Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Exploring open-source tools for synthetic biology and circular economy.
Week 2 — DNA Read, Write, & Edit
This week explores the read–write–edit toolkit: sequencing and synthesis workflows, restriction digests and gel electrophoresis, and early genome-editing frameworks.
Molecular weight calculation of eGFP via adjacent charge state analysis of LC-MS data and assessment of experimental measurement accuracy. The work includes the identification and quantification of Lysine and Arginine residues through bioinformatics-based sequence analysis. This approach integrates analytical chemistry and computational tools to achieve precise protein characterization.
Week 4 HW: Protein Design Part I
Analysis of protein structure and sequence through 3D visualization and machine learning models such as ESMFold and ProteinMPNN. Implementation of mutational scanning and latent space analysis to explore protein design space and optimization. Development of computational strategies for bacteriophage engineering aimed at enhancing stability and functional outcomes.
Week 5 HW: Protein Design Part II
In silico design of therapeutic peptides targeting mutant SOD1 using advanced generative models such as PepMLM and moPPIt. Structural validation and property prediction were conducted through AlphaFold3 and PeptiVerse to assess binding affinity and solubility. The work focused on multi-objective optimization to enhance the stability and folding of the MS2 phage lysis protein.
Week 6 HW: Genetic Circuits Part I
Exploration of molecular biology techniques for DNA assembly, focusing on PCR and Gibson Assembly protocols for genetic construct preparation. Implementation of the Asimov Kernel platform to design, simulate, and validate complex genetic circuits such as the repressilator. The work involves comparative analysis of assembly methods and the characterization of bacterial parts to engineer functional biological systems.
Week 7 HW: Genetic Circuits Part II
Investigation of neuromorphic genetic circuits and the implementation of Intracellular Artificial Neural Networks (IANNs) to perform "perceptron"-like computations. The work includes the design of multi-layer genetic perceptrons using endoribonucleases and an exploration of fungal materials as a chassis for synthetic biology. Additionally, it covers the initial DNA design and synthesis orders for the individual final project.
Study of cell-free protein synthesis (CFPS) systems for protein expression outside of cellular boundaries, emphasizing flexibility and control over experimental variables. Implementation of synthetic minimal cells for biosensing applications and the development of integrated biological sensors for architecture, textiles, and space exploration. The work includes optimizing energy regeneration and designing DNA constructs for specialized protein production in cell-free environments.
Week 10 HW: Advanced Imaging & Measurement Technology
Characterization of recombinant eGFP protein using liquid chromatography and mass spectrometry to determine molecular weight, charge state distribution, and primary sequence via peptide mapping. Comparison of native versus denatured protein conformations and identification of oligomeric states in high-molecular-weight complexes through charge detection mass spectrometry.
Week 11 HW: Bioproduction & Cloud Labs
Exploration of cloud laboratories for decentralized bioproduction and collaborative bioart experiments. The work focuses on optimizing cell-free protein synthesis (CFPS) through master mix design and biophysical characterization of fluorescent proteins using automated remote platforms.
This week focuses on designing, synthesizing, and editing whole genomes, from minimal cells to refactored microbes and synthetic chromosomes.
Week 13 HW: AI, SynBio, and Scaling Health Innovation (ARPA-H)
This week focuses on designing, synthesizing, and editing whole genomes, from minimal cells to refactored microbes and synthetic chromosomes.
Bio Design & Bio Fabrication.