Homework
Weekly homework submissions:
week-01-hw-principles-and-practices
Biological Engineering Application or Tool The proposed application is an AI-guided protein therapeutic discovery and bioproduction platform. The system uses machine learning–based protein design models to generate novel therapeutic protein candidates, such as antimicrobial proteins, enzymes, or biologics optimized for stability and activity. These candidates are then evaluated for manufacturability and functional performance using controlled bioproduction workflows, including microbial expression or cell-free systems. This application reflects an emerging paradigm in biopharmaceutical development, where AI accelerates early-stage discovery while scalable bioproduction determines clinical and commercial feasibility. However, as AI enables rapid de novo protein design, many generated sequences may lack homology to known natural proteins, introducing novel biosecurity and safety risks if not properly governed.
week-02-hw-dna-read-write-and-edit
This week, we were tasked to utilize different tools to be able to virtually read, write, and visualize using samples like lambda DNA from Escherichia coli and the Tumor suppressor gene from humans. Part 1 - Introduction and DNA digest. Gel Electrophoresis Gel - material Electro - Electric Phoresis - to transport It is a method used to transport charged materials using an electric field through a gel (a Semi-liquid substance). Digested fragments of Lambda DNA
Bioart Using Opentrons Goal of learning this lesson and doing the OpenTron automation. Utilizing different tools to automate different lab work using programmed robots. Be able to design, coordinate, code, and print one’s design using OpenTron robots. Code CLICK HERE SEE THE CODE USED from opentrons import types
week-04-hw-protein-design-part-i
A. Conceptual Questions 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) Answer 1 Dalton ≈ 1 g/mol Average amino acid ≈ 100 g/mol If you eat 500 g of (pure) amino acids: number of moles = Gm/ Tm = 500g/100g/mol
week-05-hw-protein-design-part-ii
Protein Design Part 2 SOD1_A4V Mutated Code Used. —> MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Part 1: PepMLM Generated Peptides Summary The four PepMLM-generated peptides were conditioned on the SOD1 A4V mutant sequence with a target length of 12 amino acids, with the exception of Peptide 2, which came out at 15 residues. Perplexity scores reflect the model’s confidence in each binder, where a lower score indicates higher confidence. Peptide 1 (WLYGAAGVRWGX) has the lowest perplexity at 13.06, making it the model’s most confident prediction, though it contains an X residue at the final position, which represents an unresolved or masked amino acid and should be noted as a potential issue before advancing it further. Peptides 2, 3, and 4 all cluster between 17 and 20, reflecting moderate confidence. The known binder FLYRWLPSRRGG is included as a structural and therapeutic benchmark and does not carry a perplexity score since it was not generated by PepMLM.
week-06-hw-genetic-circuits-part-ii
Part - 1 What are some components in the Phusion High-Fidelity PCR Master Mix, and what is their purpose? Phusion High-Fidelity PCR Master Mix, commonly produced by Thermo Fisher Scientific, contains a high-fidelity DNA polymerase with proofreading ability, a reaction buffer that maintains optimal conditions, Mg²⁺ ions as a cofactor, dNTPs as building blocks, and stabilizing additives. Together, these components enable accurate and efficient DNA amplification with a low error rate. What are some factors that determine primer annealing temperature during PCR?
week-07-hw-genetic-circuits-part-ii
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Intracellular artificial neural networks provide more flexible and nuanced behavior than traditional Boolean genetic circuits because they can process inputs in a graded, continuous manner rather than simple on or off states. This allows cells to integrate multiple signals and produce proportional responses, making them better suited for complex decision making and pattern recognition inside biological systems. Describe a useful application for an IANN; include a detailed description of input/output behavior, as well as any limitations an IANN might face to achieve your goal.
Homework question from Kate Adamala. Design an example of a useful synthetic minimal cell as follows: Pick a function and describe it. a. What would your synthetic cell do? What is the input, and what is the output? The cell-free genetic circuit that I plan to make for the final project aims to detect different biological signals and produce a measurable output. The input will be one among the environmental signals, IL-6 or low O₂, and the output will be a green fluorescence signal or a therapeutic peptide. Could this function be realized by cell-free Tx/Tl alone, without encapsulation? The system that I am thinking of needs to be encapsulated inside a hydrogel. Could this function be realized by genetically modified natural cells? Cells do have a mechanism to respond to real signals in the body, but getting therapeutic peptides and other luminescent signals as an output from a signal is achieved if the cell is preprogrammed and the genetic circuit is assembled in a way to detect the signal and respond accordingly. Describe the desired outcome of your synthetic cell operation. Output will be a Green Fluorescence Signal. Design all components that would need to be part of your synthetic cell. What would the membrane be made of?
week-10-hw-imaging-and-measurement
Protein Characterization: eGFP and KLH Homework: Final Project Project Title: A Hydrogel-Embedded Multiple Input-Output (MIMO) Genetic Circuit for IL-6 and Hypoxia Detection What I Will Measure My final project centers on engineering a cell-free genetic circuit embedded within a hydrogel matrix that responds to two physiological disease signals, IL-6 (an inflammatory cytokine) and low oxygen tension (hypoxia), and produces two corresponding outputs: sfGFP fluorescence as a reporter signal and a therapeutic peptide as a functional output.
Bioproduction & Cloud Labs Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork My Contribution I contributed pixels forming part of the DNA helix structure on the lower left quadrant of the collective canvas, using a blue-green palette consistent with the biological theme of the artwork.