TVI: Theoretical Biological Physics (Prof. Erwin Frey)
This lecture is intended as an introduction to the theoretical concepts used in describing biological systems and biologically relevant soft materials such as polymers and membranes. It builds on the course "thermodynamics and statistical mechanics". The course starts with an introduction into the the theories of stochastic processes and nonlinear systems. These methods are of particular importance in the molecular world of cellular systems but have broad range of applications far beyond biologically relevant systems. Building on these theoretical concepts the course will cover a range of topics:
- Theory of Stochastic Processes and Brownian Motion
- Nonlinear Dynamics
- Brownian Dynamics Simulations
- Hydrodynamics at Low Reynolds Number
- Entropic Forces
- Molecular Machines and Enzymes
- Polymers and Membranes
- Population Genetics and Gene Regulation
- Reaction Diffusion Models and Pattern Formation
- Game Theory and Evolution
- System Theory and Networks
Vorlesung:
- 4- stündig, Mo 9 - 11 Uhr, Do 11 - 13 Uhr
- Sommerfeld Raum 348/349, Theresienstr. 37, 3. Stock
Begleitendes Seminar & Übungen:
- 2- stündig, Mi 13 - 15 Uhr, Sommerfeld Raum (Beginn am 26. Oktober)
Seminar Schedule:
- 26.10. Wolfram Möbius: How to generate random numbers
- 02.11. Jonas Kraus: The Ehrenfest model and the Jarzynski relation
- 16.11. Stephanie Kappler: Delbrück-Luria Experiment
- 30.11. Benjamin Terjung: Stochastic Gene Expression in Fluctuating Environments
- 07.12. Axel Kammerer: Intrinsic noise in gene regulatory networks
- 07.12. Borysova Elina: Polymerization Ratchets
- 14.12. Special Sommerfeld Lectures
- 20.12. Anton Winkler: Forced Thermal Ratchets
- 11.01. Boris Schäfer: Fluctuation Driven Ratchets: Molecular Motors
- 11.01. Louis Reese: Fluctuation-Driven Molecular Transport through an asymmetric Membrane Channel
- 18.01. Tobias Reichenbach: Stochastic Resonance in Biology
- 18.01. Gerald Raoul Ryseck: Models of Circadian Rhythms
- 25.01. Stephanie Kappler: Statistical Fluctuations in Autocatalytic Reactions
- 25.01. Karen Winkler: Kinetic Proofreading
- 02.02. Michael Hecht: Distribution Function of Semiflexible Polymers
- 02.02. Daniel Nicklas: Voltage Gated Ion Channels
- 08.02. Georg Fritz: Stochastic description of gene regulatory mechanisms
- 08.02. Matthias Schmitt: Force Spectroscopy on Single Macromolecules
Topics for Seminar Talks:
- Delbrück-Luria Experiment [Stephanie Kappler]
- Theoretical modeling of prion disease incubation
Material: R.V. Kulkarni [cond-mat/011053] - Life and death in an expanding cage and at the edge of a receding cliff
Material: P.L. Krapivski and S. Redner [Am. J. Phys. 64, 546 (1996)]. - Stochastic Gene Expression in Fluctuating Environments [Benjamin Terjung]
Material: M. Thattai and A. van Oudenaarden, [Genetics 167, 523 (2004)]. - Intrinsic noise in gene regulatory networks [Axel Kammerer]
Material: M. Thattai and A. van Oudenaarden, [PNAS 98, 8614 (2001)]. - Polymerization Ratchets [Borysova Elina]
Material:- A. Mogilner and G. Oster, Review article in [Current Biology 13, R721 (2003)],
- C.S. Peskin et al., [Biophys. J. 65, 316 (1993)]
- Simulations in Java [Link]
- Forced Thermal Ratchets [Anton Winkler]
Material: M.O. Magnasco, [Phys. Rev. Lett. 71, 1477 (1993)] - Fluctuation-Driven Molecular Transport through an asymmetric Membrane Channel [Louis Reese]
Material: I. Kosztin and K. Schulten, [Phys. Rev. Lett. 93, 238102 (2004)] - Fluctuation Driven Ratchets: Molecular Motors [Boris Schäfer]
Material:- R.D. Astumian and M. Bier, [Phys. Rev. Lett. 72, 1766 (1994)]
- R.D. Astumian and I. Derenyi, Review article in [Eur. Biophys. J. 27, 474 (1998)]
- Voltage Gated Ion Channels [Daniel Nicklas]
Material: Book chapter in 'Computational Cell Biology', ed. by C.P. Fall et al., Springer Verlag
(A copy of the book chapter is available at the office of Frau Lesperance) - Stochastic Resonance in Biology [Tobias Reichenbach]
Material:- P. Hänggi, [ChemPhysChem 3, 285 (2005)]
- L. Gammaitoni et al., [Rev. Mod. Phys. 70, 223 (1998)]
- Models of Circadian Rhythms [Gerald Raoul Ryseck]
Material:- D. Beersma, [Journal of Biological Rhythms, Vol. 20, No. 4, 304-313 (2005)]
- F. Naef, Review in Molecular Systems Biology [Link]
- D. Gonze et al., [PNAS 99, 673 (2002)]
- Statistical Fluctuations in Autocatalytic Reactions [Stephanie Kappler]
Material: M. Delbrueck [Article] - Kinetic Proofreading [Karen Winkler]
Material:- J.J. Hopfileld, [PNAS, 71, 4135 (1979)]
- J.J. Hopfield, [PNAS, 74, 2246 (1977)]
- Force Response of semiflexible Polymers (statistical mechanics calculation)
Material: - Distribution Function of Semiflexible Polymers [Michael Hecht]
Material: Wilhelm, Frey [Article] - Force Spectroscopy on Single Macromolecules [Matthias Schmitt]
Material: - Inequivalence of statistical ensembles in finite systems
Material:
Contents:
please report any errors and typos in the script to Jan-Timm Kuhr
Supplementary material:
- Supplement_1 (password required)
- Numerical recipes in C
- Gambler's Ruin Java Applet
- Random Walk Notebook for Mathematica
- P.A. Pury, Asymmetry and convergence in the central limit theorem: An approach for physicists, Am. J. Phys. 58, 62 (1990) [Article]
- E. Frey and K. Kroy, Im Zickzack zwischen Physik und Biologie [Article]
- E. Frey and K. Kroy, Brownian motion: a paradigm of soft matter and biological physics, Annalen der Physik (Leipzig) 14, 20 (2005). [Article]
- E. Frey, Physics in Cell Biology: On the physics of Biopolymers and Molecular Motors, ChemPhysChem 3, 270 (2002). [Article]
- E. Frey, Physikalische Fragestellungen aus der Zellbiologie, Physikalische Blätter 57, 63 (2001). [PDF]
- Poisson Process - Notebook for Mathematica
- Yule Process - Notebook for Mathematica
- Molecular motors - pdf slides
- Supplement 2 (password required)
- Malthus-Verhulst Gillespie simulation - Notebook for Mathematica
- Methode der Charakteristiken (password required)
- Introduction to Biopolymers and Biomembranes (password required)
- Ideal chains (password required)
Literature:
- L.J.S. Allen, Stochastic Processes with Applications to Biology
- C.W. Gardiner, Handbook of Stochastic Methods
Sprechstunde Prof. Dr. Frey:
- Fr 13.30 - 15 Uhr, Raum 335, Theresienstr. 37