In this course, we will explore how general physical principles govern the organization of biological processes. We will for example discuss how matter moves around in cells, how cells process information, how genomes are organized, or how biology exploits self-organization principles.
During the course, we will use frequently use mathematical derivations and concepts from physics that should be familiar to you from high school or the introductory lectures in semesters 1 and 2. Furthermore, many exercises will involve programming and you will use the computer to solve problems. The preferred programming language for this is Python, but you can use what ever programming language you like.
This course will be mostly taught remotely and asynchronously. For each week, I will record multiple short videos in which either present the material, or go through iPython notebooks that explore the material quantitatively. In addition, I will suggest material by third parties (for example the excellent videos on mathematics by 3Blue1Brown) to give additional background and revise necessary mathematical techniques.
- The relevant scales and dimensions of biophysics
- Refresher: Growth processes and simple differential equations
- Random walks, diffusion and Stokes-Einstein relation
- Elements of polymer physics
- Chromatin organization
- Models of gene regulation
- Membraneless organelles and liquid-liquid phase transitions
- Discrimination and fidelity.
- The physical biology of the Cell by Rob Phillips et al
- Cell biology by the numbers by Rob Phillips and Ron Milo
- Preparatory material
- Week 1 -- The relevant scales: sizes, energies, concentrations
- Week 2 -- Growth processes and differential equations
- Week 3 -- Brownian motion, diffusion, and Fick's law