Seminar: Statistische Physik in der Biologie (Prof. Erwin Frey, Prof. Ulrich Gerland)
Zeit und Ort
2-stündig, Mo 16:00-18:00 Uhr,
Theresienstr. 37, A 449,
Vorbesprechung: 13.10.2008
Theresienstr. 37, A 449,
Vorbesprechung: 13.10.2008
Seminartermine
Termin | Vortragende/r, Thema | Betreuer/in |
---|---|---|
03.11.08 | Severin Schink | Karen Alim |
6.
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10.11.08 | Stefan Mauerberger | Marta Balbás Gambra |
3.
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17.11.08 | Sebastian Gude | Wolfram Möbius |
10.
Peeling and Sliding in Nucleosome Repositioning
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24.11.08 | Thomas Allesch | Marta Balbás Gambra |
8.
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01.12.08 | Lasma Alberte | Steffen Rulands |
13.
Rare event statistics in reaction-diffusion systems
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08.12.08 | Martin Weidl | Georg Fritz |
12.
Sequence alignment
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15.12.08 | Stephan Humeniuk | Benedikt Obermayer |
1.
|
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Nicola Tyler | Ulrich Gerland | |
4.
Physical constraints and functional characteristics of transcription factor–DNA interaction
|
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22.12.08 | Christian Matek | Georg Fritz |
11.
Models of stochastic gene expression
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19.01.09 | Delia Brick | Georg Fritz |
9.
Allostery and cooperativity in biochemical reactions
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Florian Rieger | Benedikt Obermayer | |
5.
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26.01.09 | Julian Hartmann | Wolfram Möbius |
7.
Knots in DNA molecules
|
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Christian Winnerlein | Karen Alim | |
2.
Statistical Mechanics of Supercoiled DNA
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02.02.09 | Vortrag von Jonathan C. Howard – TUM, Garching | |
Molecular Control of Cellular Size: How the motor protein kinesin-8 measures microtubule length |
Themen
- The application of statistical physics to evolutionary biology ∗
- G. Sella and A. E. Hirsh, PNAS 102:9541 (2005)
- Statistical Mechanics of Supercoiled DNA
- J.F. Marko and E.D.Siggia, Phys. Rev. E. 52, 2912 (1995)
- Statistical Mechanics of Complex Networks ∗
- Réka Albert and Albert-László Barabási, Rev. Mod. Phys. 74, 47-97 (2002)
- Physical constraints and functional characteristics of transcription factor–DNA interaction ∗
- Ulrich Gerland, J. David Moroz, and Terence Hwa, Proc. Natl. Acad. Sci. 99, 12015–12020 (2002)
- Statistical Mechanics of Semiflexible Polymers ∗
- J. Wilhelm, E. Frey, Phys. Rev. Lett. 77, 2581 (1996)
- Denaturation and unzipping of DNA: statistical mechanics of interacting loops ∗
- Y. Kafri, D. Mukamel, and L. Peliti, Physica A 306, 39–50 (2002)
- Knots in DNA molecules ∗
- Metzler et al., Title: Single DNA conformations and biological function.
J Comput Theor Nanos 4, 1 (2007) - W. Moebius, E. Frey, and U. Gerland, Knotted DNA in a Nanochannel
- Metzler et al., Title: Single DNA conformations and biological function.
- A Statistical-Thermodynamic Model of Viral Budding
- Shelly Tzlil, Markus Deserno, William M. Gelbart and Avinoam Ben-Shaul,
Biophys. J. 86, 2037-2048 (2004)
- Shelly Tzlil, Markus Deserno, William M. Gelbart and Avinoam Ben-Shaul,
- Allostery and cooperativity in biochemical reactions ∗
- Changeux et al., Allosteric mechanisms of signal transduction.
Science 308, 1424-1428 (2005) - Keymer et al., Chemosensing in Escherichia coli: two regimes of two-state receptors.
PNAS 103, 1786-1791 (2006)
- Changeux et al., Allosteric mechanisms of signal transduction.
- Peeling and Sliding in Nucleosome Repositioning ∗
- T. Chou, Peeling and Sliding in Nucleosome Repositioning.
Phys. Rev. Lett. 99, 058105 (2007)
- T. Chou, Peeling and Sliding in Nucleosome Repositioning.
- Models of stochastic gene expression ∗
- J. Paulsson, Models of stochastic gene expression.
Physics of Life Reviews 2 (2) 157-175 (2005) - Thattai et al., Intrinsic noise in gene regulatory networks.
PNAS 98, 8614-8619 (2001)
- J. Paulsson, Models of stochastic gene expression.
- Sequence Alignment
- S. B. Needleman, C. D. Wunsch,
A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins. J. Mol. Biol. 48, 443453 (1970) - R. Bundschuh, T. Hwa,
An analytic study of the phase transition line in local sequence alignment with gaps.
Discrete Applied Mathematics 104, 113–142 (2000)
- S. B. Needleman, C. D. Wunsch,
- Rare event statistics in reaction-diffusion systems (Thema ersetzt RNA-Matrixtheorie) ∗
(Warnung: sehr anspruchsvoll und zeitintensiv)- Vlad Elgart and Alex Kamenev, Rare event statistics in reaction-diffusion systems.
Phys. Rev. E 70, 041106 (2004)
- Vlad Elgart and Alex Kamenev, Rare event statistics in reaction-diffusion systems.
- Molecular Crowding in cells ∗
- R. J. Ellis, Macromolecular crowding: obvious but underappreciated.
Trends Biochem. Sci. 26, 597 (2001)
- R. J. Ellis, Macromolecular crowding: obvious but underappreciated.
Zugriff auf die Online-Zeitschriften der Universitätsbibliotheken (LRZ)
Buchempfehlungen
- Biological Physics, by Philip Nelson
- Physics With Illustrative Examples From Medicine and Biology, Volume 2: Statistical Physics,
by George B. Benedek, Felix M. H. Villars - The Molecular Biology of the Cell, by Alberts et al., is fully available online.
References
- Review article on "Brownian motion: a paradigm of soft matter and biological physics",
E. Frey, K. Kroy, Annalen der Physik (Leipzig) 14, 20 (2005). [arXiv:cond-mat/0502602]