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
- Membraneless 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

### Lectures

- Preparatory material
- Lecture 1 -- The relevant scales: sizes, energies, concentrations
- Quantitative problems, dimensions, and units
- How big are biological entities? lecture, notebook, notebook-PDF

- Lecture 2 -- scales continued, differential equations, friction.
- Volumes and concentrations? lecture, notebook, notebook-PDF
- Energies and Forces lecture, notebook, notebook-PDF
- Genome sizes lecture, notebook, notebook-PDF
- Differential Equations notebook, notebook-PDF

- Lecture 3 -- Biological growth processes, gene regulation
- Logistic growth, notebook, notebook-PDF
- SIR and predator-prey notebook, notebook-PDF
- Dynamical Systems notebook, notebook-PDF
- Gene Regulation Basics lecture, notebook, notebook-PDF
- Gene Regulation Basics lecture, notebook, notebook-PDF
- Auto-activation and repression. lecture, notebook, notebook-PDF

- Lecture 4 -- Random walks and diffusion
- Random protein production: notebook, notebook-PDF
- Random walks: lecture, notebook, notebook-PDF
- Diffusion equation: lecture, notebook, notebook-PDF
- Boundary and initial conditions: lecture, notebook, notebook-PDF
- Diffusive transport: lecture, notebook, notebook-PDF
- Stokes-Einstein relation: lecture, notebook, notebook-PDF
- Background: Introduction to partial differential equations (3Blue1Brown)
- Background: Solutions to the heat and diffusion equation (3Blue1Brown)