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
