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Lecture course Theoretical Biophysics summer term 2015
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.
Contents
The exact choice of subjects depends also on the background and suggestions of the students.- biomolecules (DNA, proteins, lipids and sugars) and their interactions
- protein folding, helix-coil transition, Zimm-Bragg model
- electrostatistics in the cell, genome compactification
- membranes, Helfrich bending energy, thermal fluctuations, Helfrich interaction
- polymers, Rouse model, force-extension curves
- allostery, cooperativity, reaction kinetics, Michaelis-Menten kinetics, homeostasis, feedback, oscillations
- diffusion and convection, life at low Reynolds number, diffusion to capture
- living polymers, polymerization ratchet, growing actin networks
- force spectroscopy, adhesion clusters, catch bonds
- molecular motors, ratchet models, cross-bridge models, force generation in muscle, Huxely model, cooperative transport
- cell shape and mechanics, cell division, physics of development and tissue
- excitable systems, ion channels, action potentials, Hodgkin-Huxley model, FitzHugh-Nagumo model, cable equation, waves
- gene expression, kinetic proofreading, sequence analysis, gene expression and protein interaction networks
- evolution, population models, game theory, dynamics of infections, range expansion
- reaction-diffusion systems, self-assembly, pattern formation, Turing-instability, Min-system
Material
- Script (updated August 21 2015)
- Script from an earlier version of this course (will be improved during this course, see link above)
- PDF from introduction during the first lecture (April 14 2015)
- PDF on molecular dynamics (April 23 2015)
- PDF on membrane shapes (May 21 2015)
- PDF on red blood cell shapes (May 28 2015)
- PDF on physics of biopolymers (June 16 2015)
Exercises
- Exercise no. 1 (April 21)
- Exercise no. 2 (April 28)
- Exercise no. 3 (May 5)
- Exercise no. 4 (May 12)
- Exercise no. 5 (May 19)
- Exercise no. 6 (May 26)
- Exercise no. 7 (June 2)
- Exercise no. 8 (June 9)
- Exercise no. 9 (June 16)
- Exercise no. 10 (June 23)
- Exercise no. 11 (June 30)
- Exercise no. 12 (July 7)
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