Seminar: Physics of Evolution – Übersicht
As minimal conditions for the emergence of an evolutionary dynamics, the three processes replication, mutation, and selection are needed. How can such an evolutionary dynamics emerge spontaneously with molecules under non-equilibrium conditions? Besides this main interest, we will also focus on game theoretical topics and related biophysical questions.
Informationen zur Vorlesung
Zeit und OrtZeit und Ort
U123 Schellingstr. 4
The Seminar is geared towards Masterstudents, however talented, late Bachelorstudents willing to digg deep into more special concepts are also welcome. Papers will focus on recent advances on the topic (last 4 years) and include theoretical treatments and also reviews of experimental methods.
Prof. Dieter Braun
Dates and Slots
11. Introduction to topics
25.  Wandrowski + Tobias Pärr
2.  Christof Beer + Jakob Knollmüller
9.  Aschmoneit + Aynin Meinhold
16.  David Butler + Christian Wolff
23.  Jurek Müller, Janik Schönmeier
30.  Krampf + Werner
6.  Berger Ricarda + Jürgen Kreiter
13.  Alexandra Götz +Niederauer Christian
20.  Perhaps Simon/Matthias/Christof??
27. "Gradients Across Self-Assembling Inorganic Membranes", Dominic Berchtold (Lab Braun)
List of topics [PDF of Papers]
1. DNA computing: Amplifying genetic logic gates (2013). Science, 340(6132).
2. Borate-Story: Ricardo, A., et al. "Borate minerals stabilize ribose." Science 303.5655 (2004): 196-196.
3. Joyce-Ligator: Robertson, Michael P., and Gerald F. Joyce. "Highly Efficient Self-Replicating RNA Enzymes." Chemistry & biology (2014)
Sczepanski, Jonathan T., and Gerald F. Joyce. "Synthetic evolving systems that implement a user-specified genetic code of arbitrary design." Chemistry & biology 19.10 (2012): 1324-1332
Ferretti, Antonio C., and Gerald F. Joyce. "Kinetic properties of an RNA enzyme that undergoes self-sustained exponential amplification." Biochemistry 52.7 (2013): 1227-1235.
4. Replicators in Lipid shells: Adamala, Katarzyna, and Jack W. Szostak. "Nonenzymatic Template-Directed RNA Synthesis Inside Model Protocells." Science 342.6162 (2013): 1098-1100
Blain, J. Craig, and Jack W. Szostak. "Progress Toward Synthetic Cells." Annual Review of Biochemistry 83.1 (2014).
5. Nick Huds Fibers: Cafferty, Brian J., et al. "Efficient self-assembly in water of long noncovalent polymers by nucleobase analogues." Journal of the American Chemical Society 135.7 (2013): 2447-2450.
6. Ribosomal Evolution. Petrov, Anton S., et al. "Secondary Structures of rRNAs from All Three Domains of Life." PloS one 9.2 (2014): e88222.
7. Recycling of Informational Units. Vaidya, Nilesh, Sara Imari Walker, and Niles Lehman. "Recycling of Informational Units Leads to Selection of Replicators in a Prebiotic Soup." Chemistry & biology 20.2 (2013): 241-252.
8. Crystal structure of RNA-based replication. Shechner, David M., and David P. Bartel. "The structural basis of RNA-catalyzed RNA polymerization." Nature structural & molecular biology 18.9 (2011): 1036-1042.
9. Role of 2-5-linkages in RNA. Sheng, Jia, et al. "Structural insights into the effects of 2′-5′ linkages on the RNA duplex." Proceedings of the National Academy of Sciences 111.8 (2014): 3050-3055.
10. Replicators in Ice:Attwater, James, Aniela Wochner, and Philipp Holliger. "In-ice evolution of RNA polymerase ribozyme activity." Nature chemistry (2013).
11. RNA-like chemical replication: Zhang, Shenglong, et al. "Fast and accurate nonenzymatic copying of an RNA-like synthetic genetic polymer." Proceedings of the National Academy of Sciences 110.44 (2013): 17732-17737.
12. Aminoacylation à la Yarus:Illangasekare, Mali, and Michael Yarus. "Small aminoacyl transfer centers at GU within a larger RNA." RNA Biol 9.1 (2012): 59-66.
13. Towards the prebiotic ribosome: Huang, Lulu, et al. "Protoribosome by quantum kernel energy method." Proceedings of the National Academy of Sciences 110.37 (2013): 14900-14905;
Villa, Elizabeth, et al. "Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis." Proceedings of the National Academy of Sciences 106.4 (2009): 1063-1068.
14. Aminoacylation à la Suga: Suga, Hiroaki, Gosuke Hayashi, and Naohiro Terasaka. "The RNA origin of transfer RNA aminoacylation and beyond." Philosophical Transactions of the Royal Society B: Biological Sciences 366.1580 (2011): 2959-2964.
15. Kiedrowski: The tale of long and fast polymers:Taran, Olga, et al. "Synthesis of information-carrying polymers of mixed sequences from double stranded short deoxynucleotides." Journal of Systems Chemistry 1.1 (2010): 1-16.
Verantwortlich für den Inhalt: Dieter Braun