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 excercises will involve programming and you will use the computer to solve problems. The preferred programming language for this is python.
Syllabus
- The relevant scales and dimensions of biophysics
- Diffusion and Stokes-Einstein relation
- Elements of polymer physics
- Membranes
- Reaction rates
- Pattern formation and reaction diffusion systems
- Liquid-liquid phase transitions in cell biology
Literature
- The physical biology of the Cell by Rob Phillips et al
- Cell biology by the numbers by Rob Phillips and Ron Milo
Lectures
- 2018-09-20 -- The relevant scales: sizes, energies, concentrations
- 2018-09-27 -- Brownian motion, diffusion, and Fick's law
- 2018-10-04 -- Diffusion coefficients and the Stokes-Einstein relation
- 2018-10-11 -- Elements of polymer physics
- 2018-10-18 -- Transcription factor search problems and polymers under force
- 2018-10-25 -- Bacterial gene regulation and signaling
- 2018-11-01 -- Elements of dynamical systems
- 2018-11-08 -- no lecture
- 2018-11-12 -- Tutorial session. Biozentrum room 612. 13-15h. Hand-written notes
- 2018-11-15 -- Linear stability analysis and oscillations
- 2018-11-22 -- Reaction rates
- 2018-11-29 -- Kinetic proofreading and percolation transitions
- 2018-12-06 -- Phase transitions in cell biology
- 2018-12-13 -- Chromosome organization and nucleosome positioning
- 2018-12-20 -- Bethedging and proportional betting