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. The University of Basel now provides a Jupyter Hub for students that you can use when you don't have a suitable computer.

This course will be partly taught remotely and asynchronously. For each week, there are multiple short videos in which either I 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. There will also be lecturing in the class room. These class room lectures will be complementary to the online videos and repeat material or cover in depth discussion of the material of the exercises.

### Syllabus

- 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.

#### 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
- Week 1 -- The relevant scales: sizes, energies, concentrations
- Quantitative problems, dimensions, and units
- How big are biological entities? lecture, notebook, notebook-PDF
- Volumes and concentrations? lecture, notebook, notebook-PDF
- Energies and Forces lecture, notebook, notebook-PDF
- Noise and Stochasticity lecture, notebook, notebook-PDF
- Genome sizes lecture, notebook, notebook-PDF

- Week 2 -- Growth processes and differential equations
- Week 3 -- Brownian motion, diffusion, and Fick's law
- 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)

- Week 11 -- Polymers
- Introduction and ideal chains: lecture, notebook, notebook-PDF
- Stiff polymers: lecture, notebook, notebook-PDF
- Polymers under force -- Pulling: lecture, notebook, notebook-PDF
- Polymers under force -- Pushing: lecture, notebook, notebook-PDF
- The dynamic cytoskeleton. lecture, notebook, notebook-PDF
- The dynamic cytoskeleton. Video by Julie Theriot
- Further information: Cell motility by Julie Theriot
- Further information: Evolution of the cytoskeleton by Julie Theriot

- Week 12 -- Gene regulation
- Introduction into gene regulation. lecture, notebook, notebook-PDF
- Simple models of gene regulation. lecture, notebook, notebook-PDF
- Elements of dynamics systems. lecture, notebook, notebook-PDF
- Auto-activation and repression. lecture, notebook, notebook-PDF
- Morphogen gradients -- regulation in space. lecture, notebook, notebook-PDF

- Week 13 -- Liquid-liquid phase transitions
- Phase transitions in biology. lecture, notebook, notebook-PDF
- Simple models of phase transitions, lecture, notebook, notebook-PDF
- Properties of membraneless organells lecture, notebook, notebook-PDF
- P granules, lecture, notebook, notebook-PDF

- Week 14 -- Fidelity, accuracy, and kinetic proof-reading
- Fidelity and accuacy. lecture, notebook, notebook-PDF
- Kinetic Proofreading. lecture, notebook, notebook-PDF