Physical Biology Module

MBL Physiology Course 2024

In our time together in the theory module of skills week, we’ll take a tour through the worlds of numerical thinking in biology and simple physical models of biological systems. We’ll try our hand at order-of-magnitude estimates and pen-and-paper models of phenomena like biological growth, diffusion, phase separation, polymerization, and more! For some topics, we’ll complement our calculations with Python simulations. You’ll also prepare and present an order-of-magnitude (‘Fermi’) estimate related to your own interests or research. Our main goal is to explore together how powerful (and fun!) numerical and physical thinking can be as a tool in understanding biology.

Date Topics Materials Videos
Monday
  • A feeling for the numbers in biology.
  • Street-Fighting Mathematics: Order-of-magnitude estimates as a tool for discovery in the living world.
  • What sets the scale of X?
Monday
  • Stuff(t) or the Protocol of Biological Dynamics.
    • Time evolution in biology.
    • Bacterial growth dynamics: Solving bacterial growth analytically and numerically.
Monday
  • Diffusion as Biology's Null Hypothesis for Dynamics.
    • Diffusion and axonal transport.
    • Diffusion by coin flips.
Monday
  • Null Hypotheses in Biology: The Poisson Distribution, Part I.
    • The Great Probability Distributions of Biology
    • The constitutive promoter.
Monday
  • A Feeling for the Numbers in Biology: Your Turn.
    • Prepare a 5 minute estimate you will present on Saturday.
    • Christina and Hernan are around to help all week. Just Slack us!
Saturday
  • Null Hypotheses in Biology: The Poisson Distribution, Part II.
    • Chemical master equation of the constitutive promoter.
    • The Poisson Distribution: Bombs over London, constitutive promoters, and sequencing the human genome.
    • Synthetic transcriptomes and the single-cell sequencing revolution.
Saturday
  • Phase Transitions in Biology.
    • Entropy maximization.
    • Free Energy Minimization.
    • Drawing Phase Diagrams.
Saturday
  • Active Matter.
Saturday
  • Physical Biology of the Cell.