https://pages.htgaa.org/2026b/mohammad-aazim/index.htmlHow To Biomanufacture Almost Anything (MAS.865) MIT Media Lab | Fall 2026 Portfolio About Me Welcome to my official How To Biomanufacture Almost Anything (HTBAA) course portfolio and research documentation space! I am a second-year Bachelor of Science student in Data Science and Applications at Indian Institute of Technology Madras (IIT Madras), taking HTBAA Fall 2026 as a committed listener affiliated with the BioPunk.Hugoenhttps://pages.htgaa.org/2026b/mohammad-aazim/week-01-hw-project-ideas/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/mohammad-aazim/week-01-hw-project-ideas/index.htmlFinal Project Proposal & Exploration 1. What You Would Like to Biomanufacture and Why? Target Product: Polyhydroxyalkanoates (PHAs) — a family of 100% bio-based, biodegradable bioplastics. The target final output is purified bioplastic pellets that can be 3D-printed or molded into single-use campus items like coffee lids, forks, and food containers. Motivation: Traditional petroleum plastics cause long-lasting environmental pollution and microplastics. Common plant-based alternatives (like PLA) require dedicated industrial composting and freshwater crops. In contrast, PHAs are naturally produced by bacteria, behave like conventional plastics, but naturally decompose in soil or ocean water within months without toxic residues. Target Audience: Campus dining halls (such as MIT dining), local coffee shops, and zero-waste campus initiatives. 2. What Living System Would You Use? Living System Chassis: Halomonas bluephagenesis — a salt-loving (halophilic) extremophile bacterium. High-Level Biological Process: Inputs: Seawater / high-salt water (30–80 g/L salt), low-cost carbon sources (like glucose or food waste hydrolysates), and basic nitrogen/minerals. Biological Process: Halomonas cells grow rapidly in salty, alkaline liquid culture. When nitrogen is limited, the cells stop multiplying and store extra carbon inside themselves as natural PHA plastic granules. Outputs: Cell biomass where up to 80% of the dry cell weight is pure PHA plastic. Breaking the cells open and washing them yields clean bioplastic resin. Key Assumptions: The extreme saltiness and high pH prevent common contaminating wild microbes from growing, allowing open, unsterile fermentation without needing expensive steam sterilization equipment. 3. How Would You Use Automation? Selected Automation Technology: A desktop liquid-handling robot (such as an Opentrons OT-2) or a remote Cloud Lab platform (such as Strateos). Automated Workflow Step: Growth media optimization and strain testing during the Design-Build-Test-Learn (DBTL) cycle. Why Automate? Finding the ideal combination of salt, pH, nutrients, and waste feedstocks across dozens of combinations is slow and prone to human error when done manually. An automated liquid handler can rapidly dispense exact liquid amounts into 96-well test plates and track cell growth and plastic accumulation automatically over 24-hour cycles. 4. How Much Would You Need to Make, and How Long Would It Take? (a) How Much? (Scale Definition & Calculations) Defined Scale: A campus dining hall scale of 100 kg of biodegradable PHA plastic per year (~275 grams of PHA per day), which replaces roughly 10,000 single-use plastic containers annually. Back-of-the-Envelope Calculation: Cell Dry Weight (CDW) Density: ~80 grams of cells per Liter of culture broth. Intracellular PHA Content: ~80% of CDW (0.80 g PHA per gram of cells). Product Yield per Liter: Yield = 80 g/L cells × 0.80 = 64 grams of PHA per Liter of broth Required Daily Fermentation Broth Volume: Daily Volume = (275 g PHA/day) / (64 g PHA/L) ≈ 4.3 Liters of broth per day Bioreactor Size: Including a 25% headspace buffer for mixing and oxygen, a modest 6-Liter benchtop bioreactor running daily (or a 35-Liter bioreactor running once per week) fulfills campus demand. (b) How Long? (Process Timeline & Automation Contrast) Batch Timeline: ~12 hours for cell growth + ~24 hours for nitrogen-starved PHA accumulation + ~4 hours for harvesting/washing = ~40 hours total per batch. Prototyping vs. Production Automation Contrast: Prototyping Scale: Small-scale 96-well plates (1 mL per well) on an Opentrons liquid handler to test many media recipes in parallel. Production Scale: A 6-Liter automated benchtop bioreactor equipped with automated sensors (pH, dissolved oxygen, feed pumps) connected to an automated centrifuge for daily harvesting. 5. What Don’t You Know Yet? (Biggest Unknowns & Bottlenecks) Feedstock Consistency: How well will Halomonas handle unpredictable variations in local food waste feedstocks from week to week? Downstream Extraction Efficiency: What is the simplest, lowest-energy method to break open the cells and recover pure plastic resin without using harsh chemical solvents? Material Quality & Durability: How do 3D-printed PHA utensils perform when holding hot food or liquids compared to traditional plastics? AI Client & Prompts Citation AI Client: Gemini Notebook (NotebookLM Workbench) Prompts Used: “Go through the HTBAA Homework #1 file along with the course syllabus document, and give a general, high-level idea for a feasible and meaningful creation in biomanufacturing that aligns with the curriculum. This will be the basis for our final project as we move along the course, allowing us to dig deeper, structure our core knowledge, and create some community impact.”https://pages.htgaa.org/2026b/mohammad-aazim/week-02-hw-dna-design/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/mohammad-aazim/week-02-hw-dna-design/index.htmlDNA Design & Expression Construct Part 0: Open-Source Software Setup & Workspace Note on Software: Per MIT course instructions regarding Kernel accounts, this DNA design was constructed and verified using Benchling (alongside open-source plasmid editing tools ApE / VectorBee). Repository / Project Name: PhaC1-Halomonas-HTBAA Live Benchling Construct Link: HTBAA HW2 PhaC1 Expression Construct on Benchling Construct Description: This live Benchling sequence file contains the complete, fully annotated, 1,762 bp 5’ → 3’ expression cassette for Polyhydroxyalkanoate Synthase Class I (PhaC1) designed for Halomonas bluephagenesis. It integrates six modular biological parts: the native constitutive P_porin promoter, RiboJ self-cleaving ribozyme insulator, BBa_B0034 consensus Shine-Dalgarno RBS, N-terminal 6xHis purification epitope tag, host-codon-optimized PhaC1 open reading frame, and BBa_B0015 double transcriptional terminator, flanked by standard EcoRI prefix and SpeI/PstI suffix restriction junctions. Part 1: Define Your Expression Target Building directly upon Homework #1 (biomanufacturing Polyhydroxyalkanoate [PHA] bioplastics for campus dining utensils), this construct encodes the core enzyme required for bioplastic polymerization.https://pages.htgaa.org/2026b/mohammad-aazim/week-03-hw-cell-free/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/mohammad-aazim/week-03-hw-cell-free/index.htmlCell-Free Reaction Design, Coopetition & CAD Assembly Section A: Compare Cell-Free Reaction Compositions Question 1: Ion Sensitivity & Role of Glutamate Salts Why do the concentrations of Potassium Glutamate (K-Glu) and Magnesium Glutamate (Mg-Glu₂) differ between CFPS formulations, and which ion is more sensitive?https://pages.htgaa.org/2026b/mohammad-aazim/final-project/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/mohammad-aazim/final-project/index.html