Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Question 1 – Application & why 1. First, describe a biological engineering application or tool you want to develop and why.
Week 2 HW: DNA Read, Write, & Edit
Part 1 – Benchling & In-silico Gel Art I used Benchling to design an in‑silico restriction digest of Lambda DNA. In Benchling, I created a customized restriction enzyme list for smoother later operations that included all the enzymes provided in the Week 2 HTGAA homework
Assignment 1: Python Script for Opentrons Artwork This week we are creating a Python file to run on an Opentrons OT-2 liquid handling robot to create flourescent designs. Using provided website I created a small “Cherry” pattern. I have little experience in coding on such platofrms, so Google Gemini was a big help to assist while writing a code: https://colab.research.google.com/drive/1kZZStiHlPdG17vqHZPM2IhAQ3vTWkMRb#scrollTo=pczDLwsq64mk&line=76&uniqifier=1
Part A Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip) How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) Since meat is not entirely made of proteins, lets assume 20% of the whole meat mass = around 100 g. An amino acid is ~100 Da (=~100g/mol). 100 g/ (100 g/mol) = 1 mol = 6.022* 10^23 AA.
Week 5 HW: Protein Design. Part 2
PART A: Computational Peptide Design — SOD1 A4V Binder Generation Background Superoxide dismutase 1 (SOD1) is a cytosolic antioxidant enzyme that converts superoxide radicals into hydrogen peroxide and oxygen. Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS) — a severe neurodegenerative disorder characterized by adult-onset loss of upper and lower motor neurons, progressive paresis, skeletal muscle atrophy, quadriplegia, and fatal respiratory failure. The A4V mutation (Alanine → Valine at residue 4) is one of the most aggressive ALS-associated variants. It subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation. The task is to design short peptides that bind mutant SOD1 and evaluate which are worth advancing toward therapy.
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion DNA Polymerase Chimeric enzyme that catalyzes the synthesis of ew DNA strand in the 5 -> 3 direction with high-fidelity dNTPs four chemical building blocks ($dATP, dTTP, dCTP, dGTP$) used to construct the DNA. They provide both the physical material and the energy required for the polymerase to grow the new strand Reaction Buffer
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
Part 1 What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Traditional genetic circuits implement Boolean logic gates (AND, OR, NOT, NAND, etc.), hence their input/output relationships are discrete - a gene is either ON or OFF. This allows only binary decision-making and makes it difficult to represent graded, continuous, or context-dependent responses. IANNs provide continuos computation where inputs and outputs exist on a continuum, allowing cells to integrate multiple signals simultaneously.
General homework questions 1. 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 protein synthesis is more flexible than in vivo expression because we can directly control the reaction conditions, such as DNA concentration, salts, cofactors, temperature, and additives. The in vivo model limits out experimet by time since we have atcually grow cells and wait for results, in cell free systems the speed of these procedures is much faster. It is more beneficial to use cell free systems for toxic proteins, membrane proteins, and rapid prototyping or diagnostics, because we do not need to keep a living cell alive while producing the protein.
Week 10 HW: Imagining and Measurement
For final project In this project, I will measure several aspects of the DNA sensing system, including sequence correctness, predicted folding behavior, target response, orthogonality, and signal output. The most important biological measurements are whether the histamine and IgE circuits are correctly designed and whether they respond only to their intended targets. I will also measure the strength of the output signal after target binding, since the goal is to convert molecular recognition into a detectable readout. In addition, I will look at background activity and nonspecific activation to estimate how cleanly the system distinguishes true signal from noise. These measurements will help determine whether the platform is suitable for future wearable use.
Week 11 HW: Bioproduction & Cloud Labs
Part A Unfortunately, I did not have the opportunity to contribute to the project before the deadline ended. However, for next semester, I think it would be a good idea to create several variations of the same artwork using different color palettes or design concepts. I noticed that many people were unsure about what exact pattern or style they were supposed to contribute, while others had their own creative ideas that did not fully match the overall design. Because everyone has different artistic preferences and interpretations, it could be helpful to divide the project into multiple themed sections or versions. This would make the collaboration process more flexible, reduce confusion, and allow more students to express their creativity in their own way.