Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Describe a biological engineering application or tool you want to develop and why I want to develop a soft material actuator powered directly by living cells rather than electronics or mechanical pumps. The system would use microbial metabolism, specifically gas produced during fermentation, to generate pressure inside a flexible chamber, allowing the material to inflate and perform mechanical work. Instead of using batteries, compressors, or microcontrollers, the material would respond to environmental conditions such as temperature or moisture because those conditions naturally regulate cellular activity. In this way, the environment becomes the control signal and biology becomes both the energy source and the actuator. If metabolic activity can reliably produce mechanical motion, it opens pathways toward deployable biohybrid interfaces, such as agricultural materials that respond to weather, environmental monitors that operate without batteries, or wearable materials that adapt to the human body. The goal is not to replace traditional machines but to investigate whether biological processes can serve as power, sensing, and control within soft matter systems.
Week 2 HW: DNA Read, Write, Edit
3.1. Choose your protein I chose miniSOG (mini Singlet Oxygen Generator) using the protein table from FPbase. It is described as a cyan fluorescent protein that can be controlled with blue light. When illuminated, the molecule absorbs energy and transfers it to nearby oxygen, briefly converting it into a reactive form called singlet oxygen. This state lasts only a few microseconds inside cells and travels about 10–20 nanometers, making it useful for nanoscale targeting. Because it can repeatedly trigger localized reactions without being consumed, it behaves more like a catalyst than a reagent.
Week 4 HW: Protein Design Part 1
Objective: Learn basic concepts of amino acid structure, 3D protein visualization, variety of ML-based design tools Part A. Conceptual Questions 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) There’s 20% of protein so there’s 100g of protein in 500g of meat. Knowing on average amino acid is 100 daltons (g/mol) so 100g divided by 100g/mol comes out to 1 mole of amino acids. 1 mole has about 6 x 10^23 molecules of AA (total in 500g of meat).
Week 5 HW: Protein Design Part II
Part A. SOD1 Binder Peptide Design Part 1: Generate Binders with PepMLM The goal of this exercise is to take a Human SOD1 sequence from UniProt (P00441) MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ A4V mutation
Week 7: Genetic Circuits Part II
Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? IANNs have an advantage over traditional genetic circuits because they can handle inputs in a more continuous way instead of just on/off logic. Regular genetic circuits are basically Boolean, so they struggle with noisy or overlapping signals. IANNs can take in multiple inputs, weigh them differently, and produce a more gradual response, which is closer to how biological systems actually behave.
Part 1 Explain the main advantages of cell-free protein synthesis over traditional in vivo methods, specifically in terms of flexibility and control over experimental variables. Name at least two cases where cell free expression is more beneficial than cell production. Describe the main components of a cell-free expression system and explain the role of each component.