Homework

Weekly homework submissions:

• Week 1 HW: Principles and Practices

  🧬 Week 1 Homework Components 📋 Professor Questions & Answers Detailed scientific answers to questions from: Professor Jacobson — DNA polymerase error rates, genetic code degeneracy Dr. LeProust — Oligonucleotide synthesis methods and limitations Professor Church — Essential amino acids and the “Lysine Contingency” 🔬 BioVolt Project - DIY Electroporation Device Complete end-to-end project documentation including governance assessment and interactive Python application.

• Week 2 HW: DNA Read, Write, & Edit

  🧬 Week 2 Homework Components DNA Read, Write, & Edit — sequencing and synthesis workflows, restriction digests and gel electrophoresis, genome-editing frameworks. 📋 Overview This week covers: Part 0: Basics of Gel Electrophoresis Part 1: Benchling & In-silico Gel Art ✓ Part 2: Gel Art — Restriction Digests and Gel Electrophoresis (wet lab, optional with lab access) Part 3: DNA Design Challenge ✓ Part 4: Prepare a Twist DNA Synthesis Order ✓ Part 5: DNA Read/Write/Edit ✓ Content to be added as you complete each part.

• Week 3 HW: Lab Automation

  Published paper on automation for novel biological applications; automation project description for gumol MD simulations + ECSOD/MSC + new-Clara microfluidic validation.

• Week 4 HW: Protein Design

  Conceptual questions from Shuguang Zhang on amino acids, protein structure, helices, and β-sheets.

• Week 5 HW: Protein Design Part II

  PepMLM peptide binder generation for human SOD1 A4V mutant; ML-conditioned peptide design.

• Week 6 HW: Genetic Circuits

  Phusion PCR, primer annealing, PCR vs restriction digests, Gibson cloning, transformation, and alternative assembly methods (Golden Gate).

• Week 7 HW: Genetic Circuits Part II

  Intracellular artificial networks (IANNs) vs Boolean circuits; multilayer perceptron diagram; fungal materials and engineering fungi.

• Week 9 HW: Cell-Free Systems & Synthetic Cells

  Cell-free expression vs in vivo; ATP regeneration; prokaryotic vs eukaryotic CFPS; membrane proteins; troubleshooting; synthetic minimal cell (SOD3/CXCR4); materials pitch; Genes in Space (BioBits).

• Week 10 HW: Advanced Imaging & Mass Spectrometry

  Final project measurement plan (SOD3); Waters eGFP LC-MS (intact, native vs denatured, peptide mapping, KLH CDMS); lab data tables.

• Week 11 HW: Cloud Laboratories & Cell-Free Master Mix

  Cell-free reagent roles; PEP-NTP vs long-run energy mix; FP properties; 36 h master-mix hypothesis. Bioart reflection completed on course site.