Ruprecht Karls Universität Heidelberg

Lecture course Theoretical Biophysics summer term 2016

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 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 lecture takes place Tue and Thu 9.15 - 10.45 in room 106 at Philosophenweg 12 and is given by Ulrich Schwarz. The exercises take place on Wed 16.15 - 17.45 in room 105 at Philosophenweg 12 and are given by Thorsten Erdmann.

If you are interested also in a seminar in this field, one possible choice is our seminar on single molecule biophysics jointly organized with Edward Lemke from EMBL.

Material

Exercises

Exercises are allowed to be done in groups of two students. First tutorial on May 11.

Contents

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

Literature

  • Bruce Alberts et al., Molecular Biology of the Cell, 6th edition 2012
  • R. Phillips, J. Kondev and J. Theriot, Physical Biology of the Cell, 2nd edition, Garland Sci. 2012
  • P. Nelson, Biological Physics, Freeman 2007
  • David Boal, Mechanics of the Cell, 2nd edition, Cambridge University Press 2012
  • KA Dill and S Bromberg, Molecular Driving Forces, Garland 2003
  • E. Sackmann und R. Merkel, Lehrbuch der Biophysik, Wiley-VCH 2010
  • J.D. Murray, Mathematical Biology I and II, 3rd edition, Springer 2002
  • James Keener and James Sneyd, Mathematical Physiology, 2nd edition Springer 2009
  • Uri Alon, An Introduction to Systems Biology, Chapman & Hall 2007
  • Edda Klipp et al., Systems Biology: A Textbook, Wiley-VCH 2009
  • Martin Novak, Evolutionary Dynamics, Harvard University Press 2006