
Lecture course Theoretical Biophysics summer term 2017
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 PhDstudents 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 nonlinear 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. 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.
Material
 script (final version July 30)
 some general information on the course from the first meeting
 Presentation on electrostatistics and genome packing
 Presentation on membranes
 Presentation on red blood cells
 Presentation on polymers
 Presentation on motors
 Presentation on diffusion
 Presentation on structure formation
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, helixcoil transition, ZimmBragg model
 electrostatistics in the cell, genome compactification
 membranes, Helfrich bending energy, thermal fluctuations, Helfrich interaction
 polymers, Rouse model, forceextension curves
 allostery, cooperativity, reaction kinetics, MichaelisMenten 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, crossbridge 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, HodgkinHuxley model, FitzHughNagumo 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
 reactiondiffusion systems, selfassembly, pattern formation, Turinginstability, Minsystem
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, WileyVCH 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, WileyVCH 2009
 Martin Novak, Evolutionary Dynamics, Harvard University Press 2006