Theoretical Biophysics

The lecture on Theoretical Biophysics takes place every Tuesday and Thursday at 9.15 am in room 106 in Philosophenweg 12.

The first lecture takes place on April 18.

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 welcome. 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 e.g. the lecture on statistical physics or the lecture on simulation methods, or with two short specialized lectures (like non-linear or stochastic dynamics). The details for the tutorial will be discussed in the first lecture. 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.

Contents

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

Literature

A script is availabe from earlier editions of this lecture. In addition we recommend the following text books:

• R. Phillips, J. Kondev and J. Theriot, Physical Biology of the Cell, 2nd edition, Garland Sci. 2012
• P. Nelson, Biological Physics: Energy, Information, Life, Student edition 2020
• KA Dill and S Bromberg, Molecular Driving Forces, 2nd edition, Garland 2011
• Jacob Israelachvili, Intermolecular and Surface Forces, 3rd ed 2011