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 selforganization 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.
Syllabus
 The relevant scales and dimensions of biophysics
 Refresher: Growth processes and simple differential equations
 Random walks, diffusion and StokesEinstein relation
 Elements of polymer physics
 Chromatin organization
 Models of gene regulation
 Membraneless organelles and liquidliquid 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, notebookPDF
 Volumes and concentrations? lecture, notebook, notebookPDF
 Energies and Forces lecture, notebook, notebookPDF
 Noise and Stochasticity lecture, notebook, notebookPDF
 Genome sizes lecture, notebook, notebookPDF
 Week 2  Growth processes and differential equations
 Week 3  Brownian motion, diffusion, and Fick's law
 Random walks: lecture, notebook, notebookPDF
 Diffusion equation: lecture, notebook, notebookPDF
 Boundary and initial conditions: lecture, notebook, notebookPDF
 Diffusive transport: lecture, notebook, notebookPDF
 StokesEinstein relation: lecture, notebook, notebookPDF
 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, notebookPDF
 Stiff polymers: lecture, notebook, notebookPDF
 Polymers under force  Pulling: lecture, notebook, notebookPDF
 Polymers under force  Pushing: lecture, notebook, notebookPDF
 The dynamic cytoskeleton. lecture, notebook, notebookPDF
 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, notebookpdf
 Simple models of gene regulation. lecture, notebook, notebookpdf
 Elements of dynamics systems. lecture, notebook, notebookpdf
 Autoactivation and repression. lecture, notebook, notebookpdf
 Morphogen gradients  regulation in space. lecture, notebook, notebookpdf