Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- Description of the Bioengineering Application Rapid-Cycle Rice System The Rapid-Cycle Rice System is a bioengineering platform designed to shorten the rice harvest cycle to approximately 45–60 days by modulating flowering-time genetic pathways in combination with controlled growth environments. The system aims to enable high-frequency and rapid-response rice production, particularly under conditions of climate stress, such as extreme droughts, floods, or disruptions to food supply chains.
Week 2 HW: DNA Read, Write, and Edit
Part 1: Benchling & In-silico Gel Art 1. IMPORTING LAMBDA DNA 1.1 Creating an Account and Accessing Benchling Purpose: To access the platform for DNA simulation.
Post-Lab Question 1 A study by the Opentrons research community demonstrated how low-cost laboratory automation platforms can accelerate biological experiments. The researchers used the Opentrons OT-2 robot to automate liquid handling tasks such as pipetting, reagent mixing, and plate preparation. In the study, the robot was programmed using Python scripts to perform repetitive experimental steps with high precision. Automation enabled researchers to run multiple biological assays simultaneously while reducing human error.
Week 4 HW: Protein Design part I
PART A — Conceptual Questions How many molecules of amino acids are in 500 g of meat? If we assume 500 g of protein: 500g÷100g/mol = 5 mol Total of molecules: 5×6.022×10²³ ≈ 3 × 10²⁴ amino acid molecules Why do humans eat beef but do not become a cow, and eat fish but do not become fish? Proteins from food are not absorbed as intact proteins. Instead, they are broken down during digestion:
Week 5 HW: Protein Design Part II
Part 1 — Generate Binders with PepMLM PepMLM was used to generate four 12-amino-acid peptides conditioned on the A4V mutant SOD1 sequence. The generated peptides showed perplexity values ranging from approximately 5.8 to 7.0, suggesting moderate model confidence in their plausibility as binders. Lower perplexity indicates that the peptide sequence better fits the model’s learned representation of protein–peptide interactions. The known SOD1-binding peptide FLYRWLPSRRGG was included as a reference for downstream structural and functional comparison.
Week 6 HW: Genetic Circuits Part I
Genetic
Week 7 HW: Genetic Circuits Part II
Genetic Circuit
Cell
Week 10 HW: Imaging and Measurement
Imaging
Genomes
Bioproduction
Week 13 HW: Bio Design Living Materials
Bio Design Living Materials
Biofabrication