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Chapters

  • 0. Configuring your computer to use Python for scientific computing
  • 1. Introduction to biological circuit design
  • 2. Introduction to Python for biological circuits
  • 3. Big functions from small circuits
  • 4. Finding biological circuit motifs
  • 5. Analysis of coherent feed forward loops
  • 6. Incoherent feed-forward loops generate pulses, speed responses, and serve as dosage compensators
  • 7. Molecular titration generates ultrasensitive responses in biological circuits
  • 8. Robustness in biological circuits
  • 9. Kinetic proofreading: Multi-step processes reduce error rates in molecular recognition
  • 10. Blinking bacteria: The repressilator enables self-sustaining oscillations
  • 11. Oscillators, part II: Uses, simplifications, and elaborations of negative feedback oscillators
  • 12. Gene expression is noisy! How stochastic effects lead to heterogeneity
  • 13. Bursty gene expression
  • 14. Stochastic simulation of biological circuits
  • 15. Stochastic differentiation
  • 16. Cellular bet-hedging
  • 17. Time-based regulation in cells
  • 18. Paradoxical regulation in intra- and intercellular circuits
  • 21. Turing patterns
  • 22. Scaling reaction-diffusion patterns
  • Appendix A: Regulatory functions and their derivatives

Homework

  • Homework 1
  • Homework 2
    • Homework 2.1: Design principles for toggles (45 pts)
    • Homework 2.2: XOR gates (55 pts)
  • Homework 3
  • Homework 4
  • Homework 5
  • Homework 6
  • Homework 7
  • Homework 8
  • Homework 9
  • Homework 10

Schedule

  • Schedule overview
  • Homework due dates
  • Lecture schedule

Policies

  • Lectures
  • Homework
  • Grading
  • Extensions
  • Course communications
  • “Ediquette”

Resources

  • Books

Package docs

  • biocircuits package documentation
Biological Circuit Design
  • »
  • Homework 2
  • View page source

Homework 2¶

  • Homework 2.1: Design principles for toggles (45 pts)
  • Homework 2.2: XOR gates (55 pts)
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Last updated on May 26, 2021.

© 2021 Michael Elowitz and Justin Bois. With the exception of pasted graphics, where the source is noted, this work is licensed under a Creative Commons Attribution License CC BY-NC-SA 4.0. All code contained herein is licensed under an MIT license.

This document was prepared at Caltech with financial support from the Donna and Benjamin M. Rosen Bioengineering Center.



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