Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
My visit at one of the 2 fungi farms in Cyprus in 2023 First weeks assignment Describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about.
Week 2 HW: DNA, READ, WRITE AND EDIT!
Geeking out over protein structures and data banks, DNA storage in plants, clouds and decoding DNA into sound I love that artist Antoine Bertin has decoded the RNA of SARS COV 2 into this track! check it out. Antoine Bertin · Meditation on SARS-CoV-2 This is the RNA of the Coronavirus translated into sound (viruses are made of RNA, not exactly DNA). Each nucleotide of the RNA (A,U,G or C) is transformed into a note so the virus sequence can be heard. The tempo of the track follows the rhythm at which the epidemic is growing (exponential curve) and how this curve flattens if we all stay home :) I wanted to create a track that can help with relaxation in times of isolation, and meditate on the fact all life on earth, including viruses, are made of the same material. We (humans, animals, trees, bacteria, viruses) are the continuation of a same common ancestor. Anyway; I hope this will helps everyone explore in their own sonic way what we are going through! Here is an extract of the RNA sequence :)
[E-INK] MICROFLUIDICS <3 I have actually been interested in microfluidics in a while because I am into inflatables and soft robotics since 2020. I started working with bodily fluids and liquids in 2023. I love this little sweat collection and analysis wearable microfluidic system device. You can find another example here and the paper.
Week 4 HW: Protein design- PART I
What is protein design? Objective: Learn basic concepts: +amino acid structure +3D protein visualization +the variety of ML-based design tools Brainstorm as a group how to apply these tools to engineer a better bacteriophage (setting the stage for the final project). Part A. INTUITIVE PART OF THE HOMEWORK! Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip)
Week 5 HW: PROTEIN DESIGN PART II
Part A: SOD1 Binder Peptide Design (From Pranam) Superoxide dismutase 1 (SOD1) is a cytosolic antioxidant enzyme that converts superoxide radicals into hydrogen peroxide and oxygen. In its native state, it forms a stable homodimer and binds copper and zinc. Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS). Among them, the A4V mutation (Alanine → Valine at residue 4) leads to one of the most aggressive forms of the disease. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation.
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
Acropora Millepora, Photo from Reefbuilders This week we learn core molecular biology tools and techniques for processing and assembling DNA, including PCR and Gibson Assembly. Here is the updated HTGAA2026 Gibson assembly lab protocol document. Homework PART A: PCR and DNA Assembly 1. What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion High-Fidelity PCR Master Mix is a 2X, ready-to-use mixture where the exact formulation is partly proprietary, but the functional components are documented in the manufacturer’s manual:
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
From the lecture with Ron Weiss "…central dogma, if you will, in synthetic biology, is the notion that almost everything that we build is based on sensing, processing, and actuation. So we want to be able to sense everything that's going on inside and outside the cell, have that information fed into some kind of controller, and have that regulate things that are going on in the cell". Week 7 Lab - Neuromorphic Circuits - Intracellular Artificial Neural Networks (IANNs) Download Neuromorphic Wizard.
This week introduces synthesis of proteins using cellular machinery outside of a cell. I LOVED THE LECTURE and I loved Kate Adamalas work. We have to solve terrestrial problems before extraterrestrial problems…we need to shift away from a petroleum based bioeconomy…we need a paradigm shift. Kate Adamala <3 General homework questions 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. A cell-free system allows biological reactions to occur outside of living cells. By extracting and using cellular components like ribosomes, RNA polymerase, amino acids, and ATP, this method enables reactions in a controlled, simplified environment. Cell-free systems allow for the engineering, expression, and analysis of genetic constructs without the complexity of living cells.
Week 10 HW: Advance imaging & Measurement technology
WEEK 10 HW Homework is based on data that will be generated in the Waters Immerse Lab in Cambridge, MA. Students will be characterizing green fluorescent protein (eGFP, a recombinant protein standard) structure (primary, secondary/tertiary) in the lab using liquid chromatography and mass spectrometry. Data generated in the lab will be available on-line for Committed Listeners.
Week 11 — Bioproduction & Cloud Labs
WEEK 11 HW This week examines how modern bioproduction pipelines, from strain engineering to fermentation and downstream processing, are increasingly designed, executed, and optimized through cloud lab platforms and automation — enabling remote, high-throughput, and reproducible synthetic biology at industrial scale. Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork How it started….
Week 12 HW This week focuses on designing, synthesizing, and editing whole genomes, from minimal cells to refactored microbes and synthetic chromosomes.
WEEK 13 HW: BIODESIGN AND ENGINEERED MATERIALS
WEEK 13 HW This week covers designing, programming, and fabricating engineered living materials — such as self-healing concretes, adaptive biofilms, and responsive biomaterials — by integrating genetic circuit design, materials science, and bioprocess engineering.
WEEK 14 HW- BIODESIGN AND BIOFABRICATION
Suzanne Lee and Christina Agapakis <3