirement. The actual amount needed would depend on the size and thickness of the final material. To determine how much biological production would be required, I would then need an experimentally measured yield, such as grams of polymer produced per liter of bacterial culture. Since I do not yet know this value, I would use an assumed yield for an initial engineering estimate and replace it with experimental data later.

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.

For an initial estimate, suppose the biological system produced 5 g of usable polymer per liter of culture and that each production batch contained 2 L of culture. 2 L × 5 g/L = 10 g of polymer per batch To produce 50 g: 50 g ÷ 10 g/batch = 5 batches If one batch took approximately 48 hours to grow and the batches were produced one after another, the total production time would be: 5 batches × 48 hours = 240 hours 240 hours ÷ 24 = 10 days This shows why scaling and parallelization would be important. Instead of running all 5 batches sequentially, multiple bioreactors could operate at the same time. These numbers are only an engineering estimate. The actual production rate, yield, batch time, and number of reactors would need to be determined experimentally.

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.

I would need to experimentally measure how much polymer is produced under different growth conditions. A second unknown is whether the polymer would actually have the properties needed for a hydrogel. Producing a material is not enough; I would need to test characteristics such as water absorption, structure, and stability. A third unknown is whether the process could be scaled efficiently. Conditions that work in a small laboratory culture may not work the same way in a much larger bioreactor. I would need to determine how production changes with culture size and whether automation could maintain consistent conditions at a larger scale. I also need more general information on how wound-healing hydrogels are created.