Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    Oncological Bacteriotherapy: Iron Sequestration in the TME via Controlled Release of Stealth Siderophores under NAND Logic Gates and Biocontainment Circuits.

  • Week 2 HW: DNA-read-write-and-edit

    Nature’s Machinery for Copying DNA - oligo synthesis

  • Week 03 HW: Lab-Automation

    1. Python Script for Opentrons Artwork This artwork was generated using the HTGAA26 Opentrons Colab environment. opentron_code The design was implemented programmatically using geometric constructions and multi-color pipetting logic. To properly render Devanagari text (e.g., “चित्”) using PIL in Google Colab, system-level fonts must be installed before executing the Opentrons script. The Noto Sans Devanagari font was installed using the following commands in a separate Colab cell:

  • Week 04 HW: Protein Design Part I

    Part A. Conceptual Questions from Shuguang Zhang 1) How many molecules of amino acids are in 500 g of meat? Assume meat is ~20–25% protein: 500 g meat → ~100–125 g protein. Using ~100 Da per amino acid (given): 100 g / (100 g/mol) = 1.0 mol amino acids → ~6.0×1023 molecules 125 g / (100 g/mol) = 1.25 mol amino acids → ~7.5×1023 molecules Answer: ~10^23

  • Week 05 HW: Protein Design Part II

    Part A: SOD1 Binder Peptide Design Part 1: Generate Binders with PepMLM Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. Original sequence sp|P00441|SODC_HUMAN Superoxide dismutase MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Variant: A4V MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Generate four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence. Using the mutant SOD1 sequence as input, PepMLM Colab generated four 12-residue candidate binders

  • Week 06 HW: Genetic Circuits Part I

    DNA Assembly Assignment 1. Components of the Phusion High-Fidelity PCR Master Mix The Phusion High-Fidelity PCR Master Mix contains the main components required for accurate DNA amplification. One key component is the Phusion DNA polymerase, which synthesizes new DNA strands with high fidelity. The mix also includes dNTPs, which serve as the nucleotide building blocks for DNA synthesis. In addition, it contains a reaction buffer that maintains the proper pH and salt conditions for enzyme activity, as well as magnesium ions, which are essential cofactors for polymerase function. Together, these components support efficient and accurate PCR amplification.

  • week-07-hw-genetic-circuits-part-ii

    Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) 1. Advantages of IANNs over traditional Boolean genetic circuits IANNs can generate graded, weighted, and more flexible input/output responses instead of only ON/OFF logic. This makes them better suited for integrating multiple noisy biological signals and for approximating complex decision boundaries.

  • week-09-hw-cell-free-systems

    Homework Part A: General and Lecturer-Specific Questions Advantages: Cell-free systems allow direct control of reaction conditions without maintaining cell viability. They are especially useful for toxic proteins and membrane proteins. Main components: Cell extract or Tx/Tl machinery, DNA template, amino acids, nucleotides, energy source, salts, and buffer. Together, these support transcription, translation, and reaction stability. Energy regeneration: ATP and GTP are rapidly consumed during transcription and translation. Continuous supply can be maintained with phosphoenolpyruvate- or maltodextrin-based regeneration systems.

  • week-10-hw-imaging-and-measurement

    Waters Part I — Molecular Weight 1) what is the calculated molecular weight? Using the amino acid sequence provided in the assignment, I calculated the theoretical molecular weight of the construct with the ExPASy Compute pI/Mw tool. The calculator (https://web.expasy.org/compute_pi/) returned the following values:

  • week-11-hw-building-genomes

    Part B: Cell-Free Protein Synthesis | Cell-Free Reagents Referencing the cell-free protein synthesis reaction composition (the middle box outlined in yellow on the image above, also listed below), provide a 1-2 sentence description of what each component’s role is in the cell-free reaction. 1.1 E. coli Lysate * BL21 (DE3) Star Lysate: Provides the essential molecular machinery, including ribosomes and translation factors, while the T7 RNA Polymerase drives the transcription of DNA into mRNA.