APh 161: Dynamics of Transcriptional Regulation

This page contains my lecture outline and notes for a set of lectures that I will be giving in [1], Rob Phillips's course on Physical Biology of the Cell. This page is mainly intended as a place for me to keep my notes, but might be useful as a reference for the lecture (the final lecture notes will be posted on the APh 161 web page).

Goals

• Motivate the role of dynamics and feedack in the physical biology of the cell
• Provide mathematical tools for analyzing the dynamics of transcriptional regulation in the cell
• Work through some case studies that serve as model systems for feedback control in cells

Lecture 1: Feedback and Dynamics in Cells

This lecture will be a powerpoint-style lecture that tries to motivate the role of dynamics and feedback in cells and describes how we can analyze models to obtain insights into the dynamics. We focus on the lac operon as the main object of study.

Lecture Outline

Lecture Materials Lecture slides MATLAB code Reading

Tutorial Interlude: Dynamical Systems 101

Tutorial Outline

Tutorial Materials Tutorial slides MATLAB code Additional Information CDS 101/110 lectures on dynamic behavior

Notes

• This material will come from CDS 101/110, Week 3 - Dynamic Behavior. Pretty much the only change is going to be to swap out the examples with ones from biology (mainly lac and repressilator)

Lecture 2: Case Studies and Calculations

Lecture Outline

Lecture Materials Lecture slides MATLAB code Reading