Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class Assignment 1. First, describe a biological engineering application or tool you want to develop and why. There is currently an urgent research focus on the biodegradation of plastics, due to the extremely long life cycle of synthetic polymers. Prior work has focused on a mix of exploring bacterial and microbial processes (e.g. anaerobic digestion) to break down plastics, and developing compositions that can be commercial compostable (e.g. for single use plastics). My personal interest is in fiber arts and sustainability, so I’d like to tackle this problem from a textile perspective. Fast fashion has exacerbated the volume of cheap, low quality clothes produced everyday. These clothes are often made with synthetic fibers and not for long term use (although the two are not necessarily interchangeable). I believe it’s incredibly important to find a way to biodegrade polyester, one of the most common synthetic polymers in fast fashion clothing.
Week 2 HW: DNA Read, Write, & Edit
Part 1: Benchling & In-silico Gel Art Had an initial mess-up where I tried to “speedrun” the process and ended up with a ladder packed with the effects of multiple restriction enzymes. Finally got success with all of the listed enzymes, separately.
Python Script for Opentrons Artwork Opentrons Art I tried to play around with math functions to create a design, like the Mathematical Heart sample. I drew up a cute fox in Desmos graphing calculator using the following functions, making sure to scale them to the 40 mm limit. Transferring that to Colab was a bit more difficult, and I had to play around with the functions, ranges, and dispense volume to find something that looked good.
Week 4 HW: Protein Design Part I
Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) Why do humans eat beef but do not become a cow, eat fish but do not become fish? Why are there only 20 natural amino acids? The natural amino acids are determined by codons, which are determined by three nucleotides (of which can be adenine, uracil, guanine, cytosine). This gives 4 x 4 x 4 = 64 total codons, but redundancy among codons produces only 20 unique amino acids.