Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
title: ‘Week 1 HW: Principles & Practices’ weight: 10 Week 1 HW: Principles & Practices Introduction and Motivation This week emphasized that biological engineering is not only about what we can build, but also how and why we choose to build it. The lectures and recitation highlighted that ethics, safety, security, and governance should not be treated as external constraints applied only after a technology is developed. Instead, they should be considered as integral design dimensions from the earliest stages of a project.
Week 2 HW: DNA Read, Write, & Edit
Part 0 — Gel Electrophoresis Basics (Concepts) This week, I reviewed how gel electrophoresis turns a DNA “mixture” into an interpretable pattern. In an agarose gel, DNA fragments migrate toward the positive electrode because DNA is negatively charged, and smaller fragments travel farther through the gel matrix than larger ones. A DNA ladder provides a size reference so unknown bands can be estimated in base pairs. When a restriction enzyme digest is performed, the DNA sequence is converted into a predictable set of fragment lengths, and those fragments appear as bands at specific positions. Band brightness is roughly related to how much DNA mass is in that fragment (longer fragments can look brighter if molar amounts are similar). Overall, the key idea is that restriction digests plus gels let you “read out” a cutting pattern, validate identity, and compare designs or conditions in a simple visual way.
Automated two-color agar art using Opentrons OT-2 and design validation with simulation.
Week 4 HW: Protein Design Part I
Conceptual questions (9/11): protein size, genetic code constraints, chirality, secondary structure, aggregation, and amyloids.
Week 5 HW: Protein Design Part II
Rational mutagenesis proposal for MS2 phage L-protein engineering.
Week 6 HW: Genetic Circuits Part I — Assembly Technologies
PCR, Gibson Assembly, DNA assembly logic, and Golden Gate Assembly modeling in Benchling.
Week 7 HW: Genetic Circuits II, Fungal Materials, and First DNA Twist Order
Intracellular artificial neural networks, fungal materials, and first DNA synthesis workflow.
Cell-free systems, synthetic minimal cells, materials-integrated CFPS, a mock Genes in Space proposal, and final project Aim 1.
Week 10 HW: Advanced Imaging & Measurement Technology
Analysis of intact eGFP and peptide mapping by LC-MS and MS/MS, with comparison of native and denatured mass spectrometry.
Week 11 HW: Bioproduction & Cloud Labs
Cloud laboratories, collaborative bioart, cell-free reagent design, fluorescent protein optimization, and automated experiment planning.
CRISPR-based metabolic engineering and bioproduction of lycopene and beta-carotene in E. coli.