Biophysics : physics of the cell

Week 1 - Introduction 

• Physical biology of the cell
• The stuff of life
• Model building in biology
• Quantitative models

Reading: PBOC Chapter 1, Phillips Numbers Snapshot

Week 2 - Construction plans for cells 

• An ode to E. coli
• Cells and the structures within them

Reading: PBOC Chapter 2.1, 2.2

Week 3 - Mechanical and chemical equilibrium in the living cell

• Biological systems as minimizers
• Entropy and hydrophobicity

Reading: PBOC Chapter 5.2, 5.5.1

Week 4 - Biological membranes

• The nature of biological membranes
• On the springiness of membranes

Reading: PBOC Chapter 11.1, 11.2

The lecture this week is on video, exercises are in-person as usual. Here is the link: Lecture04_2025_video

Week 5 - Biological membranes

• Structure, energetics, and function of vesicles
• Membranes and shape

Reading: PBOC Chapters 11.3, 11.4

Week 6 - Proteins: Entropy rules

• Statistical mechanics
• The calculus of equilibrium
  

Reading: PBOC Chapter 6.1.1, 6.1.2, 6.4 (except 6.4.4)

Week 7 - Proteins: Ion channels

• Ion channels, a two-state system
• The active membrane

Week 8 - Diffusive dynamics

• Diffusion in the cell
• Concentration fields and diffusive dynamics
• Diffusion in crowded environments

Reading: PBOC Chapter 13.1, 13.2.1-13.2.3, 14.3.2

Easter break. No lecture or exercises

Week 9 - Directed dynamics

• Dynamics of molecular motors
• Model: Translocation ratchet

Reading: PBOC Chapter 16.1, 16.3.3

Week 10 - Genomes: Central Dogma of molecular biology

• Machines and processes
• Statistical mechanics of gene expression
  
• Genetic networks

Reading: PBOC Chapter 3.2.1, 6.1.2, 19.2 (except 19.2.5)

Week 11 - Genomes: Network theory

Flipped class: Uri Alon (see Flipped Class questions Part 1)

Reading: Alon Network Motifs

Week 12 - Genomes: Network theory

Flipped class: Uri Alon (see Flipped Class questions Part 2)

Reading: Alon Network Motifs (from Week 11)

• Genetic switches
• Genetic oscillators

Reading: PBOC Chapter 19.3.2, 19.3.3