Lecture course Theoretical Biophysics summer term 2012
This course is addressed to master students in physics and related
disciplines with a background in statistical mechanics. Motivated
bachelor or PhD-students are also encouraged to attend. There
are two lectures each week, each for 1.5 hours, plus weekly homework and
exercises. Together you can earn 6 credit points from this course.
The lectures take place Mon and Wed 11.15 - 12.45 in HS2 of KIP.
At some point, we considered shifting the Mon lecture
to the afternoon in order to avoid overlap with the condensed matter
theory course given by Andreas Komnik, but because
this created even more overlap, we now leave it like
before.
This
is the entry in the LSF-database. The exercises take
place Wed at 16.15 in seminar room 41 in the BioQuant-building and are
held by Thorsten Erdmann.
Contents
- biomolecules (DNA, proteins, lipids and sugars) and their interactions
- electrostatics in the cell, genome compactification
- membranes, Helfrich bending energy, thermal fluctuations, Helfrich interaction
- polymers, Rouse model, force-extension curves
- protein folding, helix-coil transition, Zimm-Bragg model
- self-assembly, (electro)chemical potential, Langmuir adsorption, allostery
- reaction kinetics, Michaelis-Menten kinetics
- homeostasis, feedback, oscillations
- diffusion and convection, life at low Reynolds number, diffusion to capture
- living polymers, polymerization ratchet
- force spectroscopy, adhesion clusters under force
- 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, cable equation, Hodgkin-Huxley model, FitzHugh-Nagumo model
- 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, pattern formation
Material
Exercises
Literature
- Bruce Alberts et al., Molecular Biology of the Cell, 5th edition 2007
- R. Phillips, J. Kondev and J. Theriot, Physical Biology of the Cell, Garland Sci. 2009
- P. Nelson, Biological Physics, Freeman 2003
- David Boal, Mechanics of the Cell, Cambridge University Press 2002
- 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
- Martin Novak, Evolutionary Dynamics, Harvard University Press 2006
Other Groups at ITP