Ruprecht Karls Universität Heidelberg

Lecture course Theoretical Biophysics summer term 2021

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 a lecture like statistical physics, nonlinear dynamics or simulation methods. It is given by Ulrich Schwarz and in summer term 2021 is streamed live by zoom from a lecture room in Philosophenweg 12. A recording will be made available afterwards on moodle. A script is available from earlier years. The lecturer is happy to include new material on request, e.g. on the physics of viruses. 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

Contents

We will cover a selection of the following subjects:
  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

  • Bruce Alberts et al., Molecular Biology of the Cell, 6th edition 2015
  • R. Phillips, J. Kondev and J. Theriot, Physical Biology of the Cell, 2nd edition, Garland Sci. 2012
  • Ron Milo and Rob Phillips, Cell biology by the numbers, Garland Sci. 2016
  • P. Nelson, Biological Physics: Energy, Information, Life, Student edition 2020
  • P. Nelson, Physical models of living systems, Freeman 2015
  • P. Nelson, From photon to neuron, Princeton University Press 2017
  • KA Dill and S Bromberg, Molecular Driving Forces, 2nd edition, Garland 2011
  • Ivet Bahar, Bob Jernigan and Ken Dill, Protein Actions, Taylor & Francis 2017
  • Jacob Israelachvili, Intermolecular and Surface Forces, 3rd ed 2011
  • J.D. Murray, Mathematical Biology I and II, 3rd edition, Springer 2002
  • James Keener and James Sneyd, Mathematical Physiology, 2nd edition Springer 2009