Homework
Weekly homework submissions:
Week 1 HW: hw-principles-and-practices
The Prometheus Symbiont 🎅1.“The Prometheus Symbiont” is a conceptual, living medical system designed to symbiotically integrate with the human body. It merges biomimetic photosynthesis, synthetic biology, and flexible electronics, aiming to shift medicine from “passive treatment” to active, sustained life maintenance and enhancement. You can think of it as a sunlight-powered, wearable or implantable “second life-support system.” 🎅The Prometheus Symbiont is not merely a technological concept; it is more akin to a philosophical proposition about the future form of life. It blurs the boundaries between therapy and enhancement, between human and machine. Its ultimate significance may lie in compelling us to re-examine: “what constitutes health, and indeed, what it means to be human.”
Week 10 HW: hw-imaging-and-measurement
Homework: Final Project Please identify at least one (ideally many) aspect(s) of your project that you will measure. It could be the mass or sequence of a protein, the presence, absence, or quantity of a biomarker, etc. 🎅All projects will be completed in two parts: Natural Photosynthesis Models A computational simulation experiment of de novo protein design that relies on self‑supplied photosynthetic energy and is driven by continuous directed evolution No directly relevant energy‑coupled evolution system exists. It is important to note that no published system to date has achieved the full loop where functional activity drives ATP regeneration, which in turn drives the evolution of the function itself. All existing continuous evolution systems, regardless of their maturity, rely on external energy input (i.e., normal host cell metabolism) to drive mutation and selection – there is no functional coupling between evolution and energy supply. This is precisely the core innovation space of our project: shifting directed evolution from “externally powered” to “self‑powered by function”.
Week 11 HW: hw-building-genomes
👩🦰Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Reflections on the HTGAA 2026 Collaborative Community Bioart Project 1. My Contribution to the Project For this collaborative bioart experiment, I made part of the DNA pattern on the bottom right plate, ensuring the engineering of the custom fragments aligned perfectly with the broader communal design layout.
Week 2 HW: DNA Read, Write, & Edit
Homework — DUE BY FEB 17 2PM MIT TIME 👨🦰Part 0: Basics of Gel Electrophoresis Keypoint: Gel Electrophoresis: Used for separating, identifying, and purifying fragments of DNA, RNA, or proteins. Gel Preparation: Add agarose powder to the buffer, heat until melted, pour the solution into the gel tray, insert the comb, and allow it to cool and solidify. Sample Loading: Remove the comb, place the gel into the electrophoresis tank, and add buffer until the gel is covered. Mix the DNA sample with loading buffer, then load the mixture into the wells.
ヾ(≧▽≦*)oAssignment: Python Script for Opentrons Artwork — DUE BY YOUR LAB TIME! The Biopunk lab hasn’t contacted me yet. The Opentrons API is a Python framework for writing automated biology lab protocols. 1.Load labware (containers, tip racks, plates); 2.Load instruments (pipettes); 3.Define your liquid handling steps; The basic artistic GUI will involve: Getting coordinates from the GUI tool; Writing a Python script that moves the pipette to those positions; Using the HTGAA26 Colab notebook as your template:https://ddls.aicell.io/course/ddls-2025/module-6/lab/#-what-is-a-code-agent;
Week 4 HW: hw-protein-design-part-i
🐉 Project Objective: Bacteriophage Engineering This document outlines the core learning experience and the collaborative framework designed to drive an optimized bacteriophage project.
- Mastery of Basic Concepts Phage Biology: Understanding the lytic and lysogenic life cycles, and the structural modularity of viral components (Capsid, Tail, Baseplate). Synthetic Biology Framework: Introduction to the “Design-Build-Test-Learn” (DBTL) cycle in viral engineering. Therapeutic Potential: Exploring the role of phages in addressing antimicrobial resistance (AMR) and precision microbiome editing. 2. Amino Acid Structure & Biochemistry Chemical Taxonomy: Categorization of the 20 standard amino acids based on hydrophobicity, charge, and polarity. Side-Chain Interactions: Analyzing how hydrogen bonds, salt bridges, and disulfide bridges dictate protein stability. Conformational Constraints: Understanding the Ramachandran plot and the energetic landscape of protein folding. 3. 3D Protein Visualization & Analysis Software Proficiency: Hands-on training with professional-grade tools such as PyMOL, ChimeraX, or NGL Viewer. Structural Mapping: Visualizing surface electrostatic potentials, hydrophobicity, and potential binding pockets. Superimposition: Learning to align wild-type and mutant structures to assess structural deviations (RMSD). 4. Diversity of ML-based Design Tools Structure Prediction: Leveraging AlphaFold 3 or RoseTTAFold for high-accuracy 3D modeling of viral proteins. Fixed-Backbone Design: Using ProteinMPNN to redesign amino acid sequences for a specific structural scaffold. Generative Scaffolding: Implementing RFdiffusion for de novo design of receptor-binding motifs and functional binders. Sequence Modeling: Utilizing Protein Language Models (e.g., ESM-3) to predict the impact of specific mutations on protein function. 👩🦰 Part A: Fundamental Principles & Frontiers in Protein Engineering This section covers fundamental inquiries into biochemistry, evolutionary biology, and structural protein design.
Week 5 HW: hw-protein-design-part-ii
🐉 Part A: SOD1 Binder Peptide Design (From Pranam) Background：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: hw-genetic-circuits-part-i
Week 6 — Genetic Circuits I: DNA Assembly Technologies Molecular Biology Lab Report: PCR & Assembly Techniques Components of Phusion High-Fidelity PCR Master MixPhusion Master Mix is a convenient 2X concentrated solution containing:Phusion DNA Polymerase: A pyrococcus-like enzyme fused with a processivity-enhancing domain. It provides extremely high fidelity ($50\times$ higher than Taq) and speed.dNTPs: The building blocks ($dATP, dTTP, dCTP, dGTP$) for the new DNA strand.Reaction Buffer: Maintains optimal pH and provides ionic strength.MgCl2: A necessary cofactor for polymerase activity.
Week 7 HW: hw-genetic-circuits-part-ii
Week 7 — Genetic Circuits Part II: Neuromorphic Circuits Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) The shift from Boolean genetic circuits to Intercellular Artificial Neural Networks (IANNs) represents a move from simple digital logic to complex, analog, and adaptive biological computing.
Week 9 HW: hw-cell-free-systems
Week 9 — Cell-Free Systems Homework Part A: General and Lecturer-Specific 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.