Readings are from the course textbook Del Vecchio, Domitilla, and Richard M. Murray. Biomolecular Feedback Systems. Princeton University Press, 2014. ISBN: 9780691161532. [Preview with Google Books]

The electronic edition of the textbook is available for free on the book’s website.

Part I: Analysis

Chapter 2: Core Processes (PDF - 4.2MB)

  • Modeling Techniques
  • Transcription and Translation
  • Transcriptional Regulation
  • Post-transcriptional Regulation
  • Cellular Subsystems

Chapter 3: Dynamic Behavior (PDF)

  • Analysis Near Equilibria
  • Robustness
  • Oscillatory Behavior
  • Bifurcations
  • Model Reduction Techniques

Chapter 4: Stochastic Modeling and Analysis (PDF)

  • Stochastic Modeling of Biochemical Systems
  • Simulation of Stochastic Systems
  • Input / Output Linear Stochastic Systems

 Part II: Design

Chapter 5: Biological Circuit Components (PDF - 2.4MB)

  • Introduction to Biological Circuit Design
  • Negative Autoregulation
  • The Toggle Switch
  • The Repressilator
  • Activator-repressor Clock
  • An Incoherent Feedforward Loop (IFFL)
  • Bacterial Chemotaxis

Chapter 6: Interconnecting Components (PDF)

  • Input / Output Modeling and the Modularity Assumption
  • Introduction to Retroactivity
  • Retroactivity in Gene Circuits
  • Retroactivity in Signaling Systems
  • Insulation Devices: Retroactivity Attenuation
  • A Case Study on the Use of Insulation Devices

Chapter 7: Design Tradeoffs (PDF)

  • Competition for Shared Cellular Resources
  • Stochastic Effects: Design Tradeoffs in Systems with Large Gains