Course materials for Physics of Life 1 at UniBas

This repository contains a script and notebooks used in Richard Neher's part of the Physics of Life 1 course (co-taught with Sebastian Hiller) for 2nd year BSc students in Biology at the University of Basel. The material is taught over 6-7 weeks, three hours per week. The main topics we touch on are

• Quantitative reasoning in biology; relevant length, time and energy scales
• Ordinary differential equations in biology, e.g. growth processes
• Simple models of gene regulation
• Random walks and diffusion
• Models of stiff and flexible polymers
• Reaction-diffusion systems
• Membrane-less organelles and liquid-liquid phase transitions

Lecture notes

The lecture notes are typeset in Latex. A rendered PDF if available here in this repository at lecture-notes.pdf.

Notebooks

Much of the course material is provided in the form of Jupyter notebooks. These notebooks are in the notebooks directory and can be viewed and executed in jupyter. Instructions to use the UniBas Jupyterhub can be found here.

Alternatively, you can use the static online version of jupyter available at

https://jupyterlite.github.io/demo/lab/index.html

This will allow you to work on and run jupyter notebooks in you web browser. However, all files you create live in your browser cache which is not persisting. So make sure to explicitly "download" whatever you want to keep.

A small collection of python and notebook basics is provided as well.

Recommended online resources

• Background: Introduction to partial differential equations (3Blue1Brown)
• Background: Solutions to the heat and diffusion equation (3Blue1Brown)
• Video lecture by Eric Wieschaus on Drosophila development
• Video lecture by Eric Wieschaus on Gradient formation in Drosophila
• Video lecture by Cliff Brangwynne on Membrane-less organelles and liquid-liquid phase transitions
• Video by Julie Theriot on The dynamic cytoskeleton

Recorded lectures from previous years

During the COVID-19 pandemic, this course was not held in person. Instead, lectures were recorded. I provide links to these recordings here in case they might be useful for some. Note, however, that the content of the course is evolving over the years and these recordings from 2020 do not correspond exactly to the current lecture content.

• The relevant scales: sizes, energies, concentrations
  • How big are biological entities?
  • Volumes and concentrations?
  • Energies and Forces
  • Noise and Stochasticity
  • Genome sizes
• Growth processes and differential equations
  • Linear and exponential growth
  • Logistic growth
  • SIR models
• Brownian motion, diffusion, and Fick's law
  • Random walks:
  • Diffusion equation:
  • Boundary and initial conditions:
  • Diffusive transport:
  • Stokes-Einstein relation:
• Polymers
  • Introduction and ideal chains:
  • Stiff polymers:
  • Polymers under force -- Pulling:
  • Polymers under force -- Pushing:
  • The dynamic cytoskeleton.
• Gene regulation
  • Introduction into gene regulation.
  • Simple models of gene regulation.
  • Elements of dynamics systems.
  • Auto-activation and repression.
  • Morphogen gradients -- regulation in space.
• Liquid-liquid phase transitions
  • Phase transitions in biology.
  • Simple models of phase transitions,
  • Properties of membrane-less organells
  • P granules,
• Fidelity, accuracy, and kinetic proof-reading
  • Fidelity and accuacy.
  • Kinetic Proofreading.