Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Exploring open-source tools for synthetic biology and circular economy.
Python Script for Opentrons Artwork Exploring the Spiral of Ouro. Artistic Concept and Motivation For this week’s assignment, I developed a “Spiral of Ouro.” This design is based on phyllotaxis principles, using the Golden Angle to distribute points across a 96-well plate. This choice reflects the core philosophy of my project: using mathematical and computational frameworks to simplify biological design. By translating natural patterns into a functional robotic protocols.
Week 4 HW: Protein Design Part I
Exploring amino acid principles, 3D protein visualization, and ML-based protein design.
Week 5 HW: Protein Design Part II
Part A: SOD1 Binder Peptide Design 🔹 Part 1 — Generate Binders with PepMLM !!! info “Description” Using PepMLM, four 12‑amino‑acid peptides were generated conditioned on the SOD1 A4V mutant sequence. SOD1‑binding peptide FLYRWLPSRRGG was added as a control, and the perplexity scores were recorded to estimate model confidence.
Week 6 HW: Genetic Circuits Part I
Part A: Assignment: DNA Assembly 1. What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Based on standard molecular biology principles, a High-Fidelity PCR Master Mix typically contains Phusion DNA Polymerase: A highly processive, proofreading polymerase responsible for synthesizing the new DNA strands accurately. Deoxynucleotide Triphosphates (dNTPs): The A, T, C, and G building blocks that the polymerase uses to build the new DNA strand. Reaction Buffer: Maintains the optimal pH and salt conditions for the enzyme. Magnesium Chloride: A crucial cofactor required for DNA polymerase activity. Specific template DNA, primers, and nuclease-free water. 2. What are some factors that determine primer annealing temperature during PCR?
Week 7 HW: Genetic Circuits Part II
Assignment Part 1: Intracellular Artificial Neural Networks 1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? IANNs provide a massive leap forward by allowing cells to process analog information instead of being stuck with binary logic. Traditional genetic circuits are brittle because they depend on strict thresholds, whereas these networks use weighted inputs to handle fuzzy or noisy data with much higher precision. This compact design enables sophisticated decision making using fewer genetic parts, which is essential for working within the tight constraints of a living organism.
Homework Part A: General and Lecturer-Specific Questions 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. Cell-free systems provide an open-access biological engine where you have direct control over every molecular dial. The main advantage over traditional in vivo methods is the lack of a cellular wall, which allows for the direct addition of non-canonical amino acids or specific inhibitors. This transparency makes it perfect for producing proteins that are normally toxic to a living host or for rapid prototyping where results are needed in hours rather than days. Two key cases where this is superior include the production of antimicrobial peptides that would lyses a host cell and the synthesis of proteins containing site-specific labels for structural NMR analysis