Seminar on Statistical Biology: Stochastic thermodynamics and biophysical applications
Johannes Berg, Tobias Bollenbach, Joachim Krug, Michael Lässig, Berenike Maier, Benedikt Sabass
This seminar covers the theoretical and experimental tools to describe stochastic
dynamics, in particular stochastic thermodynamics.
We then look at biological systems as key applications of stochastic dynamics: large enough to warrant a statistical description but too small
to invoke the thermodynamic limit.
We then look at biological systems as key applications of stochastic dynamics: large enough to warrant a statistical description but too small
to invoke the thermodynamic limit.
- Foundations of stochastic dynamics (G. Lalovski, JK, 3.11., see here for notes)
- Langevin equations, thermodynamics, and fluctuation theorems (S. Ganguly, JK, 10.11, see here for notes)
- Master equations and thermodynamics, and fluctuation theorems (C. Zachow, JK, 17.11, see here for notes)
- Irreversibility and the arrow of time (N. Sharma, JB, 24.11.)
- Brownian and molecular motors (C. Lakshmisha, BM, 1.12)
- Biomolecules (Experiment) (R. Kirina, BM, 8.12)
- Accuracy limits to cellular sensing (M. Srivastava, TB, 15.12,, see here for notes)
- Thermodynamic uncertainty relations and statistical kinetics (J. Cordes, TB, 22.12)
- Feedback and information (J. Müller, JB, 12.1)
- Stochastic gene expression (R. Moran, JB, 19.1)
- Fitness flux and adaptive evolution (D. Augustin, ML, 26.1)
Schedule
Fridays 10:00, Seminar Room 2 New Building Theoretical Physics
The first meeting is Friday 13.10. Please contact the faculty member in charge of your topic for literature pointers well in advance of your presentation.
The first meeting is Friday 13.10. Please contact the faculty member in charge of your topic for literature pointers well in advance of your presentation.
Literature
Introduction to stochastic systems:
N.G. van Kampen, Stochastic Processes in Physics and Chemistry, North Holland
Review articles and overviews:
Bustamante, C., Liphardt, J., Ritort, F. (2005) The nonequilibrium thermodynamics of small systems. Physics Today, p. 43.
Ciliberto, S. (2017). Experiments in stochastic thermodynamics: Short history and perspectives. Phys. Rev. X 7, 021051.
Ritort, F. (2008). Nonequilibrium fluctuations in small systems: From physics to biology. Advances in chemical physics, 137, 31.
Seifert, U. (2008). Stochastic thermodynamics. IFF Jülich lecture notes.
Seifert, U. (2012). Stochastic thermodynamics, fluctuation theorems and molecular machines. Reports on Progress in Physics, 75(12), 126001.
Materials for the individual seminar topics will be provided separately.
N.G. van Kampen, Stochastic Processes in Physics and Chemistry, North Holland
Review articles and overviews:
Bustamante, C., Liphardt, J., Ritort, F. (2005) The nonequilibrium thermodynamics of small systems. Physics Today, p. 43.
Ciliberto, S. (2017). Experiments in stochastic thermodynamics: Short history and perspectives. Phys. Rev. X 7, 021051.
Ritort, F. (2008). Nonequilibrium fluctuations in small systems: From physics to biology. Advances in chemical physics, 137, 31.
Seifert, U. (2008). Stochastic thermodynamics. IFF Jülich lecture notes.
Seifert, U. (2012). Stochastic thermodynamics, fluctuation theorems and molecular machines. Reports on Progress in Physics, 75(12), 126001.
Materials for the individual seminar topics will be provided separately.
Picture credit: Brownian Motion on a Sphere, picture created by
Christian Bayer and Thomas Steiner. See here for
details and licensing.
