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 whatever programming language you like (for example R or Matlab). The University of Basel now provides a Jupyter Hub for students that you can use when you don't have a suitable computer.
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.
Syllabus
- The relevant scales and dimensions of biophysics
- Laws of physics and differential equations
- Growth processes
- Models of gene regulation
- Random walks, diffusion and Stokes-Einstein relation
- Elements of polymer physics
- Chromatin organization
- Membrane-less organelles and liquid-liquid phase transitions
- Discrimination and fidelity.
Literature
- The physical biology of the Cell by Rob Phillips et al
- Cell biology by the numbers by Rob Phillips and Ron Milo
Course materials
The course materials are provided on GitHub in PoL-1-course-materials repository. Exercise sheets and exercise submissions will be handled via ADAM.
Older recorded lectures
- Arrays in NumPy.mp4
- Auto-activation and repression.mp4
- Boundary and initial conditions.mp4
- Diffusion Equation.mp4
- Diffusive Transport and Fick's law.mp4
- Elements of dynamical systems.mp4
- Extra_ SIR models.mp4
- Genome sizes.mp4
- Introduction into gene regulation.mp4
- Introduction to polymer physics.mp4
- Logistic growth.mp4
- Morphogen gradients -- regulation in space.mp4
- P Granules and their liquid properties.mp4
- Phase Transitions in Biology.mp4
- Properties of membrane-less organelles.mp4
- Pulling on polymers.mp4
- Random Walks.mp4
- Relevant length scales in biological systems.mp4
- Relevant volumes and concentrations.mp4
- Simple growth processes.mp4
- Simple models of demixing.mp4
- Simple models of gene regulation.mp4
- Stiff polymers.mp4
- Stochastic effects and low copy numbers.mp4
- Stokes-Einstein relation.mp4
- The dynamic cytoskeleton.mp4
- Typical energy scales and forces.mp4
- Units, dimensions, and laws of physics.mp4