Theoretical Biophysics

Course description

This course is MVBP2 in the modul handbook and is addressed to master students in physics with a background in statistical physics. Motivated bachelor or PhD-students are also encouraged to attend. There are two lectures each week, each for 90 minutes, plus weekly homework and exercises. Together you can earn 6 credit points from this course. This lecture can be used for the oral master examination if combined with a lecture like statistical physics, nonlinear dynamics or simulation methods. It is given by Ulrich Schwarz and in summer term 2021 is streamed live by zoom from a lecture room in Philosophenweg 12. A recording will be made available afterwards on moodle. A script is available from earlier years. The lecturer is happy to include new material on request, e.g. on the physics of viruses. Earlier exposure to biology and biophysics (e.g. the experimental biophysics course in the winter term, bachelor courses on biophysics, biology courses) is helpful, but not required.

Content

We will cover a selection of the following subjects:

1. biomolecules (DNA, RNA, proteins, lipids and sugars) and their interactions
2. protein folding, helix-coil transition, Zimm-Bragg model
3. electrostatistics in the cell, genome compactification
4. self-assembly, nucleation and growth, aggregation-fragmentation model, micelles, filaments, virus capsides, clathrin cages
5. membranes, Helfrich bending energy, thermal fluctuations, Helfrich interaction
6. virus entry, endocytosis, fusion, uncoating, virus assembly, virus exit, budding, maturation
7. polymers, Rouse model, force spectroscopy, force-extension curves
8. allostery, cooperativity, reaction kinetics, Michaelis-Menten kinetics, homeostasis, feedback, oscillations
9. diffusion and convection, life at low Reynolds number, diffusion to capture
10. living polymers, polymerization ratchet, growing actin networks
11. force spectroscopy for clusters, adhesion clusters, catch bonds
12. molecular motors, ratchet models, cross-bridge models, force generation in muscle, Huxely model, cooperative transport
13. cell shape and mechanics, cell division, physics of development and tissue
14. excitable systems, ion channels, action potentials, Hodgkin-Huxley model, FitzHugh-Nagumo model, cable equation, waves 
15. gene expression, kinetic proofreading, sequence analysis, gene expression and protein interaction networks
16. evolution, population models, game theory, dynamics of infections, range expansion
17. reaction-diffusion systems, self-assembly, pattern formation, Turing-instability, Min-system